From 12a31f4c130c551f82232d9ef7dfb608bd52c53f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 27 Sep 2016 23:00:48 +0200 Subject: Reorganise repository using standard package layout --- pkg/.Rbuildignore | 3 - pkg/DESCRIPTION | 25 - pkg/NAMESPACE | 29 - pkg/R/FOCUS_GW_scenarios_2012.R | 11 - pkg/R/GUS.R | 98 - pkg/R/PEC_soil.R | 215 - pkg/R/PEC_sw_drainage_UK.R | 66 - pkg/R/PEC_sw_drift.R | 65 - pkg/R/PEC_sw_sed.R | 50 - pkg/R/SFO_actual_twa.R | 36 - pkg/R/SSLRC_mobility_classification.R | 42 - pkg/R/TOXSWA_cwa.R | 380 -- pkg/R/drift_data_JKI.R | 44 - pkg/R/endpoint.R | 110 - pkg/R/geomean.R | 38 - pkg/R/pfm_degradation.R | 48 - pkg/R/soil_scenario_data_EFSA_2015.R | 40 - pkg/data/FOCUS_GW_scenarios_2012.RData | Bin 993 -> 0 bytes pkg/data/drift_data_JKI.RData | Bin 966 -> 0 bytes pkg/data/soil_scenario_data_EFSA_2015.RData | Bin 522 -> 0 bytes pkg/inst/extdata/FOCUS_GW_scenarios_2012.R | 59 - pkg/inst/staticdocs/index.r | 42 - pkg/inst/testdata/SwashProjects.zip | Bin 7989179 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delete mode 100644 pkg/tests/testthat/test_PEC_sw_drift.R delete mode 100644 pkg/tests/testthat/test_SFO_actual_twa.R delete mode 100644 pkg/tests/testthat/test_TOXSWA_cwa.R delete mode 100644 pkg/tests/testthat/test_UK_drainage.R delete mode 100644 pkg/tests/testthat/test_geomean.R (limited to 'pkg') diff --git a/pkg/.Rbuildignore b/pkg/.Rbuildignore deleted file mode 100644 index c48d8e3..0000000 --- a/pkg/.Rbuildignore +++ /dev/null @@ -1,3 +0,0 @@ -inst/testdata/SwashProjects/project_H_sw/MACRO/*/*.bin -inst/testdata/Swash/ -inst/extdata/Tabelle\ der\ Abdrifteckwerte.xls diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION deleted file mode 100644 index f9de23c..0000000 --- a/pkg/DESCRIPTION +++ /dev/null @@ -1,25 +0,0 @@ -Package: pfm -Type: Package -Title: Utilities for Pesticide Fate Modelling -Version: 0.3-8 -Date: 2016-09-26 -Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", - role = c("aut", "cre", "cph")) -Description: Utilities for simple calculations of predicted environmental - concentrations (PECs) and for dealing with data from some FOCUS pesticide - fate modelling software packages. -Depends: - R6, - mkin -Imports: - graphics, - readr, - methods -Suggests: - testthat, - chents -License: GPL -LazyLoad: yes -LazyData: yes -Encoding: UTF-8 -RoxygenNote: 5.0.1 diff --git a/pkg/NAMESPACE b/pkg/NAMESPACE deleted file mode 100644 index 572ec80..0000000 --- a/pkg/NAMESPACE +++ /dev/null @@ -1,29 +0,0 @@ -# Generated by roxygen2: do not edit by hand - -S3method(GUS,chent) -S3method(GUS,numeric) -S3method(plot,TOXSWA_cwa) -S3method(print,GUS_result) -export(GUS) -export(PEC_soil) -export(PEC_sw_drainage_UK) -export(PEC_sw_drift) -export(PEC_sw_sed) -export(SFO_actual_twa) -export(SSLRC_mobility_classification) -export(TOXSWA_cwa) -export(endpoint) -export(geomean) -export(pfm_degradation) -export(read.TOXSWA_cwa) -export(soil_DT50) -export(soil_Kfoc) -export(soil_N) -export(soil_sorption) -import(chents) -import(graphics) -import(mkin) -importFrom(R6,R6Class) -importFrom(methods,is) -importFrom(readr,fwf_empty) -importFrom(readr,read_fwf) diff --git a/pkg/R/FOCUS_GW_scenarios_2012.R b/pkg/R/FOCUS_GW_scenarios_2012.R deleted file mode 100644 index 49cf7dd..0000000 --- a/pkg/R/FOCUS_GW_scenarios_2012.R +++ /dev/null @@ -1,11 +0,0 @@ -#' A very small subset of the FOCUS Groundwater scenario defitions -#' -#' Currently, only a small subset of the soil definitions are provided. -#' -#' @name FOCUS_GW_scenarios_2012 -#' @references FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. -#' FOrum for the Co-ordination of pesticde fate models and their USe. -#' http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf -#' @examples -#' FOCUS_GW_scenarios_2012 -NULL diff --git a/pkg/R/GUS.R b/pkg/R/GUS.R deleted file mode 100644 index 4a6532d..0000000 --- a/pkg/R/GUS.R +++ /dev/null @@ -1,98 +0,0 @@ -# Copyright (C) 2015 Johannes Ranke -# Contact: jranke@uni-bremen.de -# This file is part of the R package pfm - -# This program is free software: you can redistribute it and/or modify it under -# the terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -#' Groundwater ubiquity score based on Gustafson (1989) -#' -#' The groundwater ubiquity score GUS is calculated according to -#' the following equation -#' \deqn{GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})}{GUS = log10 DT50soil * (4 - log10 Koc)} -#' -#' @references Gustafson, David I. (1989) Groundwater ubiquity score: a simple -#' method for assessing pesticide leachability. \emph{Environmental -#' toxicology and chemistry} \bold{8}(4) 339–57. -#' @inheritParams endpoint -#' @param DT50 Half-life of the chemical in soil. Should be a field -#' half-life according to Gustafson (1989). However, leaching to the sub-soil -#' can not completely be excluded in field dissipation experiments and Gustafson -#' did not refer to any normalisation procedure, but says the field study should -#' be conducted under use conditions. -#' @param Koc The sorption constant normalised to organic carbon. Gustafson -#' does not mention the nonlinearity of the sorption constant commonly -#' found and usually described by Freundlich sorption, therefore it is -#' unclear at which reference concentration the Koc should be observed -#' (and if the reference concentration would be in soil or in porewater). -#' @param chent If a chent is given with appropriate information present in its -#' chyaml field, this information is used, with defaults specified below. -#' @param degradation_value Which of the available degradation values should -#' be used? -#' @param lab_field Should laboratory or field half-lives be used? This -#' defaults to lab in this implementation, in order to avoid -#' double-accounting for mobility. If comparability with the original GUS -#' values given by Gustafson (1989) is desired, non-normalised first-order -#' field half-lives obtained under actual use conditions should be used. -#' @param redox Aerobic or anaerobic degradation data -#' @param sorption_value Which of the available sorption values should be used? -#' Defaults to Kfoc as this is what is generally available from the European -#' pesticide peer review process. These values generally use a reference -#' concentration of 1 mg/L in porewater, that means they would be expected to -#' be Koc values at a concentration of 1 mg/L in the water phase. -#' @param degradation_aggregator Function for aggregating half-lives -#' @param sorption_aggregator Function for aggregation Koc values -#' @param ... Included in the generic to allow for further arguments later. Therefore -#' this also had to be added to the specific methods. -#' @return A list with the DT50 and Koc used as well as the resulting score -#' of class GUS_result -#' @author Johannes Ranke -#' @export -GUS <- function(...) UseMethod("GUS") - -#' @rdname GUS -#' @export -GUS.numeric <- function(DT50, Koc, ...) { - score <- log10(DT50) * (4 - log10(Koc)) - res <- list(DT50 = DT50, Koc = Koc, score = score) - class(res) <- "GUS_result" - return(res) -} - -#' @rdname GUS -#' @export -GUS.chent <- function(chent, - degradation_value = "DT50ref", - lab_field = "laboratory", - redox = "aerobic", - sorption_value = "Kfoc", - degradation_aggregator = geomean, - sorption_aggregator = geomean, - ...) -{ - DT50 = soil_DT50(chent, lab_field = lab_field, redox = redox, - value = degradation_value, - aggregator = degradation_aggregator, signif = 5) - Koc = soil_Kfoc(chent, value = sorption_value, - aggregator = sorption_aggregator, signif = 5) - GUS.numeric(DT50, Koc) -} - -#' @rdname GUS -#' @export -#' @param x An object of class GUS_result to be printed -#' @param digits The number of digits used in the print method -print.GUS_result = function(x, ..., digits = 1) { - cat("GUS: ", round(x$score, digits = 1), "\n") - cat("calculated from DT50 ", x$DT50, " and Koc ", x$Koc, "\n") -} diff --git a/pkg/R/PEC_soil.R b/pkg/R/PEC_soil.R deleted file mode 100644 index 0263e47..0000000 --- a/pkg/R/PEC_soil.R +++ /dev/null @@ -1,215 +0,0 @@ -# Copyright (C) 2015 Johannes Ranke -# Contact: jranke@uni-bremen.de -# This file is part of the R package pfm - -# This program is free software: you can redistribute it and/or modify it under -# the terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -# Register global variables -if(getRversion() >= '2.15.1') utils::globalVariables(c("destination", "study_type", "TP_identifier", - "soil_scenario_data_EFSA_2015")) - -#' Calculate predicted environmental concentrations in soil -#' -#' This is a basic calculation of a contaminant concentration in bulk soil -#' based on complete, instantaneous mixing. If an interval is given, an -#' attempt is made at calculating a long term maximum concentration using -#' the concepts layed out for example in the PPR panel opinion (EFSA 2012). -#' -#' This assumes that the complete load to soil during the time specified by -#' 'interval' (typically 365 days) is dosed at once. As in the PPR panel -#' opinion cited below (PPR panel 2012), only temperature correction using the -#' Arrhenius equation is performed. -#' -#' Total soil and porewater PEC values for the scenarios as defined in the EFSA -#' guidance (2015, p. 13) can easily be calculated. -#' -#' @note If temperature information is available in the selected scenarios, as -#' e.g. in the EFSA scenarios, the DT50 for groundwater modelling -#' (destination 'PECgw') is taken from the chent object, otherwise the DT50 -#' with destination 'PECsoil'. -#' @importFrom methods is -#' @param rate Application rate in units specified below -#' @param rate_units Defaults to g/ha -#' @param interception The fraction of the application rate that does not reach the soil -#' @param mixing_depth Mixing depth in cm -#' @param interval Period of the deeper mixing, defaults to 365, which is a year if -#' rate units are in days -#' @param n_periods Number of periods to be considered for long term PEC calculations -#' @param PEC_units Requested units for the calculated PEC. Only mg/kg currently supported -#' @param PEC_pw_units Only mg/L currently supported -#' @param tillage_depth Periodic (see interval) deeper mixing in cm -#' @param chent An optional chent object holding substance specific information. Can -#' also be a name for the substance as a character string -#' @param DT50 If specified, overrides soil DT50 endpoints from a chent object -#' If DT50 is not specified here and not available from the chent object, zero -#' degradation is assumed -#' @param Koc If specified, overrides Koc endpoints from a chent object -#' @param Kom Calculated from Koc by default, but can explicitly be specified -#' as Kom here -#' @param t_avg Averaging times for time weighted average concentrations -#' @param scenarios If this is 'default', the DT50 will be used without correction -#' and soil properties as specified in the REACH guidance (R.16, Table -#' R.16-9) are used for porewater PEC calculations. If this is "EFSA_2015", -#' the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when -#' 'chents' is specified, the DegT50 with destination 'PECgw' will be used), -#' and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also -#' model and scenario adjustment factors from the EFSA guidance are used. -#' @param porewater Should equilibrium porewater concentrations be estimated -#' based on Kom and the organic carbon fraction of the soil instead of total -#' soil concentrations? Based on equation (7) given in the PPR panel opinion -#' (EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015, -#' p. 13). -#' @return The predicted concentration in soil -#' @references EFSA Panel on Plant Protection Products and their Residues (2012) -#' Scientific Opinion on the science behind the guidance for scenario -#' selection and scenario parameterisation for predicting environmental -#' concentrations of plant protection products in soil. \emph{EFSA Journal} -#' \bold{10}(2) 2562, doi:10.2903/j.efsa.2012.2562 -#' -#' EFSA (European Food Safety Authority) (2015) EFSA guidance document for -#' predicting environmental concentrations of active substances of plant -#' protection products and transformation products of these active substances -#' in soil. \emph{EFSA Journal} \bold{13}(4) 4093 -#' doi:10.2903/j.efsa.2015.4093 -#' @author Johannes Ranke -#' @export -#' @examples -#' PEC_soil(100, interception = 0.25) -#' -#' # This is example 1 starting at p. 79 of the EFSA guidance (2015) -#' PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), -#' scenarios = "EFSA_2015") -#' PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), -#' Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE) -#' -#' # The following is from example 4 starting at p. 85 of the EFSA guidance (2015) -#' # Metabolite M2 -#' # Calculate total and porewater soil concentrations for tier 1 scenarios -#' # Relative molar mass is 100/300, formation fraction is 0.7 * 1 -#' results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21), -#' scenarios = "EFSA_2015") -#' results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21), -#' Kom = 100, scenarios = "EFSA_2015", porewater = TRUE) - -PEC_soil <- function(rate, rate_units = "g/ha", interception = 0, - mixing_depth = 5, - PEC_units = "mg/kg", PEC_pw_units = "mg/L", - interval = NA, n_periods = Inf, - tillage_depth = 20, - chent = NA, - DT50 = NA, - Koc = NA, Kom = Koc / 1.724, - t_avg = 0, - scenarios = c("default", "EFSA_2015"), - porewater = FALSE) -{ - rate_to_soil = (1 - interception) * rate - rate_units = match.arg(rate_units) - PEC_units = match.arg(PEC_units) - scenarios = match.arg(scenarios) - sce <- switch(scenarios, - default = data.frame(rho = 1.5, T_arr = NA, theta_fc = 0.2, f_oc = 0.02, - f_sce = 1, f_mod = 1, row.names = "default"), - EFSA_2015 = if (porewater) soil_scenario_data_EFSA_2015[4:6, ] - else soil_scenario_data_EFSA_2015[1:3, ] - ) - n_sce = nrow(sce) - - soil_volume = 100 * 100 * (mixing_depth/100) # in m3 - soil_mass = soil_volume * sce$rho * 1000 # in kg - - # The following is C_T,ini from EFSA 2012, p. 22, but potentially with interception > 0 - PEC_soil_ini = rate_to_soil * 1000 / soil_mass # in mg/kg - - # Decide which DT50 to take, or set degradation to zero if no DT50 available - if (is.na(DT50) & is(chent, "chent")) { - if (all(is.na(sce$T_arr))) { # No temperature correction - DT50 <- subset(chent$soil_degradation_endpoints, destination == "PECsoil")$DT50 - } else { - DT50 <- subset(chent$soil_degradation_endpoints, destination == "PECgw")$DT50 - } - if (length(DT50) > 1) stop("More than one PECsoil DT50 in chent object") - if (length(DT50) == 0) DT50 <- Inf - } - k = log(2)/DT50 - - # Temperature correction of degradation (accumulation) - if (all(is.na(sce$T_arr))) { # No temperature correction - f_T = 1 - } else { - # Temperature correction as in EFSA 2012 p. 23 - f_T = ifelse(sce$T_arr == 0, - 0, - exp(- (65.4 / 0.008314) * (1/(sce$T_arr + 273.15) - 1/293.15))) - } - - # X is the fraction left after one period (EFSA guidance p. 23) - X = exp(- k * f_T * interval) - - # f_accu is the fraction left after n periods (X + X^2 + ...) - f_accu = 0 - if (!is.na(interval)) { - if (n_periods == Inf) { - f_accu = X/(1 - X) - } else { - for (i in 1:n_periods) { - f_accu = f_accu + X^i - } - } - } - - f_tillage = mixing_depth / tillage_depth - - PEC_background = f_accu * f_tillage * PEC_soil_ini - - PEC_soil = (1 + f_accu * f_tillage) * PEC_soil_ini - - # Get porewater PEC if requested - if (porewater) { - - # If Kom is not specified, try to get K(f)oc - if (is.na(Kom)) { - # If Koc not specified, try to get K(f)oc from chent - if (is.na(Koc) & is(chent, "chent")) { - Koc <- soil_Kfoc(chent) - } - Kom <- Koc / 1.724 - } - - if (is.na(Kom)) stop("No Kom information specified") - - PEC_soil = PEC_soil/((sce$theta_fc/sce$rho) + sce$f_om * Kom) - } - - # Scenario adjustment factors - PEC_soil_sce = PEC_soil * sce$f_sce - - # Model adjustment factors - PEC_soil_sce_mod = PEC_soil_sce * sce$f_mod - - result <- matrix(NA, ncol = n_sce, nrow = length(t_avg), - dimnames = list(t_avg = t_avg, scenario = rownames(sce))) - - result[1, ] <- PEC_soil_sce_mod - - for (i in seq_along(t_avg)) { - t_av_i <- t_avg[i] - if (t_av_i > 0) { - # Equation 10 from p. 24 (EFSA 2015) - result[i, ] <- PEC_soil_sce_mod/(t_av_i * f_T * k) * (1 - exp(- f_T * k * t_av_i)) - } - } - - return(result) -} diff --git a/pkg/R/PEC_sw_drainage_UK.R b/pkg/R/PEC_sw_drainage_UK.R deleted file mode 100644 index e53f179..0000000 --- a/pkg/R/PEC_sw_drainage_UK.R +++ /dev/null @@ -1,66 +0,0 @@ -# Copyright (C) 2015 Johannes Ranke -# Contact: jranke@uni-bremen.de -# This file is part of the R package pfm - -# This program is free software: you can redistribute it and/or modify it under -# the terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -#' Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method -#' -#' This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet -#' published on the CRC website -#' -#' @param rate Application rate in g/ha -#' @param interception The fraction of the application rate that does not reach the soil -#' @param Koc The sorption coefficient normalised to organic carbon in L/kg -#' @param latest_application Latest application date, formatted as e.g. "01 July" -#' @param soil_DT50 Soil degradation half-life, if SFO kinetics are to be used -#' @param model The soil degradation model to be used. Either one of "FOMC", -#' "DFOP", "HS", or "IORE", or an mkinmod object -#' @param model_parms A named numeric vector containing the model parameters -#' @return The predicted concentration in surface water in µg/L -#' @export -#' @author Johannes Ranke -#' @examples -#' PEC_sw_drainage_UK(150, Koc = 100) -PEC_sw_drainage_UK <- function(rate, interception = 0, Koc, - latest_application = NULL, soil_DT50 = NULL, - model = NULL, model_parms = NULL) -{ - percentage_lost <- SSLRC_mobility_classification(Koc)[[2]] - amount_available <- rate * (1 - interception) # g/ha - - if (!missing(latest_application)) { - lct <- Sys.getlocale("LC_TIME") - tmp <- Sys.setlocale("LC_TIME", "C") - latest <- as.Date(paste(latest_application, "1999"), "%d %b %Y") - tmp <- Sys.setlocale("LC_TIME", lct) - degradation_time <- as.numeric(difftime(as.Date("1999-10-01"), units = "days", latest)) - if (!missing(soil_DT50)) { - k = log(2)/soil_DT50 - as.Date(paste(latest_application, "1999"), "%d %B %Y") - - amount_available <- amount_available * exp(-k * degradation_time) - if (!missing(model)) stop("You already supplied a soil_DT50 value, implying SFO kinetics") - } - if (!missing(model)) { - fraction_left <- pfm_degradation(model, parms = model_parms, - times = degradation_time)[1, "parent"] - amount_available <- fraction_left * amount_available - } - } - - volume = 130000 # L/ha - PEC = 1e6 * (percentage_lost/100) * amount_available / volume - return(PEC) -} diff --git a/pkg/R/PEC_sw_drift.R b/pkg/R/PEC_sw_drift.R deleted file mode 100644 index 261706c..0000000 --- a/pkg/R/PEC_sw_drift.R +++ /dev/null @@ -1,65 +0,0 @@ -# Copyright (C) 2015 Johannes Ranke -# Contact: jranke@uni-bremen.de -# This file is part of the R package pfm - -# This program is free software: you can redistribute it and/or modify it under -# the terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -#' Calculate predicted environmental concentrations in surface water due to drift -#' -#' This is a basic, vectorised form of a simple calculation of a contaminant -#' concentration in surface water based on complete, instantaneous mixing -#' with input via spray drift. -#' -#' @param rate Application rate in units specified below -#' @param applications Number of applications for selection of drift percentile -#' @param drift_percentages Percentage drift values for which to calculate PECsw. -#' 'drift_data' and 'distances' if not NULL. -#' @param drift_data Source of drift percentage data -#' @param crop Crop name (use German names for JKI data), defaults to "Ackerbau" -#' @param distances The distances in m for which to get PEC values -#' @param water_depth Depth of the water body in cm -#' @param rate_units Defaults to g/ha -#' @param PEC_units Requested units for the calculated PEC. Only µg/L currently supported -#' @return The predicted concentration in surface water -#' @export -#' @author Johannes Ranke -#' @examples -#' PEC_sw_drift(100) -PEC_sw_drift <- function(rate, - applications = 1, - water_depth = 30, - drift_percentages = NULL, - drift_data = "JKI", - crop = "Ackerbau", - distances = c(1, 5, 10, 20), - rate_units = "g/ha", - PEC_units = "\u00B5g/L") -{ - rate_units <- match.arg(rate_units) - PEC_units <- match.arg(PEC_units) - drift_data <- match.arg(drift_data) - water_volume <- 100 * 100 * (water_depth/100) * 1000 # in L (for 1 ha) - PEC_sw_overspray <- rate * 1e6 / water_volume # in µg/L - dist_index <- as.character(distances) - - if (is.null(drift_percentages)) { - drift_percentages <- pfm::drift_data_JKI[[applications]][dist_index, crop] - names(drift_percentages) <- paste(dist_index, "m") - } else { - names(drift_percentages) <- paste(drift_percentages, "%") - } - - PEC_sw_drift <- PEC_sw_overspray * drift_percentages / 100 - return(PEC_sw_drift) -} diff --git a/pkg/R/PEC_sw_sed.R b/pkg/R/PEC_sw_sed.R deleted file mode 100644 index a4a3d6a..0000000 --- a/pkg/R/PEC_sw_sed.R +++ /dev/null @@ -1,50 +0,0 @@ -# Copyright (C) 2015 Johannes Ranke -# Contact: jranke@uni-bremen.de -# This file is part of the R package pfm - -# This program is free software: you can redistribute it and/or modify it under -# the terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -#' Calculate predicted environmental concentrations in sediment from surface -#' water concentrations -#' -#' The method 'percentage' is equivalent to what is used in the CRD spreadsheet -#' PEC calculator -#' -#' @param PEC_sw Numeric vector or matrix of surface water concentrations in µg/L for -#' which the corresponding sediment concentration is to be estimated -#' @param percentage The percentage in sediment, used for the percentage method -#' @param method The method used for the calculation -#' @param sediment_depth Depth of the sediment layer -#' @param water_depth Depth of the water body in cm -#' @param sediment_density The density of the sediment in L/kg (equivalent to -#' g/cm3) -#' @param PEC_sed_units The units of the estimated sediment PEC value -#' @return The predicted concentration in sediment -#' @export -#' @author Johannes Ranke -#' @examples -#' PEC_sw_sed(PEC_sw_drift(100, distances = 1), percentage = 50) -PEC_sw_sed <- function(PEC_sw, percentage = 100, method = "percentage", - sediment_depth = 5, water_depth = 30, - sediment_density = 1.3, - PEC_sed_units = c("\u00B5g/kg", "mg/kg")) -{ - method = match.arg(method) - PEC_sed_units = match.arg(PEC_sed_units) - if (method == "percentage") { - PEC_sed = PEC_sw * (percentage/100) * (water_depth / sediment_depth) * (1 / sediment_density) - if (PEC_sed_units == "mg/kg") PEC_sed <- PEC_sed / 1000 - } - return(PEC_sed) -} diff --git a/pkg/R/SFO_actual_twa.R b/pkg/R/SFO_actual_twa.R deleted file mode 100644 index 7facb6a..0000000 --- a/pkg/R/SFO_actual_twa.R +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright (C) 2015 Johannes Ranke -# Contact: jranke@uni-bremen.de -# This file is part of the R package pfm - -# This program is free software: you can redistribute it and/or modify it under -# the terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -#' Actual and maximum moving window time average concentrations for SFO kinetics -#' -#' @param DT50 The half-life. -#' @param times The output times, and window sizes for time weighted average concentrations -#' @export -#' @author Johannes Ranke -#' @source FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation -#' Kinetics from Environmental Fate Studies on Pesticides in EU Registratin, Version 1.1, -#' 18 December 2014, p. 251 -#' @examples -#' SFO_actual_twa(10) -SFO_actual_twa <- function(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100)) -{ - k = log(2)/DT50 - result <- data.frame(actual = 1 * exp(-k * times), - twa = (1 - exp(-k * times))/(k * times), - row.names = times) - return(result) -} diff --git a/pkg/R/SSLRC_mobility_classification.R b/pkg/R/SSLRC_mobility_classification.R deleted file mode 100644 index deda5cf..0000000 --- a/pkg/R/SSLRC_mobility_classification.R +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright (C) 2015 Johannes Ranke -# Contact: jranke@uni-bremen.de -# This file is part of the R package pfm - -# This program is free software: you can redistribute it and/or modify it under -# the terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -#' Determine the SSLRC mobility classification for a chemical substance from its Koc -#' -#' This implements the method specified in the UK data requirements handbook and was -#' checked against the spreadsheet published on the CRC website -#' -#' @param Koc The sorption coefficient normalised to organic carbon in L/kg -#' @return A list containing the classification and the percentage of the -#' compound transported per 10 mm drain water -#' @export -#' @author Johannes Ranke -#' @examples -#' SSLRC_mobility_classification(100) -SSLRC_mobility_classification <- function(Koc) -{ - if (!is.numeric(Koc) | length(Koc) != 1) stop("Please give a single number") - result <- list("Non mobile", 0.01) - if (Koc < 4000) result <- list("Slightly mobile", 0.02) - if (Koc < 1000) result <- list("Slightly mobile", 0.5) - if (Koc < 500) result <- list("Moderately mobile", 0.7) - if (Koc < 75) result <- list("Mobile", 1.9) - if (Koc < 15) result <- list("Very mobile", 1.9) - names(result) <- c("Mobility classification", - "Percentage drained per mm of drain water") - return(result) -} diff --git a/pkg/R/TOXSWA_cwa.R b/pkg/R/TOXSWA_cwa.R deleted file mode 100644 index c5ddce9..0000000 --- a/pkg/R/TOXSWA_cwa.R +++ /dev/null @@ -1,380 +0,0 @@ -# Copyright (C) 2014,2015,2016 Johannes Ranke -# Contact: jranke@uni-bremen.de -# This file is part of the R package pfm - -# This program is free software: you can redistribute it and/or modify it under -# the terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -#' Read TOXSWA surface water concentrations -#' -#' Read TOXSWA hourly concentrations of a chemical substance in a specific -#' segment of a TOXSWA surface water body. Per default, the data for the last -#' segment are imported. As TOXSWA 4 reports the values at the end of the hour -#' (ConLiqWatLayCur) in its summary file, we use this value as well instead -#' of the hourly averages (ConLiqWatLay). -#' -#' @param filename The filename of the cwa file (TOXSWA 2.x.y or similar) or the -#' out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar). -#' @param basedir The path to the directory where the cwa file resides. -#' @param zipfile Optional path to a zip file containing the cwa file. -#' @param segment The segment for which the data should be read. Either "last", or -#' the segment number. -#' @param total Set this to TRUE in order to read total concentrations as well. This is -#' only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa -#' files. For .cwa files, the total concentration is always read as well. -#' @param substance For TOXSWA 4 .out files, the default value "parent" leads -#' to reading concentrations of the parent compound. Alternatively, the substance -#' of interested can be selected by its code name. -#' @param windows Numeric vector of width of moving windows in days, for calculating -#' maximum time weighted average concentrations and areas under the curve. -#' @param thresholds Numeric vector of threshold concentrations in µg/L for -#' generating event statistics. -#' @importFrom readr read_fwf fwf_empty -#' @return An instance of an R6 object of class -#' \code{\link{TOXSWA_cwa}}. -#' @export -#' @author Johannes Ranke -#' @examples -#' H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", -#' basedir = "SwashProjects/project_H_sw/TOXSWA", -#' zipfile = system.file("testdata/SwashProjects.zip", -#' package = "pfm")) -read.TOXSWA_cwa <- function(filename, basedir = ".", zipfile = NULL, - segment = "last", substance = "parent", - total = FALSE, - windows = NULL, thresholds = NULL) -{ - if (!missing(filename)) { - cwa <- TOXSWA_cwa$new(filename, basedir, zipfile, - substance = substance, total = total) - if (!is.null(windows[1])) cwa$moving_windows(windows) - if (!is.null(thresholds[1])) cwa$get_events(thresholds) - invisible(cwa) - } else { - message("You need to specify a filename for the cwa file to be read") - } -} - -#' Plot TOXSWA surface water concentrations -#' -#' Plot TOXSWA hourly concentrations of a chemical substance in a specific -#' segment of a TOXSWA surface water body. -#' -#' @import graphics -#' @param x The TOXSWA_cwa object to be plotted. -#' @param xlab,ylab Labels for x and y axis. -#' @param time_column What should be used for the time axis. If "t_firstjan" is chosen, -#' the time is given in days relative to the first of January in the first year. -#' @param add Should we add to an existing plot? -#' @param total Should the total concentration in water be plotted, including substance sorbed -#' to suspended matter? -#' @param LC_TIME Specification of the locale used to format dates -#' @param ... Further arguments passed to \code{plot} if we are not adding to an existing plot -#' @export -#' @author Johannes Ranke -#' @examples -#' H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", -#' basedir = "SwashProjects/project_H_sw/TOXSWA", -#' zipfile = system.file("testdata/SwashProjects.zip", -#' package = "pfm")) -#' plot(H_sw_D4_pond) -plot.TOXSWA_cwa <- function(x, time_column = c("datetime", "t", "t_firstjan", "t_rel_to_max"), - xlab = "default", ylab = "default", - add = FALSE, - total = FALSE, LC_TIME = "C", ...) -{ - time_column = match.arg(time_column) - cwa_column = ifelse(total, "cwa_tot_mug_per_L", "cwa_mug_per_L") - lct <- Sys.getlocale("LC_TIME") - tmp <- Sys.setlocale("LC_TIME", LC_TIME) - if (xlab == "default") { - xlab = switch(time_column, - datetime = "Time", - t = "Time [days]", - t_firstjan = "Time since first of January [days]", - t_rel_to_max = "Time relative to maximum concentration [days]") - } - if (ylab == "default") { - ylab = paste( ifelse(total, "Total concentration", "Concentration"), "[\u03bcg/L]") - } - if (add) { - lines(x$cwas[c(time_column, cwa_column)], xlab = xlab, ylab = ylab, ...) - } else{ - if (time_column == "datetime") { - plot(x$cwas$datetime, x$cwas[[cwa_column]], type = "l", - xlab = xlab, ylab = ylab, xaxt = "n", ...) - seq_x <- seq(min(x$cwas$datetime), max(x$cwas$datetime), by = "quarter") - axis(1, at = seq_x, labels = format(seq_x, "%b %Y")) - } else { - plot(x$cwas[c(time_column, cwa_column)], type = "l", - xlab = xlab, ylab = ylab, ...) - } - } - tmp <- Sys.setlocale("LC_TIME", lct) -} - -#' R6 class for holding TOXSWA cwa concentration data and associated statistics -#' -#' An R6 class for holding TOXSWA cwa concentration data and some associated statistics. -#' Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_cwa}}. -#' -#' @docType class -#' @importFrom R6 R6Class -#' @export -#' @format An \code{\link{R6Class}} generator object. -#' @field filename Length one character vector. -#' @field basedir Length one character vector. -#' @field segment Length one integer, specifying for which segment the cwa data were read. -#' @field cwas Dataframe holding the concentrations. -#' @field events List of dataframes holding the event statistics for each threshold. -#' @field windows Matrix of maximum time weighted average concentrations (TWAC_max) -#' and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) -#' for the requested moving window sizes in days. -#' @section Methods: -#' \describe{ -#' \item{\code{get_events(threshold, total = FALSE)}}{ -#' Populate a datataframe with event information for the specified threshold value -#' in µg/L. If \code{total = TRUE}, the total concentration including the amount -#' adsorbed to suspended matter will be used. The resulting dataframe is stored in the -#' \code{events} field of the object. -#' } -#' \item{\code{moving_windows(windows, total = FALSE)}}{ -#' Add to the \code{windows} field described above. -#' Again, if \code{total = TRUE}, the total concentration including the amount -#' adsorbed to suspended matter will be used. -#' } -#' } -#' @examples -#' H_sw_R1_stream <- read.TOXSWA_cwa("00003s_pa.cwa", -#' basedir = "SwashProjects/project_H_sw/TOXSWA", -#' zipfile = system.file("testdata/SwashProjects.zip", -#' package = "pfm")) -#' H_sw_R1_stream$get_events(c(2, 10)) -#' H_sw_R1_stream$moving_windows(c(7, 21)) -#' print(H_sw_R1_stream) -#' @keywords data - -TOXSWA_cwa <- R6Class("TOXSWA_cwa", - public = list( - filename = NULL, - basedir = NULL, - zipfile = NULL, - segment = NULL, - substance = NULL, - cwas = NULL, - windows = NULL, - events = list(), - initialize = function(filename, basedir, zipfile = NULL, - segment = "last", substance = "parent", total = FALSE) { - self$filename <- filename - self$basedir <- basedir - self$zipfile <- zipfile - if (!is.null(zipfile)) { - try(file_connection <- unz(zipfile, paste0(basedir, "/", filename))) - } else { - try(file_connection <- file(file.path(basedir, filename), "rt")) - } - - - if (grepl(".cwa$", filename)) { - # cwa file from FOCUS TOXSWA 3 (TOXSWA 2.x.y) - cwa_all_segments <- try( - read.table(file_connection, - sep = "", skip = 40, - encoding = "UTF-8", - colClasses = c("character", "numeric", - "integer", rep("numeric", 5)), - col.names = c("datetime", "t", "segment", - "xcd", "cwa_tot", "cwa", "Xss", "Xmp"))) - - if (is.null(zipfile)) close(file_connection) # only needed for files - - if (!inherits(cwa_all_segments, "try-error")) { - available_segments = 1:max(cwa_all_segments$segment) - if (segment == "last") segment = max(available_segments) - if (!segment %in% available_segments) stop("Invalid segment specified") - self$segment <- segment - cwa <- subset(cwa_all_segments, segment == self$segment, - c("datetime", "t", "segment", "cwa", "cwa_tot")) - lct <- Sys.getlocale("LC_TIME"); Sys.setlocale("LC_TIME", "C") - cwa$datetime <- strptime(cwa$datetime, "%d-%b-%Y-%H:%M") - Sys.setlocale("LC_TIME", lct) - startyear = format(cwa$datetime[1], "%Y") - firstjan <- strptime(paste0(startyear, "-01-01"), "%Y-%m-%d") - cwa$t_firstjan <- as.numeric(difftime(cwa$datetime, - firstjan, units = "days")) - - t_max = cwa[which.max(cwa$cwa), "t"] - cwa$t_rel_to_max = cwa$t - t_max - cwa$cwa_mug_per_L <- cwa$cwa * 1000 - cwa$cwa_tot_mug_per_L <- cwa$cwa_tot * 1000 - self$cwas <- cwa[c("datetime", "t", "t_firstjan", - "t_rel_to_max", - "cwa_mug_per_L", - "cwa_tot_mug_per_L")] - } else { - stop("Could not read ", filename) - } - } else { - # out file from FOCUS TOXSWA 4 (TOXSWA 4.4.2 or similar) - outfile <- try(readLines(file_connection)) - - close(file_connection) # only needed for files - - if (inherits(outfile, "try-error")) { - stop("Could not read ", filename) - } else { - # Get the substance name(s) - sub_lines <- grep(".*0.000.*ConLiqWatLayCur_", outfile[1:50], value = TRUE) - substances <- gsub(".*ConLiqWatLayCur_(.*?) *[0-9].*", "\\1", sub_lines) - if (!substance %in% c("parent", substances)) { - stop("No data for substance ", substance, " present in the .out file.") - } - - # Generate field name for the concentrations at end of hour for the - # substance of interest - if (substance == "parent") { - cwa_string = paste0("ConLiqWatLayCur_", substances[1]) - } else { - cwa_string = paste0("ConLiqWatLayCur_", substance) - } - - cwa_lines <- grep(cwa_string, outfile, value = TRUE) - - cwa_all_segments <- read_fwf(paste(cwa_lines, collapse = "\n"), - fwf_empty(paste(tail(cwa_lines), collapse = "\n"))) - - # Append time "-00h00" to datetime in first row, as this is not (always?) present - # in the line ConLiqWatLayCur - if (nchar(cwa_all_segments[1, "X2"]) == 11) { - cwa_all_segments[1, "X2"] = paste0(cwa_all_segments[1, "X2"], "-00h00") - } - - available_segments = 1:(ncol(cwa_all_segments) - 3) - if (segment == "last") segment = max(available_segments) - if (!segment %in% available_segments) stop("Invalid segment specified") - self$segment <- segment - cwa <- data.frame( - datetime = as.character(cwa_all_segments$X2), - t = cwa_all_segments$X1, - cwa = cwa_all_segments[[3 + segment]] - ) - if (total) { - cwa_tot_lines <- outfile[grep("ConSysWatLay_", outfile)] # hourly total conc. - cwa_tot_all_segments <- read.table(text = cwa_lines) - cwa$cwa_tot = cwa_tot_all_segments[[3 + segment]] - } - lct <- Sys.getlocale("LC_TIME"); Sys.setlocale("LC_TIME", "C") - cwa$datetime <- strptime(cwa$datetime, "%d-%b-%Y-%Hh%M") - Sys.setlocale("LC_TIME", lct) - - startyear = format(cwa$datetime[1], "%Y") - firstjan <- strptime(paste0(startyear, "-01-01"), "%Y-%m-%d") - cwa$t_firstjan <- as.numeric(difftime(cwa$datetime, - firstjan, units = "days")) - t_max = cwa[which.max(cwa$cwa), "t"] - cwa$t_rel_to_max = cwa$t - t_max - cwa$cwa_mug_per_L <- cwa$cwa * 1000 - self$cwas <- cwa[c("datetime", "t", "t_firstjan", - "t_rel_to_max", - "cwa_mug_per_L")] - if (total) { - self$cwas$cwa_tot_mug_per_L <- cwa$cwa_tot * 1000 - } - } - } - }, - moving_windows = function(windows, total = FALSE) { - window_names = paste(windows, "days") - n = length(window_names) - self$windows <- data.frame(window = window_names, - max_TWAC = numeric(n), - max_AUC_h = numeric(n), - max_AUC_d = numeric(n)) - if (missing(windows)) { - stop("You need to specify at least one moving window size in days") - } - cwa_column = ifelse(total, "cwa_tot_mug_per_L", "cwa_mug_per_L") - for (i in seq_along(windows)) { - window_size = windows[i] - filter_size = window_size * 24 - max_TWAC = max(filter(self$cwas[cwa_column], rep(1/filter_size, filter_size), - "convolution"), na.rm = TRUE) - max_AUC_h = max_TWAC * filter_size - max_AUC_d = max_TWAC * window_size - - self$windows[i, -1] = c(max_TWAC, max_AUC_h, max_AUC_d) - } - invisible(self) - }, - get_events = function(thresholds, total = FALSE) { - if (missing(thresholds)) { - stop("You need to specify at least one threshold concentration in \u03bcg/L") - } - for (threshold in thresholds) { - events = data.frame(t_start = numeric(), cwa_max = numeric(), - duration = numeric(), pre_interval = numeric(), - AUC_h = numeric(), AUC_d = numeric()) - cwa_column = ifelse(total, "cwa_tot_mug_per_L", "cwa_mug_per_L") - - event_end = 0 - event = FALSE - event_max = 0 - event_nr = 0 - n_rows = nrow(self$cwas) - for (i in 1:n_rows) { - cwa_cur = self$cwas[i, cwa_column] - if (event == FALSE) { - if (cwa_cur > threshold) { - event_start = self$cwas[i, "t"] - pre_interval = event_start - event_end - i_start = i - event = TRUE - event_max = cwa_cur - } - } else { - if (cwa_cur > event_max) event_max = cwa_cur - if (cwa_cur < threshold || i == n_rows) { - event_nr = event_nr + 1 - i_end = i - if (i == n_rows) i_end = i - event_end = self$cwas[i_end, "t"] - event_length = event_end - event_start - event_cwas <- self$cwas[i_start:(i_end - 1), cwa_column] - event_AUC_h = sum(event_cwas) - event_AUC_d = event_AUC_h / 24 - events[event_nr, ] = c(event_start, event_max, event_length, - pre_interval, event_AUC_h, event_AUC_d) - event = FALSE - } - } - } - - self$events[[as.character(threshold)]] <- events - } - invisible(self) - }, - print = function() { - cat(" data from file", self$filename, "segment", self$segment, "\n") - print(head(self$cwas)) - cat("Moving window analysis\n") - print(self$windows) - for (threshold in names(self$events)) { - cat("Event statistics for threshold", threshold, "\n") - if (nrow(self$events[[threshold]]) == 0) cat("No events found\n") - else print(self$events[[threshold]]) - } - } - ) -) -# vim: set ts=2 sw=2 expandtab: diff --git a/pkg/R/drift_data_JKI.R b/pkg/R/drift_data_JKI.R deleted file mode 100644 index 888d3b5..0000000 --- a/pkg/R/drift_data_JKI.R +++ /dev/null @@ -1,44 +0,0 @@ -#' Deposition from spray drift expressed as percent of the applied dose as -#' published by the JKI -#' -#' Deposition from spray drift expressed as percent of the applied dose as -#' published by the German Julius-Kühn Institute (JKI). -#' -#' The data were extracted from the spreadsheet cited below using the R code -#' given in the example section. The spreadsheet is not included in the package -#' as its licence is not clear. -#' -#' -#' @name drift_data_JKI -#' @docType data -#' @format A list currently containing matrices with spray drift percentage -#' data for field crops (Ackerbau), and Pome/stone fruit, early and late -#' (Obstbau frueh, spaet). -#' @source JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved -#' from -#' http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html -#' on 2015-06-11 -#' @keywords datasets -#' @examples -#' -#' \dontrun{ -#' # This is the code that was used to extract the data -#' library(readxl) -#' abdrift_path <- "inst/extdata/Tabelle der Abdrifteckwerte.xls" -#' JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet") -#' names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late") -#' drift_data_JKI <- list() -#' -#' for (n in 1:8) { -#' drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2) -#' drift_data <- as.matrix(drift_data_raw[1:9, 2:4]) -#' dimnames(drift_data) <- list(distance = as.integer(drift_data_raw[1:9, 1]), -#' crop = JKI_crops) -#' drift_data_JKI[[n]] <- drift_data -#' } -#' save(drift_data_JKI, file = "data/drift_data_JKI.RData") -#' } -#' -#' # And this is the resulting data -#' drift_data_JKI -NULL diff --git a/pkg/R/endpoint.R b/pkg/R/endpoint.R deleted file mode 100644 index 314acd2..0000000 --- a/pkg/R/endpoint.R +++ /dev/null @@ -1,110 +0,0 @@ -#' Retrieve endpoint information from the chyaml field of a chent object -#' -#' R6 class objects of class \code{\link{chent}} represent chemical entities -#' and can hold a list of information loaded from a chemical yaml file in their -#' chyaml field. Such information is extracted and optionally aggregated by -#' this function. -#' -#' The functions \code{soil_*} are functions to extract soil specific endpoints. -#' For the Freundlich exponent, the capital letter \code{N} is used in order to -#' facilitate dealing with such data in R. In pesticide fate modelling, this -#' exponent is often called 1/n. -#' -#' @import chents -#' @export -#' @param chent The \code{\link{chent}} object to get the information from -#' @param medium The medium for which information is sought -#' @param type The information type -#' @param lab_field If not NA, do we want laboratory or field endpoints -#' @param redox If not NA, are we looking for aerobic or anaerobic data -#' @param value The name of the value we want. The list given in the -#' usage section is not exclusive -#' @param aggregator The aggregator function. Can be mean, -#' \code{\link{geomean}}, or identity, for example. -#' @param raw Should the number(s) be returned as stored in the chent -#' object (could be a character value) to retain original information -#' about precision? -#' @param signif How many significant digits do we want -#' @return The result from applying the aggregator function to -#' the values converted to a numeric vector, rounded to the -#' given number of significant digits, or, if raw = TRUE, -#' the values as a character value, retaining any implicit -#' information on precision that may be present. -#' -endpoint <- function(chent, - medium = "soil", - type = c("degradation", "sorption"), - lab_field = c(NA, "laboratory", "field"), - redox = c(NA, "aerobic", "anaerobic"), - value = c("DT50ref", "Kfoc", "N"), - aggregator = geomean, - raw = FALSE, - signif = 3) -{ - if (!is(chent, "chent")) { - stop("Please supply a chent object as created using the package 'chents' available from jrwb.de") - } - ep_list <- chent$chyaml[[medium]][[type]] - if (!is.na(lab_field[1])) { - ep_list <- ep_list[[lab_field]] - } - if (!is.na(redox[1])) { - ep_list <- ep_list[[redox]] - } - values <- ep_list$data[[value]] - if (raw) return(values) - else return(signif(aggregator(as.numeric(values)), signif)) -} - -#' @inheritParams endpoint -#' @rdname endpoint -#' @export -soil_DT50 <- function(chent, aggregator = geomean, signif = 3, - lab_field = "laboratory", value = "DT50ref", - redox = "aerobic", raw = FALSE) { - ep <- endpoint(chent, medium = "soil", type = "degradation", - lab_field = "laboratory", redox = redox, - signif = signif, - value = value, aggregator = aggregator, raw = raw) - return(ep) -} - -#' @inheritParams endpoint -#' @rdname endpoint -#' @export -soil_Kfoc <- function(chent, aggregator = geomean, signif = 3, - value = "Kfoc", raw = FALSE) { - ep <- endpoint(chent, medium = "soil", type = "sorption", - signif = signif, - value = value, aggregator = aggregator, raw = raw) - return(ep) -} - -#' @inheritParams endpoint -#' @rdname endpoint -#' @export -soil_N <- function(chent, aggregator = mean, signif = 3, raw = FALSE) { - ep <- endpoint(chent, medium = "soil", type = "sorption", - signif = signif, - value = "N", aggregator = aggregator, raw = raw) - return(ep) -} - -#' @inheritParams endpoint -#' @rdname endpoint -#' @param values The values to be returned -#' @param aggregators A named vector of aggregator functions to be used -#' @export -soil_sorption <- function(chent, values = c("Kfoc", "N"), - aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), - signif = c(Kfoc = 3, N = 3), - raw = FALSE) { - res <- sapply(values, - function(x) { - endpoint(chent, medium = "soil", type = "sorption", - signif = signif[[x]], - value = x, aggregator = aggregators[[x]], raw = raw) - } - ) - return(res) -} diff --git a/pkg/R/geomean.R b/pkg/R/geomean.R deleted file mode 100644 index 626829b..0000000 --- a/pkg/R/geomean.R +++ /dev/null @@ -1,38 +0,0 @@ -# Copyright (C) 2015 Johannes Ranke -# Contact: jranke@uni-bremen.de -# This file is part of the R package pfm - -# This program is free software: you can redistribute it and/or modify it under -# the terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -#' Calculate the geometric mean -#' -#' Based on some posts in a thread on Stackoverflow -#' \url{http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in} -#' This function checks for negative values, removes NA values per default and -#' returns 0 if at least one element of the vector is 0. -#' -#' @param x Vector of numbers -#' @param na.rm Should NA values be omitted? -#' @return The geometric mean -#' @export -#' @author Johannes Ranke -#' @examples -#' geomean(c(1, 3, 9)) -#' geomean(c(1, 3, NA, 9)) -#' \dontrun{geomean(c(1, -3, 9)) # returns an error} -geomean = function(x, na.rm = TRUE){ - if (any(is.na(x)) & na.rm == FALSE) stop("Removal of NA values was not requested") - if (any(x < 0, na.rm = na.rm)) stop("Only defined for positive numbers") - exp(mean(log(x), na.rm = na.rm)) -} diff --git a/pkg/R/pfm_degradation.R b/pkg/R/pfm_degradation.R deleted file mode 100644 index 6c8610e..0000000 --- a/pkg/R/pfm_degradation.R +++ /dev/null @@ -1,48 +0,0 @@ -# Copyright (C) 2015 Johannes Ranke -# Contact: jranke@uni-bremen.de -# This file is part of the R package pfm - -# This program is free software: you can redistribute it and/or modify it under -# the terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -#' Calculate a time course of relative concentrations based on an mkinmod model -#' -#' @import mkin -#' @param model The degradation model to be used. Either a parent only model like -#' 'SFO' or 'FOMC', or an mkinmod object -#' @param DT50 The half-life. This is only used when simple exponential decline -#' is calculated (SFO model). -#' @param parms The parameters used for the degradation model -#' @param years For how many years should the degradation be predicted? -#' @param step_days What step size in days should the output have? -#' @param times The output times -#' @export -#' @author Johannes Ranke -#' @examples -#' head(pfm_degradation("SFO", DT50 = 10)) -pfm_degradation <- function(model = "SFO", DT50 = 1000, parms = c(k_parent_sink = log(2)/DT50), - years = 1, step_days = 1, - times = seq(0, years * 365, by = step_days)) -{ - if (model %in% c("SFO", "FOMC", "DFOP", "HS", "IORE")) { - model <- mkinmod(parent = list(type = model)) - } - initial_state = c(1, rep(0, length(model$diffs) - 1)) - names(initial_state) <- names(model$diffs) - time_course <- mkinpredict(model, odeparms = parms, - odeini = initial_state, - outtimes = times, - solution_type = ifelse(length(model$spec) == 1, - "analytical", "deSolve")) - invisible(time_course) -} diff --git a/pkg/R/soil_scenario_data_EFSA_2015.R b/pkg/R/soil_scenario_data_EFSA_2015.R deleted file mode 100644 index fb096bc..0000000 --- a/pkg/R/soil_scenario_data_EFSA_2015.R +++ /dev/null @@ -1,40 +0,0 @@ -#' Properties of the predefined scenarios from the EFSA guidance from 2015 -#' -#' Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the -#' concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the -#' scenario and model adjustment factors from p. 15 and p. 17 are included. -#' -#' @name soil_scenario_data_EFSA_2015 -#' @docType data -#' @format A data frame with one row for each scenario. Row names are the scenario codes, -#' e.g. CTN for the Northern scenario for the total concentration in soil. Columns are -#' mostly self-explanatory. \code{rho} is the dry bulk density of the top soil. -#' @source EFSA (European Food Safety Authority) (2015) -#' EFSA guidance document for predicting environmental concentrations -#' of active substances of plant protection products and transformation products of these -#' active substances in soil. \emph{EFSA Journal} \bold{13}(4) 4093 -#' doi:10.2903/j.efsa.2015.4093 -#' @keywords datasets -#' @examples -#' \dontrun{ -#' # This is the code that was used to define the data -#' soil_scenario_data_EFSA_2015 <- data.frame( -#' Zone = rep(c("North", "Central", "South"), 2), -#' Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"), -#' T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8), -#' T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7), -#' Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"), -#' f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011), -#' theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347), -#' rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51), -#' f_sce = c(3, 2, 2, 2, 1.5, 1.5), -#' f_mod = c(2, 2, 2, 4, 4, 4), -#' stringsAsFactors = FALSE, -#' row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS") -#' ) -#' save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData') -#' } -#' -#' # And this is the resulting dataframe -#' soil_scenario_data_EFSA_2015 -NULL diff --git a/pkg/data/FOCUS_GW_scenarios_2012.RData b/pkg/data/FOCUS_GW_scenarios_2012.RData deleted file mode 100644 index 4b2622e..0000000 Binary files a/pkg/data/FOCUS_GW_scenarios_2012.RData and /dev/null differ diff --git a/pkg/data/drift_data_JKI.RData b/pkg/data/drift_data_JKI.RData deleted file mode 100644 index 0a2f05e..0000000 Binary files a/pkg/data/drift_data_JKI.RData and /dev/null differ diff --git a/pkg/data/soil_scenario_data_EFSA_2015.RData b/pkg/data/soil_scenario_data_EFSA_2015.RData deleted file mode 100644 index b30076f..0000000 Binary files a/pkg/data/soil_scenario_data_EFSA_2015.RData and /dev/null differ diff --git a/pkg/inst/extdata/FOCUS_GW_scenarios_2012.R b/pkg/inst/extdata/FOCUS_GW_scenarios_2012.R deleted file mode 100644 index 3715325..0000000 --- a/pkg/inst/extdata/FOCUS_GW_scenarios_2012.R +++ /dev/null @@ -1,59 +0,0 @@ -# FOCUS 2012 p. 46 ff -FOCUS_GW_scenarios_2012 = list() - -n_layers = c(7, 6, 6, 5, 5, 6, 4, 6, 6) -acronyms = c("Cha", "Ham", "Jok", "Kre", "Oke", "Pia", "Por", "Sev", "Thi") -FOCUS_GW_scenarios_2012$names = c("Ch\u00e2teadun", "Hamburg", "Jokioinen", - "Kremsm\u00fcnster", "Okehampton", - "Piacenza", "Porto", "Sevilla", "Thiva") - -names(FOCUS_GW_scenarios_2012$names) = acronyms -FOCUS_GW_scenarios_2012$soils <- data.frame( - location= rep(acronyms, times = n_layers), - horizon = c("Ap", "B1", "B2", "II C1", "II C1", "II C2", "M", - "Ap", "BvI", "BvII", "Bv/Cv", "Cv", "Cv", - "Ap", "Bs", "BC1", "BC2", "BC2", "Cg", - rep(NA, 5), - "A", "Bw1", "BC", "C", "C", - "Ap", "Ap", "Bw", "Bw", "2C", "2C", - rep(NA, 4), - rep(NA, 6), - "Ap1", "Ap2", "Bw", "Bw", "Ck1", "Ck1"), - number = unlist(sapply(n_layers, function(x) 1:x)), - pH_H2O = c(8.0, 8.1, 8.2, 8.5, 8.5, 8.5, 8.3, - 6.4, 5.6, 5.6, 5.7, 5.5, 5.5, - 6.2, 5.6, 5.4, 5.4, 5.4, 5.3, - 7.7, 7.0, 7.1, 7.1, 7.1, - 5.8, 6.3, 6.5, 6.6, 6.6, - 7, 7, 6.3, 6.3, 6.4, 6.4, - 4.9, 4.8, 4.8, 4.8, - 7.3, 7.3, 7.8, 8.1, 8.1, 8.2, - 7.7, 7.7, 7.8, 7.8, 7.8, 7.8), - perc_clay = c(30, 31, 25, 26, 26, 24, 31, - 7.2, 6.7, 0.9, 0, 0, 0, - 3.6, 1.8, 1.2, 1.7, 1.7, 1.9, - 14, 25, 27, 27, 27, - 18, 17, 14, 9, 9, - 15, 15, 7, 7, 0, 0, - 10, 8, 8, 8, - 14, 13, 15, 16, 16, 22, - 25.3, 25.3, 29.6, 31.9, 32.9, 32.9), - perc_oc = c(1.39, 0.93, 0.7, 0.3, 0.3, 0.27, 0.21, - 1.5, 1, 0.2, 0, 0, 0, - 4.06, 0.84, 0.36, 0.29, 0.29, 0.21, - 3.6, 1.0, 0.5, 0.5, 0.5, - 2.2, 0.7, 0.4, 0.1, 0.1, - 1.26, 1.26, 0.47, 0.47, 0, 0, - 1.42, 0.78, 0.78, 0.78, - 0.93, 0.93, 0.70, 0.58, 0.58, 0.49, - 0.74, 0.74, 0.57, 0.31, 0.18, 0.18), - rel_deg = c(1, 0.5, 0.5, 0.3, 0, 0, 0, - 1, 0.5, 0.3, 0.3, 0.3, 0, - 1, 0.5, 0.3, 0.3, 0, 0, - 1, 0.5, 0.5, 0.3, 0, - 1, 0.5, 0.3, 0.3, 0, - 1, 0.5, 0.5, 0.3, 0.3, 0, - 1, 0.5, 0.3, 0, - 1, 1, 0.5, 0.3, 0, 0, - 1, 0.5, 0.5, 0.3, 0.3, 0)) -save(FOCUS_GW_scenarios_2012, file = "../../data/FOCUS_GW_scenarios_2012.RData") diff --git a/pkg/inst/staticdocs/index.r b/pkg/inst/staticdocs/index.r deleted file mode 100644 index 421071c..0000000 --- a/pkg/inst/staticdocs/index.r +++ /dev/null @@ -1,42 +0,0 @@ -sd_section( - "Degradation", - "Functions related to degradation", - c("pfm_degradation", "SFO_actual_twa") -) -sd_section( - "Mobility", - "Indicators related to mobility", - c("GUS", "SSLRC_mobility_classification") -) -sd_section( - "Soil", - "Predicted environmental concentrations in soil", - c("PEC_soil", "soil_scenario_data_EFSA_2015") -) -sd_section( - "Surface water", - "Predicted environmental concentrations in surface water", - c( - "PEC_sw_drift", "PEC_sw_sed", - "drift_data_JKI", - "PEC_sw_drainage_UK", - "TOXSWA_cwa", - "read.TOXSWA_cwa", - "plot.TOXSWA_cwa" - ) -) -sd_section( - "Groundwater", - "Predicted environmental concentrations in groundwater", - c("FOCUS_GW_scenarios_2012") -) -sd_section( - "Chemical entities", - "Work with input stored in chemical entites as R objects using the chent package", - c("endpoint") -) -sd_section( - "General", - "Utilities that are generally useful", - c("geomean") -) diff --git a/pkg/inst/testdata/SwashProjects.zip b/pkg/inst/testdata/SwashProjects.zip deleted file mode 100644 index 5b9ff49..0000000 Binary files a/pkg/inst/testdata/SwashProjects.zip and /dev/null differ diff --git a/pkg/inst/web/FOCUS_GW_scenarios_2012.html b/pkg/inst/web/FOCUS_GW_scenarios_2012.html deleted file mode 100644 index 43ac090..0000000 --- a/pkg/inst/web/FOCUS_GW_scenarios_2012.html +++ /dev/null @@ -1,154 +0,0 @@ - - - - -FOCUS_GW_scenarios_2012. pfm 0.3-7 - - - - - - - - - - - - - - - -
-
-
- pfm 0.3-7 -
- -
-
-
-
- -
-
- -
- -

A very small subset of the FOCUS Groundwater scenario defitions

- -
-
- -
-

Description

- -

Currently, only a small subset of the soil definitions are provided.

- -
- -
-

References

- -

FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. - FOrum for the Co-ordination of pesticde fate models and their USe. - http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf

- -
- -

Examples

- 
FOCUS_GW_scenarios_2012
-

-
$names
-           Cha            Ham            Jok            Kre            Oke 
-  "Châteaudun"      "Hamburg"    "Jokioinen" "Kremsmünster"   "Okehampton" 
-           Pia            Por            Sev            Thi 
-    "Piacenza"        "Porto"      "Sevilla"        "Thiva" 
-
-$soils
-   location horizon number pH_H2O perc_clay perc_oc rel_deg
-1       Cha      Ap      1    8.0      30.0    1.39     1.0
-2       Cha      B1      2    8.1      31.0    0.93     0.5
-3       Cha      B2      3    8.2      25.0    0.70     0.5
-4       Cha   II C1      4    8.5      26.0    0.30     0.3
-5       Cha   II C1      5    8.5      26.0    0.30     0.0
-6       Cha   II C2      6    8.5      24.0    0.27     0.0
-7       Cha       M      7    8.3      31.0    0.21     0.0
-8       Ham      Ap      1    6.4       7.2    1.50     1.0
-9       Ham     BvI      2    5.6       6.7    1.00     0.5
-10      Ham    BvII      3    5.6       0.9    0.20     0.3
-11      Ham   Bv/Cv      4    5.7       0.0    0.00     0.3
-12      Ham      Cv      5    5.5       0.0    0.00     0.3
-13      Ham      Cv      6    5.5       0.0    0.00     0.0
-14      Jok      Ap      1    6.2       3.6    4.06     1.0
-15      Jok      Bs      2    5.6       1.8    0.84     0.5
-16      Jok     BC1      3    5.4       1.2    0.36     0.3
-17      Jok     BC2      4    5.4       1.7    0.29     0.3
-18      Jok     BC2      5    5.4       1.7    0.29     0.0
-19      Jok      Cg      6    5.3       1.9    0.21     0.0
-20      Kre    <NA>      1    7.7      14.0    3.60     1.0
-21      Kre    <NA>      2    7.0      25.0    1.00     0.5
-22      Kre    <NA>      3    7.1      27.0    0.50     0.5
-23      Kre    <NA>      4    7.1      27.0    0.50     0.3
-24      Kre    <NA>      5    7.1      27.0    0.50     0.0
-25      Oke       A      1    5.8      18.0    2.20     1.0
-26      Oke     Bw1      2    6.3      17.0    0.70     0.5
-27      Oke      BC      3    6.5      14.0    0.40     0.3
-28      Oke       C      4    6.6       9.0    0.10     0.3
-29      Oke       C      5    6.6       9.0    0.10     0.0
-30      Pia      Ap      1    7.0      15.0    1.26     1.0
-31      Pia      Ap      2    7.0      15.0    1.26     0.5
-32      Pia      Bw      3    6.3       7.0    0.47     0.5
-33      Pia      Bw      4    6.3       7.0    0.47     0.3
-34      Pia      2C      5    6.4       0.0    0.00     0.3
-35      Pia      2C      6    6.4       0.0    0.00     0.0
-36      Por    <NA>      1    4.9      10.0    1.42     1.0
-37      Por    <NA>      2    4.8       8.0    0.78     0.5
-38      Por    <NA>      3    4.8       8.0    0.78     0.3
-39      Por    <NA>      4    4.8       8.0    0.78     0.0
-40      Sev    <NA>      1    7.3      14.0    0.93     1.0
-41      Sev    <NA>      2    7.3      13.0    0.93     1.0
-42      Sev    <NA>      3    7.8      15.0    0.70     0.5
-43      Sev    <NA>      4    8.1      16.0    0.58     0.3
-44      Sev    <NA>      5    8.1      16.0    0.58     0.0
-45      Sev    <NA>      6    8.2      22.0    0.49     0.0
-46      Thi     Ap1      1    7.7      25.3    0.74     1.0
-47      Thi     Ap2      2    7.7      25.3    0.74     0.5
-48      Thi      Bw      3    7.8      29.6    0.57     0.5
-49      Thi      Bw      4    7.8      31.9    0.31     0.3
-50      Thi     Ck1      5    7.8      32.9    0.18     0.3
-51      Thi     Ck1      6    7.8      32.9    0.18     0.0
-
-
-
-
- - - -
-
- - -
- - \ No newline at end of file diff --git a/pkg/inst/web/GUS.html b/pkg/inst/web/GUS.html deleted file mode 100644 index a330be2..0000000 --- a/pkg/inst/web/GUS.html +++ /dev/null @@ -1,160 +0,0 @@ - - - - -GUS. pfm 0.3-7 - - - - - - - - - - - - - - - -
-
-
- pfm 0.3-7 -
- -
-
-
-
- -
-
- -
- -

Groundwater ubiquity score based on Gustafson (1989)

- -
-
-

Usage

- 
GUS(...)

-
"GUS"(DT50, Koc, ...)

-
"GUS"(chent, degradation_value = "DT50ref", lab_field = "laboratory", redox = "aerobic", sorption_value = "Kfoc", degradation_aggregator = geomean, sorption_aggregator = geomean, ...)

-
"print"(x, ..., digits = 1)
- -

Arguments

-
-
...
-
Included in the generic to allow for further arguments later. Therefore -this also had to be added to the specific methods.
-
DT50
-
Half-life of the chemical in soil. Should be a field -half-life according to Gustafson (1989). However, leaching to the sub-soil -can not completely be excluded in field dissipation experiments and Gustafson -did not refer to any normalisation procedure, but says the field study should -be conducted under use conditions.
-
Koc
-
The sorption constant normalised to organic carbon. Gustafson -does not mention the nonlinearity of the sorption constant commonly -found and usually described by Freundlich sorption, therefore it is -unclear at which reference concentration the Koc should be observed -(and if the reference concentration would be in soil or in porewater).
-
chent
-
If a chent is given with appropriate information present in its -chyaml field, this information is used, with defaults specified below.
-
degradation_value
-
Which of the available degradation values should -be used?
-
lab_field
-
Should laboratory or field half-lives be used? This -defaults to lab in this implementation, in order to avoid -double-accounting for mobility. If comparability with the original GUS -values given by Gustafson (1989) is desired, non-normalised first-order -field half-lives obtained under actual use conditions should be used.
-
redox
-
Aerobic or anaerobic degradation data
-
sorption_value
-
Which of the available sorption values should be used? -Defaults to Kfoc as this is what is generally available from the European -pesticide peer review process. These values generally use a reference -concentration of 1 mg/L in porewater, that means they would be expected to -be Koc values at a concentration of 1 mg/L in the water phase.
-
degradation_aggregator
-
Function for aggregating half-lives
-
sorption_aggregator
-
Function for aggregation Koc values
-
x
-
An object of class GUS_result to be printed
-
digits
-
The number of digits used in the print method
-
- -
-

Value

- -

-A list with the DT50 and Koc used as well as the resulting score - of class GUS_result -

- -
- -
-

Description

- -

The groundwater ubiquity score GUS is calculated according to -the following equation -$$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$

- -
- -
-

References

- -

Gustafson, David I. (1989) Groundwater ubiquity score: a simple -method for assessing pesticide leachability. Environmental -toxicology and chemistry 8(4) 339–57.

- -
-
-
- - - -

Author

- -Johannes Ranke - - -
-
- - -
- - \ No newline at end of file diff --git a/pkg/inst/web/PEC_soil.html b/pkg/inst/web/PEC_soil.html deleted file mode 100644 index 1304d19..0000000 --- a/pkg/inst/web/PEC_soil.html +++ /dev/null @@ -1,228 +0,0 @@ - - - - -PEC_soil. pfm 0.3-7 - - - - - - - - - - - - - - - -
-
-
- pfm 0.3-7 -
- -
-
-
-
- -
-
- -
- -

Calculate predicted environmental concentrations in soil

- -
-
-

Usage

- 
PEC_soil(rate, rate_units = "g/ha", interception = 0, mixing_depth = 5, PEC_units = "mg/kg", PEC_pw_units = "mg/L", interval = NA, n_periods = Inf, tillage_depth = 20, chent = NA, DT50 = NA, Koc = NA, Kom = Koc/1.724, t_avg = 0, scenarios = c("default", "EFSA_2015"), porewater = FALSE)
- -

Arguments

-
-
rate
-
Application rate in units specified below
-
rate_units
-
Defaults to g/ha
-
interception
-
The fraction of the application rate that does not reach the soil
-
mixing_depth
-
Mixing depth in cm
-
PEC_units
-
Requested units for the calculated PEC. Only mg/kg currently supported
-
PEC_pw_units
-
Only mg/L currently supported
-
interval
-
Period of the deeper mixing, defaults to 365, which is a year if -rate units are in days
-
n_periods
-
Number of periods to be considered for long term PEC calculations
-
tillage_depth
-
Periodic (see interval) deeper mixing in cm
-
chent
-
An optional chent object holding substance specific information. Can -also be a name for the substance as a character string
-
DT50
-
If specified, overrides soil DT50 endpoints from a chent object -If DT50 is not specified here and not available from the chent object, zero -degradation is assumed
-
Koc
-
If specified, overrides Koc endpoints from a chent object
-
Kom
-
Calculated from Koc by default, but can explicitly be specified -as Kom here
-
t_avg
-
Averaging times for time weighted average concentrations
-
scenarios
-
If this is 'default', the DT50 will be used without correction -and soil properties as specified in the REACH guidance (R.16, Table -R.16-9) are used for porewater PEC calculations. If this is "EFSA_2015", -the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when -'chents' is specified, the DegT50 with destination 'PECgw' will be used), -and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also -model and scenario adjustment factors from the EFSA guidance are used.
-
porewater
-
Should equilibrium porewater concentrations be estimated -based on Kom and the organic carbon fraction of the soil instead of total -soil concentrations? Based on equation (7) given in the PPR panel opinion -(EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015, -p. 13).
-
- -
-

Value

- -

-The predicted concentration in soil -

- -
- -
-

Description

- -

This is a basic calculation of a contaminant concentration in bulk soil -based on complete, instantaneous mixing. If an interval is given, an -attempt is made at calculating a long term maximum concentration using -the concepts layed out for example in the PPR panel opinion (EFSA 2012).

- -
- -
-

Details

- -

This assumes that the complete load to soil during the time specified by -'interval' (typically 365 days) is dosed at once. As in the PPR panel -opinion cited below (PPR panel 2012), only temperature correction using the -Arrhenius equation is performed.

- -

Total soil and porewater PEC values for the scenarios as defined in the EFSA -guidance (2015, p. 13) can easily be calculated.

- -
- -
-

Note

- -

If temperature information is available in the selected scenarios, as - e.g. in the EFSA scenarios, the DT50 for groundwater modelling - (destination 'PECgw') is taken from the chent object, otherwise the DT50 - with destination 'PECsoil'.

- -
- -
-

References

- -

EFSA Panel on Plant Protection Products and their Residues (2012) - Scientific Opinion on the science behind the guidance for scenario - selection and scenario parameterisation for predicting environmental - concentrations of plant protection products in soil. EFSA Journal - 10(2) 2562, doi:10.2903/j.efsa.2012.2562

- -

EFSA (European Food Safety Authority) (2015) EFSA guidance document for - predicting environmental concentrations of active substances of plant - protection products and transformation products of these active substances - in soil. EFSA Journal 13(4) 4093 - doi:10.2903/j.efsa.2015.4093

- -
- -

Examples

- 
PEC_soil(100, interception = 0.25)
-

-
     scenario
-t_avg default
-    0     0.1
-

-

-# This is example 1 starting at p. 79 of the EFSA guidance (2015)
-PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21),
-               scenarios = "EFSA_2015")
-

-
     scenario
-t_avg      CTN      CTC      CTS
-   0  21.96827 11.53750 9.145259
-   21 21.78517 11.40701 9.017370
-

-
PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21),
-               Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE)
-

-
     scenario
-t_avg       CLN       CLC       CLS
-   0  0.7589401 0.6674322 0.9147861
-   21 0.7506036 0.6590345 0.8987279
-

-

-# The following is from example 4 starting at p. 85 of the EFSA guidance (2015)
-# Metabolite M2
-# Calculate total and porewater soil concentrations for tier 1 scenarios
-# Relative molar mass is 100/300, formation fraction is 0.7 * 1
-results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21),
-                        scenarios = "EFSA_2015")
-results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21),
-                           Kom = 100, scenarios = "EFSA_2015", porewater = TRUE)
-
-
-
- - - -

Author

- -Johannes Ranke - - -
-
- - -
- - \ No newline at end of file diff --git a/pkg/inst/web/PEC_soil_product.html b/pkg/inst/web/PEC_soil_product.html deleted file mode 100644 index 9704de2..0000000 --- a/pkg/inst/web/PEC_soil_product.html +++ /dev/null @@ -1,141 +0,0 @@ - - - - -PEC_soil_product. pfm 0.2-4 - - - - - - - - - - - - - - - -
-
-
- pfm 0.2-4 -
- -
-
-
-
- -
-
- -
- -

Calculate predicted environmental concentrations in soil for a product

- -
-
-

Usage

- 
PEC_soil_product(product, rate, rate_units = "L/ha", interception = 0, mixing_depth = 5, tillage_depth = 20, interval = 365, PEC_units = "mg/kg", scenarios = "EFSA_2015")
- -

Arguments

-
-
product
-
An object of class pp
-
rate
-
Application rate in units specified below
-
rate_units
-
Defaults to g/ha
-
interception
-
The fraction of the application rate that does not reach the soil
-
mixing_depth
-
Mixing depth in cm
-
tillage_depth
-
Periodic (see interval) deeper mixing in cm
-
interval
-
Period of the deeper mixing, defaults to 365, which is a year if -rate units are in days
-
PEC_units
-
Requested units for the calculated PEC. Only mg/kg currently supported
-
- -
-

Source

- -

EFSA Panel on Plant Protection Products and their Residues (2012) -Scientific Opinion on the science behind the guidance for scenario selection -and scenario parameterisation for predicting environmental concentrations -of plant protection products in soil. EFSA Journal 10(2) 2562, -doi:10.2903/j.efsa.2012.2562

- -

EFSA (European Food Safety Authority) (2015) -EFSA guidance document for predicting environmental concentrations -of active substances of plant protection products and transformation products of these -active substances in soil. EFSA Journal 13(4) 4093 -doi:10.2903/j.efsa.2015.4093

- -
- -
-

Value

- -

-A data frame with compound names, and initial, background (plateau minimum) - and long term maximum predicted concentrations in soil -

- -
- -
-

Description

- -

Calculates long term accumulation PEC values. Assumes that the complete load to soil during the -time specified by 'interval' (typically 365 days) is dosed at once. As in the PPR panel opinion -cited below (PPR panel 2012), only temperature correction using the Arrhenius equation is performed. -By default, PEC values for the scenarios as defined in the EFSA guidance -(2015, p. 13) are calculated.

- -
-
-
- - - -

Author

- -Johannes Ranke - - -
-
- - -
- - \ No newline at end of file diff --git a/pkg/inst/web/PEC_sw_drainage_UK.html b/pkg/inst/web/PEC_sw_drainage_UK.html deleted file mode 100644 index bf97fea..0000000 --- a/pkg/inst/web/PEC_sw_drainage_UK.html +++ /dev/null @@ -1,124 +0,0 @@ - - - - -PEC_sw_drainage_UK. pfm 0.3-7 - - - - - - - - - - - - - - - -
-
-
- pfm 0.3-7 -
- -
-
-
-
- -
-
- -
- -

Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method

- -
-
-

Usage

- 
PEC_sw_drainage_UK(rate, interception = 0, Koc, latest_application = NULL, soil_DT50 = NULL, model = NULL, model_parms = NULL)
- -

Arguments

-
-
rate
-
Application rate in g/ha
-
interception
-
The fraction of the application rate that does not reach the soil
-
Koc
-
The sorption coefficient normalised to organic carbon in L/kg
-
latest_application
-
Latest application date, formatted as e.g. "01 July"
-
soil_DT50
-
Soil degradation half-life, if SFO kinetics are to be used
-
model
-
The soil degradation model to be used. Either one of "FOMC", -"DFOP", "HS", or "IORE", or an mkinmod object
-
model_parms
-
A named numeric vector containing the model parameters
-
- -
-

Value

- -

-The predicted concentration in surface water in µg/L -

- -
- -
-

Description

- -

This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet -published on the CRC website

- -
- -

Examples

- 
PEC_sw_drainage_UK(150, Koc = 100)
-

-
[1] 8.076923
-
-
-
- - - -

Author

- -Johannes Ranke - - -
-
- - -
- - \ No newline at end of file diff --git a/pkg/inst/web/PEC_sw_drainage_UK_ini.html b/pkg/inst/web/PEC_sw_drainage_UK_ini.html deleted file mode 100644 index 0d55bd9..0000000 --- a/pkg/inst/web/PEC_sw_drainage_UK_ini.html +++ /dev/null @@ -1,124 +0,0 @@ - - - - -PEC_sw_drainage_UK_ini. pfm 0.2-4 - - - - - - - - - - - - - - - -
-
-
- pfm 0.2-4 -
- -
-
-
-
- -
-
- -
- -

Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method

- -
-
-

Usage

- 
PEC_sw_drainage_UK_ini(rate, interception = 0, Koc, latest_application = NULL, soil_DT50 = NULL, model = NULL, model_parms = NULL)
- -

Arguments

-
-
rate
-
Application rate in g/ha
-
interception
-
The fraction of the application rate that does not reach the soil
-
Koc
-
The sorption coefficient normalised to organic carbon in L/kg
-
latest_application
-
Latest application date, formatted as e.g. "01 July"
-
soil_DT50
-
Soil degradation half-life, if SFO kinetics are to be used
-
model
-
The degradation model to be used. Either one of "FOMC", "DFOP", -"HS", or "IORE", or an mkinmod object
-
model_parms
-
A named numeric vector containing the model parameters
-
- -
-

Value

- -

-The predicted concentration in surface water in µg/L -

- -
- -
-

Description

- -

This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet -published on the CRC website

- -
- -

Examples

- 
PEC_sw_drainage_UK_ini(150, Koc = 100)
-

-
[1] 8.076923
-
-
-
- - - -

Author

- -Johannes Ranke - - -
-
- - -
- - \ No newline at end of file diff --git a/pkg/inst/web/PEC_sw_drift.html b/pkg/inst/web/PEC_sw_drift.html deleted file mode 100644 index 5d4bb47..0000000 --- a/pkg/inst/web/PEC_sw_drift.html +++ /dev/null @@ -1,130 +0,0 @@ - - - - -PEC_sw_drift. pfm 0.3-7 - - - - - - - - - - - - - - - -
-
-
- pfm 0.3-7 -
- -
-
-
-
- -
-
- -
- -

Calculate predicted environmental concentrations in surface water due to drift

- -
-
-

Usage

- 
PEC_sw_drift(rate, applications = 1, water_depth = 30, drift_percentages = NULL, drift_data = "JKI", crop = "Ackerbau", distances = c(1, 5, 10, 20), rate_units = "g/ha", PEC_units = "µg/L")
- -

Arguments

-
-
rate
-
Application rate in units specified below
-
applications
-
Number of applications for selection of drift percentile
-
water_depth
-
Depth of the water body in cm
-
drift_percentages
-
Percentage drift values for which to calculate PECsw. -'drift_data' and 'distances' if not NULL.
-
drift_data
-
Source of drift percentage data
-
crop
-
Crop name (use German names for JKI data), defaults to "Ackerbau"
-
distances
-
The distances in m for which to get PEC values
-
rate_units
-
Defaults to g/ha
-
PEC_units
-
Requested units for the calculated PEC. Only µg/L currently supported
-
- -
-

Value

- -

-The predicted concentration in surface water -

- -
- -
-

Description

- -

This is a basic, vectorised form of a simple calculation of a contaminant -concentration in surface water based on complete, instantaneous mixing -with input via spray drift.

- -
- -

Examples

- 
PEC_sw_drift(100)
-

-
       1 m        5 m       10 m       20 m 
-0.92333333 0.19000000 0.09666667 0.05000000 
-
-
-
- - - -

Author

- -Johannes Ranke - - -
-
- - -
- - \ No newline at end of file diff --git a/pkg/inst/web/PEC_sw_drift_ini.html b/pkg/inst/web/PEC_sw_drift_ini.html deleted file mode 100644 index bc7eed5..0000000 --- a/pkg/inst/web/PEC_sw_drift_ini.html +++ /dev/null @@ -1,127 +0,0 @@ - - - - -PEC_sw_drift_ini. pfm 0.2-4 - - - - - - - - - - - - - - - -
-
-
- pfm 0.2-4 -
- -
-
-
-
- -
-
- -
- -

Calculate initial predicted environmental concentrations in surface water due to drift

- -
-
-

Usage

- 
PEC_sw_drift_ini(rate, applications = 1, water_depth = 30, drift_data = "JKI", crop = "Ackerbau", distances = c(1, 5, 10, 20), rate_units = "g/ha", PEC_units = "µg/L")
- -

Arguments

-
-
rate
-
Application rate in units specified below
-
applications
-
Number of applications for selection of drift percentile
-
water_depth
-
Depth of the water body in cm
-
drift_data
-
Source of drift percentage data
-
crop
-
Crop name (use German names for JKI data), defaults to "Ackerbau"
-
distances
-
The distances in m for which to get PEC values
-
rate_units
-
Defaults to g/ha
-
PEC_units
-
Requested units for the calculated PEC. Only µg/L currently supported
-
- -
-

Value

- -

-The predicted concentration in surface water -

- -
- -
-

Description

- -

This is a basic, vectorised form of a simple calculation of a contaminant -concentration in surface water based on complete, instantaneous mixing -with input via spray drift.

- -
- -

Examples

- 
PEC_sw_drift_ini(100)
-

-
       1 m        5 m       10 m       20 m 
-0.92333333 0.19000000 0.09666667 0.05000000 
-
-
-
- - - -

Author

- -Johannes Ranke - - -
-
- - -
- - \ No newline at end of file diff --git a/pkg/inst/web/PEC_sw_sed.html b/pkg/inst/web/PEC_sw_sed.html deleted file mode 100644 index 4eda1d7..0000000 --- a/pkg/inst/web/PEC_sw_sed.html +++ /dev/null @@ -1,127 +0,0 @@ - - - - -PEC_sw_sed. pfm 0.3-7 - - - - - - - - - - - - - - - -
-
-
- pfm 0.3-7 -
- -
-
-
-
- -
-
- -
- -

Calculate predicted environmental concentrations in sediment from surface -water concentrations

- -
-
-

Usage

- 
PEC_sw_sed(PEC_sw, percentage = 100, method = "percentage", sediment_depth = 5, water_depth = 30, sediment_density = 1.3, PEC_sed_units = c("µg/kg", "mg/kg"))
- -

Arguments

-
-
PEC_sw
-
Numeric vector or matrix of surface water concentrations in µg/L for -which the corresponding sediment concentration is to be estimated
-
percentage
-
The percentage in sediment, used for the percentage method
-
method
-
The method used for the calculation
-
sediment_depth
-
Depth of the sediment layer
-
water_depth
-
Depth of the water body in cm
-
sediment_density
-
The density of the sediment in L/kg (equivalent to -g/cm3)
-
PEC_sed_units
-
The units of the estimated sediment PEC value
-
- -
-

Value

- -

-The predicted concentration in sediment -

- -
- -
-

Description

- -

The method 'percentage' is equivalent to what is used in the CRD spreadsheet -PEC calculator

- -
- -

Examples

- 
PEC_sw_sed(PEC_sw_drift(100, distances = 1), percentage = 50)
-

-
     1 m 
-2.130769 
-
-
-
- - - -

Author

- -Johannes Ranke - - -
-
- - -
- - \ No newline at end of file diff --git a/pkg/inst/web/SFO_actual_twa.html b/pkg/inst/web/SFO_actual_twa.html deleted file mode 100644 index 3ce9220..0000000 --- a/pkg/inst/web/SFO_actual_twa.html +++ /dev/null @@ -1,123 +0,0 @@ - - - - -SFO_actual_twa. pfm 0.3-7 - - - - - - - - - - - - - - - -
-
-
- pfm 0.3-7 -
- -
-
-
-
- -
-
- -
- -

Actual and maximum moving window time average concentrations for SFO kinetics

- -
-
-

Usage

- 
SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100))
- -

Arguments

-
-
DT50
-
The half-life.
-
times
-
The output times, and window sizes for time weighted average concentrations
-
- -
-

Source

- -

FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation - Kinetics from Environmental Fate Studies on Pesticides in EU Registratin, Version 1.1, - 18 December 2014, p. 251

- -
- -
-

Description

- -

Actual and maximum moving window time average concentrations for SFO kinetics

- -
- -

Examples

- 
SFO_actual_twa(10)
-

-
          actual       twa
-0   1.0000000000       NaN
-1   0.9330329915 0.9661297
-2   0.8705505633 0.9337803
-4   0.7578582833 0.8733416
-7   0.6155722067 0.7923030
-14  0.3789291416 0.6400113
-21  0.2332582479 0.5267498
-28  0.1435872944 0.4412651
-42  0.0544094102 0.3248093
-50  0.0312500000 0.2795222
-100 0.0009765625 0.1441286
-
-
-
- - - -

Author

- -Johannes Ranke - - -
-
- - -
- - \ No newline at end of file diff --git a/pkg/inst/web/SSLRC_mobility_classification.html b/pkg/inst/web/SSLRC_mobility_classification.html deleted file mode 100644 index 43d701e..0000000 --- a/pkg/inst/web/SSLRC_mobility_classification.html +++ /dev/null @@ -1,117 +0,0 @@ - - - - -SSLRC_mobility_classification. pfm 0.3-7 - - - - - - - - - - - - - - - -
-
-
- pfm 0.3-7 -
- -
-
-
-
- -
-
- -
- -

Determine the SSLRC mobility classification for a chemical substance from its Koc

- -
-
-

Usage

- 
SSLRC_mobility_classification(Koc)
- -

Arguments

-
-
Koc
-
The sorption coefficient normalised to organic carbon in L/kg
-
- -
-

Value

- -

-A list containing the classification and the percentage of the - compound transported per 10 mm drain water -

- -
- -
-

Description

- -

This implements the method specified in the UK data requirements handbook and was -checked against the spreadsheet published on the CRC website

- -
- -

Examples

- 
SSLRC_mobility_classification(100)
-

-
$`Mobility classification`
-[1] "Moderately mobile"
-
-$`Percentage drained per mm of drain water`
-[1] 0.7
-
-
-
-
- - - -

Author

- -Johannes Ranke - - -
-
- - -
- - \ No newline at end of file diff --git a/pkg/inst/web/TOXSWA_cwa.html b/pkg/inst/web/TOXSWA_cwa.html deleted file mode 100644 index 0d8ae17..0000000 --- a/pkg/inst/web/TOXSWA_cwa.html +++ /dev/null @@ -1,176 +0,0 @@ - - - - -TOXSWA_cwa. pfm 0.3-7 - - - - - - - - - - - - - - - -
-
-
- pfm 0.3-7 -
- -
-
-
-
- -
-
- -
- -

R6 class for holding TOXSWA cwa concentration data and associated statistics

- -
-
-

Usage

- 
TOXSWA_cwa
- -
-

Format

- -

An R6Class generator object.

- -
- -
-

Description

- -

An R6 class for holding TOXSWA cwa concentration data and some associated statistics. -Usually, an instance of this class will be generated by read.TOXSWA_cwa.

- -
- -
-

Fields

- -

- -

-
filename
Length one character vector.

- -

basedir
Length one character vector.

- -

segment
Length one integer, specifying for which segment the cwa data were read.

- -

cwas
Dataframe holding the concentrations.

- -

events
List of dataframes holding the event statistics for each threshold.

- -

windows
Matrix of maximum time weighted average concentrations (TWAC_max) -and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) -for the requested moving window sizes in days.

- -

- -
- -
-

Methods

- -

- -

-
get_events(threshold, total = FALSE)
- Populate a datataframe with event information for the specified threshold value - in µg/L. If total = TRUE, the total concentration including the amount - adsorbed to suspended matter will be used. The resulting dataframe is stored in the - events field of the object. -

- -

moving_windows(windows, total = FALSE)
- Add to the windows field described above. - Again, if total = TRUE, the total concentration including the amount - adsorbed to suspended matter will be used. -

- -

- -

- -
- -

Examples

- 
H_sw_R1_stream  <- read.TOXSWA_cwa("00003s_pa.cwa",
-                                 basedir = "SwashProjects/project_H_sw/TOXSWA",
-                                 zipfile = system.file("testdata/SwashProjects.zip",
-                                             package = "pfm"))
-H_sw_R1_stream$get_events(c(2, 10))
-H_sw_R1_stream$moving_windows(c(7, 21))
-print(H_sw_R1_stream)
-

-
<TOXSWA_cwa> data from file 00003s_pa.cwa segment 20 
-               datetime     t t_firstjan t_rel_to_max cwa_mug_per_L
-20  1978-10-01 00:00:00 0.000   273.0000      -55.333             0
-40  1978-10-01 01:00:00 0.042   273.0417      -55.291             0
-60  1978-10-01 02:00:00 0.083   273.0833      -55.250             0
-80  1978-10-01 03:00:00 0.125   273.1250      -55.208             0
-100 1978-10-01 04:00:00 0.167   273.1667      -55.166             0
-120 1978-10-01 05:00:00 0.208   273.2083      -55.125             0
-    cwa_tot_mug_per_L
-20                  0
-40                  0
-60                  0
-80                  0
-100                 0
-120                 0
-Moving window analysis
-   window  max_TWAC max_AUC_h max_AUC_d
-1  7 days 2.3926551  401.9660  16.74859
-2 21 days 0.8369248  421.8101  17.57542
-Event statistics for threshold 2 
-  t_start   cwa_max duration pre_interval     AUC_h     AUC_d
-1  44.375  4.167238    0.208       44.375  17.77202  0.740501
-2  55.042 40.584010    0.583       10.459 398.21189 16.592162
-Event statistics for threshold 10 
-  t_start  cwa_max duration pre_interval   AUC_h    AUC_d
-1  55.083 40.58401    0.459       55.083 379.433 15.80971
-
-
-
- - - -
-
- - -
- - \ No newline at end of file diff --git a/pkg/inst/web/css/bootstrap-responsive.css b/pkg/inst/web/css/bootstrap-responsive.css deleted file mode 100644 index 06e55c0..0000000 --- a/pkg/inst/web/css/bootstrap-responsive.css +++ /dev/null @@ -1,815 +0,0 @@ -/*! - * Bootstrap Responsive v2.0.4 - * - * Copyright 2012 Twitter, Inc - * Licensed under the Apache License v2.0 - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Designed and built with all the love in the world @twitter by @mdo and @fat. - */ - -.clearfix { - *zoom: 1; -} - -.clearfix:before, -.clearfix:after { - display: table; - content: ""; -} - -.clearfix:after { - clear: both; -} - -.hide-text { - font: 0/0 a; - color: transparent; - text-shadow: none; - background-color: transparent; - border: 0; -} - -.input-block-level { - display: block; - width: 100%; - min-height: 28px; - -webkit-box-sizing: border-box; - -moz-box-sizing: border-box; - -ms-box-sizing: border-box; - box-sizing: border-box; -} - -.hidden { - display: none; - visibility: hidden; -} - -.visible-phone { - display: none !important; -} - -.visible-tablet { - display: none !important; -} - -.hidden-desktop { - display: none !important; -} - -@media (max-width: 767px) { - .visible-phone { - display: inherit !important; - } - .hidden-phone { - display: none !important; - } - .hidden-desktop { - display: inherit !important; - } - .visible-desktop { - display: none !important; - } -} - -@media (min-width: 768px) and (max-width: 979px) { - .visible-tablet { - display: inherit !important; - } - .hidden-tablet { - display: none !important; - } - .hidden-desktop { - display: inherit !important; - } - .visible-desktop { - display: none !important ; - } -} - -@media (max-width: 480px) { - .nav-collapse { - -webkit-transform: translate3d(0, 0, 0); - } - .page-header h1 small { - display: block; - line-height: 18px; - } - input[type="checkbox"], - input[type="radio"] { - border: 1px solid #ccc; - } - .form-horizontal .control-group > label { - float: none; - width: auto; - padding-top: 0; - text-align: left; - } - .form-horizontal .controls { - margin-left: 0; - } - .form-horizontal .control-list { - padding-top: 0; - } - .form-horizontal .form-actions { - padding-right: 10px; - padding-left: 10px; - } - .modal { - position: absolute; - top: 10px; - right: 10px; - left: 10px; - width: auto; - margin: 0; - } - .modal.fade.in { - top: auto; - } - .modal-header .close { - padding: 10px; - margin: -10px; - } - .carousel-caption { - position: static; - } -} - -@media (max-width: 767px) { - body { - padding-right: 20px; - padding-left: 20px; - } - .navbar-fixed-top, - .navbar-fixed-bottom { - margin-right: -20px; - margin-left: -20px; - } - .container-fluid { - padding: 0; - } - .dl-horizontal dt { - float: none; - width: auto; - clear: none; - text-align: left; - } - .dl-horizontal dd { - margin-left: 0; - } - .container { - width: auto; - } - .row-fluid { - width: 100%; - } - .row, - .thumbnails { - margin-left: 0; - } - [class*="span"], - .row-fluid [class*="span"] { - display: block; - float: none; - width: auto; - margin-left: 0; - } - .input-large, - .input-xlarge, - .input-xxlarge, - input[class*="span"], - select[class*="span"], - textarea[class*="span"], - .uneditable-input { - display: block; - width: 100%; - min-height: 28px; - -webkit-box-sizing: border-box; - -moz-box-sizing: border-box; - -ms-box-sizing: border-box; - box-sizing: border-box; - } - .input-prepend input, - .input-append input, - .input-prepend input[class*="span"], - .input-append input[class*="span"] { - display: inline-block; - width: auto; - } -} - -@media (min-width: 768px) and (max-width: 979px) { - .row { - margin-left: -20px; - *zoom: 1; - } - .row:before, - .row:after { - display: table; - content: ""; - } - .row:after { - clear: both; - } - [class*="span"] { - float: left; - margin-left: 20px; - } - .container, - .navbar-fixed-top .container, - .navbar-fixed-bottom .container { - width: 724px; - } - .span12 { - 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.row-fluid [class*="span"] { - display: block; - float: left; - width: 100%; - min-height: 28px; - margin-left: 2.762430939%; - *margin-left: 2.709239449638298%; - -webkit-box-sizing: border-box; - -moz-box-sizing: border-box; - -ms-box-sizing: border-box; - box-sizing: border-box; - } - .row-fluid [class*="span"]:first-child { - margin-left: 0; - } - .row-fluid .span12 { - width: 99.999999993%; - *width: 99.9468085036383%; - } - .row-fluid .span11 { - width: 91.436464082%; - *width: 91.38327259263829%; - } - .row-fluid .span10 { - width: 82.87292817100001%; - *width: 82.8197366816383%; - } - .row-fluid .span9 { - width: 74.30939226%; - *width: 74.25620077063829%; - } - .row-fluid .span8 { - width: 65.74585634900001%; - *width: 65.6926648596383%; - } - .row-fluid .span7 { - width: 57.182320438000005%; - *width: 57.129128948638304%; - } - .row-fluid .span6 { - width: 48.618784527%; - *width: 48.5655930376383%; - } - .row-fluid .span5 { - width: 40.055248616%; - *width: 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-o-transition: opacity 0.3s linear, top 0.3s ease-out; - transition: opacity 0.3s linear, top 0.3s ease-out; -} - -.modal.fade.in { - top: 50%; -} - -.modal-header { - padding: 9px 15px; - border-bottom: 1px solid #eee; -} - -.modal-header .close { - margin-top: 2px; -} - -.modal-body { - max-height: 400px; - padding: 15px; - overflow-y: auto; -} - -.modal-form { - margin-bottom: 0; -} - -.modal-footer { - padding: 14px 15px 15px; - margin-bottom: 0; - text-align: right; - background-color: #f5f5f5; - border-top: 1px solid #ddd; - -webkit-border-radius: 0 0 6px 6px; - -moz-border-radius: 0 0 6px 6px; - border-radius: 0 0 6px 6px; - *zoom: 1; - -webkit-box-shadow: inset 0 1px 0 #ffffff; - -moz-box-shadow: inset 0 1px 0 #ffffff; - box-shadow: inset 0 1px 0 #ffffff; -} - -.modal-footer:before, -.modal-footer:after { - display: table; - content: ""; -} - -.modal-footer:after { - clear: both; -} - -.modal-footer .btn + .btn { - margin-bottom: 0; - margin-left: 5px; -} - -.modal-footer 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linear-gradient(top, #149bdf, #0480be); - background-image: -ms-linear-gradient(top, #149bdf, #0480be); - background-repeat: repeat-x; - filter: progid:dximagetransform.microsoft.gradient(startColorstr='#149bdf', endColorstr='#0480be', GradientType=0); - -webkit-box-shadow: inset 0 -1px 0 rgba(0, 0, 0, 0.15); - -moz-box-shadow: inset 0 -1px 0 rgba(0, 0, 0, 0.15); - box-shadow: inset 0 -1px 0 rgba(0, 0, 0, 0.15); - -webkit-box-sizing: border-box; - -moz-box-sizing: border-box; - -ms-box-sizing: border-box; - box-sizing: border-box; - -webkit-transition: width 0.6s ease; - -moz-transition: width 0.6s ease; - -ms-transition: width 0.6s ease; - -o-transition: width 0.6s ease; - transition: width 0.6s ease; -} - -.progress-striped .bar { - background-color: #149bdf; - background-image: -o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); - background-image: 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100%,from(#5bc0de),to(#339bb9));background-image:-webkit-linear-gradient(top,#5bc0de,#339bb9);background-image:-o-linear-gradient(top,#5bc0de,#339bb9);background-image:linear-gradient(top,#5bc0de,#339bb9);background-repeat:repeat-x;filter:progid:dximagetransform.microsoft.gradient(startColorstr='#5bc0de',endColorstr='#339bb9',GradientType=0)}.progress-info.progress-striped .bar{background-color:#5bc0de;background-image:-webkit-gradient(linear,0 100%,100% 0,color-stop(0.25,rgba(255,255,255,0.15)),color-stop(0.25,transparent),color-stop(0.5,transparent),color-stop(0.5,rgba(255,255,255,0.15)),color-stop(0.75,rgba(255,255,255,0.15)),color-stop(0.75,transparent),to(transparent));background-image:-webkit-linear-gradient(-45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:-moz-linear-gradient(-45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:-ms-linear-gradient(-45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:-o-linear-gradient(-45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:linear-gradient(-45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent)}.progress-warning .bar{background-color:#faa732;background-image:-moz-linear-gradient(top,#fbb450,#f89406);background-image:-ms-linear-gradient(top,#fbb450,#f89406);background-image:-webkit-gradient(linear,0 0,0 100%,from(#fbb450),to(#f89406));background-image:-webkit-linear-gradient(top,#fbb450,#f89406);background-image:-o-linear-gradient(top,#fbb450,#f89406);background-image:linear-gradient(top,#fbb450,#f89406);background-repeat:repeat-x;filter:progid:dximagetransform.microsoft.gradient(startColorstr='#fbb450',endColorstr='#f89406',GradientType=0)}.progress-warning.progress-striped .bar{background-color:#fbb450;background-image:-webkit-gradient(linear,0 100%,100% 0,color-stop(0.25,rgba(255,255,255,0.15)),color-stop(0.25,transparent),color-stop(0.5,transparent),color-stop(0.5,rgba(255,255,255,0.15)),color-stop(0.75,rgba(255,255,255,0.15)),color-stop(0.75,transparent),to(transparent));background-image:-webkit-linear-gradient(-45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:-moz-linear-gradient(-45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:-ms-linear-gradient(-45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:-o-linear-gradient(-45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:linear-gradient(-45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent)}.accordion{margin-bottom:18px}.accordion-group{margin-bottom:2px;border:1px solid #e5e5e5;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px}.accordion-heading{border-bottom:0}.accordion-heading .accordion-toggle{display:block;padding:8px 15px}.accordion-toggle{cursor:pointer}.accordion-inner{padding:9px 15px;border-top:1px solid #e5e5e5}.carousel{position:relative;margin-bottom:18px;line-height:1}.carousel-inner{position:relative;width:100%;overflow:hidden}.carousel .item{position:relative;display:none;-webkit-transition:.6s ease-in-out left;-moz-transition:.6s ease-in-out left;-ms-transition:.6s ease-in-out left;-o-transition:.6s ease-in-out left;transition:.6s ease-in-out left}.carousel .item>img{display:block;line-height:1}.carousel .active,.carousel .next,.carousel .prev{display:block}.carousel .active{left:0}.carousel .next,.carousel .prev{position:absolute;top:0;width:100%}.carousel .next{left:100%}.carousel .prev{left:-100%}.carousel .next.left,.carousel .prev.right{left:0}.carousel .active.left{left:-100%}.carousel .active.right{left:100%}.carousel-control{position:absolute;top:40%;left:15px;width:40px;height:40px;margin-top:-20px;font-size:60px;font-weight:100;line-height:30px;color:#fff;text-align:center;background:#222;border:3px solid #fff;-webkit-border-radius:23px;-moz-border-radius:23px;border-radius:23px;opacity:.5;filter:alpha(opacity=50)}.carousel-control.right{right:15px;left:auto}.carousel-control:hover{color:#fff;text-decoration:none;opacity:.9;filter:alpha(opacity=90)}.carousel-caption{position:absolute;right:0;bottom:0;left:0;padding:10px 15px 5px;background:#333;background:rgba(0,0,0,0.75)}.carousel-caption h4,.carousel-caption p{color:#fff}.hero-unit{padding:60px;margin-bottom:30px;background-color:#eee;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px}.hero-unit h1{margin-bottom:0;font-size:60px;line-height:1;letter-spacing:-1px;color:inherit}.hero-unit p{font-size:18px;font-weight:200;line-height:27px;color:inherit}.pull-right{float:right}.pull-left{float:left}.hide{display:none}.show{display:block}.invisible{visibility:hidden} diff --git a/pkg/inst/web/css/highlight.css b/pkg/inst/web/css/highlight.css deleted file mode 100644 index 4b85237..0000000 --- a/pkg/inst/web/css/highlight.css +++ /dev/null @@ -1,28 +0,0 @@ -/* Syntax highlighting ---------------------------------------------------- */ - -pre .input { - border-left: 3px solid #ccc; - padding-left: 0.5em; -} -pre .output { - background-color: #eee; -} - -.number {color:rgb(21,20,181);} -.functioncall {color:#264D66 ;} -.string {color:#375D81 ;} -.keyword {font-weight:bolder ;color:black;} -.argument {color:#264D66 ;} -.comment {color: #333;} -.formalargs {color: #264D66;} -.eqformalargs {color:#264D66;} -.slot {font-style:italic;} -.symbol {color:black ;} -.prompt {color:black ;} - -pre img { - background-color: #fff; - border: 1px solid #ccc; - display: block; - margin: 0.5em auto 0.5em auto; -} diff --git a/pkg/inst/web/css/staticdocs.css b/pkg/inst/web/css/staticdocs.css deleted file mode 100644 index 9fee28b..0000000 --- a/pkg/inst/web/css/staticdocs.css +++ /dev/null @@ -1,18 +0,0 @@ -h2 {padding-top: 20px} - -.icon img { - float: right; - border: 1px solid #ccc; -} -.index .internal {display: none;} -ul.index li {margin-bottom: 0.5em; clear: both;} - -footer { - margin-top: 45px; - padding: 35px 0 36px; - border-top: 1px solid #e5e5e5; -} -footer p { - margin-bottom: 0; - color: #555; -} diff --git a/pkg/inst/web/drift_data_JKI.html b/pkg/inst/web/drift_data_JKI.html deleted file mode 100644 index c3471c9..0000000 --- a/pkg/inst/web/drift_data_JKI.html +++ /dev/null @@ -1,239 +0,0 @@ - - - - -drift_data_JKI. pfm 0.3-7 - - - - - - - - - - - - - - - -
-
-
- pfm 0.3-7 -
- -
-
-
-
- -
-
- -
- -

Deposition from spray drift expressed as percent of the applied dose as -published by the JKI

- -
-
- -
-

Format

- -

A list currently containing matrices with spray drift percentage -data for field crops (Ackerbau), and Pome/stone fruit, early and late -(Obstbau frueh, spaet).

- -
- -
-

Source

- -

JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved -from -http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html -on 2015-06-11

- -
- -
-

Description

- -

Deposition from spray drift expressed as percent of the applied dose as -published by the German Julius-Kühn Institute (JKI).

- -
- -
-

Details

- -

The data were extracted from the spreadsheet cited below using the R code -given in the example section. The spreadsheet is not included in the package -as its licence is not clear.

- -
- -

Examples

- 

-## Not run: 
-#   # This is the code that was used to extract the data
-#   library(readxl)
-#   abdrift_path <- "inst/extdata/Tabelle der Abdrifteckwerte.xls"
-#   JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet")
-#   names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late")
-#   drift_data_JKI <- list()
-# 
-#   for (n in 1:8) {
-#     drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2)
-#     drift_data <- as.matrix(drift_data_raw[1:9, 2:4]) 
-#     dimnames(drift_data) <- list(distance = as.integer(drift_data_raw[1:9, 1]),
-#                                             crop = JKI_crops)
-#     drift_data_JKI[[n]] <- drift_data
-#   }
-#   save(drift_data_JKI, file = "data/drift_data_JKI.RData")
-# ## End(Not run)
-
-# And this is the resulting data
-drift_data_JKI
-

-
[[1]]
-        crop
-distance Ackerbau Obstbau frueh Obstbau spaet
-      1      2.77            NA            NA
-      3        NA         29.20         15.73
-      5      0.57         19.89          8.41
-      10     0.29         11.81          3.60
-      15     0.20          5.55          1.81
-      20     0.15          2.77          1.09
-      30     0.10          1.04          0.54
-      40     0.07          0.52          0.32
-      50     0.06          0.30          0.22
-
-[[2]]
-        crop
-distance Ackerbau Obstbau frueh Obstbau spaet
-      1      2.38            NA            NA
-      3        NA         25.53         12.13
-      5      0.47         16.87          6.81
-      10     0.24          9.61          3.11
-      15     0.16          5.61          1.58
-      20     0.12          2.59          0.90
-      30     0.08          0.87          0.40
-      40     0.06          0.40          0.23
-      50     0.05          0.22          0.15
-
-[[3]]
-        crop
-distance Ackerbau Obstbau frueh Obstbau spaet
-      1      2.01            NA            NA
-      3        NA         23.96         11.01
-      5      0.41         15.79          6.04
-      10     0.20          8.96          2.67
-      15     0.14          4.24          1.39
-      20     0.10          2.01          0.80
-      30     0.07          0.70          0.36
-      40     0.05          0.33          0.21
-      50     0.04          0.19          0.13
-
-[[4]]
-        crop
-distance Ackerbau Obstbau frueh Obstbau spaet
-      1      1.85            NA            NA
-      3        NA         23.61         10.12
-      5      0.38         15.42          5.60
-      10     0.19          8.66          2.50
-      15     0.13          4.01          1.28
-      20     0.10          1.89          0.75
-      30     0.06          0.66          0.35
-      40     0.05          0.31          0.20
-      50     0.04          0.17          0.13
-
-[[5]]
-        crop
-distance Ackerbau Obstbau frueh Obstbau spaet
-      1      1.75            NA            NA
-      3        NA         23.12          9.74
-      5      0.36         15.06          5.41
-      10     0.18          8.42          2.43
-      15     0.12          3.83          1.24
-      20     0.09          1.81          0.72
-      30     0.06          0.63          0.34
-      40     0.05          0.30          0.20
-      50     0.04          0.17          0.13
-
-[[6]]
-        crop
-distance Ackerbau Obstbau frueh Obstbau spaet
-      1      1.64            NA            NA
-      3        NA         22.76          9.21
-      5      0.34         14.64          5.18
-      10     0.17          8.04          2.38
-      15     0.11          3.71          1.20
-      20     0.09          1.75          0.68
-      30     0.06          0.61          0.31
-      40     0.04          0.29          0.17
-      50     0.03          0.16          0.11
-
-[[7]]
-        crop
-distance Ackerbau Obstbau frueh Obstbau spaet
-      1      1.61            NA            NA
-      3        NA         22.69          9.10
-      5      0.33         14.45          5.11
-      10     0.17          7.83          2.33
-      15     0.11          3.62          1.20
-      20     0.08          1.71          0.67
-      30     0.06          0.60          0.30
-      40     0.04          0.28          0.17
-      50     0.03          0.16          0.11
-
-[[8]]
-        crop
-distance Ackerbau Obstbau frueh Obstbau spaet
-      1      1.52            NA            NA
-      3        NA         22.24          8.66
-      5      0.31         14.09          4.92
-      10     0.16          7.58          2.29
-      15     0.11          3.48          1.14
-      20     0.08          1.65          0.65
-      30     0.05          0.57          0.29
-      40     0.04          0.27          0.16
-      50     0.03          0.15          0.11
-
-
-
-
- - - -
-
- - -
- - \ No newline at end of file diff --git a/pkg/inst/web/endpoint.html b/pkg/inst/web/endpoint.html deleted file mode 100644 index 521f7f4..0000000 --- a/pkg/inst/web/endpoint.html +++ /dev/null @@ -1,142 +0,0 @@ - - - - -endpoint. pfm 0.3-7 - - - - - - - - - - - - - - - -
-
-
- pfm 0.3-7 -
- -
-
-
-
- -
-
- -
- -

Retrieve endpoint information from the chyaml field of a chent object

- -
-
-

Usage

- 
endpoint(chent, medium = "soil", type = c("degradation", "sorption"), lab_field = c(NA, "laboratory", "field"), redox = c(NA, "aerobic", "anaerobic"), value = c("DT50ref", "Kfoc", "N"), aggregator = geomean, raw = FALSE, signif = 3)

-
soil_DT50(chent, aggregator = geomean, signif = 3, lab_field = "laboratory", value = "DT50ref", redox = "aerobic", raw = FALSE)

-
soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc", raw = FALSE)

-
soil_N(chent, aggregator = mean, signif = 3, raw = FALSE)

-
soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3), raw = FALSE)
- -

Arguments

-
-
chent
-
The chent object to get the information from
-
medium
-
The medium for which information is sought
-
type
-
The information type
-
lab_field
-
If not NA, do we want laboratory or field endpoints
-
redox
-
If not NA, are we looking for aerobic or anaerobic data
-
value
-
The name of the value we want. The list given in the -usage section is not exclusive
-
aggregator
-
The aggregator function. Can be mean, -geomean, or identity, for example.
-
raw
-
Should the number(s) be returned as stored in the chent -object (could be a character value) to retain original information -about precision?
-
signif
-
How many significant digits do we want
-
values
-
The values to be returned
-
aggregators
-
A named vector of aggregator functions to be used
-
- -
-

Value

- -

-The result from applying the aggregator function to - the values converted to a numeric vector, rounded to the - given number of significant digits, or, if raw = TRUE, - the values as a character value, retaining any implicit - information on precision that may be present. -

- -
- -
-

Description

- -

R6 class objects of class chent represent chemical entities -and can hold a list of information loaded from a chemical yaml file in their -chyaml field. Such information is extracted and optionally aggregated by -this function.

- -
- -
-

Details

- -

The functions soil_* are functions to extract soil specific endpoints. -For the Freundlich exponent, the capital letter N is used in order to -facilitate dealing with such data in R. In pesticide fate modelling, this -exponent is often called 1/n.

- -
-
-
- - - -
-
- - -
- - \ No newline at end of file diff --git a/pkg/inst/web/geomean.html b/pkg/inst/web/geomean.html deleted file mode 100644 index 672e9b5..0000000 --- a/pkg/inst/web/geomean.html +++ /dev/null @@ -1,121 +0,0 @@ - - - - -geomean. pfm 0.3-7 - - - - - - - - - - - - - - - -
-
-
- pfm 0.3-7 -
- -
-
-
-
- -
-
- -
- -

Calculate the geometric mean

- -
-
-

Usage

- 
geomean(x, na.rm = TRUE)
- -

Arguments

-
-
x
-
Vector of numbers
-
na.rm
-
Should NA values be omitted?
-
- -
-

Value

- -

-The geometric mean -

- -
- -
-

Description

- -

Based on some posts in a thread on Stackoverflow -http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in -This function checks for negative values, removes NA values per default and -returns 0 if at least one element of the vector is 0.

- -
- -

Examples

- 
geomean(c(1, 3, 9))
-

-
[1] 3
-

-
geomean(c(1, 3, NA, 9))
-

-
[1] 3
-

-
## Not run: geomean(c(1, -3, 9)) # returns an error
-
-
-
- - - -

Author

- -Johannes Ranke - - -
-
- - -
- - \ No newline at end of file diff --git a/pkg/inst/web/img/glyphicons-halflings-white.png b/pkg/inst/web/img/glyphicons-halflings-white.png deleted file mode 100644 index 3bf6484..0000000 Binary files a/pkg/inst/web/img/glyphicons-halflings-white.png and /dev/null differ diff --git a/pkg/inst/web/img/glyphicons-halflings.png b/pkg/inst/web/img/glyphicons-halflings.png deleted file mode 100644 index 79bc568..0000000 Binary files a/pkg/inst/web/img/glyphicons-halflings.png and /dev/null differ diff --git a/pkg/inst/web/index.html b/pkg/inst/web/index.html deleted file mode 100644 index 54f0f35..0000000 --- a/pkg/inst/web/index.html +++ /dev/null @@ -1,182 +0,0 @@ - - - - -Index. pfm 0.3-7 - - - - - - - - - - - - - - - -
-
-
- pfm 0.3-7 -
- -
-
-
-
- -
-
- -
- -
-
- Utilities for simple calculations of predicted environmental -concentrations (PECs) and for dealing with data from some FOCUS pesticide -fate modelling software packages. - -

Help topics

- -

Degradation

-

Functions related to degradation

- - -
    - -
  • - pfm_degradation
    Calculate a time course of relative concentrations based on an mkinmod model
    • - -
  • - SFO_actual_twa
    Actual and maximum moving window time average concentrations for SFO kinetics
    • - -
-

Mobility

-

Indicators related to mobility

- - -
    - -
  • - GUS(GUS.chent, GUS.numeric, print.GUS_result)
    Groundwater ubiquity score based on Gustafson (1989)
    • - -
  • - SSLRC_mobility_classification
    Determine the SSLRC mobility classification for a chemical substance from its Koc
    • - -
-

Soil

-

Predicted environmental concentrations in soil

- - -
    - -
  • - PEC_soil
    Calculate predicted environmental concentrations in soil
    • - -
  • - soil_scenario_data_EFSA_2015
    Properties of the predefined scenarios from the EFSA guidance from 2015
    • - -
-

Surface water

-

Predicted environmental concentrations in surface water

- - -
    - -
  • - PEC_sw_drift
    Calculate predicted environmental concentrations in surface water due to drift
    • - -
  • - PEC_sw_sed
    Calculate predicted environmental concentrations in sediment from surface -
    • - -
  • - drift_data_JKI
    Deposition from spray drift expressed as percent of the applied dose as -
    • - -
  • - PEC_sw_drainage_UK
    Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method
    • - -
  • - TOXSWA_cwa
    R6 class for holding TOXSWA cwa concentration data and associated statistics
    • - -
  • - read.TOXSWA_cwa
    Read TOXSWA surface water concentrations
    • - -
  • - plot.TOXSWA_cwa
    Plot TOXSWA surface water concentrations
    • - -
-

Groundwater

-

Predicted environmental concentrations in groundwater

- - - -

Chemical entities

-

Work with input stored in chemical entites as R objects using the chent package

- - -
    - -
  • - endpoint(soil_DT50, soil_Kfoc, soil_N, soil_sorption)
    Retrieve endpoint information from the chyaml field of a chent object
    • - -
-

General

-

Utilities that are generally useful

- - -
    - -
  • - geomean
    Calculate the geometric mean
    • - -
-
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Dependencies

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  • Depends: R6, mkin
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  • Imports: graphics, chents, readr, methods
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  • Suggests: testthat
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Authors

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- - \ No newline at end of file diff --git a/pkg/inst/web/js/bootstrap.js b/pkg/inst/web/js/bootstrap.js deleted file mode 100644 index 5d6e65b..0000000 --- a/pkg/inst/web/js/bootstrap.js +++ /dev/null @@ -1,1825 +0,0 @@ -/* =================================================== - * bootstrap-transition.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#transitions - * =================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ========================================================== */ - - -!function ($) { - - $(function () { - - "use strict"; // jshint ;_; - - - /* CSS TRANSITION SUPPORT (http://www.modernizr.com/) - * ======================================================= */ - - $.support.transition = (function () { - - var transitionEnd = (function () { - - var el = document.createElement('bootstrap') - , transEndEventNames = { - 'WebkitTransition' : 'webkitTransitionEnd' - , 'MozTransition' : 'transitionend' - , 'OTransition' : 'oTransitionEnd' - , 'msTransition' : 'MSTransitionEnd' - , 'transition' : 'transitionend' - } - , name - - for (name in transEndEventNames){ - if (el.style[name] !== undefined) { - return transEndEventNames[name] - } - } - - }()) - - return transitionEnd && { - end: transitionEnd - } - - })() - - }) - -}(window.jQuery);/* ========================================================== - * bootstrap-alert.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#alerts - * ========================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ========================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* ALERT CLASS DEFINITION - * ====================== */ - - var dismiss = '[data-dismiss="alert"]' - , Alert = function (el) { - $(el).on('click', dismiss, this.close) - } - - Alert.prototype.close = function (e) { - var $this = $(this) - , selector = $this.attr('data-target') - , $parent - - if (!selector) { - selector = $this.attr('href') - selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 - } - - $parent = $(selector) - - e && e.preventDefault() - - $parent.length || ($parent = $this.hasClass('alert') ? $this : $this.parent()) - - $parent.trigger(e = $.Event('close')) - - if (e.isDefaultPrevented()) return - - $parent.removeClass('in') - - function removeElement() { - $parent - .trigger('closed') - .remove() - } - - $.support.transition && $parent.hasClass('fade') ? - $parent.on($.support.transition.end, removeElement) : - removeElement() - } - - - /* ALERT PLUGIN DEFINITION - * ======================= */ - - $.fn.alert = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('alert') - if (!data) $this.data('alert', (data = new Alert(this))) - if (typeof option == 'string') data[option].call($this) - }) - } - - $.fn.alert.Constructor = Alert - - - /* ALERT DATA-API - * ============== */ - - $(function () { - $('body').on('click.alert.data-api', dismiss, Alert.prototype.close) - }) - -}(window.jQuery);/* ============================================================ - * bootstrap-button.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#buttons - * ============================================================ - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ============================================================ */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* BUTTON PUBLIC CLASS DEFINITION - * ============================== */ - - var Button = function (element, options) { - this.$element = $(element) - this.options = $.extend({}, $.fn.button.defaults, options) - } - - Button.prototype.setState = function (state) { - var d = 'disabled' - , $el = this.$element - , data = $el.data() - , val = $el.is('input') ? 'val' : 'html' - - state = state + 'Text' - data.resetText || $el.data('resetText', $el[val]()) - - $el[val](data[state] || this.options[state]) - - // push to event loop to allow forms to submit - setTimeout(function () { - state == 'loadingText' ? - $el.addClass(d).attr(d, d) : - $el.removeClass(d).removeAttr(d) - }, 0) - } - - Button.prototype.toggle = function () { - var $parent = this.$element.parent('[data-toggle="buttons-radio"]') - - $parent && $parent - .find('.active') - .removeClass('active') - - this.$element.toggleClass('active') - } - - - /* BUTTON PLUGIN DEFINITION - * ======================== */ - - $.fn.button = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('button') - , options = typeof option == 'object' && option - if (!data) $this.data('button', (data = new Button(this, options))) - if (option == 'toggle') data.toggle() - else if (option) data.setState(option) - }) - } - - $.fn.button.defaults = { - loadingText: 'loading...' - } - - $.fn.button.Constructor = Button - - - /* BUTTON DATA-API - * =============== */ - - $(function () { - $('body').on('click.button.data-api', '[data-toggle^=button]', function ( e ) { - var $btn = $(e.target) - if (!$btn.hasClass('btn')) $btn = $btn.closest('.btn') - $btn.button('toggle') - }) - }) - -}(window.jQuery);/* ========================================================== - * bootstrap-carousel.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#carousel - * ========================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ========================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* CAROUSEL CLASS DEFINITION - * ========================= */ - - var Carousel = function (element, options) { - this.$element = $(element) - this.options = options - this.options.slide && this.slide(this.options.slide) - this.options.pause == 'hover' && this.$element - .on('mouseenter', $.proxy(this.pause, this)) - .on('mouseleave', $.proxy(this.cycle, this)) - } - - Carousel.prototype = { - - cycle: function (e) { - if (!e) this.paused = false - this.options.interval - && !this.paused - && (this.interval = setInterval($.proxy(this.next, this), this.options.interval)) - return this - } - - , to: function (pos) { - var $active = this.$element.find('.active') - , children = $active.parent().children() - , activePos = children.index($active) - , that = this - - if (pos > (children.length - 1) || pos < 0) return - - if (this.sliding) { - return this.$element.one('slid', function () { - that.to(pos) - }) - } - - if (activePos == pos) { - return this.pause().cycle() - } - - return this.slide(pos > activePos ? 'next' : 'prev', $(children[pos])) - } - - , pause: function (e) { - if (!e) this.paused = true - clearInterval(this.interval) - this.interval = null - return this - } - - , next: function () { - if (this.sliding) return - return this.slide('next') - } - - , prev: function () { - if (this.sliding) return - return this.slide('prev') - } - - , slide: function (type, next) { - var $active = this.$element.find('.active') - , $next = next || $active[type]() - , isCycling = this.interval - , direction = type == 'next' ? 'left' : 'right' - , fallback = type == 'next' ? 'first' : 'last' - , that = this - , e = $.Event('slide') - - this.sliding = true - - isCycling && this.pause() - - $next = $next.length ? $next : this.$element.find('.item')[fallback]() - - if ($next.hasClass('active')) return - - if ($.support.transition && this.$element.hasClass('slide')) { - this.$element.trigger(e) - if (e.isDefaultPrevented()) return - $next.addClass(type) - $next[0].offsetWidth // force reflow - $active.addClass(direction) - $next.addClass(direction) - this.$element.one($.support.transition.end, function () { - $next.removeClass([type, direction].join(' ')).addClass('active') - $active.removeClass(['active', direction].join(' ')) - that.sliding = false - setTimeout(function () { that.$element.trigger('slid') }, 0) - }) - } else { - this.$element.trigger(e) - if (e.isDefaultPrevented()) return - $active.removeClass('active') - $next.addClass('active') - this.sliding = false - this.$element.trigger('slid') - } - - isCycling && this.cycle() - - return this - } - - } - - - /* CAROUSEL PLUGIN DEFINITION - * ========================== */ - - $.fn.carousel = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('carousel') - , options = $.extend({}, $.fn.carousel.defaults, typeof option == 'object' && option) - if (!data) $this.data('carousel', (data = new Carousel(this, options))) - if (typeof option == 'number') data.to(option) - else if (typeof option == 'string' || (option = options.slide)) data[option]() - else if (options.interval) data.cycle() - }) - } - - $.fn.carousel.defaults = { - interval: 5000 - , pause: 'hover' - } - - $.fn.carousel.Constructor = Carousel - - - /* CAROUSEL DATA-API - * ================= */ - - $(function () { - $('body').on('click.carousel.data-api', '[data-slide]', function ( e ) { - var $this = $(this), href - , $target = $($this.attr('data-target') || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7 - , options = !$target.data('modal') && $.extend({}, $target.data(), $this.data()) - $target.carousel(options) - e.preventDefault() - }) - }) - -}(window.jQuery);/* ============================================================= - * bootstrap-collapse.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#collapse - * ============================================================= - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ============================================================ */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* COLLAPSE PUBLIC CLASS DEFINITION - * ================================ */ - - var Collapse = function (element, options) { - this.$element = $(element) - this.options = $.extend({}, $.fn.collapse.defaults, options) - - if (this.options.parent) { - this.$parent = $(this.options.parent) - } - - this.options.toggle && this.toggle() - } - - Collapse.prototype = { - - constructor: Collapse - - , dimension: function () { - var hasWidth = this.$element.hasClass('width') - return hasWidth ? 'width' : 'height' - } - - , show: function () { - var dimension - , scroll - , actives - , hasData - - if (this.transitioning) return - - dimension = this.dimension() - scroll = $.camelCase(['scroll', dimension].join('-')) - actives = this.$parent && this.$parent.find('> .accordion-group > .in') - - if (actives && actives.length) { - hasData = actives.data('collapse') - if (hasData && hasData.transitioning) return - actives.collapse('hide') - hasData || actives.data('collapse', null) - } - - this.$element[dimension](0) - this.transition('addClass', $.Event('show'), 'shown') - this.$element[dimension](this.$element[0][scroll]) - } - - , hide: function () { - var dimension - if (this.transitioning) return - dimension = this.dimension() - this.reset(this.$element[dimension]()) - this.transition('removeClass', $.Event('hide'), 'hidden') - this.$element[dimension](0) - } - - , reset: function (size) { - var dimension = this.dimension() - - this.$element - .removeClass('collapse') - [dimension](size || 'auto') - [0].offsetWidth - - this.$element[size !== null ? 'addClass' : 'removeClass']('collapse') - - return this - } - - , transition: function (method, startEvent, completeEvent) { - var that = this - , complete = function () { - if (startEvent.type == 'show') that.reset() - that.transitioning = 0 - that.$element.trigger(completeEvent) - } - - this.$element.trigger(startEvent) - - if (startEvent.isDefaultPrevented()) return - - this.transitioning = 1 - - this.$element[method]('in') - - $.support.transition && this.$element.hasClass('collapse') ? - this.$element.one($.support.transition.end, complete) : - complete() - } - - , toggle: function () { - this[this.$element.hasClass('in') ? 'hide' : 'show']() - } - - } - - - /* COLLAPSIBLE PLUGIN DEFINITION - * ============================== */ - - $.fn.collapse = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('collapse') - , options = typeof option == 'object' && option - if (!data) $this.data('collapse', (data = new Collapse(this, options))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.collapse.defaults = { - toggle: true - } - - $.fn.collapse.Constructor = Collapse - - - /* COLLAPSIBLE DATA-API - * ==================== */ - - $(function () { - $('body').on('click.collapse.data-api', '[data-toggle=collapse]', function ( e ) { - var $this = $(this), href - , target = $this.attr('data-target') - || e.preventDefault() - || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '') //strip for ie7 - , option = $(target).data('collapse') ? 'toggle' : $this.data() - $(target).collapse(option) - }) - }) - -}(window.jQuery);/* ============================================================ - * bootstrap-dropdown.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#dropdowns - * ============================================================ - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ============================================================ */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* DROPDOWN CLASS DEFINITION - * ========================= */ - - var toggle = '[data-toggle="dropdown"]' - , Dropdown = function (element) { - var $el = $(element).on('click.dropdown.data-api', this.toggle) - $('html').on('click.dropdown.data-api', function () { - $el.parent().removeClass('open') - }) - } - - Dropdown.prototype = { - - constructor: Dropdown - - , toggle: function (e) { - var $this = $(this) - , $parent - , selector - , isActive - - if ($this.is('.disabled, :disabled')) return - - selector = $this.attr('data-target') - - if (!selector) { - selector = $this.attr('href') - selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 - } - - $parent = $(selector) - $parent.length || ($parent = $this.parent()) - - isActive = $parent.hasClass('open') - - clearMenus() - - if (!isActive) $parent.toggleClass('open') - - return false - } - - } - - function clearMenus() { - $(toggle).parent().removeClass('open') - } - - - /* DROPDOWN PLUGIN DEFINITION - * ========================== */ - - $.fn.dropdown = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('dropdown') - if (!data) $this.data('dropdown', (data = new Dropdown(this))) - if (typeof option == 'string') data[option].call($this) - }) - } - - $.fn.dropdown.Constructor = Dropdown - - - /* APPLY TO STANDARD DROPDOWN ELEMENTS - * =================================== */ - - $(function () { - $('html').on('click.dropdown.data-api', clearMenus) - $('body') - .on('click.dropdown', '.dropdown form', function (e) { e.stopPropagation() }) - .on('click.dropdown.data-api', toggle, Dropdown.prototype.toggle) - }) - -}(window.jQuery);/* ========================================================= - * bootstrap-modal.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#modals - * ========================================================= - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ========================================================= */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* MODAL CLASS DEFINITION - * ====================== */ - - var Modal = function (content, options) { - this.options = options - this.$element = $(content) - .delegate('[data-dismiss="modal"]', 'click.dismiss.modal', $.proxy(this.hide, this)) - } - - Modal.prototype = { - - constructor: Modal - - , toggle: function () { - return this[!this.isShown ? 'show' : 'hide']() - } - - , show: function () { - var that = this - , e = $.Event('show') - - this.$element.trigger(e) - - if (this.isShown || e.isDefaultPrevented()) return - - $('body').addClass('modal-open') - - this.isShown = true - - escape.call(this) - backdrop.call(this, function () { - var transition = $.support.transition && that.$element.hasClass('fade') - - if (!that.$element.parent().length) { - that.$element.appendTo(document.body) //don't move modals dom position - } - - that.$element - .show() - - if (transition) { - that.$element[0].offsetWidth // force reflow - } - - that.$element.addClass('in') - - transition ? - that.$element.one($.support.transition.end, function () { that.$element.trigger('shown') }) : - that.$element.trigger('shown') - - }) - } - - , hide: function (e) { - e && e.preventDefault() - - var that = this - - e = $.Event('hide') - - this.$element.trigger(e) - - if (!this.isShown || e.isDefaultPrevented()) return - - this.isShown = false - - $('body').removeClass('modal-open') - - escape.call(this) - - this.$element.removeClass('in') - - $.support.transition && this.$element.hasClass('fade') ? - hideWithTransition.call(this) : - hideModal.call(this) - } - - } - - - /* MODAL PRIVATE METHODS - * ===================== */ - - function hideWithTransition() { - var that = this - , timeout = setTimeout(function () { - that.$element.off($.support.transition.end) - hideModal.call(that) - }, 500) - - this.$element.one($.support.transition.end, function () { - clearTimeout(timeout) - hideModal.call(that) - }) - } - - function hideModal(that) { - this.$element - .hide() - .trigger('hidden') - - backdrop.call(this) - } - - function backdrop(callback) { - var that = this - , animate = this.$element.hasClass('fade') ? 'fade' : '' - - if (this.isShown && this.options.backdrop) { - var doAnimate = $.support.transition && animate - - this.$backdrop = $('
') - .appendTo(document.body) - - if (this.options.backdrop != 'static') { - this.$backdrop.click($.proxy(this.hide, this)) - } - - if (doAnimate) this.$backdrop[0].offsetWidth // force reflow - - this.$backdrop.addClass('in') - - doAnimate ? - this.$backdrop.one($.support.transition.end, callback) : - callback() - - } else if (!this.isShown && this.$backdrop) { - this.$backdrop.removeClass('in') - - $.support.transition && this.$element.hasClass('fade')? - this.$backdrop.one($.support.transition.end, $.proxy(removeBackdrop, this)) : - removeBackdrop.call(this) - - } else if (callback) { - callback() - } - } - - function removeBackdrop() { - this.$backdrop.remove() - this.$backdrop = null - } - - function escape() { - var that = this - if (this.isShown && this.options.keyboard) { - $(document).on('keyup.dismiss.modal', function ( e ) { - e.which == 27 && that.hide() - }) - } else if (!this.isShown) { - $(document).off('keyup.dismiss.modal') - } - } - - - /* MODAL PLUGIN DEFINITION - * ======================= */ - - $.fn.modal = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('modal') - , options = $.extend({}, $.fn.modal.defaults, $this.data(), typeof option == 'object' && option) - if (!data) $this.data('modal', (data = new Modal(this, options))) - if (typeof option == 'string') data[option]() - else if (options.show) data.show() - }) - } - - $.fn.modal.defaults = { - backdrop: true - , keyboard: true - , show: true - } - - $.fn.modal.Constructor = Modal - - - /* MODAL DATA-API - * ============== */ - - $(function () { - $('body').on('click.modal.data-api', '[data-toggle="modal"]', function ( e ) { - var $this = $(this), href - , $target = $($this.attr('data-target') || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7 - , option = $target.data('modal') ? 'toggle' : $.extend({}, $target.data(), $this.data()) - - e.preventDefault() - $target.modal(option) - }) - }) - -}(window.jQuery);/* =========================================================== - * bootstrap-tooltip.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#tooltips - * Inspired by the original jQuery.tipsy by Jason Frame - * =========================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ========================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* TOOLTIP PUBLIC CLASS DEFINITION - * =============================== */ - - var Tooltip = function (element, options) { - this.init('tooltip', element, options) - } - - Tooltip.prototype = { - - constructor: Tooltip - - , init: function (type, element, options) { - var eventIn - , eventOut - - this.type = type - this.$element = $(element) - this.options = this.getOptions(options) - this.enabled = true - - if (this.options.trigger != 'manual') { - eventIn = this.options.trigger == 'hover' ? 'mouseenter' : 'focus' - eventOut = this.options.trigger == 'hover' ? 'mouseleave' : 'blur' - this.$element.on(eventIn, this.options.selector, $.proxy(this.enter, this)) - this.$element.on(eventOut, this.options.selector, $.proxy(this.leave, this)) - } - - this.options.selector ? - (this._options = $.extend({}, this.options, { trigger: 'manual', selector: '' })) : - this.fixTitle() - } - - , getOptions: function (options) { - options = $.extend({}, $.fn[this.type].defaults, options, this.$element.data()) - - if (options.delay && typeof options.delay == 'number') { - options.delay = { - show: options.delay - , hide: options.delay - } - } - - return options - } - - , enter: function (e) { - var self = $(e.currentTarget)[this.type](this._options).data(this.type) - - if (!self.options.delay || !self.options.delay.show) return self.show() - - clearTimeout(this.timeout) - self.hoverState = 'in' - this.timeout = setTimeout(function() { - if (self.hoverState == 'in') self.show() - }, self.options.delay.show) - } - - , leave: function (e) { - var self = $(e.currentTarget)[this.type](this._options).data(this.type) - - if (this.timeout) clearTimeout(this.timeout) - if (!self.options.delay || !self.options.delay.hide) return self.hide() - - self.hoverState = 'out' - this.timeout = setTimeout(function() { - if (self.hoverState == 'out') self.hide() - }, self.options.delay.hide) - } - - , show: function () { - var $tip - , inside - , pos - , actualWidth - , actualHeight - , placement - , tp - - if (this.hasContent() && this.enabled) { - $tip = this.tip() - this.setContent() - - if (this.options.animation) { - $tip.addClass('fade') - } - - placement = typeof this.options.placement == 'function' ? - this.options.placement.call(this, $tip[0], this.$element[0]) : - this.options.placement - - inside = /in/.test(placement) - - $tip - .remove() - .css({ top: 0, left: 0, display: 'block' }) - .appendTo(inside ? this.$element : document.body) - - pos = this.getPosition(inside) - - actualWidth = $tip[0].offsetWidth - actualHeight = $tip[0].offsetHeight - - switch (inside ? placement.split(' ')[1] : placement) { - case 'bottom': - tp = {top: pos.top + pos.height, left: pos.left + pos.width / 2 - actualWidth / 2} - break - case 'top': - tp = {top: pos.top - actualHeight, left: pos.left + pos.width / 2 - actualWidth / 2} - break - case 'left': - tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left - actualWidth} - break - case 'right': - tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left + pos.width} - break - } - - $tip - .css(tp) - .addClass(placement) - .addClass('in') - } - } - - , isHTML: function(text) { - // html string detection logic adapted from jQuery - return typeof text != 'string' - || ( text.charAt(0) === "<" - && text.charAt( text.length - 1 ) === ">" - && text.length >= 3 - ) || /^(?:[^<]*<[\w\W]+>[^>]*$)/.exec(text) - } - - , setContent: function () { - var $tip = this.tip() - , title = this.getTitle() - - $tip.find('.tooltip-inner')[this.isHTML(title) ? 'html' : 'text'](title) - $tip.removeClass('fade in top bottom left right') - } - - , hide: function () { - var that = this - , $tip = this.tip() - - $tip.removeClass('in') - - function removeWithAnimation() { - var timeout = setTimeout(function () { - $tip.off($.support.transition.end).remove() - }, 500) - - $tip.one($.support.transition.end, function () { - clearTimeout(timeout) - $tip.remove() - }) - } - - $.support.transition && this.$tip.hasClass('fade') ? - removeWithAnimation() : - $tip.remove() - } - - , fixTitle: function () { - var $e = this.$element - if ($e.attr('title') || typeof($e.attr('data-original-title')) != 'string') { - $e.attr('data-original-title', $e.attr('title') || '').removeAttr('title') - } - } - - , hasContent: function () { - return this.getTitle() - } - - , getPosition: function (inside) { - return $.extend({}, (inside ? {top: 0, left: 0} : this.$element.offset()), { - width: this.$element[0].offsetWidth - , height: this.$element[0].offsetHeight - }) - } - - , getTitle: function () { - var title - , $e = this.$element - , o = this.options - - title = $e.attr('data-original-title') - || (typeof o.title == 'function' ? o.title.call($e[0]) : o.title) - - return title - } - - , tip: function () { - return this.$tip = this.$tip || $(this.options.template) - } - - , validate: function () { - if (!this.$element[0].parentNode) { - this.hide() - this.$element = null - this.options = null - } - } - - , enable: function () { - this.enabled = true - } - - , disable: function () { - this.enabled = false - } - - , toggleEnabled: function () { - this.enabled = !this.enabled - } - - , toggle: function () { - this[this.tip().hasClass('in') ? 'hide' : 'show']() - } - - } - - - /* TOOLTIP PLUGIN DEFINITION - * ========================= */ - - $.fn.tooltip = function ( option ) { - return this.each(function () { - var $this = $(this) - , data = $this.data('tooltip') - , options = typeof option == 'object' && option - if (!data) $this.data('tooltip', (data = new Tooltip(this, options))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.tooltip.Constructor = Tooltip - - $.fn.tooltip.defaults = { - animation: true - , placement: 'top' - , selector: false - , template: '
' - , trigger: 'hover' - , title: '' - , delay: 0 - } - -}(window.jQuery); -/* =========================================================== - * bootstrap-popover.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#popovers - * =========================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * =========================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* POPOVER PUBLIC CLASS DEFINITION - * =============================== */ - - var Popover = function ( element, options ) { - this.init('popover', element, options) - } - - - /* NOTE: POPOVER EXTENDS BOOTSTRAP-TOOLTIP.js - ========================================== */ - - Popover.prototype = $.extend({}, $.fn.tooltip.Constructor.prototype, { - - constructor: Popover - - , setContent: function () { - var $tip = this.tip() - , title = this.getTitle() - , content = this.getContent() - - $tip.find('.popover-title')[this.isHTML(title) ? 'html' : 'text'](title) - $tip.find('.popover-content > *')[this.isHTML(content) ? 'html' : 'text'](content) - - $tip.removeClass('fade top bottom left right in') - } - - , hasContent: function () { - return this.getTitle() || this.getContent() - } - - , getContent: function () { - var content - , $e = this.$element - , o = this.options - - content = $e.attr('data-content') - || (typeof o.content == 'function' ? o.content.call($e[0]) : o.content) - - return content - } - - , tip: function () { - if (!this.$tip) { - this.$tip = $(this.options.template) - } - return this.$tip - } - - }) - - - /* POPOVER PLUGIN DEFINITION - * ======================= */ - - $.fn.popover = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('popover') - , options = typeof option == 'object' && option - if (!data) $this.data('popover', (data = new Popover(this, options))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.popover.Constructor = Popover - - $.fn.popover.defaults = $.extend({} , $.fn.tooltip.defaults, { - placement: 'right' - , content: '' - , template: '

' - }) - -}(window.jQuery);/* ============================================================= - * bootstrap-scrollspy.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#scrollspy - * ============================================================= - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ============================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* SCROLLSPY CLASS DEFINITION - * ========================== */ - - function ScrollSpy( element, options) { - var process = $.proxy(this.process, this) - , $element = $(element).is('body') ? $(window) : $(element) - , href - this.options = $.extend({}, $.fn.scrollspy.defaults, options) - this.$scrollElement = $element.on('scroll.scroll.data-api', process) - this.selector = (this.options.target - || ((href = $(element).attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7 - || '') + ' .nav li > a' - this.$body = $('body') - this.refresh() - this.process() - } - - ScrollSpy.prototype = { - - constructor: ScrollSpy - - , refresh: function () { - var self = this - , $targets - - this.offsets = $([]) - this.targets = $([]) - - $targets = this.$body - .find(this.selector) - .map(function () { - var $el = $(this) - , href = $el.data('target') || $el.attr('href') - , $href = /^#\w/.test(href) && $(href) - return ( $href - && href.length - && [[ $href.position().top, href ]] ) || null - }) - .sort(function (a, b) { return a[0] - b[0] }) - .each(function () { - self.offsets.push(this[0]) - self.targets.push(this[1]) - }) - } - - , process: function () { - var scrollTop = this.$scrollElement.scrollTop() + this.options.offset - , scrollHeight = this.$scrollElement[0].scrollHeight || this.$body[0].scrollHeight - , maxScroll = scrollHeight - this.$scrollElement.height() - , offsets = this.offsets - , targets = this.targets - , activeTarget = this.activeTarget - , i - - if (scrollTop >= maxScroll) { - return activeTarget != (i = targets.last()[0]) - && this.activate ( i ) - } - - for (i = offsets.length; i--;) { - activeTarget != targets[i] - && scrollTop >= offsets[i] - && (!offsets[i + 1] || scrollTop <= offsets[i + 1]) - && this.activate( targets[i] ) - } - } - - , activate: function (target) { - var active - , selector - - this.activeTarget = target - - $(this.selector) - .parent('.active') - .removeClass('active') - - selector = this.selector - + '[data-target="' + target + '"],' - + this.selector + '[href="' + target + '"]' - - active = $(selector) - .parent('li') - .addClass('active') - - if (active.parent('.dropdown-menu')) { - active = active.closest('li.dropdown').addClass('active') - } - - active.trigger('activate') - } - - } - - - /* SCROLLSPY PLUGIN DEFINITION - * =========================== */ - - $.fn.scrollspy = function ( option ) { - return this.each(function () { - var $this = $(this) - , data = $this.data('scrollspy') - , options = typeof option == 'object' && option - if (!data) $this.data('scrollspy', (data = new ScrollSpy(this, options))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.scrollspy.Constructor = ScrollSpy - - $.fn.scrollspy.defaults = { - offset: 10 - } - - - /* SCROLLSPY DATA-API - * ================== */ - - $(function () { - $('[data-spy="scroll"]').each(function () { - var $spy = $(this) - $spy.scrollspy($spy.data()) - }) - }) - -}(window.jQuery);/* ======================================================== - * bootstrap-tab.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#tabs - * ======================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ======================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* TAB CLASS DEFINITION - * ==================== */ - - var Tab = function ( element ) { - this.element = $(element) - } - - Tab.prototype = { - - constructor: Tab - - , show: function () { - var $this = this.element - , $ul = $this.closest('ul:not(.dropdown-menu)') - , selector = $this.attr('data-target') - , previous - , $target - , e - - if (!selector) { - selector = $this.attr('href') - selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 - } - - if ( $this.parent('li').hasClass('active') ) return - - previous = $ul.find('.active a').last()[0] - - e = $.Event('show', { - relatedTarget: previous - }) - - $this.trigger(e) - - if (e.isDefaultPrevented()) return - - $target = $(selector) - - this.activate($this.parent('li'), $ul) - this.activate($target, $target.parent(), function () { - $this.trigger({ - type: 'shown' - , relatedTarget: previous - }) - }) - } - - , activate: function ( element, container, callback) { - var $active = container.find('> .active') - , transition = callback - && $.support.transition - && $active.hasClass('fade') - - function next() { - $active - .removeClass('active') - .find('> .dropdown-menu > .active') - .removeClass('active') - - element.addClass('active') - - if (transition) { - element[0].offsetWidth // reflow for transition - element.addClass('in') - } else { - element.removeClass('fade') - } - - if ( element.parent('.dropdown-menu') ) { - element.closest('li.dropdown').addClass('active') - } - - callback && callback() - } - - transition ? - $active.one($.support.transition.end, next) : - next() - - $active.removeClass('in') - } - } - - - /* TAB PLUGIN DEFINITION - * ===================== */ - - $.fn.tab = function ( option ) { - return this.each(function () { - var $this = $(this) - , data = $this.data('tab') - if (!data) $this.data('tab', (data = new Tab(this))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.tab.Constructor = Tab - - - /* TAB DATA-API - * ============ */ - - $(function () { - $('body').on('click.tab.data-api', '[data-toggle="tab"], [data-toggle="pill"]', function (e) { - e.preventDefault() - $(this).tab('show') - }) - }) - -}(window.jQuery);/* ============================================================= - * bootstrap-typeahead.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#typeahead - * ============================================================= - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ============================================================ */ - - -!function($){ - - "use strict"; // jshint ;_; - - - /* TYPEAHEAD PUBLIC CLASS DEFINITION - * ================================= */ - - var Typeahead = function (element, options) { - this.$element = $(element) - this.options = $.extend({}, $.fn.typeahead.defaults, options) - this.matcher = this.options.matcher || this.matcher - this.sorter = this.options.sorter || this.sorter - this.highlighter = this.options.highlighter || this.highlighter - this.updater = this.options.updater || this.updater - this.$menu = $(this.options.menu).appendTo('body') - this.source = this.options.source - this.shown = false - this.listen() - } - - Typeahead.prototype = { - - constructor: Typeahead - - , select: function () { - var val = this.$menu.find('.active').attr('data-value') - this.$element - .val(this.updater(val)) - .change() - return this.hide() - } - - , updater: function (item) { - return item - } - - , show: function () { - var pos = $.extend({}, this.$element.offset(), { - height: this.$element[0].offsetHeight - }) - - this.$menu.css({ - top: pos.top + pos.height - , left: pos.left - }) - - this.$menu.show() - this.shown = true - return this - } - - , hide: function () { - this.$menu.hide() - this.shown = false - return this - } - - , lookup: function (event) { - var that = this - , items - , q - - this.query = this.$element.val() - - if (!this.query) { - return this.shown ? this.hide() : this - } - - items = $.grep(this.source, function (item) { - return that.matcher(item) - }) - - items = this.sorter(items) - - if (!items.length) { - return this.shown ? this.hide() : this - } - - return this.render(items.slice(0, this.options.items)).show() - } - - , matcher: function (item) { - return ~item.toLowerCase().indexOf(this.query.toLowerCase()) - } - - , sorter: function (items) { - var beginswith = [] - , caseSensitive = [] - , caseInsensitive = [] - , item - - while (item = items.shift()) { - if (!item.toLowerCase().indexOf(this.query.toLowerCase())) beginswith.push(item) - else if (~item.indexOf(this.query)) caseSensitive.push(item) - else caseInsensitive.push(item) - } - - return beginswith.concat(caseSensitive, caseInsensitive) - } - - , highlighter: function (item) { - var query = this.query.replace(/[\-\[\]{}()*+?.,\\\^$|#\s]/g, '\\$&') - return item.replace(new RegExp('(' + query + ')', 'ig'), function ($1, match) { - return '' + match + '' - }) - } - - , render: function (items) { - var that = this - - items = $(items).map(function (i, item) { - i = $(that.options.item).attr('data-value', item) - i.find('a').html(that.highlighter(item)) - return i[0] - }) - - items.first().addClass('active') - this.$menu.html(items) - return this - } - - , next: function (event) { - var active = this.$menu.find('.active').removeClass('active') - , next = active.next() - - if (!next.length) { - next = $(this.$menu.find('li')[0]) - } - - next.addClass('active') - } - - , prev: function (event) { - var active = this.$menu.find('.active').removeClass('active') - , prev = active.prev() - - if (!prev.length) { - prev = this.$menu.find('li').last() - } - - prev.addClass('active') - } - - , listen: function () { - this.$element - .on('blur', $.proxy(this.blur, this)) - .on('keypress', $.proxy(this.keypress, this)) - .on('keyup', $.proxy(this.keyup, this)) - - if ($.browser.webkit || $.browser.msie) { - this.$element.on('keydown', $.proxy(this.keypress, this)) - } - - this.$menu - .on('click', $.proxy(this.click, this)) - .on('mouseenter', 'li', $.proxy(this.mouseenter, this)) - } - - , keyup: function (e) { - switch(e.keyCode) { - case 40: // down arrow - case 38: // up arrow - break - - case 9: // tab - case 13: // enter - if (!this.shown) return - this.select() - break - - case 27: // escape - if (!this.shown) return - this.hide() - break - - default: - this.lookup() - } - - e.stopPropagation() - e.preventDefault() - } - - , keypress: function (e) { - if (!this.shown) return - - switch(e.keyCode) { - case 9: // tab - case 13: // enter - case 27: // escape - e.preventDefault() - break - - case 38: // up arrow - if (e.type != 'keydown') break - e.preventDefault() - this.prev() - break - - case 40: // down arrow - if (e.type != 'keydown') break - e.preventDefault() - this.next() - break - } - - e.stopPropagation() - 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      ',item:'
      • '},a.fn.typeahead.Constructor=b,a(function(){a("body").on("focus.typeahead.data-api",'[data-provide="typeahead"]',function(b){var c=a(this);if(c.data("typeahead"))return;b.preventDefault(),c.typeahead(c.data())})})}(window.jQuery); \ No newline at end of file diff --git a/pkg/inst/web/pfm_degradation.html b/pkg/inst/web/pfm_degradation.html deleted file mode 100644 index fad64be..0000000 --- a/pkg/inst/web/pfm_degradation.html +++ /dev/null @@ -1,119 +0,0 @@ - - - - -pfm_degradation. pfm 0.3-7 - - - - - - - - - - - - - - - -
      -
      -
      - pfm 0.3-7 -
      - -
      -
      -
      -
      - -
      -
      - -
      - -

      Calculate a time course of relative concentrations based on an mkinmod model

      - -
      -
      -

      Usage

      - 
      pfm_degradation(model = "SFO", DT50 = 1000, parms = c(k_parent_sink = log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365, by = step_days))
      - -

      Arguments

      -
      -
      model
      -
      The degradation model to be used. Either a parent only model like -'SFO' or 'FOMC', or an mkinmod object
      -
      DT50
      -
      The half-life. This is only used when simple exponential decline -is calculated (SFO model).
      -
      parms
      -
      The parameters used for the degradation model
      -
      years
      -
      For how many years should the degradation be predicted?
      -
      step_days
      -
      What step size in days should the output have?
      -
      times
      -
      The output times
      -
      - -
      -

      Description

      - -

      Calculate a time course of relative concentrations based on an mkinmod model

      - -
      - -

      Examples

      - 
      head(pfm_degradation("SFO", DT50 = 10))
-
      
-
        time    parent
-1    0 1.0000000
-2    1 0.9330330
-3    2 0.8705506
-4    3 0.8122524
-5    4 0.7578583
-6    5 0.7071068
-
      -
      -
      - - - -

      Author

      - -Johannes Ranke - - -
      -
      - - -
      - - \ No newline at end of file diff --git a/pkg/inst/web/plot.TOXSWA_cwa-2.png b/pkg/inst/web/plot.TOXSWA_cwa-2.png deleted file mode 100644 index 764c7f4..0000000 Binary files a/pkg/inst/web/plot.TOXSWA_cwa-2.png and /dev/null differ diff --git a/pkg/inst/web/plot.TOXSWA_cwa-4.png b/pkg/inst/web/plot.TOXSWA_cwa-4.png deleted file mode 100644 index 764c7f4..0000000 Binary files a/pkg/inst/web/plot.TOXSWA_cwa-4.png and /dev/null differ diff --git a/pkg/inst/web/plot.TOXSWA_cwa.html b/pkg/inst/web/plot.TOXSWA_cwa.html deleted file mode 100644 index a6118df..0000000 --- a/pkg/inst/web/plot.TOXSWA_cwa.html +++ /dev/null @@ -1,119 +0,0 @@ - - - - -plot.TOXSWA_cwa. pfm 0.3-7 - - - - - - - - - - - - - - - -
      -
      -
      - pfm 0.3-7 -
      - -
      -
      -
      -
      - -
      -
      - -
      - -

      Plot TOXSWA surface water concentrations

      - -
      -
      -

      Usage

      - 
      "plot"(x, time_column = c("datetime", "t", "t_firstjan", "t_rel_to_max"), xlab = "default", ylab = "default", add = FALSE, total = FALSE, LC_TIME = "C", ...)
      - -

      Arguments

      -
      -
      x
      -
      The TOXSWA_cwa object to be plotted.
      -
      time_column
      -
      What should be used for the time axis. If "t_firstjan" is chosen, -the time is given in days relative to the first of January in the first year.
      -
      xlab, ylab
      -
      Labels for x and y axis.
      -
      add
      -
      Should we add to an existing plot?
      -
      total
      -
      Should the total concentration in water be plotted, including substance sorbed -to suspended matter?
      -
      LC_TIME
      -
      Specification of the locale used to format dates
      -
      ...
      -
      Further arguments passed to plot if we are not adding to an existing plot
      -
      - -
      -

      Description

      - -

      Plot TOXSWA hourly concentrations of a chemical substance in a specific -segment of a TOXSWA surface water body.

      - -
      - -

      Examples

      - 
      H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
-                                 basedir = "SwashProjects/project_H_sw/TOXSWA",
-                                 zipfile = system.file("testdata/SwashProjects.zip",
-                                             package = "pfm"))
-plot(H_sw_D4_pond)
-
      
-
      -
      -
      - - - -

      Author

      - -Johannes Ranke - - -
      -
      - - -
      - - \ No newline at end of file diff --git a/pkg/inst/web/read.TOXSWA_cwa.html b/pkg/inst/web/read.TOXSWA_cwa.html deleted file mode 100644 index 3f2d997..0000000 --- a/pkg/inst/web/read.TOXSWA_cwa.html +++ /dev/null @@ -1,138 +0,0 @@ - - - - -read.TOXSWA_cwa. pfm 0.3-7 - - - - - - - - - - - - - - - -
      -
      -
      - pfm 0.3-7 -
      - -
      -
      -
      -
      - -
      -
      - -
      - -

      Read TOXSWA surface water concentrations

      - -
      -
      -

      Usage

      - 
      read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last", substance = "parent", total = FALSE, windows = NULL, thresholds = NULL)
      - -

      Arguments

      -
      -
      filename
      -
      The filename of the cwa file (TOXSWA 2.x.y or similar) or the -out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).
      -
      basedir
      -
      The path to the directory where the cwa file resides.
      -
      zipfile
      -
      Optional path to a zip file containing the cwa file.
      -
      segment
      -
      The segment for which the data should be read. Either "last", or -the segment number.
      -
      substance
      -
      For TOXSWA 4 .out files, the default value "parent" leads -to reading concentrations of the parent compound. Alternatively, the substance -of interested can be selected by its code name.
      -
      total
      -
      Set this to TRUE in order to read total concentrations as well. This is -only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa -files. For .cwa files, the total concentration is always read as well.
      -
      windows
      -
      Numeric vector of width of moving windows in days, for calculating -maximum time weighted average concentrations and areas under the curve.
      -
      thresholds
      -
      Numeric vector of threshold concentrations in µg/L for -generating event statistics.
      -
      - -
      -

      Value

      - -

      -An instance of an R6 object of class -TOXSWA_cwa. -

      - -
      - -
      -

      Description

      - -

      Read TOXSWA hourly concentrations of a chemical substance in a specific -segment of a TOXSWA surface water body. Per default, the data for the last -segment are imported. As TOXSWA 4 reports the values at the end of the hour -(ConLiqWatLayCur) in its summary file, we use this value as well instead -of the hourly averages (ConLiqWatLay).

      - -
      - -

      Examples

      - 
      H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
-                                 basedir = "SwashProjects/project_H_sw/TOXSWA",
-                                 zipfile = system.file("testdata/SwashProjects.zip",
-                                                       package = "pfm"))
-
      -
      -
      - - - -

      Author

      - -Johannes Ranke - - -
      -
      - - -
      - - \ No newline at end of file diff --git a/pkg/inst/web/soil_DT50.html b/pkg/inst/web/soil_DT50.html deleted file mode 100644 index 0e142ae..0000000 --- a/pkg/inst/web/soil_DT50.html +++ /dev/null @@ -1,104 +0,0 @@ - - - - -soil_DT50. pfm 0.2-4 - - - - - - - - - - - - - - - -
      -
      -
      - pfm 0.2-4 -
      - -
      -
      -
      -
      - -
      -
      - -
      - -

      Obtain soil DT50

      - -
      -
      -

      Usage

      - 
      soil_DT50(chent, aggregator = geomean, signif = 3, lab_field = "laboratory", value = "DT50ref", redox = "aerobic", raw = FALSE)
      - -

      Arguments

      -
      -
      chent
      -
      The chent object to get the information from
      -
      aggregator
      -
      The aggregator function. Can be mean, -geomean, or identity, for example.
      -
      signif
      -
      How many significant digits do we want
      -
      lab_field
      -
      If not NA, do we want laboratory or field endpoints
      -
      value
      -
      The name of the value we want. The list given in the -usage section is not exclusive
      -
      redox
      -
      If not NA, are we looking for aerobic or anaerobic data
      -
      raw
      -
      Should the number(s) be returned as stored in the chent -object (could be a character value) to retain original information -about precision?
      -
      - -
      -

      Description

      - -

      Obtain soil DT50

      - -
      -
      -
      - - - -
      -
      - - -
      - - \ No newline at end of file diff --git a/pkg/inst/web/soil_Kfoc.html b/pkg/inst/web/soil_Kfoc.html deleted file mode 100644 index ace5f4b..0000000 --- a/pkg/inst/web/soil_Kfoc.html +++ /dev/null @@ -1,100 +0,0 @@ - - - - -soil_Kfoc. pfm 0.2-4 - - - - - - - - - - - - - - - -
      -
      -
      - pfm 0.2-4 -
      - -
      -
      -
      -
      - -
      -
      - -
      - -

      Obtain soil Kfoc

      - -
      -
      -

      Usage

      - 
      soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc", raw = FALSE)
      - -

      Arguments

      -
      -
      chent
      -
      The chent object to get the information from
      -
      aggregator
      -
      The aggregator function. Can be mean, -geomean, or identity, for example.
      -
      signif
      -
      How many significant digits do we want
      -
      value
      -
      The name of the value we want. The list given in the -usage section is not exclusive
      -
      raw
      -
      Should the number(s) be returned as stored in the chent -object (could be a character value) to retain original information -about precision?
      -
      - -
      -

      Description

      - -

      Obtain soil Kfoc

      - -
      -
      -
      - - - -
      -
      - - -
      - - \ No newline at end of file diff --git a/pkg/inst/web/soil_N.html b/pkg/inst/web/soil_N.html deleted file mode 100644 index 886bbc7..0000000 --- a/pkg/inst/web/soil_N.html +++ /dev/null @@ -1,98 +0,0 @@ - - - - -soil_N. pfm 0.2-4 - - - - - - - - - - - - - - - -
      -
      -
      - pfm 0.2-4 -
      - -
      -
      -
      -
      - -
      -
      - -
      - -

      Obtain soil Freundlich exponent

      - -
      -
      -

      Usage

      - 
      soil_N(chent, aggregator = mean, signif = 3, raw = FALSE)
      - -

      Arguments

      -
      -
      chent
      -
      The chent object to get the information from
      -
      aggregator
      -
      The aggregator function. Can be mean, -geomean, or identity, for example.
      -
      signif
      -
      How many significant digits do we want
      -
      raw
      -
      Should the number(s) be returned as stored in the chent -object (could be a character value) to retain original information -about precision?
      -
      - -
      -

      Description

      - -

      In pesticide fate modelling, this exponent is often called 1/n. Here, in -order to facilitate dealing with such data in R, it is called N.

      - -
      -
      -
      - - - -
      -
      - - -
      - - \ No newline at end of file diff --git a/pkg/inst/web/soil_scenario_data_EFSA_2015.html b/pkg/inst/web/soil_scenario_data_EFSA_2015.html deleted file mode 100644 index 0230afb..0000000 --- a/pkg/inst/web/soil_scenario_data_EFSA_2015.html +++ /dev/null @@ -1,141 +0,0 @@ - - - - -soil_scenario_data_EFSA_2015. pfm 0.3-7 - - - - - - - - - - - - - - - -
      -
      -
      - pfm 0.3-7 -
      - -
      -
      -
      -
      - -
      -
      - -
      - -

      Properties of the predefined scenarios from the EFSA guidance from 2015

      - -
      -
      - -
      -

      Format

      - -

      A data frame with one row for each scenario. Row names are the scenario codes, - e.g. CTN for the Northern scenario for the total concentration in soil. Columns are - mostly self-explanatory. rho is the dry bulk density of the top soil.

      - -
      - -
      -

      Source

      - -

      EFSA (European Food Safety Authority) (2015) -EFSA guidance document for predicting environmental concentrations -of active substances of plant protection products and transformation products of these -active substances in soil. EFSA Journal 13(4) 4093 -doi:10.2903/j.efsa.2015.4093

      - -
      - -
      -

      Description

      - -

      Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the -concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the -scenario and model adjustment factors from p. 15 and p. 17 are included.

      - -
      - -

      Examples

      - 
      ## Not run: 
-#   # This is the code that was used to define the data
-#   soil_scenario_data_EFSA_2015 <- data.frame(
-#     Zone = rep(c("North", "Central", "South"), 2),
-#     Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"),
-#     T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8),
-#     T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7),
-#     Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"),
-#     f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011),
-#     theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347),
-#     rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51),
-#     f_sce = c(3, 2, 2, 2, 1.5, 1.5),
-#     f_mod = c(2, 2, 2, 4, 4, 4),
-#     stringsAsFactors = FALSE,
-#     row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS")
-#   )
-#   save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData')
-# ## End(Not run)
-
-# And this is the resulting dataframe
-soil_scenario_data_EFSA_2015
-
      
-
             Zone        Country T_arit T_arr     Texture  f_om theta_fc  rho f_sce
-CTN   North        Estonia    4.7   7.0      Coarse 0.118    0.244 0.95   3.0
-CTC Central        Germany    8.0  10.1      Coarse 0.086    0.244 1.05   2.0
-CTS   South         France   11.0  12.3 Medium fine 0.048    0.385 1.22   2.0
-CLN   North        Denmark    8.2   9.8      Medium 0.023    0.347 1.39   2.0
-CLC Central Czech Republik    9.1  11.2      Medium 0.018    0.347 1.43   1.5
-CLS   South          Spain   12.8  14.7      Medium 0.011    0.347 1.51   1.5
-    f_mod
-CTN     2
-CTC     2
-CTS     2
-CLN     4
-CLC     4
-CLS     4
-
      -
      -
      - - - -
      -
      - - -
      - - \ No newline at end of file diff --git a/pkg/inst/web/soil_sorption.html b/pkg/inst/web/soil_sorption.html deleted file mode 100644 index 152fc5e..0000000 --- a/pkg/inst/web/soil_sorption.html +++ /dev/null @@ -1,98 +0,0 @@ - - - - -soil_sorption. pfm 0.2-4 - - - - - - - - - - - - - - - -
      -
      -
      - pfm 0.2-4 -
      - -
      -
      -
      -
      - -
      -
      - -
      - -

      Obtain soil sorption data

      - -
      -
      -

      Usage

      - 
      soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), signif = rep(3, length(values)), raw = FALSE)
      - -

      Arguments

      -
      -
      chent
      -
      The chent object to get the information from
      -
      values
      -
      The values to be returned
      -
      aggregators
      -
      A named vector of aggregator functions to be used
      -
      signif
      -
      How many significant digits do we want
      -
      raw
      -
      Should the number(s) be returned as stored in the chent -object (could be a character value) to retain original information -about precision?
      -
      - -
      -

      Description

      - -

      Obtain soil sorption data

      - -
      -
      -
      - - - -
      -
      - - -
      - - \ No newline at end of file diff --git a/pkg/man/FOCUS_GW_scenarios_2012.Rd b/pkg/man/FOCUS_GW_scenarios_2012.Rd deleted file mode 100644 index 3ae151b..0000000 --- a/pkg/man/FOCUS_GW_scenarios_2012.Rd +++ /dev/null @@ -1,17 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/FOCUS_GW_scenarios_2012.R -\name{FOCUS_GW_scenarios_2012} -\alias{FOCUS_GW_scenarios_2012} -\title{A very small subset of the FOCUS Groundwater scenario defitions} -\description{ -Currently, only a small subset of the soil definitions are provided. -} -\examples{ -FOCUS_GW_scenarios_2012 -} -\references{ -FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. - FOrum for the Co-ordination of pesticde fate models and their USe. - http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf -} - diff --git a/pkg/man/GUS.Rd b/pkg/man/GUS.Rd deleted file mode 100644 index f1f5f28..0000000 --- a/pkg/man/GUS.Rd +++ /dev/null @@ -1,81 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/GUS.R -\name{GUS} -\alias{GUS} -\alias{GUS.chent} -\alias{GUS.numeric} -\alias{print.GUS_result} -\title{Groundwater ubiquity score based on Gustafson (1989)} -\usage{ -GUS(...) - -\method{GUS}{numeric}(DT50, Koc, ...) - -\method{GUS}{chent}(chent, degradation_value = "DT50ref", - lab_field = "laboratory", redox = "aerobic", sorption_value = "Kfoc", - degradation_aggregator = geomean, sorption_aggregator = geomean, ...) - -\method{print}{GUS_result}(x, ..., digits = 1) -} -\arguments{ -\item{...}{Included in the generic to allow for further arguments later. Therefore -this also had to be added to the specific methods.} - -\item{DT50}{Half-life of the chemical in soil. Should be a field -half-life according to Gustafson (1989). However, leaching to the sub-soil -can not completely be excluded in field dissipation experiments and Gustafson -did not refer to any normalisation procedure, but says the field study should -be conducted under use conditions.} - -\item{Koc}{The sorption constant normalised to organic carbon. Gustafson -does not mention the nonlinearity of the sorption constant commonly -found and usually described by Freundlich sorption, therefore it is -unclear at which reference concentration the Koc should be observed -(and if the reference concentration would be in soil or in porewater).} - -\item{chent}{If a chent is given with appropriate information present in its -chyaml field, this information is used, with defaults specified below.} - -\item{degradation_value}{Which of the available degradation values should -be used?} - -\item{lab_field}{Should laboratory or field half-lives be used? This -defaults to lab in this implementation, in order to avoid -double-accounting for mobility. If comparability with the original GUS -values given by Gustafson (1989) is desired, non-normalised first-order -field half-lives obtained under actual use conditions should be used.} - -\item{redox}{Aerobic or anaerobic degradation data} - -\item{sorption_value}{Which of the available sorption values should be used? -Defaults to Kfoc as this is what is generally available from the European -pesticide peer review process. These values generally use a reference -concentration of 1 mg/L in porewater, that means they would be expected to -be Koc values at a concentration of 1 mg/L in the water phase.} - -\item{degradation_aggregator}{Function for aggregating half-lives} - -\item{sorption_aggregator}{Function for aggregation Koc values} - -\item{x}{An object of class GUS_result to be printed} - -\item{digits}{The number of digits used in the print method} -} -\value{ -A list with the DT50 and Koc used as well as the resulting score - of class GUS_result -} -\description{ -The groundwater ubiquity score GUS is calculated according to -the following equation -\deqn{GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})}{GUS = log10 DT50soil * (4 - log10 Koc)} -} -\author{ -Johannes Ranke -} -\references{ -Gustafson, David I. (1989) Groundwater ubiquity score: a simple -method for assessing pesticide leachability. \emph{Environmental -toxicology and chemistry} \bold{8}(4) 339–57. -} - diff --git a/pkg/man/PEC_soil.Rd b/pkg/man/PEC_soil.Rd deleted file mode 100644 index c0b5201..0000000 --- a/pkg/man/PEC_soil.Rd +++ /dev/null @@ -1,119 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/PEC_soil.R -\name{PEC_soil} -\alias{PEC_soil} -\title{Calculate predicted environmental concentrations in soil} -\usage{ -PEC_soil(rate, rate_units = "g/ha", interception = 0, mixing_depth = 5, - PEC_units = "mg/kg", PEC_pw_units = "mg/L", interval = NA, - n_periods = Inf, tillage_depth = 20, chent = NA, DT50 = NA, - Koc = NA, Kom = Koc/1.724, t_avg = 0, scenarios = c("default", - "EFSA_2015"), porewater = FALSE) -} -\arguments{ -\item{rate}{Application rate in units specified below} - -\item{rate_units}{Defaults to g/ha} - -\item{interception}{The fraction of the application rate that does not reach the soil} - -\item{mixing_depth}{Mixing depth in cm} - -\item{PEC_units}{Requested units for the calculated PEC. Only mg/kg currently supported} - -\item{PEC_pw_units}{Only mg/L currently supported} - -\item{interval}{Period of the deeper mixing, defaults to 365, which is a year if -rate units are in days} - -\item{n_periods}{Number of periods to be considered for long term PEC calculations} - -\item{tillage_depth}{Periodic (see interval) deeper mixing in cm} - -\item{chent}{An optional chent object holding substance specific information. Can -also be a name for the substance as a character string} - -\item{DT50}{If specified, overrides soil DT50 endpoints from a chent object -If DT50 is not specified here and not available from the chent object, zero -degradation is assumed} - -\item{Koc}{If specified, overrides Koc endpoints from a chent object} - -\item{Kom}{Calculated from Koc by default, but can explicitly be specified -as Kom here} - -\item{t_avg}{Averaging times for time weighted average concentrations} - -\item{scenarios}{If this is 'default', the DT50 will be used without correction -and soil properties as specified in the REACH guidance (R.16, Table -R.16-9) are used for porewater PEC calculations. If this is "EFSA_2015", -the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when -'chents' is specified, the DegT50 with destination 'PECgw' will be used), -and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also -model and scenario adjustment factors from the EFSA guidance are used.} - -\item{porewater}{Should equilibrium porewater concentrations be estimated -based on Kom and the organic carbon fraction of the soil instead of total -soil concentrations? Based on equation (7) given in the PPR panel opinion -(EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015, -p. 13).} -} -\value{ -The predicted concentration in soil -} -\description{ -This is a basic calculation of a contaminant concentration in bulk soil -based on complete, instantaneous mixing. If an interval is given, an -attempt is made at calculating a long term maximum concentration using -the concepts layed out for example in the PPR panel opinion (EFSA 2012). -} -\details{ -This assumes that the complete load to soil during the time specified by -'interval' (typically 365 days) is dosed at once. As in the PPR panel -opinion cited below (PPR panel 2012), only temperature correction using the -Arrhenius equation is performed. - -Total soil and porewater PEC values for the scenarios as defined in the EFSA -guidance (2015, p. 13) can easily be calculated. -} -\note{ -If temperature information is available in the selected scenarios, as - e.g. in the EFSA scenarios, the DT50 for groundwater modelling - (destination 'PECgw') is taken from the chent object, otherwise the DT50 - with destination 'PECsoil'. -} -\examples{ -PEC_soil(100, interception = 0.25) - -# This is example 1 starting at p. 79 of the EFSA guidance (2015) -PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), - scenarios = "EFSA_2015") -PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), - Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE) - -# The following is from example 4 starting at p. 85 of the EFSA guidance (2015) -# Metabolite M2 -# Calculate total and porewater soil concentrations for tier 1 scenarios -# Relative molar mass is 100/300, formation fraction is 0.7 * 1 -results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21), - scenarios = "EFSA_2015") -results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21), - Kom = 100, scenarios = "EFSA_2015", porewater = TRUE) -} -\author{ -Johannes Ranke -} -\references{ -EFSA Panel on Plant Protection Products and their Residues (2012) - Scientific Opinion on the science behind the guidance for scenario - selection and scenario parameterisation for predicting environmental - concentrations of plant protection products in soil. \emph{EFSA Journal} - \bold{10}(2) 2562, doi:10.2903/j.efsa.2012.2562 - - EFSA (European Food Safety Authority) (2015) EFSA guidance document for - predicting environmental concentrations of active substances of plant - protection products and transformation products of these active substances - in soil. \emph{EFSA Journal} \bold{13}(4) 4093 - doi:10.2903/j.efsa.2015.4093 -} - diff --git a/pkg/man/PEC_sw_drainage_UK.Rd b/pkg/man/PEC_sw_drainage_UK.Rd deleted file mode 100644 index cb64bde..0000000 --- a/pkg/man/PEC_sw_drainage_UK.Rd +++ /dev/null @@ -1,39 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/PEC_sw_drainage_UK.R -\name{PEC_sw_drainage_UK} -\alias{PEC_sw_drainage_UK} -\title{Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method} -\usage{ -PEC_sw_drainage_UK(rate, interception = 0, Koc, latest_application = NULL, - soil_DT50 = NULL, model = NULL, model_parms = NULL) -} -\arguments{ -\item{rate}{Application rate in g/ha} - -\item{interception}{The fraction of the application rate that does not reach the soil} - -\item{Koc}{The sorption coefficient normalised to organic carbon in L/kg} - -\item{latest_application}{Latest application date, formatted as e.g. "01 July"} - -\item{soil_DT50}{Soil degradation half-life, if SFO kinetics are to be used} - -\item{model}{The soil degradation model to be used. Either one of "FOMC", -"DFOP", "HS", or "IORE", or an mkinmod object} - -\item{model_parms}{A named numeric vector containing the model parameters} -} -\value{ -The predicted concentration in surface water in µg/L -} -\description{ -This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet -published on the CRC website -} -\examples{ -PEC_sw_drainage_UK(150, Koc = 100) -} -\author{ -Johannes Ranke -} - diff --git a/pkg/man/PEC_sw_drift.Rd b/pkg/man/PEC_sw_drift.Rd deleted file mode 100644 index 20fa921..0000000 --- a/pkg/man/PEC_sw_drift.Rd +++ /dev/null @@ -1,45 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/PEC_sw_drift.R -\name{PEC_sw_drift} -\alias{PEC_sw_drift} -\title{Calculate predicted environmental concentrations in surface water due to drift} -\usage{ -PEC_sw_drift(rate, applications = 1, water_depth = 30, - drift_percentages = NULL, drift_data = "JKI", crop = "Ackerbau", - distances = c(1, 5, 10, 20), rate_units = "g/ha", PEC_units = "µg/L") -} -\arguments{ -\item{rate}{Application rate in units specified below} - -\item{applications}{Number of applications for selection of drift percentile} - -\item{water_depth}{Depth of the water body in cm} - -\item{drift_percentages}{Percentage drift values for which to calculate PECsw. -'drift_data' and 'distances' if not NULL.} - -\item{drift_data}{Source of drift percentage data} - -\item{crop}{Crop name (use German names for JKI data), defaults to "Ackerbau"} - -\item{distances}{The distances in m for which to get PEC values} - -\item{rate_units}{Defaults to g/ha} - -\item{PEC_units}{Requested units for the calculated PEC. Only µg/L currently supported} -} -\value{ -The predicted concentration in surface water -} -\description{ -This is a basic, vectorised form of a simple calculation of a contaminant -concentration in surface water based on complete, instantaneous mixing -with input via spray drift. -} -\examples{ -PEC_sw_drift(100) -} -\author{ -Johannes Ranke -} - diff --git a/pkg/man/PEC_sw_sed.Rd b/pkg/man/PEC_sw_sed.Rd deleted file mode 100644 index 3140eb0..0000000 --- a/pkg/man/PEC_sw_sed.Rd +++ /dev/null @@ -1,42 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/PEC_sw_sed.R -\name{PEC_sw_sed} -\alias{PEC_sw_sed} -\title{Calculate predicted environmental concentrations in sediment from surface -water concentrations} -\usage{ -PEC_sw_sed(PEC_sw, percentage = 100, method = "percentage", - sediment_depth = 5, water_depth = 30, sediment_density = 1.3, - PEC_sed_units = c("µg/kg", "mg/kg")) -} -\arguments{ -\item{PEC_sw}{Numeric vector or matrix of surface water concentrations in µg/L for -which the corresponding sediment concentration is to be estimated} - -\item{percentage}{The percentage in sediment, used for the percentage method} - -\item{method}{The method used for the calculation} - -\item{sediment_depth}{Depth of the sediment layer} - -\item{water_depth}{Depth of the water body in cm} - -\item{sediment_density}{The density of the sediment in L/kg (equivalent to -g/cm3)} - -\item{PEC_sed_units}{The units of the estimated sediment PEC value} -} -\value{ -The predicted concentration in sediment -} -\description{ -The method 'percentage' is equivalent to what is used in the CRD spreadsheet -PEC calculator -} -\examples{ -PEC_sw_sed(PEC_sw_drift(100, distances = 1), percentage = 50) -} -\author{ -Johannes Ranke -} - diff --git a/pkg/man/SFO_actual_twa.Rd b/pkg/man/SFO_actual_twa.Rd deleted file mode 100644 index 573ea03..0000000 --- a/pkg/man/SFO_actual_twa.Rd +++ /dev/null @@ -1,29 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/SFO_actual_twa.R -\name{SFO_actual_twa} -\alias{SFO_actual_twa} -\title{Actual and maximum moving window time average concentrations for SFO kinetics} -\source{ -FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation - Kinetics from Environmental Fate Studies on Pesticides in EU Registratin, Version 1.1, - 18 December 2014, p. 251 -} -\usage{ -SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, - 100)) -} -\arguments{ -\item{DT50}{The half-life.} - -\item{times}{The output times, and window sizes for time weighted average concentrations} -} -\description{ -Actual and maximum moving window time average concentrations for SFO kinetics -} -\examples{ -SFO_actual_twa(10) -} -\author{ -Johannes Ranke -} - diff --git a/pkg/man/SSLRC_mobility_classification.Rd b/pkg/man/SSLRC_mobility_classification.Rd deleted file mode 100644 index 04aa01d..0000000 --- a/pkg/man/SSLRC_mobility_classification.Rd +++ /dev/null @@ -1,26 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/SSLRC_mobility_classification.R -\name{SSLRC_mobility_classification} -\alias{SSLRC_mobility_classification} -\title{Determine the SSLRC mobility classification for a chemical substance from its Koc} -\usage{ -SSLRC_mobility_classification(Koc) -} -\arguments{ -\item{Koc}{The sorption coefficient normalised to organic carbon in L/kg} -} -\value{ -A list containing the classification and the percentage of the - compound transported per 10 mm drain water -} -\description{ -This implements the method specified in the UK data requirements handbook and was -checked against the spreadsheet published on the CRC website -} -\examples{ -SSLRC_mobility_classification(100) -} -\author{ -Johannes Ranke -} - diff --git a/pkg/man/TOXSWA_cwa.Rd b/pkg/man/TOXSWA_cwa.Rd deleted file mode 100644 index de87510..0000000 --- a/pkg/man/TOXSWA_cwa.Rd +++ /dev/null @@ -1,58 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/TOXSWA_cwa.R -\docType{class} -\name{TOXSWA_cwa} -\alias{TOXSWA_cwa} -\title{R6 class for holding TOXSWA cwa concentration data and associated statistics} -\format{An \code{\link{R6Class}} generator object.} -\usage{ -TOXSWA_cwa -} -\description{ -An R6 class for holding TOXSWA cwa concentration data and some associated statistics. -Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_cwa}}. -} -\section{Fields}{ - -\describe{ -\item{\code{filename}}{Length one character vector.} - -\item{\code{basedir}}{Length one character vector.} - -\item{\code{segment}}{Length one integer, specifying for which segment the cwa data were read.} - -\item{\code{cwas}}{Dataframe holding the concentrations.} - -\item{\code{events}}{List of dataframes holding the event statistics for each threshold.} - -\item{\code{windows}}{Matrix of maximum time weighted average concentrations (TWAC_max) -and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) -for the requested moving window sizes in days.} -}} -\section{Methods}{ - -\describe{ - \item{\code{get_events(threshold, total = FALSE)}}{ - Populate a datataframe with event information for the specified threshold value - in µg/L. If \code{total = TRUE}, the total concentration including the amount - adsorbed to suspended matter will be used. The resulting dataframe is stored in the - \code{events} field of the object. - } - \item{\code{moving_windows(windows, total = FALSE)}}{ - Add to the \code{windows} field described above. - Again, if \code{total = TRUE}, the total concentration including the amount - adsorbed to suspended matter will be used. - } -} -} -\examples{ -H_sw_R1_stream <- read.TOXSWA_cwa("00003s_pa.cwa", - basedir = "SwashProjects/project_H_sw/TOXSWA", - zipfile = system.file("testdata/SwashProjects.zip", - package = "pfm")) -H_sw_R1_stream$get_events(c(2, 10)) -H_sw_R1_stream$moving_windows(c(7, 21)) -print(H_sw_R1_stream) -} -\keyword{data} - diff --git a/pkg/man/drift_data_JKI.Rd b/pkg/man/drift_data_JKI.Rd deleted file mode 100644 index c193c0d..0000000 --- a/pkg/man/drift_data_JKI.Rd +++ /dev/null @@ -1,50 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/drift_data_JKI.R -\docType{data} -\name{drift_data_JKI} -\alias{drift_data_JKI} -\title{Deposition from spray drift expressed as percent of the applied dose as -published by the JKI} -\format{A list currently containing matrices with spray drift percentage -data for field crops (Ackerbau), and Pome/stone fruit, early and late -(Obstbau frueh, spaet).} -\source{ -JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved -from -http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html -on 2015-06-11 -} -\description{ -Deposition from spray drift expressed as percent of the applied dose as -published by the German Julius-Kühn Institute (JKI). -} -\details{ -The data were extracted from the spreadsheet cited below using the R code -given in the example section. The spreadsheet is not included in the package -as its licence is not clear. -} -\examples{ - -\dontrun{ - # This is the code that was used to extract the data - library(readxl) - abdrift_path <- "inst/extdata/Tabelle der Abdrifteckwerte.xls" - JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet") - names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late") - drift_data_JKI <- list() - - for (n in 1:8) { - drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2) - drift_data <- as.matrix(drift_data_raw[1:9, 2:4]) - dimnames(drift_data) <- list(distance = as.integer(drift_data_raw[1:9, 1]), - crop = JKI_crops) - drift_data_JKI[[n]] <- drift_data - } - save(drift_data_JKI, file = "data/drift_data_JKI.RData") -} - -# And this is the resulting data -drift_data_JKI -} -\keyword{datasets} - diff --git a/pkg/man/endpoint.Rd b/pkg/man/endpoint.Rd deleted file mode 100644 index fd16650..0000000 --- a/pkg/man/endpoint.Rd +++ /dev/null @@ -1,75 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/endpoint.R -\name{endpoint} -\alias{endpoint} -\alias{soil_DT50} -\alias{soil_Kfoc} -\alias{soil_N} -\alias{soil_sorption} -\title{Retrieve endpoint information from the chyaml field of a chent object} -\usage{ -endpoint(chent, medium = "soil", type = c("degradation", "sorption"), - lab_field = c(NA, "laboratory", "field"), redox = c(NA, "aerobic", - "anaerobic"), value = c("DT50ref", "Kfoc", "N"), aggregator = geomean, - raw = FALSE, signif = 3) - -soil_DT50(chent, aggregator = geomean, signif = 3, - lab_field = "laboratory", value = "DT50ref", redox = "aerobic", - raw = FALSE) - -soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc", - raw = FALSE) - -soil_N(chent, aggregator = mean, signif = 3, raw = FALSE) - -soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc = - geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3), - raw = FALSE) -} -\arguments{ -\item{chent}{The \code{\link{chent}} object to get the information from} - -\item{medium}{The medium for which information is sought} - -\item{type}{The information type} - -\item{lab_field}{If not NA, do we want laboratory or field endpoints} - -\item{redox}{If not NA, are we looking for aerobic or anaerobic data} - -\item{value}{The name of the value we want. The list given in the -usage section is not exclusive} - -\item{aggregator}{The aggregator function. Can be mean, -\code{\link{geomean}}, or identity, for example.} - -\item{raw}{Should the number(s) be returned as stored in the chent -object (could be a character value) to retain original information -about precision?} - -\item{signif}{How many significant digits do we want} - -\item{values}{The values to be returned} - -\item{aggregators}{A named vector of aggregator functions to be used} -} -\value{ -The result from applying the aggregator function to - the values converted to a numeric vector, rounded to the - given number of significant digits, or, if raw = TRUE, - the values as a character value, retaining any implicit - information on precision that may be present. -} -\description{ -R6 class objects of class \code{\link{chent}} represent chemical entities -and can hold a list of information loaded from a chemical yaml file in their -chyaml field. Such information is extracted and optionally aggregated by -this function. -} -\details{ -The functions \code{soil_*} are functions to extract soil specific endpoints. -For the Freundlich exponent, the capital letter \code{N} is used in order to -facilitate dealing with such data in R. In pesticide fate modelling, this -exponent is often called 1/n. -} - diff --git a/pkg/man/geomean.Rd b/pkg/man/geomean.Rd deleted file mode 100644 index ed82294..0000000 --- a/pkg/man/geomean.Rd +++ /dev/null @@ -1,31 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/geomean.R -\name{geomean} -\alias{geomean} -\title{Calculate the geometric mean} -\usage{ -geomean(x, na.rm = TRUE) -} -\arguments{ -\item{x}{Vector of numbers} - -\item{na.rm}{Should NA values be omitted?} -} -\value{ -The geometric mean -} -\description{ -Based on some posts in a thread on Stackoverflow -\url{http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in} -This function checks for negative values, removes NA values per default and -returns 0 if at least one element of the vector is 0. -} -\examples{ -geomean(c(1, 3, 9)) -geomean(c(1, 3, NA, 9)) -\dontrun{geomean(c(1, -3, 9)) # returns an error} -} -\author{ -Johannes Ranke -} - diff --git a/pkg/man/pfm_degradation.Rd b/pkg/man/pfm_degradation.Rd deleted file mode 100644 index 9ab1d0a..0000000 --- a/pkg/man/pfm_degradation.Rd +++ /dev/null @@ -1,35 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/pfm_degradation.R -\name{pfm_degradation} -\alias{pfm_degradation} -\title{Calculate a time course of relative concentrations based on an mkinmod model} -\usage{ -pfm_degradation(model = "SFO", DT50 = 1000, parms = c(k_parent_sink = - log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365, by = - step_days)) -} -\arguments{ -\item{model}{The degradation model to be used. Either a parent only model like -'SFO' or 'FOMC', or an mkinmod object} - -\item{DT50}{The half-life. This is only used when simple exponential decline -is calculated (SFO model).} - -\item{parms}{The parameters used for the degradation model} - -\item{years}{For how many years should the degradation be predicted?} - -\item{step_days}{What step size in days should the output have?} - -\item{times}{The output times} -} -\description{ -Calculate a time course of relative concentrations based on an mkinmod model -} -\examples{ -head(pfm_degradation("SFO", DT50 = 10)) -} -\author{ -Johannes Ranke -} - diff --git a/pkg/man/plot.TOXSWA_cwa.Rd b/pkg/man/plot.TOXSWA_cwa.Rd deleted file mode 100644 index b5f0163..0000000 --- a/pkg/man/plot.TOXSWA_cwa.Rd +++ /dev/null @@ -1,42 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/TOXSWA_cwa.R -\name{plot.TOXSWA_cwa} -\alias{plot.TOXSWA_cwa} -\title{Plot TOXSWA surface water concentrations} -\usage{ -\method{plot}{TOXSWA_cwa}(x, time_column = c("datetime", "t", "t_firstjan", - "t_rel_to_max"), xlab = "default", ylab = "default", add = FALSE, - total = FALSE, LC_TIME = "C", ...) -} -\arguments{ -\item{x}{The TOXSWA_cwa object to be plotted.} - -\item{time_column}{What should be used for the time axis. If "t_firstjan" is chosen, -the time is given in days relative to the first of January in the first year.} - -\item{xlab, ylab}{Labels for x and y axis.} - -\item{add}{Should we add to an existing plot?} - -\item{total}{Should the total concentration in water be plotted, including substance sorbed -to suspended matter?} - -\item{LC_TIME}{Specification of the locale used to format dates} - -\item{...}{Further arguments passed to \code{plot} if we are not adding to an existing plot} -} -\description{ -Plot TOXSWA hourly concentrations of a chemical substance in a specific -segment of a TOXSWA surface water body. -} -\examples{ -H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", - basedir = "SwashProjects/project_H_sw/TOXSWA", - zipfile = system.file("testdata/SwashProjects.zip", - package = "pfm")) -plot(H_sw_D4_pond) -} -\author{ -Johannes Ranke -} - diff --git a/pkg/man/read.TOXSWA_cwa.Rd b/pkg/man/read.TOXSWA_cwa.Rd deleted file mode 100644 index 84ef3da..0000000 --- a/pkg/man/read.TOXSWA_cwa.Rd +++ /dev/null @@ -1,56 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/TOXSWA_cwa.R -\name{read.TOXSWA_cwa} -\alias{read.TOXSWA_cwa} -\title{Read TOXSWA surface water concentrations} -\usage{ -read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last", - substance = "parent", total = FALSE, windows = NULL, - thresholds = NULL) -} -\arguments{ -\item{filename}{The filename of the cwa file (TOXSWA 2.x.y or similar) or the -out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).} - -\item{basedir}{The path to the directory where the cwa file resides.} - -\item{zipfile}{Optional path to a zip file containing the cwa file.} - -\item{segment}{The segment for which the data should be read. Either "last", or -the segment number.} - -\item{substance}{For TOXSWA 4 .out files, the default value "parent" leads -to reading concentrations of the parent compound. Alternatively, the substance -of interested can be selected by its code name.} - -\item{total}{Set this to TRUE in order to read total concentrations as well. This is -only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa -files. For .cwa files, the total concentration is always read as well.} - -\item{windows}{Numeric vector of width of moving windows in days, for calculating -maximum time weighted average concentrations and areas under the curve.} - -\item{thresholds}{Numeric vector of threshold concentrations in µg/L for -generating event statistics.} -} -\value{ -An instance of an R6 object of class -\code{\link{TOXSWA_cwa}}. -} -\description{ -Read TOXSWA hourly concentrations of a chemical substance in a specific -segment of a TOXSWA surface water body. Per default, the data for the last -segment are imported. As TOXSWA 4 reports the values at the end of the hour -(ConLiqWatLayCur) in its summary file, we use this value as well instead -of the hourly averages (ConLiqWatLay). -} -\examples{ -H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", - basedir = "SwashProjects/project_H_sw/TOXSWA", - zipfile = system.file("testdata/SwashProjects.zip", - package = "pfm")) -} -\author{ -Johannes Ranke -} - diff --git a/pkg/man/soil_scenario_data_EFSA_2015.Rd b/pkg/man/soil_scenario_data_EFSA_2015.Rd deleted file mode 100644 index b45af4a..0000000 --- a/pkg/man/soil_scenario_data_EFSA_2015.Rd +++ /dev/null @@ -1,46 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/soil_scenario_data_EFSA_2015.R -\docType{data} -\name{soil_scenario_data_EFSA_2015} -\alias{soil_scenario_data_EFSA_2015} -\title{Properties of the predefined scenarios from the EFSA guidance from 2015} -\format{A data frame with one row for each scenario. Row names are the scenario codes, - e.g. CTN for the Northern scenario for the total concentration in soil. Columns are - mostly self-explanatory. \code{rho} is the dry bulk density of the top soil.} -\source{ -EFSA (European Food Safety Authority) (2015) -EFSA guidance document for predicting environmental concentrations -of active substances of plant protection products and transformation products of these -active substances in soil. \emph{EFSA Journal} \bold{13}(4) 4093 -doi:10.2903/j.efsa.2015.4093 -} -\description{ -Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the -concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the -scenario and model adjustment factors from p. 15 and p. 17 are included. -} -\examples{ -\dontrun{ - # This is the code that was used to define the data - soil_scenario_data_EFSA_2015 <- data.frame( - Zone = rep(c("North", "Central", "South"), 2), - Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"), - T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8), - T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7), - Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"), - f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011), - theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347), - rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51), - f_sce = c(3, 2, 2, 2, 1.5, 1.5), - f_mod = c(2, 2, 2, 4, 4, 4), - stringsAsFactors = FALSE, - row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS") - ) - save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData') -} - -# And this is the resulting dataframe -soil_scenario_data_EFSA_2015 -} -\keyword{datasets} - diff --git a/pkg/tests/testthat.R b/pkg/tests/testthat.R deleted file mode 100644 index d2df1cc..0000000 --- a/pkg/tests/testthat.R +++ /dev/null @@ -1,4 +0,0 @@ -library(testthat) -library(pfm) - -test_check("pfm") diff --git a/pkg/tests/testthat/EXSW2_R1_stream_printed.txt b/pkg/tests/testthat/EXSW2_R1_stream_printed.txt deleted file mode 100644 index 60bb5ac..0000000 --- a/pkg/tests/testthat/EXSW2_R1_stream_printed.txt +++ /dev/null @@ -1,10 +0,0 @@ - data from file 3.out segment 20 - datetime t t_firstjan t_rel_to_max cwa_mug_per_L -1 1978-10-01 00:00:00 0.000 273.0000 -55.083 0 -2 1978-10-01 01:00:00 0.042 273.0417 -55.041 0 -3 1978-10-01 02:00:00 0.083 273.0833 -55.000 0 -4 1978-10-01 03:00:00 0.125 273.1250 -54.958 0 -5 1978-10-01 04:00:00 0.167 273.1667 -54.916 0 -6 1978-10-01 05:00:00 0.208 273.2083 -54.875 0 -Moving window analysis -NULL diff --git a/pkg/tests/testthat/H_sw_D4_pond_printed.txt b/pkg/tests/testthat/H_sw_D4_pond_printed.txt deleted file mode 100644 index 5730be6..0000000 --- a/pkg/tests/testthat/H_sw_D4_pond_printed.txt +++ /dev/null @@ -1,10 +0,0 @@ - data from file 00001p_pa.cwa segment 1 - datetime t t_firstjan t_rel_to_max cwa_mug_per_L cwa_tot_mug_per_L -1 1985-01-01 00:00:00 0.000 0.00000000 -396.167 0.00000000 0.00000000 -2 1985-01-01 01:00:00 0.042 0.04166667 -396.125 0.08323064 0.08323716 -3 1985-01-01 02:00:00 0.083 0.08333333 -396.084 0.16626900 0.16628210 -4 1985-01-01 03:00:00 0.125 0.12500000 -396.042 0.24911240 0.24913190 -5 1985-01-01 04:00:00 0.167 0.16666667 -396.000 0.33172050 0.33174650 -6 1985-01-01 05:00:00 0.208 0.20833333 -395.959 0.41401430 0.41404670 -Moving window analysis -NULL diff --git a/pkg/tests/testthat/H_sw_R1_stream_events.rds b/pkg/tests/testthat/H_sw_R1_stream_events.rds deleted file mode 100644 index ba6557b..0000000 Binary files a/pkg/tests/testthat/H_sw_R1_stream_events.rds and /dev/null differ diff --git a/pkg/tests/testthat/H_sw_R1_stream_printed.txt b/pkg/tests/testthat/H_sw_R1_stream_printed.txt deleted file mode 100644 index 572ad6d..0000000 --- a/pkg/tests/testthat/H_sw_R1_stream_printed.txt +++ /dev/null @@ -1,10 +0,0 @@ - data from file 00003s_pa.cwa segment 20 - datetime t t_firstjan t_rel_to_max cwa_mug_per_L cwa_tot_mug_per_L -20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0 0 -40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0 0 -60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0 0 -80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0 0 -100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0 0 -120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0 0 -Moving window analysis -NULL diff --git a/pkg/tests/testthat/H_sw_R1_stream_windows.rds b/pkg/tests/testthat/H_sw_R1_stream_windows.rds deleted file mode 100644 index 2531189..0000000 Binary files a/pkg/tests/testthat/H_sw_R1_stream_windows.rds and /dev/null differ diff --git a/pkg/tests/testthat/test_PEC_sed.R b/pkg/tests/testthat/test_PEC_sed.R deleted file mode 100644 index 443f789..0000000 --- a/pkg/tests/testthat/test_PEC_sed.R +++ /dev/null @@ -1,9 +0,0 @@ -context("Simple PEC sediment calculations") - -test_that("PEC_sw_sed calculates correctly using the percentage method", { - # Application of 100 g/ha, 1 m spray drift distance (2.77% drift input), 50% in sediment, - # default assumptions of CRD spreadsheet (5 cm sediment depth, 1.3 kg/L sediment density) - # Reference value calculated with CRD spreadsheet - PEC_sw_100_1_m <- PEC_sw_drift(100, distances = 1) - expect_equivalent(round(PEC_sw_sed(PEC_sw_100_1_m, percentage = 50), 3), 2.131) -}) diff --git a/pkg/tests/testthat/test_PEC_soil.R b/pkg/tests/testthat/test_PEC_soil.R deleted file mode 100644 index 0661a52..0000000 --- a/pkg/tests/testthat/test_PEC_soil.R +++ /dev/null @@ -1,95 +0,0 @@ -library(pfm) -context("Simple PEC soil calculations") - -test_that("PEC_soil calculates correctly", { - # Application of 100 g/ha gives 0.133 mg/kg under default assumptions - expect_equal(as.numeric(PEC_soil(100)), 0.1 * 4/3) - - # or 0.1 mg/kg assuming 25% interception - expect_equal(as.numeric(PEC_soil(100, interception = 0.25)), 0.1) - - # Mixing depth of 1 cm gives five-fold PEC - expect_equal(as.numeric(PEC_soil(100, interception = 0.25, mixing_depth = 1)), 0.5) -}) - -test_that("Tier 1 PEC soil example for Pesticide A in EFSA guidance can be reproduced", { - # Calculate total soil concentrations for tier 1 scenarios - results_pfm <- PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), - scenarios = "EFSA_2015") - - # From Table I.5, p. 80 - results_guidance <- matrix(c(22.0, 11.5, 9.1, 21.8, 11.4, 9.0), - ncol = 3, byrow = TRUE) - dimnames(results_guidance) <- list(t_avg = c(0, 21), - scenario = c("CTN", "CTC", "CTS")) - - - expect_equal(round(results_pfm, 1), results_guidance) - - # Calculate porewater soil concentrations for tier 1 scenarios - results_pfm_pw <- PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), - Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE) - - # From Table I.5, p. 80 - results_guidance_pw <- matrix(c(0.76, 0.67, 0.91, 0.75, 0.66, 0.90), - ncol = 3, byrow = TRUE) - dimnames(results_guidance_pw) <- list(t_avg = c(0, 21), - scenario = c("CLN", "CLC", "CLS")) - - expect_equal(round(results_pfm_pw, 2), results_guidance_pw) -}) - -test_that("Tier 1 PEC soil example for Pesticide F in EFSA guidance can be reproduced", { - # Parent F - # Calculate total and porewater soil concentrations for tier 1 scenarios - results_pfm <- PEC_soil(1000, interval = 365, DT50 = 25, t_avg = c(0, 21), - scenarios = "EFSA_2015") - results_pfm_pw <- PEC_soil(1000, interval = 365, DT50 = 25, t_av = c(0, 21), - Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE) - - # From Table I.14, p. 88 - results_guidance <- matrix(c(12.8, 7.7, 6.6, 11.8, 6.8, 5.7), - ncol = 3, byrow = TRUE) - results_guidance_pw <- matrix(c(0.50, 0.46, 0.71, 0.45, 0.41, 0.60), - ncol = 3, byrow = TRUE) - - # Skip checking dimnames by using expect_equivalent() - expect_equivalent(round(results_pfm, 1), results_guidance) - expect_equivalent(round(results_pfm_pw, 2), results_guidance_pw) - - # Metabolite M1 - # Calculate total and porewater soil concentrations for tier 1 scenarios - # Relative molar mass is 200/300, formation fraction is 0.7 - results_pfm <- PEC_soil(200/300 * 0.7 * 1000, interval = 365, DT50 = 100, t_avg = c(0, 21), - scenarios = "EFSA_2015") - results_pfm_pw <- PEC_soil(200/300 * 0.7 * 1000, interval = 365, DT50 = 100, t_av = c(0, 21), - Kom = 10, scenarios = "EFSA_2015", porewater = TRUE) - - # From Table I.15, p. 88 - results_guidance <- matrix(c(7.27, 4.08, 3.38, 7.12, 3.97, 3.26), - ncol = 3, byrow = TRUE) - results_guidance_pw <- matrix(c(12.93, 10.42, 11.66, 12.58, 10.09, 11.15), - ncol = 3, byrow = TRUE) - - # Skip checking dimnames by using expect_equivalent() - expect_equivalent(round(results_pfm, 2), results_guidance) - expect_equivalent(round(results_pfm_pw, 2), results_guidance_pw) - - # Metabolite M2 - # Calculate total and porewater soil concentrations for tier 1 scenarios - # Relative molar mass is 100/300, formation fraction is 0.7 * 1 - results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21), - scenarios = "EFSA_2015") - results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21), - Kom = 100, scenarios = "EFSA_2015", porewater = TRUE) - - # From Table I.16, p. 89 - results_guidance <- matrix(c(5.13, 2.69, 2.13, 5.08, 2.66, 2.10), - ncol = 3, byrow = TRUE) - results_guidance_pw <- matrix(c(1.61, 1.39, 1.80, 1.60, 1.37, 1.77), - ncol = 3, byrow = TRUE) - - # Skip checking dimnames by using expect_equivalent() - expect_equivalent(round(results_pfm, 2), results_guidance) - expect_equivalent(round(results_pfm_pw, 2), results_guidance_pw) -}) diff --git a/pkg/tests/testthat/test_PEC_sw_drift.R b/pkg/tests/testthat/test_PEC_sw_drift.R deleted file mode 100644 index d09d578..0000000 --- a/pkg/tests/testthat/test_PEC_sw_drift.R +++ /dev/null @@ -1,15 +0,0 @@ -library(pfm) -context("Simple PEC surface water calculations with drift entry") - -test_that("PEC_sw_drift gives the same results as the CRD PEC calculator", { - # One application of 30 g/ha to field crops calculated with UK PEC calculator published by CRD - expect_equal(round(PEC_sw_drift(30), 3), - c('1 m' = 0.277, '5 m' = 0.057, '10 m' = 0.029, '20 m' = 0.015)) - - # 7 applications of 30 g/ha to field crops calculated with UK PEC calculator, initial PEC - expect_equal(round(PEC_sw_drift(30, 7), 3), - c('1 m' = 0.161, '5 m' = 0.033, '10 m' = 0.017, '20 m' = 0.008)) - - # 4 applications of 30 g/ha to late fruit crops calculated with UK PEC calculator published by CRD (uses different drift values from SANCO aquatic guidance) - #expect_equal(round(PEC_sw_drift(30, 4, crop = "Obstbau spät", distances = c(3, 20, 50)), 3), c('3 m' = 1.101, '20 m' = 0.080, '50 m' = 0.013)) -}) diff --git a/pkg/tests/testthat/test_SFO_actual_twa.R b/pkg/tests/testthat/test_SFO_actual_twa.R deleted file mode 100644 index b0a5537..0000000 --- a/pkg/tests/testthat/test_SFO_actual_twa.R +++ /dev/null @@ -1,13 +0,0 @@ -library(pfm) -context("Actual and time weighted average concentrations for SFO kinetics") - -test_that("SFO_actual_twa calculates correctly", { - test_times <- c(0, 1, 7, 21, 42) - # This was calculated with the CRD spreadsheet for multiple applications - reference <- data.frame( - actual = c(10, 9.330, 6.156, 2.333, 0.544), - twa = c(NaN, 9.661, 7.923, 5.267, 3.248), - row.names = test_times) - result <- round(10 * SFO_actual_twa(10, times = test_times), 3) - expect_equal(result, reference) -}) diff --git a/pkg/tests/testthat/test_TOXSWA_cwa.R b/pkg/tests/testthat/test_TOXSWA_cwa.R deleted file mode 100644 index 7c9a73c..0000000 --- a/pkg/tests/testthat/test_TOXSWA_cwa.R +++ /dev/null @@ -1,56 +0,0 @@ -library(pfm) -context("Read and analyse TOXSWA cwa files") - -zipfile_test = system.file("testdata/SwashProjects.zip", package = "pfm") -basedir_test = "SwashProjects/project_H_sw/TOXSWA" - -H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", - basedir = basedir_test, - zipfile = zipfile_test) - -H_sw_R1_stream <- read.TOXSWA_cwa("00003s_pa.cwa", - basedir = basedir_test, - zipfile = zipfile_test) - -basedir_test_2 = "SwashProjects/Project_1/TOXSWA" - -EXSW2_R1_stream <- read.TOXSWA_cwa("3.out", - basedir = basedir_test_2, - zipfile = zipfile_test) - - - -test_that("TOXSWA cwa file is correctly read and printed", { - - # This was the setting when printing the output into text files - options(width = 100) - - # Most content of the R6 object is at least partially printed - - H_sw_D4_pond_printed <- capture.output(print(H_sw_D4_pond)) - - expect_equal(H_sw_D4_pond_printed, readLines("H_sw_D4_pond_printed.txt")) - - H_sw_R1_stream_printed <- capture.output(print(H_sw_R1_stream)) - expect_equal(H_sw_R1_stream_printed, readLines("H_sw_R1_stream_printed.txt")) - - # The basedir is not printed, therefore tested separately - expect_equal(H_sw_D4_pond$basedir, basedir_test) - - EXSW2_R1_stream_printed <- capture.output(print(EXSW2_R1_stream)) - expect_equal(EXSW2_R1_stream_printed, readLines("EXSW2_R1_stream_printed.txt")) - - # The basedir is not printed, therefore tested separately - expect_equal(H_sw_D4_pond$basedir, basedir_test) -}) - -test_that("Getting events and moving window analysis works", { - - # Event analysis with two different thresholds - H_sw_R1_stream$get_events(c(2, 10)) - expect_equal_to_reference(H_sw_R1_stream$events, file = "H_sw_R1_stream_events.rds") - - # Moving window analysis - H_sw_R1_stream$moving_windows(c(7, 21)) - expect_equal_to_reference(H_sw_R1_stream$windows, file = "H_sw_R1_stream_windows.rds") -}) diff --git a/pkg/tests/testthat/test_UK_drainage.R b/pkg/tests/testthat/test_UK_drainage.R deleted file mode 100644 index 859f145..0000000 --- a/pkg/tests/testthat/test_UK_drainage.R +++ /dev/null @@ -1,33 +0,0 @@ -library(pfm) -context("UK drainage PEC calculations") - -test_that("The mobility classification and the drained percentage are correct", { - # Expected results are from the CRD drainage calculator, retrieved 2015-06-11 - - expect_equivalent(SSLRC_mobility_classification(1), list("Very mobile", 1.9)) - expect_equivalent(SSLRC_mobility_classification(15), list("Mobile", 1.9)) - expect_equivalent(SSLRC_mobility_classification(30), list("Mobile", 1.9)) - expect_equivalent(SSLRC_mobility_classification(74.9), list("Mobile", 1.9)) - expect_equivalent(SSLRC_mobility_classification(75), list("Moderately mobile", 0.7)) - expect_equivalent(SSLRC_mobility_classification(100), list("Moderately mobile", 0.7)) - expect_equivalent(SSLRC_mobility_classification(800), list("Slightly mobile", 0.5)) - expect_equivalent(SSLRC_mobility_classification(2000), list("Slightly mobile", 0.02)) - expect_equivalent(SSLRC_mobility_classification(5000), list("Non mobile", 0.01)) -}) - -test_that("UK drainflow PECs are correct", { - # Expected results are from the CRD drainage calculator, retrieved 2015-06-11, except - # for the third example from the data requirements handbook - - # This is the first example calculation from the data requirements handbook, where they give - # 8.07 µg/L as the result (obviously a rounding error). - expect_equal(round(PEC_sw_drainage_UK(150, interception = 0, Koc = 100), 4), 8.0769) - - # This is the second example calculation from the data requirements handbook - expect_equal(round(PEC_sw_drainage_UK(90, interception = 0, Koc = 10), 4), 13.1538) - - # This is the third example calculation from the data requirements handbook, - expect_equal(round(PEC_sw_drainage_UK(60, interception = 0.5, Koc = 550, - latest_application = "01 July", - soil_DT50 = 200), 2), 0.84) -}) diff --git a/pkg/tests/testthat/test_geomean.R b/pkg/tests/testthat/test_geomean.R deleted file mode 100644 index 0cc3416..0000000 --- a/pkg/tests/testthat/test_geomean.R +++ /dev/null @@ -1,11 +0,0 @@ -library(pfm) -context("Geometric mean calculation") - -test_that("The geometric mean is correctly calculated", { - expect_equal(geomean(c(1, 3, 9)), 3) - expect_equal(geomean(c(0, 3, 9)), 0) - expect_error(geomean(c(1, 3, NA, 9), na.rm = FALSE), "NA") - expect_equal(geomean(c(1, 3, NA, 9), na.rm = TRUE), 3) - expect_error(geomean(c(1, -3, 9)), "positive") - expect_error(geomean(c(1, -3, NA, 9)), "positive") -}) -- cgit v1.2.1