From d81550d0cccae824cc748de48e7fd50ea8d8033a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 16 Apr 2020 18:02:18 +0200 Subject: Make na.rm = FALSE the default for geomean() This makes more sense and is in line with mean() from base R. Adapt tests and update docs. --- man/FOCUS_Step_12_scenarios.Rd | 4 +- man/FOMC_actual_twa.Rd | 7 ++- man/GUS.Rd | 14 ++++-- man/PEC_soil.Rd | 30 +++++++++--- man/PEC_sw_drainage_UK.Rd | 12 +++-- man/PEC_sw_drift.Rd | 15 ++++-- man/PEC_sw_exposit_drainage.Rd | 15 ++++-- man/PEC_sw_exposit_runoff.Rd | 14 ++++-- man/PEC_sw_focus.Rd | 25 +++++++--- man/PEC_sw_sed.Rd | 12 +++-- man/SFO_actual_twa.Rd | 3 +- man/TOXSWA_cwa.Rd | 106 +++++++++++++++++++++++++++++++++-------- man/chent_focus_sw.Rd | 15 ++++-- man/endpoint.Rd | 40 +++++++++++----- man/geomean.Rd | 7 +-- man/one_box.Rd | 6 +-- man/pfm_degradation.Rd | 11 +++-- man/plot.TOXSWA_cwa.Rd | 16 +++++-- man/plot.one_box.Rd | 13 +++-- man/read.TOXSWA_cwa.Rd | 13 +++-- man/sawtooth.Rd | 8 +++- man/set_nd_nq.Rd | 10 +++- 22 files changed, 296 insertions(+), 100 deletions(-) (limited to 'man') diff --git a/man/FOCUS_Step_12_scenarios.Rd b/man/FOCUS_Step_12_scenarios.Rd index f58dea7..0547d61 100644 --- a/man/FOCUS_Step_12_scenarios.Rd +++ b/man/FOCUS_Step_12_scenarios.Rd @@ -19,14 +19,14 @@ The text file is not included in the package as its licence is not clear. scenario_path <- "inst/extdata/FOCUS_Step_12_scenarios.txt" scenarios <- readLines(scenario_path)[9:38] FOCUS_Step_12_scenarios <- list() - sce <- read.table(text = scenarios, sep = "\\t", header = TRUE, check.names = FALSE, + sce <- read.table(text = scenarios, sep = "\t", header = TRUE, check.names = FALSE, stringsAsFactors = FALSE) FOCUS_Step_12_scenarios$names = sce$Crop rownames(sce) <- sce$Crop FOCUS_Step_12_scenarios$drift = sce[, 3:11] FOCUS_Step_12_scenarios$interception = sce[, 12:15] sce_2 <- readLines(scenario_path)[41:46] - rd <- read.table(text = sce_2, sep = "\\t")[1:2] + rd <- read.table(text = sce_2, sep = "\t")[1:2] rd_mat <- matrix(rd$V2, nrow = 3, byrow = FALSE) dimnames(rd_mat) = list(Time = c("Oct-Feb", "Mar-May", "Jun-Sep"), Region = c("North", "South")) diff --git a/man/FOMC_actual_twa.Rd b/man/FOMC_actual_twa.Rd index 2c40048..a0c7284 100644 --- a/man/FOMC_actual_twa.Rd +++ b/man/FOMC_actual_twa.Rd @@ -9,8 +9,11 @@ FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation 18 December 2014, p. 251 } \usage{ -FOMC_actual_twa(alpha = 1.0001, beta = 10, times = c(0, 1, 2, 4, 7, - 14, 21, 28, 42, 50, 100)) +FOMC_actual_twa( + alpha = 1.0001, + beta = 10, + times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100) +) } \arguments{ \item{alpha}{Parameter of the FOMC model} diff --git a/man/GUS.Rd b/man/GUS.Rd index adc1bb3..cd1a332 100644 --- a/man/GUS.Rd +++ b/man/GUS.Rd @@ -11,10 +11,16 @@ 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{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) } diff --git a/man/PEC_soil.Rd b/man/PEC_soil.Rd index a9e6c49..a198f24 100644 --- a/man/PEC_soil.Rd +++ b/man/PEC_soil.Rd @@ -4,14 +4,30 @@ \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, - leaching_depth = tillage_depth, crop = "annual", - cultivation = FALSE, chent = NA, DT50 = NA, FOMC = NA, - Koc = NA, Kom = Koc/1.724, t_avg = 0, t_act = NULL, +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, + leaching_depth = tillage_depth, + crop = "annual", + cultivation = FALSE, + chent = NA, + DT50 = NA, + FOMC = NA, + Koc = NA, + Kom = Koc/1.724, + t_avg = 0, + t_act = NULL, scenarios = c("default", "EFSA_2017", "EFSA_2015"), - leaching = scenarios == "EFSA_2017", porewater = FALSE) + leaching = scenarios == "EFSA_2017", + porewater = FALSE +) } \arguments{ \item{rate}{Application rate in units specified below} diff --git a/man/PEC_sw_drainage_UK.Rd b/man/PEC_sw_drainage_UK.Rd index c9f8ed4..98aa868 100644 --- a/man/PEC_sw_drainage_UK.Rd +++ b/man/PEC_sw_drainage_UK.Rd @@ -4,9 +4,15 @@ \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) +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} diff --git a/man/PEC_sw_drift.Rd b/man/PEC_sw_drift.Rd index dfc3f39..cde3c78 100644 --- a/man/PEC_sw_drift.Rd +++ b/man/PEC_sw_drift.Rd @@ -4,10 +4,17 @@ \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") +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} diff --git a/man/PEC_sw_exposit_drainage.Rd b/man/PEC_sw_exposit_drainage.Rd index 237d8cf..5a543c8 100644 --- a/man/PEC_sw_exposit_drainage.Rd +++ b/man/PEC_sw_exposit_drainage.Rd @@ -8,10 +8,17 @@ Excel 3.02 spreadsheet available from \url{https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3} } \usage{ -PEC_sw_exposit_drainage(rate, interception = 0, Koc = NA, - mobility = c(NA, "low", "high"), DT50 = Inf, t_drainage = 3, - V_ditch = 30, V_drainage = c(spring = 10, autumn = 100), - dilution = 2) +PEC_sw_exposit_drainage( + rate, + interception = 0, + Koc = NA, + mobility = c(NA, "low", "high"), + DT50 = Inf, + t_drainage = 3, + V_ditch = 30, + V_drainage = c(spring = 10, autumn = 100), + dilution = 2 +) } \arguments{ \item{rate}{The application rate in g/ha} diff --git a/man/PEC_sw_exposit_runoff.Rd b/man/PEC_sw_exposit_runoff.Rd index c73270b..a415a63 100644 --- a/man/PEC_sw_exposit_runoff.Rd +++ b/man/PEC_sw_exposit_runoff.Rd @@ -8,9 +8,17 @@ Excel 3.02 spreadsheet available from \url{https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3} } \usage{ -PEC_sw_exposit_runoff(rate, interception = 0, Koc, DT50 = Inf, - t_runoff = 3, exposit_reduction_version = c("3.02", "3.01a", - "3.01a2", "2.0"), V_ditch = 30, V_event = 100, dilution = 2) +PEC_sw_exposit_runoff( + rate, + interception = 0, + Koc, + DT50 = Inf, + t_runoff = 3, + exposit_reduction_version = c("3.02", "3.01a", "3.01a2", "2.0"), + V_ditch = 30, + V_event = 100, + dilution = 2 +) } \arguments{ \item{rate}{The application rate in g/ha} diff --git a/man/PEC_sw_focus.Rd b/man/PEC_sw_focus.Rd index 836ed86..3ad1ad0 100644 --- a/man/PEC_sw_focus.Rd +++ b/man/PEC_sw_focus.Rd @@ -4,12 +4,25 @@ \alias{PEC_sw_focus} \title{Calculate PEC surface water at FOCUS Step 1} \usage{ -PEC_sw_focus(parent, rate, n = 1, i = NA, comment = "", met = NULL, - f_drift = NA, f_rd = 0.1, scenario = FOCUS_Step_12_scenarios$names, - region = c("n", "s"), season = c(NA, "of", "mm", "js"), - interception = c("no interception", "minimal crop cover", - "average crop cover", "full canopy"), met_form_water = TRUE, - txt_file = "pesticide.txt", overwrite = FALSE, append = TRUE) +PEC_sw_focus( + parent, + rate, + n = 1, + i = NA, + comment = "", + met = NULL, + f_drift = NA, + f_rd = 0.1, + scenario = FOCUS_Step_12_scenarios$names, + region = c("n", "s"), + season = c(NA, "of", "mm", "js"), + interception = c("no interception", "minimal crop cover", "average crop cover", + "full canopy"), + met_form_water = TRUE, + txt_file = "pesticide.txt", + overwrite = FALSE, + append = TRUE +) } \arguments{ \item{parent}{A list containing substance specific parameters, e.g. diff --git a/man/PEC_sw_sed.Rd b/man/PEC_sw_sed.Rd index 1feb146..bc82ee3 100644 --- a/man/PEC_sw_sed.Rd +++ b/man/PEC_sw_sed.Rd @@ -5,9 +5,15 @@ \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")) +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 diff --git a/man/SFO_actual_twa.Rd b/man/SFO_actual_twa.Rd index 30039f2..bdf4c4d 100644 --- a/man/SFO_actual_twa.Rd +++ b/man/SFO_actual_twa.Rd @@ -9,8 +9,7 @@ FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation 18 December 2014, p. 251 } \usage{ -SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, - 50, 100)) +SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100)) } \arguments{ \item{DT50}{The half-life.} diff --git a/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd index f073180..eb3fe38 100644 --- a/man/TOXSWA_cwa.Rd +++ b/man/TOXSWA_cwa.Rd @@ -5,31 +5,10 @@ \alias{TOXSWA_cwa} \title{R6 class for holding TOXSWA water concentration data and associated statistics} \format{An \code{\link{R6Class}} generator object.} -\usage{ -TOXSWA_cwa -} \description{ An R6 class for holding TOXSWA water concentration (cwa) 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{ @@ -57,3 +36,88 @@ H_sw_R1_stream$moving_windows(c(7, 21)) print(H_sw_R1_stream) } \keyword{data} +\section{Public fields}{ +\if{html}{\out{
}} +\describe{ +\item{\code{filename}}{Length one character vector.} + +\item{\code{basedir}}{Length one character vector.} + +\item{\code{segment}}{Length one integer, specifying for which segment the cwa data were read.} + +\item{\code{cwas}}{Dataframe holding the concentrations.} + +\item{\code{events}}{List of dataframes holding the event statistics for each threshold.} + +\item{\code{windows}}{Matrix of maximum time weighted average concentrations (TWAC_max) +and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) +for the requested moving window sizes in days.} +} +\if{html}{\out{
}} +} +\section{Methods}{ +\subsection{Public methods}{ +\itemize{ +\item \href{#method-new}{\code{TOXSWA_cwa$new()}} +\item \href{#method-moving_windows}{\code{TOXSWA_cwa$moving_windows()}} +\item \href{#method-get_events}{\code{TOXSWA_cwa$get_events()}} +\item \href{#method-print}{\code{TOXSWA_cwa$print()}} +\item \href{#method-clone}{\code{TOXSWA_cwa$clone()}} +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\subsection{Method \code{new()}}{ +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{TOXSWA_cwa$new( + filename, + basedir, + zipfile = NULL, + segment = "last", + substance = "parent", + total = FALSE +)}\if{html}{\out{
}} +} + +} +\if{html}{\out{
}} +\if{html}{\out{}} +\subsection{Method \code{moving_windows()}}{ +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{TOXSWA_cwa$moving_windows(windows, total = FALSE)}\if{html}{\out{
}} +} + +} +\if{html}{\out{
}} +\if{html}{\out{}} +\subsection{Method \code{get_events()}}{ +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{TOXSWA_cwa$get_events(thresholds, total = FALSE)}\if{html}{\out{
}} +} + +} +\if{html}{\out{
}} +\if{html}{\out{}} +\subsection{Method \code{print()}}{ +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{TOXSWA_cwa$print()}\if{html}{\out{
}} +} + +} +\if{html}{\out{
}} +\if{html}{\out{}} +\subsection{Method \code{clone()}}{ +The objects of this class are cloneable with this method. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{TOXSWA_cwa$clone(deep = FALSE)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{deep}}{Whether to make a deep clone.} +} +\if{html}{\out{
}} +} +} +} diff --git a/man/chent_focus_sw.Rd b/man/chent_focus_sw.Rd index 9830ade..5f595d8 100644 --- a/man/chent_focus_sw.Rd +++ b/man/chent_focus_sw.Rd @@ -4,9 +4,18 @@ \alias{chent_focus_sw} \title{Create a chemical compound object for FOCUS Step 1 calculations} \usage{ -chent_focus_sw(name, Koc, DT50_ws = NA, DT50_soil = NA, - DT50_water = NA, DT50_sediment = NA, cwsat = 1000, mw = NA, - max_soil = 1, max_ws = 1) +chent_focus_sw( + name, + Koc, + DT50_ws = NA, + DT50_soil = NA, + DT50_water = NA, + DT50_sediment = NA, + cwsat = 1000, + mw = NA, + max_soil = 1, + max_ws = 1 +) } \arguments{ \item{name}{Length one character vector containing the name} diff --git a/man/endpoint.Rd b/man/endpoint.Rd index 204905b..2b66c21 100644 --- a/man/endpoint.Rd +++ b/man/endpoint.Rd @@ -8,23 +8,39 @@ \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) +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_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_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) +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 chent object to get the information from} diff --git a/man/geomean.Rd b/man/geomean.Rd index 2887929..506e64d 100644 --- a/man/geomean.Rd +++ b/man/geomean.Rd @@ -4,7 +4,7 @@ \alias{geomean} \title{Calculate the geometric mean} \usage{ -geomean(x, na.rm = TRUE) +geomean(x, na.rm = FALSE) } \arguments{ \item{x}{Vector of numbers} @@ -17,8 +17,9 @@ 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. +This function returns NA if NA values are present and na.rm = FALSE +(default). If negative values are present, it gives an error message. +If at least one element of the vector is 0, it returns 0. } \examples{ geomean(c(1, 3, 9)) diff --git a/man/one_box.Rd b/man/one_box.Rd index 3c34dae..a60aa39 100644 --- a/man/one_box.Rd +++ b/man/one_box.Rd @@ -11,11 +11,9 @@ one_box(x, ini, ..., t_end = 100, res = 0.01) \method{one_box}{numeric}(x, ini = 1, ..., t_end = 100, res = 0.01) -\method{one_box}{character}(x, ini = 1, parms, ..., t_end = 100, - res = 0.01) +\method{one_box}{character}(x, ini = 1, parms, ..., t_end = 100, res = 0.01) -\method{one_box}{mkinfit}(x, ini = "model", ..., t_end = 100, - res = 0.01) +\method{one_box}{mkinfit}(x, ini = "model", ..., t_end = 100, res = 0.01) } \arguments{ \item{x}{When numeric, this is the half-life to be used for an exponential diff --git a/man/pfm_degradation.Rd b/man/pfm_degradation.Rd index fdc99fe..6684fa4 100644 --- a/man/pfm_degradation.Rd +++ b/man/pfm_degradation.Rd @@ -4,9 +4,14 @@ \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)) +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 diff --git a/man/plot.TOXSWA_cwa.Rd b/man/plot.TOXSWA_cwa.Rd index f06d3c7..7eeb3fc 100644 --- a/man/plot.TOXSWA_cwa.Rd +++ b/man/plot.TOXSWA_cwa.Rd @@ -4,10 +4,18 @@ \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, threshold_factor = 1000, thin_low = 1, - total = FALSE, LC_TIME = "C", ...) +\method{plot}{TOXSWA_cwa}( + x, + time_column = c("datetime", "t", "t_firstjan", "t_rel_to_max"), + xlab = "default", + ylab = "default", + add = FALSE, + threshold_factor = 1000, + thin_low = 1, + total = FALSE, + LC_TIME = "C", + ... +) } \arguments{ \item{x}{The TOXSWA_cwa object to be plotted.} diff --git a/man/plot.one_box.Rd b/man/plot.one_box.Rd index a212c11..35e7bf7 100644 --- a/man/plot.one_box.Rd +++ b/man/plot.one_box.Rd @@ -4,9 +4,16 @@ \alias{plot.one_box} \title{Plot time series of decline data} \usage{ -\method{plot}{one_box}(x, xlim = range(time(x)), ylim = c(0, max(x)), - xlab = "Time", ylab = "Residue", max_twa = NULL, - max_twa_var = dimnames(x)[[2]][1], ...) +\method{plot}{one_box}( + x, + xlim = range(time(x)), + ylim = c(0, max(x)), + xlab = "Time", + ylab = "Residue", + max_twa = NULL, + max_twa_var = dimnames(x)[[2]][1], + ... +) } \arguments{ \item{x}{The object of type \code{\link{one_box}} to be plotted} diff --git a/man/read.TOXSWA_cwa.Rd b/man/read.TOXSWA_cwa.Rd index ccd403a..b6ee4f6 100644 --- a/man/read.TOXSWA_cwa.Rd +++ b/man/read.TOXSWA_cwa.Rd @@ -4,9 +4,16 @@ \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) +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 diff --git a/man/sawtooth.Rd b/man/sawtooth.Rd index 007f00d..44ab2be 100644 --- a/man/sawtooth.Rd +++ b/man/sawtooth.Rd @@ -4,8 +4,12 @@ \alias{sawtooth} \title{Create decline time series for multiple applications} \usage{ -sawtooth(x, n = 1, i = 365, applications = data.frame(time = seq(0, - (n - 1) * i, length.out = n), amount = 1)) +sawtooth( + x, + n = 1, + i = 365, + applications = data.frame(time = seq(0, (n - 1) * i, length.out = n), amount = 1) +) } \arguments{ \item{x}{A \code{\link{one_box}} object} diff --git a/man/set_nd_nq.Rd b/man/set_nd_nq.Rd index 47b7e33..7135d0d 100644 --- a/man/set_nd_nq.Rd +++ b/man/set_nd_nq.Rd @@ -7,8 +7,14 @@ \usage{ set_nd_nq(res_raw, lod, loq = NA, time_zero_presence = FALSE) -set_nd_nq_focus(res_raw, lod, loq = NA, set_first_sample_nd = TRUE, - first_sample_nd_value = 0, ignore_below_loq_after_first_nd = TRUE) +set_nd_nq_focus( + res_raw, + lod, + loq = NA, + set_first_sample_nd = TRUE, + first_sample_nd_value = 0, + ignore_below_loq_after_first_nd = TRUE +) } \arguments{ \item{res_raw}{Character vector of a residue time series, or matrix of -- cgit v1.2.1