From 8989a484b9b2d23463c95e0a3927e307ec0a5e64 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 4 Jul 2018 10:59:47 +0200 Subject: Some documentation updates Document that TOXSWA 5.5.3 is supported in the help files --- ChangeLog | 18 ++++++++++++++++++ DESCRIPTION | 2 +- R/PEC_soil.R | 4 ++-- R/TOXSWA_cwa.R | 11 ++++++----- README.html | 8 ++++++-- docs/reference/PEC_soil.html | 2 +- docs/reference/PELMO_runs.html | 2 +- docs/reference/TOXSWA_cwa.html | 10 +++++----- docs/reference/index.html | 2 +- docs/reference/pesticide.txt | 2 ++ docs/reference/read.TOXSWA_cwa.html | 10 ++++++---- man/PEC_soil.Rd | 2 +- man/TOXSWA_cwa.Rd | 4 ++-- man/read.TOXSWA_cwa.Rd | 7 ++++--- 14 files changed, 56 insertions(+), 28 deletions(-) diff --git a/ChangeLog b/ChangeLog index 926bcd6..2960fbe 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,21 @@ +commit 6ca8bdb8636141fac592688a6794ae092f0bc85a +Author: Johannes Ranke +Date: 2018-06-20 14:58:44 +0200 + + Advertise drat repo + +commit 6acfd0dfb2670e3eeab6144c90586f28105583a8 +Author: Johannes Ranke +Date: 2018-06-20 14:53:02 +0200 + + Update static docs + +commit cac29c8c1cc0f6004ef0cd63229cfb993a24496c +Author: Johannes Ranke +Date: 2018-06-11 16:27:22 +0200 + + Adapt to TOXSWA 5.5.3 + commit bd15236d5dedb4067bd29e58e655c5352aca1db4 Author: Johannes Ranke Date: 2018-06-08 16:20:40 +0200 diff --git a/DESCRIPTION b/DESCRIPTION index 0851224..c1d967f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: pfm Type: Package Title: Utilities for Pesticide Fate Modelling Version: 0.4-6 -Date: 2018-06-11 +Date: 2018-07-04 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-4371-6538")) diff --git a/R/PEC_soil.R b/R/PEC_soil.R index ea1cb71..15ccc90 100644 --- a/R/PEC_soil.R +++ b/R/PEC_soil.R @@ -1,4 +1,4 @@ -# Copyright (C) 2015 Johannes Ranke +# Copyright (C) 2015,2016,2018 Johannes Ranke # Contact: jranke@uni-bremen.de # This file is part of the R package pfm @@ -44,7 +44,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("destination", "study_typ #' @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 +#' degradation 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 diff --git a/R/TOXSWA_cwa.R b/R/TOXSWA_cwa.R index 576c7d3..5b1e8f2 100644 --- a/R/TOXSWA_cwa.R +++ b/R/TOXSWA_cwa.R @@ -22,10 +22,11 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("cwa")) #' 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). +#' of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was +#' renamed to ConLiqWatLay in the out file. #' #' @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). +#' out file when using FOCUS TOXSWA 4 (i.e. TOXSWA 4.4.2) or higher. #' @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 @@ -33,7 +34,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("cwa")) #' @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 +#' @param substance For .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 @@ -155,9 +156,9 @@ plot.TOXSWA_cwa <- function(x, time_column = c("datetime", "t", "t_firstjan", "t tmp <- Sys.setlocale("LC_TIME", lct) } -#' R6 class for holding TOXSWA cwa concentration data and associated statistics +#' R6 class for holding TOXSWA water concentration data and associated statistics #' -#' An R6 class for holding TOXSWA cwa concentration data and some associated statistics. +#' 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}}. #' #' @docType class diff --git a/README.html b/README.html index 026f011..ef6dfca 100644 --- a/README.html +++ b/README.html @@ -15,7 +15,7 @@ - + @@ -138,7 +138,11 @@ You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>

Installation

-

You can install the package from github, e.g. using the devtools package. Using quick = TRUE skips docs, multiple-architecture builds, demos, and vignettes, to make installation as fast and painless as possible.

+

The easiest way to install the package is probably to use drat:

+
install.packages("drat")
+drat::addRepo("jranke")
+install.packages("pfm")
+

Alternatively you can install the package using the devtools package. Using quick = TRUE skips docs, multiple-architecture builds, demos, and vignettes.

library(devtools)
 install_github("jranke/pfm", quick = TRUE)
diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index feed9d5..5073067 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -150,7 +150,7 @@ the concepts layed out for example in the PPR panel opinion (EFSA 2012).

interval

Period of the deeper mixing, defaults to 365, which is a year if -rate units are in days

+degradation rate units are in days

n_periods diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html index 1eac49b..5d53104 100644 --- a/docs/reference/PELMO_runs.html +++ b/docs/reference/PELMO_runs.html @@ -229,7 +229,7 @@ the period.plm file generated by the FOCUS PELMO GUI.

#> #>
# We get exactly the same PECgw values (on Linux, calling PELMO using Wine). print(time_1)
#> User System verstrichen -#> 0.398 0.100 30.624
if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) { +#> 0.384 0.095 30.954
if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) { cat(gsub("model name\t: ", "CPU model: ", cpuinfo[grep("model name", cpuinfo)[1]])) }
#> CPU model: AMD Ryzen 7 1700 Eight-Core Processor
# Demonstrate some results with metabolites. diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html index 3b11804..932e6ef 100644 --- a/docs/reference/TOXSWA_cwa.html +++ b/docs/reference/TOXSWA_cwa.html @@ -6,7 +6,7 @@ -R6 class for holding TOXSWA cwa concentration data and associated statistics — TOXSWA_cwa • pfm +R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa • pfm @@ -30,9 +30,9 @@ - + - @@ -98,14 +98,14 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." />
-

R6 class for holding TOXSWA cwa concentration data and associated statistics

+

R6 class for holding TOXSWA water concentration data and associated statistics

Source: R/TOXSWA_cwa.R
-

An R6 class for holding TOXSWA cwa concentration data and some associated statistics. +

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

diff --git a/docs/reference/index.html b/docs/reference/index.html index c153b50..162298b 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -311,7 +311,7 @@ water concentrations

TOXSWA_cwa

-

R6 class for holding TOXSWA cwa concentration data and associated statistics

+

R6 class for holding TOXSWA water concentration data and associated statistics

diff --git a/docs/reference/pesticide.txt b/docs/reference/pesticide.txt index 85f103d..d4fd84e 100644 --- a/docs/reference/pesticide.txt +++ b/docs/reference/pesticide.txt @@ -35,3 +35,5 @@ Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Du M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 +Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 +M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html index 60e236a..aa18ec4 100644 --- a/docs/reference/read.TOXSWA_cwa.html +++ b/docs/reference/read.TOXSWA_cwa.html @@ -36,7 +36,8 @@ 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)." /> +of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was +renamed to ConLiqWatLay in the out file." /> @@ -112,7 +113,8 @@ of the hourly averages (ConLiqWatLay)." /> 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).

+of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was +renamed to ConLiqWatLay in the out file.

@@ -126,7 +128,7 @@ of the hourly averages (ConLiqWatLay).

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).

+out file when using FOCUS TOXSWA 4 (i.e. TOXSWA 4.4.2) or higher.

basedir @@ -143,7 +145,7 @@ the segment number.

substance -

For TOXSWA 4 .out files, the default value "parent" leads +

For .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.

diff --git a/man/PEC_soil.Rd b/man/PEC_soil.Rd index dd780cf..1491790 100644 --- a/man/PEC_soil.Rd +++ b/man/PEC_soil.Rd @@ -24,7 +24,7 @@ PEC_soil(rate, rate_units = "g/ha", interception = 0, mixing_depth = 5, \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} +degradation rate units are in days} \item{n_periods}{Number of periods to be considered for long term PEC calculations} diff --git a/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd index 3152c6e..f073180 100644 --- a/man/TOXSWA_cwa.Rd +++ b/man/TOXSWA_cwa.Rd @@ -3,13 +3,13 @@ \docType{class} \name{TOXSWA_cwa} \alias{TOXSWA_cwa} -\title{R6 class for holding TOXSWA cwa concentration data and associated statistics} +\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 cwa concentration data and some associated statistics. +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}{ diff --git a/man/read.TOXSWA_cwa.Rd b/man/read.TOXSWA_cwa.Rd index 2541c9b..c76fdbd 100644 --- a/man/read.TOXSWA_cwa.Rd +++ b/man/read.TOXSWA_cwa.Rd @@ -10,7 +10,7 @@ read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last", } \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).} +out file when using FOCUS TOXSWA 4 (i.e. TOXSWA 4.4.2) or higher.} \item{basedir}{The path to the directory where the cwa file resides.} @@ -19,7 +19,7 @@ out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).} \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 +\item{substance}{For .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.} @@ -42,7 +42,8 @@ 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). +of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was +renamed to ConLiqWatLay in the out file. } \examples{ H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", -- cgit v1.2.1