diff options
| -rw-r--r-- | DESCRIPTION | 3 | ||||
| -rw-r--r-- | NAMESPACE | 1 | ||||
| -rw-r--r-- | NEWS.md | 2 | ||||
| -rw-r--r-- | R/pfm_degradation.R | 35 | ||||
| -rw-r--r-- | R/twa.R | 33 | ||||
| -rw-r--r-- | log/check.log | 28 | ||||
| -rw-r--r-- | man/one_box.Rd | 23 | ||||
| -rw-r--r-- | man/pfm_degradation.Rd | 27 |
8 files changed, 129 insertions, 23 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 696eb3e..b0eeac3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: pfm Type: Package Title: Utilities for Pesticide Fate Modelling Version: 0.6.5 -Date: 2026-06-22 +Date: 2026-09-10 Authors@R: c( person("Johannes Ranke", email = "johannes.ranke@agroscope.admin.ch", role = c("aut", "cre"), @@ -25,5 +25,6 @@ LazyLoad: true LazyData: true Encoding: UTF-8 URL: https://pkgdown.jrwb.de/pfm, https://github.com/jranke/pfm, http://jranke.github.io/pfm/ +Additional_repositories: https://agroscope-ch.r-universe.dev, https://jranke.r-universe.dev Roxygen: list(markdown = TRUE, r6 = TRUE) Config/roxygen2/version: 8.0.0 @@ -6,6 +6,7 @@ S3method(max_twa,mkinfit) S3method(max_twa,one_box) S3method(one_box,character) S3method(one_box,mkinfit) +S3method(one_box,mkinmod) S3method(one_box,numeric) S3method(plot,TOXSWA_cwa) S3method(plot,one_box) @@ -1,5 +1,7 @@ ## version 0.6.5 +- Add a `one_box` method for `mkinmod` objects to facilitate generating `sawtooth` curves also for metabolites +- R/pfm_degradation.R: Fix using an mkinmod model and add an SFO-SFO example - R/PEC_sw_drift.R: Support specifying units for distances and widths using the units package. - R/TOXSWA_cwa.R: Adapt to readr (>= 2.2.0) requiring to wrap literal input as used for reading .out files with I(). - R/PEC_sw_drainage_UK.R: Create a function `drainage_date_UK` that does not only respect the beginning of the drainage period on 1 October, but also the end of the drainage period on 30 April, and use it for determining the degradation time. Applications early in the year before 1 May will now correctly be calculated without degradation time. diff --git a/R/pfm_degradation.R b/R/pfm_degradation.R index 832a797..63a6e19 100644 --- a/R/pfm_degradation.R +++ b/R/pfm_degradation.R @@ -9,21 +9,48 @@ #' @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 +#' @return A data frame containing the output times and the concentrations +#' assuming initial concentrations of 1 for the parent and zero for +#' metabolites, if any. #' @export #' @author Johannes Ranke #' @examples -#' head(pfm_degradation("SFO", DT50 = 10)) +#' # Simple example of an SFO decline curve +#' sfo_out <- pfm_degradation("SFO", DT50 = 10) +#' head(sfo_out) +#' +#' # Fictive example with a metabolite where we first generate an SFO-SFO model +#' sfo_sfo <- mkinmod( +#' parent = mkinsub("SFO", to = "metabolite"), +#' metabolite = mkinsub("SFO")) +#' +#' sfo_sfo_out <- pfm_degradation(sfo_sfo, +#' parms = c(k_parent = 0.1, f_parent_to_metabolite = 0.5, k_metabolite = 0.02)) +#' +#' plot( +#' sfo_sfo_out[, "time"], +#' sfo_sfo_out[, "parent"], type = "l", +#' xlab = "Time", ylab = "Relative concentration", +#' xlim = c(0, 100)) +#' lines( +#' sfo_sfo_out[, "time"], +#' sfo_sfo_out[, "metabolite"], lty = 2) +#' pfm_degradation <- function(model = "SFO", DT50 = 1000, parms = c(k_parent = 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)) + if (!inherits(model, "mkinmod")) { + if (model[1] %in% c("SFO", "FOMC", "DFOP", "HS", "IORE")) { + model <- mkinmod(parent = list(type = model)) + } else { + stop("Please specify the model with a suitable name or an mkinmod object") + } } initial_state = c(1, rep(0, length(model$diffs) - 1)) names(initial_state) <- names(model$diffs) - time_course <- mkinpredict(model, odeparms = parms, + time_course <- mkinpredict(model, odeparms = parms, odeini = initial_state, outtimes = times, solution_type = ifelse(length(model$spec) == 1, "analytical", "deSolve")) @@ -82,8 +82,41 @@ one_box.character <- function(x, ini = 1, parms, ..., } #' @rdname one_box +#' @param odeparms Will be passed to [mkinpredict] +#' @param solution_type Will be passed to [mkinpredict] #' @importFrom mkin mkinpredict #' @export +#' @examples +#' library(mkin) +#' SFO_SFO <- mkinmod( +#' parent = mkinsub("SFO", to = "m1"), +#' m1 = mkinsub("SFO")) +#' c_0 = c(parent = 100, m1 = 0) +#' deg_parms = c(k_parent = 0.15, f_parent_to_m1 = 0.5, k_m1 = 0.01) +#' sfo_sfo_box <- one_box(SFO_SFO, odeparms = deg_parms, ini = c_0) +#' head(sfo_sfo_box) +one_box.mkinmod <- function(x, + ini = c(1, rep(0, length(x$diffs) - 1)), + odeparms, + solution_type = "deSolve", + ..., + t_end = 100, res = 0.01) +{ + + # Set names for initial amounts to be compatible with the model + if (is.null(names(ini))) names(ini) <- names(x$diffs) + + t_out = seq(0, t_end, by = res) + + tmp <- mkinpredict(x, odeparms = odeparms, odeini = ini, + outtimes = t_out, solution_type = solution_type)[, -1, drop = FALSE] + result <- ts(tmp, 0, t_end, frequency = 1/res) + class(result) <- c("one_box", "ts") + return(result) +} + +#' @rdname one_box +#' @export one_box.mkinfit <- function(x, ini = "model", ..., t_end = 100, res = 0.01) { fit <- x if (ini[1] == "model") { diff --git a/log/check.log b/log/check.log index 3c0c083..0897357 100644 --- a/log/check.log +++ b/log/check.log @@ -1,12 +1,12 @@ -* using log directory ‘/home/f80868656/projects/pfm/pfm.Rcheck’ -* using R version 4.6.0 (2026-04-24) +* using log directory ‘/home/jranke/git/pfm/pfm.Rcheck’ +* using R version 4.6.1 (2026-06-24) * using platform: x86_64-pc-linux-gnu * R was compiled by - gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0 - GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0 -* running under: Ubuntu 24.04.4 LTS + x86_64-linux-gnu-gcc (Debian 14.2.0-19) 14.2.0 + GNU Fortran (Debian 14.2.0-19) 14.2.0 +* running under: Debian GNU/Linux 13 (trixie) * using session charset: UTF-8 -* current time: 2026-06-22 16:48:14 UTC +* current time: 2026-09-10 10:31:00 UTC * using options ‘--no-tests --as-cran’ * checking for file ‘pfm/DESCRIPTION’ ... OK * checking extension type ... Package @@ -23,9 +23,9 @@ * checking for sufficient/correct file permissions ... OK * checking whether package ‘pfm’ can be installed ... OK * checking installed package size ... INFO - installed size is 10.4Mb + installed size is 10.3Mb sub-directories of 1Mb or more: - testdata 10.0Mb + testdata 9.9Mb * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK @@ -60,20 +60,14 @@ * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK -* checking examples ... [11s/10s] OK +* checking examples ... [10s/10s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking PDF version of manual ... OK -* checking HTML version of manual ... NOTE -Skipping checking HTML validation: no command 'tidy' found. -Please obtain a recent version of HTML Tidy by downloading a binary -release or compiling the source code from <https://www.html-tidy.org/>. +* checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE -Status: 1 NOTE -See - ‘/home/f80868656/projects/pfm/pfm.Rcheck/00check.log’ -for details. +Status: OK diff --git a/man/one_box.Rd b/man/one_box.Rd index 16f4859..cf8a91a 100644 --- a/man/one_box.Rd +++ b/man/one_box.Rd @@ -4,6 +4,7 @@ \alias{one_box} \alias{one_box.numeric} \alias{one_box.character} +\alias{one_box.mkinmod} \alias{one_box.mkinfit} \title{Create a time series of decline data} \usage{ @@ -13,6 +14,16 @@ one_box(x, ini, ..., t_end = 100, res = 0.01) \method{one_box}{character}(x, ini = 1, parms, ..., t_end = 100, res = 0.01) +\method{one_box}{mkinmod}( + x, + ini = c(1, rep(0, length(x$diffs) - 1)), + odeparms, + solution_type = "deSolve", + ..., + t_end = 100, + res = 0.01 +) + \method{one_box}{mkinfit}(x, ini = "model", ..., t_end = 100, res = 0.01) } \arguments{ @@ -35,6 +46,10 @@ all observed variables.} \item{res}{Resolution of the time series} \item{parms}{A named numeric vector containing the model parameters} + +\item{odeparms}{Will be passed to \link[mkin:mkinpredict]{mkinpredict}} + +\item{solution_type}{Will be passed to \link[mkin:mkinpredict]{mkinpredict}} } \value{ An object of class \code{one_box}, inheriting from \link{ts}. @@ -58,4 +73,12 @@ m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) pred_2 <- one_box(fit_2, ini = "model") plot(pred_2) +library(mkin) +SFO_SFO <- mkinmod( + parent = mkinsub("SFO", to = "m1"), + m1 = mkinsub("SFO")) +c_0 = c(parent = 100, m1 = 0) +deg_parms = c(k_parent = 0.15, f_parent_to_m1 = 0.5, k_m1 = 0.01) +sfo_sfo_box <- one_box(SFO_SFO, odeparms = deg_parms, ini = c_0) +head(sfo_sfo_box) } diff --git a/man/pfm_degradation.Rd b/man/pfm_degradation.Rd index 81f2e81..163bcee 100644 --- a/man/pfm_degradation.Rd +++ b/man/pfm_degradation.Rd @@ -28,11 +28,36 @@ is calculated (SFO model).} \item{times}{The output times} } +\value{ +A data frame containing the output times and the concentrations +assuming initial concentrations of 1 for the parent and zero for +metabolites, if any. +} \description{ Calculate a time course of relative concentrations based on an mkinmod model } \examples{ -head(pfm_degradation("SFO", DT50 = 10)) +# Simple example of an SFO decline curve +sfo_out <- pfm_degradation("SFO", DT50 = 10) +head(sfo_out) + +# Fictive example with a metabolite where we first generate an SFO-SFO model +sfo_sfo <- mkinmod( + parent = mkinsub("SFO", to = "metabolite"), + metabolite = mkinsub("SFO")) + +sfo_sfo_out <- pfm_degradation(sfo_sfo, + parms = c(k_parent = 0.1, f_parent_to_metabolite = 0.5, k_metabolite = 0.02)) + +plot( + sfo_sfo_out[, "time"], + sfo_sfo_out[, "parent"], type = "l", + xlab = "Time", ylab = "Relative concentration", + xlim = c(0, 100)) +lines( + sfo_sfo_out[, "time"], + sfo_sfo_out[, "metabolite"], lty = 2) + } \author{ Johannes Ranke |