From dd30f0d0ff1d8d0cc46aaef6e0917c51fe798f52 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 19 Jan 2017 10:36:19 +0100 Subject: Move mkin::twa to pfm::max_twa.mkinfit - Add max_twa.mkinfit() recently introduced to mkin as mkin::twa() but never released with it - Add a test to check max_twa.one_box() against analytical solutions in max_twa.mkinfit(). - Clean up R CMD check - Update docs --- .Rbuildignore | 1 + ChangeLog | 6 +++ NAMESPACE | 3 ++ R/twa.R | 88 +++++++++++++++++++++++++++++++++++--- docs/reference/max_twa.html | 45 ++++++++++++++++++- docs/reference/one_box-4.png | Bin 5743 -> 5587 bytes docs/reference/one_box-8.png | Bin 9901 -> 9860 bytes docs/reference/one_box.html | 12 ++++-- docs/reference/plot.one_box-8.png | Bin 13603 -> 13490 bytes docs/reference/sawtooth-6.png | Bin 13603 -> 13490 bytes docs/reference/sawtooth.html | 4 +- man/max_twa.Rd | 19 ++++++++ man/one_box.Rd | 12 ++++-- tests/testthat/test_max_twa.R | 11 +++++ 14 files changed, 182 insertions(+), 19 deletions(-) create mode 100644 tests/testthat/test_max_twa.R diff --git a/.Rbuildignore b/.Rbuildignore index 48acd64..59d7984 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -7,4 +7,5 @@ ^build.log$ ^test.log$ ^inst/extdata/Tabelle\ der\ Abdrifteckwerte.xls$ +^_pkgdown.yml$ ^docs$ diff --git a/ChangeLog b/ChangeLog index 3aff70c..f7a68ea 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,9 @@ +commit 3ead7acba845b4f2552f555dfb29da889ed0cda8 +Author: Johannes Ranke +Date: 2017-01-19 09:42:21 +0100 + + Make max_twa() a bit safer + commit 74ed85b07f09ea99476208749cd274a476ba4536 Author: Johannes Ranke Date: 2017-01-19 09:27:36 +0100 diff --git a/NAMESPACE b/NAMESPACE index c4d671f..35245d9 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -2,6 +2,7 @@ S3method(GUS,chent) S3method(GUS,numeric) +S3method(max_twa,mkinfit) S3method(max_twa,one_box) S3method(one_box,character) S3method(one_box,mkinfit) @@ -37,8 +38,10 @@ importFrom(methods,is) importFrom(mkin,mkinpredict) importFrom(readr,fwf_empty) importFrom(readr,read_fwf) +importFrom(stats,end) importFrom(stats,filter) importFrom(stats,frequency) importFrom(stats,plot.ts) +importFrom(stats,start) importFrom(stats,time) importFrom(stats,ts) diff --git a/R/twa.R b/R/twa.R index fcf49c0..88cfec3 100644 --- a/R/twa.R +++ b/R/twa.R @@ -1,4 +1,4 @@ -# Copyright (C) 2017 Johannes Ranke +# Copyright (C) 2016,2017 Johannes Ranke # Contact: jranke@uni-bremen.de # This file is part of the R package pfm @@ -23,6 +23,7 @@ #' #' @param x When numeric, this is the half-life to be used for an exponential #' decline. If x is an mkinfit object, the decline is calculated from this object +#' @param ini The initial amount for each compound #' @param t_end End of the time series #' @param res Resolution of the time series #' @param ... Further arguments passed to methods @@ -44,7 +45,7 @@ #' fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) #' pred_2 <- one_box(fit_2) #' plot(pred_2) -one_box <- function(x, ..., +one_box <- function(x, ini, ..., t_end = 100, res = 0.01) { UseMethod("one_box") @@ -52,7 +53,7 @@ one_box <- function(x, ..., #' @rdname one_box #' @export -one_box.numeric <- function(x, ..., +one_box.numeric <- function(x, ini = 1, ..., t_end = 100, res = 0.01) { half_life = x @@ -68,7 +69,7 @@ one_box.numeric <- function(x, ..., #' @rdname one_box #' @param parms A named numeric vector containing the model parameters #' @export -one_box.character <- function(x, parms, ..., +one_box.character <- function(x, ini = 1, parms, ..., t_end = 100, res = 0.01) { parent_models_available = c("SFO", "FOMC", "DFOP", "HS", "SFORB", "IORE") @@ -96,11 +97,18 @@ one_box.character <- function(x, parms, ..., #' @rdname one_box #' @importFrom mkin mkinpredict #' @export -one_box.mkinfit <- function(x, ..., t_end = 100, res = 0.01) { +one_box.mkinfit <- function(x, ini = c("model", 1), ..., t_end = 100, res = 0.01) { fit <- x + + ini = match.arg(ini) + if (ini == "model") { + odeini = x$bparms.state + } else { + odeini <- c(1, rep(0, length(fit$mkinmod$spec) - 1)) + names(odeini) <- names(fit$mkinmod$spec) + } + t_out = seq(0, t_end, by = res) - odeini <- c(1, rep(0, length(fit$mkinmod$spec) - 1)) - names(odeini) <- names(fit$mkinmod$spec) if (length(fit$mkinmod$spec) == 1) solution_type = "analytical" else solution_type = "deSolve" @@ -216,6 +224,7 @@ sawtooth <- function(x, n = 1, i = 365, #' @param x An object of type \code{\link{one_box}} #' @param window The size of the moving window #' @seealso \code{\link{max_twa}} +#' @importFrom stats start end #' @export #' @examples #' pred <- sawtooth(one_box(10), @@ -247,11 +256,76 @@ twa.one_box <- function(x, window = 21) #' for finding the maximum. It is therefore recommended to check this using #' \code{\link{plot.one_box}} using the window size for the argument #' \code{max_twa}. +#' +#' The method working directly on fitted \code{\link{mkinfit}} objects uses the +#' equations given in the PEC soil section of the FOCUS guidance and is restricted +#' SFO, FOMC and DFOP models and to the parent compound +#' @references FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and +#' Degradation Kinetics from Environmental Fate Studies on Pesticides in EU +#' Registration} Report of the FOCUS Work Group on Degradation Kinetics, +#' EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +#' \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} #' @seealso \code{\link{twa}} #' @inheritParams twa #' @export +#' @examples +#' pred <- sawtooth(one_box(10), +#' applications = data.frame(time = c(0, 7), amount = c(1, 1))) +#' max_twa(pred) +#' pred_FOMC <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) +#' max_twa(pred_FOMC) max_twa <- function(x, window = 21) UseMethod("max_twa") +#' @export +max_twa.mkinfit <- function(x, window = 21) { + fit <- x + parms.all <- c(fit$bparms.optim, fit$bparms.fixed) + obs_vars <- fit$obs_vars + if (length(obs_vars) > 1) { + warning("Calculation of maximum time weighted average concentrations is", + "currently only implemented for the parent compound using", + "analytical solutions") + } + obs_var <- obs_vars[1] + spec = fit$mkinmod$spec + type = spec[[1]]$type + + M0 <- parms.all[paste0(obs_var, "_0")] + + if (type == "SFO") { + k_name <- paste0("k_", obs_var) + if (fit$mkinmod$use_of_ff == "min") { + k_name <- paste0(k_name, "_sink") + } + k <- parms.all[k_name] + twafunc <- function(t) { + M0 * (1 - exp(- k * t)) / (k * t) + } + } + if (type == "FOMC") { + alpha <- parms.all["alpha"] + beta <- parms.all["beta"] + twafunc <- function(t) { + M0 * (beta)/(t * (1 - alpha)) * ((t/beta + 1)^(1 - alpha) - 1) + } + } + if (type == "DFOP") { + k1 <- parms.all["k1"] + k2 <- parms.all["k2"] + g <- parms.all["g"] + twafunc <- function(t) { + M0/t * ((g/k1) * (1 - exp(- k1 * t)) + ((1 - g)/k2) * (1 - exp(- k2 * t))) + } + } + if (type %in% c("HS", "IORE", "SFORB")) { + stop("Calculation of maximum time weighted average concentrations is currently ", + "not implemented for the ", type, " model.") + } + res <- twafunc(t = window) + names(res) <- window + return(res) +} + #' @export max_twa.one_box <- function(x, window = 21) { diff --git a/docs/reference/max_twa.html b/docs/reference/max_twa.html index 4bb1be9..f78da58 100644 --- a/docs/reference/max_twa.html +++ b/docs/reference/max_twa.html @@ -70,7 +70,11 @@ -

The maximum time weighted average concentration for a moving window

+

If you generate your time series using sawtooth, +you need to make sure that the length of the time series allows +for finding the maximum. It is therefore recommended to check this using +plot.one_box using the window size for the argument +max_twa.

max_twa(x, window = 21)
@@ -83,19 +87,56 @@
The size of the moving window
+

Details

+ +

The method working directly on fitted mkinfit objects uses the +equations given in the PEC soil section of the FOCUS guidance and is restricted +SFO, FOMC and DFOP models and to the parent compound

+ +

References

+ +

FOCUS (2006) “Guidance Document on Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration” Report of the FOCUS Work Group on Degradation Kinetics, + EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

+

See also

twa

+

Examples

+ 
pred <- sawtooth(one_box(10),
+  applications = data.frame(time = c(0, 7), amount = c(1, 1)))
+max_twa(pred)
#> $max
+#>    parent 
+#> 0.9537545 
+#> 
+#> $window_start
+#> parent 
+#>      0 
+#> 
+#> $window_end
+#> parent 
+#>     21 
+#> 
pred_FOMC <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
+max_twa(pred_FOMC)
#>       21 
+#> 18.22124
diff --git a/docs/reference/one_box-4.png b/docs/reference/one_box-4.png index 10ebb35..3c6dadb 100644 Binary files a/docs/reference/one_box-4.png and b/docs/reference/one_box-4.png differ diff --git a/docs/reference/one_box-8.png b/docs/reference/one_box-8.png index 31e2f4b..897737e 100644 Binary files a/docs/reference/one_box-8.png and b/docs/reference/one_box-8.png differ diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html index 698f887..cb49c02 100644 --- a/docs/reference/one_box.html +++ b/docs/reference/one_box.html @@ -74,22 +74,26 @@ This does not create objects of type ts.

- 
one_box(x, ..., t_end = 100, res = 0.01)
+    
one_box(x, ini, ..., t_end = 100, res = 0.01)
 
 # S3 method for numeric
-one_box(x, ..., t_end = 100, res = 0.01)
+one_box(x, ini = 1, ..., t_end = 100, res = 0.01)
 
 # S3 method for character
-one_box(x, parms, ..., t_end = 100, res = 0.01)
+one_box(x, ini = 1, parms, ..., t_end = 100,
+  res = 0.01)
 
 # S3 method for mkinfit
-one_box(x, ..., t_end = 100, res = 0.01)

+one_box(x, ini = c("model", 1), ..., t_end = 100,
+  res = 0.01)

Arguments

x
When numeric, this is the half-life to be used for an exponential decline. If x is an mkinfit object, the decline is calculated from this object
+
ini
+
The initial amount for each compound
...
Further arguments passed to methods
t_end
diff --git a/docs/reference/plot.one_box-8.png b/docs/reference/plot.one_box-8.png index 161ecb4..f534444 100644 Binary files a/docs/reference/plot.one_box-8.png and b/docs/reference/plot.one_box-8.png differ diff --git a/docs/reference/sawtooth-6.png b/docs/reference/sawtooth-6.png index 161ecb4..f534444 100644 Binary files a/docs/reference/sawtooth-6.png and b/docs/reference/sawtooth-6.png differ diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html index cf33630..216f64a 100644 --- a/docs/reference/sawtooth.html +++ b/docs/reference/sawtooth.html @@ -102,8 +102,8 @@ the corresponding amounts applied in the second column. pred_2_saw <- sawtooth(pred_2, 2, 7) plot(pred_2_saw, max_twa = 21, max_twa_var = "m1")
max_twa(pred_2_saw)
#> $max -#> parent m1 -#> 0.6627707 0.8542785 +#> parent m1 +#> 66.01096 85.08484 #> #> $window_start #> parent m1 diff --git a/man/max_twa.Rd b/man/max_twa.Rd index e39165a..0a8dcca 100644 --- a/man/max_twa.Rd +++ b/man/max_twa.Rd @@ -18,6 +18,25 @@ for finding the maximum. It is therefore recommended to check this using \code{\link{plot.one_box}} using the window size for the argument \code{max_twa}. } +\details{ +The method working directly on fitted \code{\link{mkinfit}} objects uses the +equations given in the PEC soil section of the FOCUS guidance and is restricted +SFO, FOMC and DFOP models and to the parent compound +} +\examples{ +pred <- sawtooth(one_box(10), + applications = data.frame(time = c(0, 7), amount = c(1, 1))) +max_twa(pred) +pred_FOMC <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) +max_twa(pred_FOMC) +} +\references{ +FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration} Report of the FOCUS Work Group on Degradation Kinetics, + EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, + \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +} \seealso{ \code{\link{twa}} } diff --git a/man/one_box.Rd b/man/one_box.Rd index 5a46142..8132a70 100644 --- a/man/one_box.Rd +++ b/man/one_box.Rd @@ -7,18 +7,22 @@ \alias{one_box.mkinfit} \title{Create a time series of decline data} \usage{ -one_box(x, ..., t_end = 100, res = 0.01) +one_box(x, ini, ..., t_end = 100, res = 0.01) -\method{one_box}{numeric}(x, ..., t_end = 100, res = 0.01) +\method{one_box}{numeric}(x, ini = 1, ..., t_end = 100, res = 0.01) -\method{one_box}{character}(x, 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, ..., t_end = 100, res = 0.01) +\method{one_box}{mkinfit}(x, ini = c("model", 1), ..., t_end = 100, + res = 0.01) } \arguments{ \item{x}{When numeric, this is the half-life to be used for an exponential decline. If x is an mkinfit object, the decline is calculated from this object} +\item{ini}{The initial amount for each compound} + \item{...}{Further arguments passed to methods} \item{t_end}{End of the time series} diff --git a/tests/testthat/test_max_twa.R b/tests/testthat/test_max_twa.R new file mode 100644 index 0000000..82d20f7 --- /dev/null +++ b/tests/testthat/test_max_twa.R @@ -0,0 +1,11 @@ +library(pfm) +context("Check max_twa for parent mkinfit models against analytical solutions") + +test_that("max_twa for simple decline curves is correct", { + fits <- mmkin(c("SFO", "FOMC", "DFOP"), list(FOCUS_2006_C), cores = 1, quiet = TRUE) + max_twa_21_analytical <- sapply(fits, max_twa, 21) + names(max_twa_21_analytical) <- rep("parent", 3) + preds <- lapply(fits, one_box) + max_twa_21_preds <- sapply(preds, function(x) max_twa(x, 21)[["max"]]) + expect_equal(max_twa_21_analytical, max_twa_21_preds, tolerance = .03, scale = 1) +}) -- cgit v1.2.1