From f30472ecd2afea6bd2153b8ad2bb2f663f3a2742 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 25 Aug 2014 10:39:40 +0200 Subject: Bug fix and unit tests for mkinerrmin See NEWS.md for details --- NEWS.md | 7 +++ R/mkinerrmin.R | 9 +-- TODO | 5 -- inst/unitTests/runit.mkinerrmin.R | 62 +++++++++++++++++++++ inst/unitTests/runit.mkinfit.R | 38 +------------ man/mkinerrmin.Rd | 10 ++++ tests/doRUnit.R | 1 - vignettes/FOCUS_L.html | 112 +++++++++++++++++++++----------------- vignettes/FOCUS_Z.pdf | Bin 220196 -> 220177 bytes 9 files changed, 146 insertions(+), 98 deletions(-) create mode 100644 inst/unitTests/runit.mkinerrmin.R diff --git a/NEWS.md b/NEWS.md index d05c2095..1ed94c97 100644 --- a/NEWS.md +++ b/NEWS.md @@ -4,12 +4,19 @@ - The initial value (state.ini) for the observed variable with the highest observed residue is set to 100 in case it has no time zero observation and `state.ini = "auto"` +- A basic unit test for `mkinerrmin()` was written + ## BUG FIXES - `mkinfit()`: The internally fitted parameter for `g` was named `g_ilr` even when `transform_fractions=FALSE` - `mkinfit()`: The initial value (state.ini) for the parent compound was not set when the parent was not the (only) variable with the highest value in the observed data. +- `mkinerrmin()`: When checking for degrees of freedom for metabolites, check + if their time zero value is fixed instead of checking if the observed value + is zero. This ensures correct calculation of degrees of freedom also in cases + where the metabolite residue at time zero is greater zero. + ## MINOR CHANGES - The formatting of differential equations in the summary was improved by wrapping overly long lines diff --git a/R/mkinerrmin.R b/R/mkinerrmin.R index 09724730..2697d0a0 100644 --- a/R/mkinerrmin.R +++ b/R/mkinerrmin.R @@ -36,10 +36,11 @@ mkinerrmin <- function(fit, alpha = 0.05) suffixes = c("_mean", "_pred")) errdata <- errdata[order(errdata$time, errdata$name), ] - # Any value that is set to exactly zero is not really an observed value - # Remove those at time 0 - those are caused by the FOCUS recommendation - # to set metabolites occurring at time 0 to 0 - errdata <- subset(errdata, !(time == 0 & value_mean == 0)) + # Remove values at time zero for variables whose value for state.ini is fixed, + # as these will not have any effect in the optimization and should therefore not + # be counted as degrees of freedom. + fixed_initials = gsub("_0$", "", rownames(subset(fit$fixed, type = "state"))) + errdata <- subset(errdata, !(time == 0 & name %in% fixed_initials)) n.optim.overall <- length(parms.optim) diff --git a/TODO b/TODO index 92a91069..f979d13a 100644 --- a/TODO +++ b/TODO @@ -2,11 +2,6 @@ TODO for version 1.0 - Think about what a user would expect from version 1.0 - Complete the main package vignette named mkin to include a method description - Improve order of parameters in output -- Write unit tests for mkinerrmin -- When checking for degrees of freedom for metabolites, check if their time - zero value (state.ini) is fixed instead of checking if the observed value is - zero (usually in regulatory kinetics it is set to zero anyway, but in the - case of known impurities this may not be the case). Nice to have: - Get starting values for formation fractions from data diff --git a/inst/unitTests/runit.mkinerrmin.R b/inst/unitTests/runit.mkinerrmin.R new file mode 100644 index 00000000..56a33ff9 --- /dev/null +++ b/inst/unitTests/runit.mkinerrmin.R @@ -0,0 +1,62 @@ +# Test SFO_SFO model with FOCUS_2006_D against Schaefer 2007 paper, tolerance = 1% # {{{ +# and check chi2 error values against values obtained with mkin 0.33 +test.FOCUS_2006_D_SFO_SFO <- function() +{ + SFO_SFO.1 <- mkinmod(parent = list(type = "SFO", to = "m1"), + m1 = list(type = "SFO"), use_of_ff = "min") + SFO_SFO.2 <- mkinmod(parent = list(type = "SFO", to = "m1"), + m1 = list(type = "SFO"), use_of_ff = "max") + + fit.1.e <- mkinfit(SFO_SFO.1, FOCUS_2006_D) + fit.1.d <- mkinfit(SFO_SFO.1, solution_type = "deSolve", FOCUS_2006_D) + fit.2.e <- mkinfit(SFO_SFO.2, FOCUS_2006_D) + fit.2.d <- mkinfit(SFO_SFO.2, solution_type = "deSolve", FOCUS_2006_D) + + FOCUS_2006_D_results_schaefer07_means <- c( + parent_0 = 99.65, DT50_parent = 7.04, DT50_m1 = 131.34) + + r.1.e <- c(fit.1.e$bparms.optim[[1]], endpoints(fit.1.e)$distimes[[1]]) + r.1.d <- c(fit.1.d$bparms.optim[[1]], endpoints(fit.1.d)$distimes[[1]]) + r.2.e <- c(fit.2.e$bparms.optim[[1]], endpoints(fit.2.e)$distimes[[1]]) + r.2.d <- c(fit.2.d$bparms.optim[[1]], endpoints(fit.2.d)$distimes[[1]]) + + dev.1.e <- 100 * (r.1.e - FOCUS_2006_D_results_schaefer07_means)/r.1.e + checkIdentical(as.numeric(abs(dev.1.e)) < 1, rep(TRUE, 3)) + dev.1.d <- 100 * (r.1.d - FOCUS_2006_D_results_schaefer07_means)/r.1.d + checkIdentical(as.numeric(abs(dev.1.d)) < 1, rep(TRUE, 3)) + dev.2.e <- 100 * (r.2.e - FOCUS_2006_D_results_schaefer07_means)/r.2.e + checkIdentical(as.numeric(abs(dev.2.e)) < 1, rep(TRUE, 3)) + dev.2.d <- 100 * (r.2.d - FOCUS_2006_D_results_schaefer07_means)/r.2.d + checkIdentical(as.numeric(abs(dev.2.d)) < 1, rep(TRUE, 3)) + + round(mkinerrmin(fit.2.e), 4) + round(mkinerrmin(fit.2.d), 4) + + errmin.FOCUS_2006_D_rounded = data.frame( + err.min = c(0.0640, 0.0646, 0.0469), + n.optim = c(4, 2, 2), + df = c(15, 7, 8), + row.names = c("All data", "parent", "m1")) + checkEqualsNumeric(round(mkinerrmin(fit.2.e), 4), + errmin.FOCUS_2006_D_rounded) +} # }}} + +# Test SFO_SFO model with FOCUS_2006_E against values obtained with mkin 0.33 {{{ +test.FOCUS_2006_E_SFO_SFO <- function() +{ + SFO_SFO.2 <- mkinmod(parent = list(type = "SFO", to = "m1"), + m1 = list(type = "SFO"), use_of_ff = "max") + + fit.2.e <- mkinfit(SFO_SFO.2, FOCUS_2006_E) + + round(mkinerrmin(fit.2.e), 4) + errmin.FOCUS_2006_E_rounded = data.frame( + err.min = c(0.1544, 0.1659, 0.1095), + n.optim = c(4, 2, 2), + df = c(13, 7, 6), + row.names = c("All data", "parent", "m1")) + checkEqualsNumeric(round(mkinerrmin(fit.2.e), 4), + errmin.FOCUS_2006_E_rounded) +} # }}} + + diff --git a/inst/unitTests/runit.mkinfit.R b/inst/unitTests/runit.mkinfit.R index fdbc86e0..8eefb995 100644 --- a/inst/unitTests/runit.mkinfit.R +++ b/inst/unitTests/runit.mkinfit.R @@ -1,6 +1,4 @@ -# $Id: runit.mkinfit.R 68 2010-09-09 22:40:04Z jranke $ - -# Copyright (C) 2010-2013 Johannes Ranke +# Copyright (C) 2010-2014 Johannes Ranke # Contact: jranke@uni-bremen.de # This file is part of the R package mkin @@ -189,40 +187,6 @@ test.FOCUS_2006_SFORB <- function() checkIdentical(dev.B.SFORB.2 < 1, rep(TRUE, length(dev.B.SFORB.2))) } # }}} -# Test SFO_SFO model with FOCUS_2006_D against Schaefer 2007 paper, tolerance = 1% # {{{ -test.FOCUS_2006_D_SFO_SFO <- function() -{ - SFO_SFO.1 <- mkinmod(parent = list(type = "SFO", to = "m1"), - m1 = list(type = "SFO"), use_of_ff = "min") - SFO_SFO.2 <- mkinmod(parent = list(type = "SFO", to = "m1"), - m1 = list(type = "SFO"), use_of_ff = "max") - - fit.1.e <- mkinfit(SFO_SFO.1, FOCUS_2006_D) - fit.1.d <- mkinfit(SFO_SFO.1, solution_type = "deSolve", FOCUS_2006_D) - fit.2.e <- mkinfit(SFO_SFO.2, FOCUS_2006_D) - SFO <- mkinmod(parent = list(type = "SFO")) - f.SFO <- mkinfit(SFO, FOCUS_2006_D) - fit.2.d <- mkinfit(SFO_SFO.2, solution_type = "deSolve", FOCUS_2006_D) - fit.2.e <- mkinfit(SFO_SFO.2, FOCUS_2006_D) - - FOCUS_2006_D_results_schaefer07_means <- c( - parent_0 = 99.65, DT50_parent = 7.04, DT50_m1 = 131.34) - - r.1.e <- c(fit.1.e$bparms.optim[[1]], endpoints(fit.1.e)$distimes[[1]]) - r.1.d <- c(fit.1.d$bparms.optim[[1]], endpoints(fit.1.d)$distimes[[1]]) - r.2.e <- c(fit.2.e$bparms.optim[[1]], endpoints(fit.2.e)$distimes[[1]]) - r.2.d <- c(fit.2.d$bparms.optim[[1]], endpoints(fit.2.d)$distimes[[1]]) - - dev.1.e <- 100 * (r.1.e - FOCUS_2006_D_results_schaefer07_means)/r.1.e - checkIdentical(as.numeric(abs(dev.1.e)) < 1, rep(TRUE, 3)) - dev.1.d <- 100 * (r.1.d - FOCUS_2006_D_results_schaefer07_means)/r.1.d - checkIdentical(as.numeric(abs(dev.1.d)) < 1, rep(TRUE, 3)) - dev.2.e <- 100 * (r.2.e - FOCUS_2006_D_results_schaefer07_means)/r.2.e - checkIdentical(as.numeric(abs(dev.2.e)) < 1, rep(TRUE, 3)) - dev.2.d <- 100 * (r.2.d - FOCUS_2006_D_results_schaefer07_means)/r.2.d - checkIdentical(as.numeric(abs(dev.2.d)) < 1, rep(TRUE, 3)) -} # }}} - # Test eigenvalue based fit to Schaefer 2007 data against solution from conference paper {{{ test.mkinfit.schaefer07_complex_example <- function() { diff --git a/man/mkinerrmin.Rd b/man/mkinerrmin.Rd index c43d87a1..78ab414e 100644 --- a/man/mkinerrmin.Rd +++ b/man/mkinerrmin.Rd @@ -34,6 +34,16 @@ mkinerrmin(fit, alpha = 0.05) \details{ This function is used internally by \code{\link{summary.mkinfit}}. } +\examples{ +SFO_SFO = mkinmod(parent = list(type = "SFO", to = "m1"), + m1 = list(type = "SFO"), + use_of_ff = "max") + +fit_FOCUS_D = mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) +round(mkinerrmin(fit_FOCUS_D), 4) +fit_FOCUS_E = mkinfit(SFO_SFO, FOCUS_2006_E, quiet = TRUE) +round(mkinerrmin(fit_FOCUS_E), 4) +} \references{ FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU diff --git a/tests/doRUnit.R b/tests/doRUnit.R index f0f82812..9faee940 100644 --- a/tests/doRUnit.R +++ b/tests/doRUnit.R @@ -1,4 +1,3 @@ -# $Id: doRUnit.R 96 2011-04-29 11:10:40Z jranke $ # Adapted from a version around 2.9 of the rcdk package by Rajarshi Guha if(require("RUnit", quietly=TRUE)) { diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index ab7ccaee..2dd186de 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -193,7 +193,13 @@ hr { report, p. 284:

library("mkin")
-FOCUS_2006_L1 = data.frame(
+
+ +
## Loading required package: minpack.lm
+## Loading required package: rootSolve
+
+ +
FOCUS_2006_L1 = data.frame(
   t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2),
   parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6, 
              72.0, 71.9, 50.3, 59.4, 47.0, 45.1,
@@ -215,17 +221,17 @@ given in the FOCUS report. 

 summary(m.L1.SFO)
-
## mkin version:    0.9.32 
+
## mkin version:    0.9.33 
 ## R version:       3.1.1 
-## Date of fit:     Thu Jul 24 10:32:09 2014 
-## Date of summary: Thu Jul 24 10:32:09 2014 
+## Date of fit:     Mon Aug 25 10:34:14 2014 
+## Date of summary: Mon Aug 25 10:34:14 2014 
 ## 
 ## Equations:
-## [1] d_parent = - k_parent_sink * parent
+## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 14 model solutions performed in 0.081 s
+## Fitted with method Marq using 14 model solutions performed in 0.083 s
 ## 
 ## Weighting: none
 ## 
@@ -318,17 +324,17 @@ is checked.

 summary(m.L1.FOMC, data = FALSE)
 

 
-
## mkin version:    0.9.32 
+
## mkin version:    0.9.33 
 ## R version:       3.1.1 
-## Date of fit:     Thu Jul 24 10:32:10 2014 
-## Date of summary: Thu Jul 24 10:32:11 2014 
+## Date of fit:     Mon Aug 25 10:34:17 2014 
+## Date of summary: Mon Aug 25 10:34:17 2014 
 ## 
 ## Equations:
-## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
+## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 53 model solutions performed in 0.321 s
+## Fitted with method Marq using 53 model solutions performed in 0.3 s
 ## 
 ## Weighting: none
 ## 
@@ -412,17 +418,17 @@ FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)
 summary(m.L2.SFO)
 

 
-
## mkin version:    0.9.32 
+
## mkin version:    0.9.33 
 ## R version:       3.1.1 
-## Date of fit:     Thu Jul 24 10:32:11 2014 
-## Date of summary: Thu Jul 24 10:32:11 2014 
+## Date of fit:     Mon Aug 25 10:34:17 2014 
+## Date of summary: Mon Aug 25 10:34:17 2014 
 ## 
 ## Equations:
-## [1] d_parent = - k_parent_sink * parent
+## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 29 model solutions performed in 0.196 s
+## Fitted with method Marq using 29 model solutions performed in 0.184 s
 ## 
 ## Weighting: none
 ## 
@@ -522,17 +528,17 @@ mkinresplot(m.L2.FOMC)
 
summary(m.L2.FOMC, data = FALSE)
 

 
-
## mkin version:    0.9.32 
+
## mkin version:    0.9.33 
 ## R version:       3.1.1 
-## Date of fit:     Thu Jul 24 10:32:11 2014 
-## Date of summary: Thu Jul 24 10:32:11 2014 
+## Date of fit:     Mon Aug 25 10:34:17 2014 
+## Date of summary: Mon Aug 25 10:34:17 2014 
 ## 
 ## Equations:
-## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
+## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 35 model solutions performed in 0.223 s
+## Fitted with method Marq using 35 model solutions performed in 0.2 s
 ## 
 ## Weighting: none
 ## 
@@ -608,17 +614,19 @@ plot(m.L2.DFOP)
 
summary(m.L2.DFOP, data = FALSE)
 

 
-
## mkin version:    0.9.32 
+
## mkin version:    0.9.33 
 ## R version:       3.1.1 
-## Date of fit:     Thu Jul 24 10:32:12 2014 
-## Date of summary: Thu Jul 24 10:32:12 2014 
+## Date of fit:     Mon Aug 25 10:34:18 2014 
+## Date of summary: Mon Aug 25 10:34:18 2014 
 ## 
 ## Equations:
-## [1] d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * parent
+## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * 
+##            time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * 
+##            time))) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 43 model solutions performed in 0.271 s
+## Fitted with method Marq using 43 model solutions performed in 0.26 s
 ## 
 ## Weighting: none
 ## 
@@ -695,17 +703,17 @@ plot(m.L3.SFO)
 
summary(m.L3.SFO)
 

 
-
## mkin version:    0.9.32 
+
## mkin version:    0.9.33 
 ## R version:       3.1.1 
-## Date of fit:     Thu Jul 24 10:32:14 2014 
-## Date of summary: Thu Jul 24 10:32:14 2014 
+## Date of fit:     Mon Aug 25 10:34:18 2014 
+## Date of summary: Mon Aug 25 10:34:18 2014 
 ## 
 ## Equations:
-## [1] d_parent = - k_parent_sink * parent
+## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 44 model solutions performed in 0.251 s
+## Fitted with method Marq using 44 model solutions performed in 0.252 s
 ## 
 ## Weighting: none
 ## 
@@ -781,17 +789,17 @@ plot(m.L3.FOMC)
 
summary(m.L3.FOMC, data = FALSE)
 

 
-
## mkin version:    0.9.32 
+
## mkin version:    0.9.33 
 ## R version:       3.1.1 
-## Date of fit:     Thu Jul 24 10:32:14 2014 
-## Date of summary: Thu Jul 24 10:32:14 2014 
+## Date of fit:     Mon Aug 25 10:34:19 2014 
+## Date of summary: Mon Aug 25 10:34:19 2014 
 ## 
 ## Equations:
-## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
+## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 26 model solutions performed in 0.154 s
+## Fitted with method Marq using 26 model solutions performed in 0.148 s
 ## 
 ## Weighting: none
 ## 
@@ -854,17 +862,19 @@ plot(m.L3.DFOP)
 
summary(m.L3.DFOP, data = FALSE)
 

 
-
## mkin version:    0.9.32 
+
## mkin version:    0.9.33 
 ## R version:       3.1.1 
-## Date of fit:     Thu Jul 24 10:32:14 2014 
-## Date of summary: Thu Jul 24 10:32:14 2014 
+## Date of fit:     Mon Aug 25 10:34:19 2014 
+## Date of summary: Mon Aug 25 10:34:19 2014 
 ## 
 ## Equations:
-## [1] d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * parent
+## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * 
+##            time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * 
+##            time))) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 37 model solutions performed in 0.228 s
+## Fitted with method Marq using 37 model solutions performed in 0.236 s
 ## 
 ## Weighting: none
 ## 
@@ -950,17 +960,17 @@ plot(m.L4.SFO)
 
summary(m.L4.SFO, data = FALSE)
 

 
-
## mkin version:    0.9.32 
+
## mkin version:    0.9.33 
 ## R version:       3.1.1 
-## Date of fit:     Thu Jul 24 10:32:15 2014 
-## Date of summary: Thu Jul 24 10:32:15 2014 
+## Date of fit:     Mon Aug 25 10:34:19 2014 
+## Date of summary: Mon Aug 25 10:34:19 2014 
 ## 
 ## Equations:
-## [1] d_parent = - k_parent_sink * parent
+## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 20 model solutions performed in 0.141 s
+## Fitted with method Marq using 20 model solutions performed in 0.123 s
 ## 
 ## Weighting: none
 ## 
@@ -1025,17 +1035,17 @@ plot(m.L4.FOMC)
 
summary(m.L4.FOMC, data = FALSE)
 

 
-
## mkin version:    0.9.32 
+
## mkin version:    0.9.33 
 ## R version:       3.1.1 
-## Date of fit:     Thu Jul 24 10:32:15 2014 
-## Date of summary: Thu Jul 24 10:32:15 2014 
+## Date of fit:     Mon Aug 25 10:34:20 2014 
+## Date of summary: Mon Aug 25 10:34:20 2014 
 ## 
 ## Equations:
-## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
+## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 48 model solutions performed in 0.296 s
+## Fitted with method Marq using 48 model solutions performed in 0.281 s
 ## 
 ## Weighting: none
 ## 
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