From 081b5f25cc4ef779175307d9ce20672e0573b7c9 Mon Sep 17 00:00:00 2001 From: jranke Date: Tue, 24 Apr 2012 17:33:56 +0000 Subject: - Added the reference fit data for FOCUS 2006 datasets from the kinfit package - Used these data in unit tests for parent only models - Fixed SFORB data and calculation of formation fractions along the way - Reintroduced the test for the Schaefer 2007 data - Got rid of the mkinmod unit tests - they are too hard to maintain and the mkinfit tests test the model definitions as well git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@32 edb9625f-4e0d-4859-8d74-9fd3b1da38cb --- R/mkinfit.R | 33 ++++- R/mkinpredict.R | 22 ++- TODO | 3 +- data/FOCUS_2006_DFOP_ref_A_to_B.rda | Bin 0 -> 723 bytes data/FOCUS_2006_FOMC_ref_A_to_F.rda | Bin 0 -> 1227 bytes data/FOCUS_2006_HS_ref_A_to_F.rda | Bin 0 -> 1360 bytes data/FOCUS_2006_SFO_ref_A_to_F.rda | Bin 0 -> 1097 bytes inst/unitTests/runit.mkinfit.R | 257 ++++++++++++++++++++++++++++++++---- inst/unitTests/runit.mkinmod.R | 134 ------------------- man/FOCUS_2006_DFOP_ref_A_to_B.Rd | 39 ++++++ man/FOCUS_2006_FOMC_ref_A_to_F.Rd | 38 ++++++ man/FOCUS_2006_HS_ref_A_to_F.Rd | 39 ++++++ man/FOCUS_2006_SFO_ref_A_to_F.Rd | 37 ++++++ man/mkinfit.Rd | 8 +- vignettes/mkin.Rnw | 4 +- 15 files changed, 443 insertions(+), 171 deletions(-) create mode 100644 data/FOCUS_2006_DFOP_ref_A_to_B.rda create mode 100644 data/FOCUS_2006_FOMC_ref_A_to_F.rda create mode 100644 data/FOCUS_2006_HS_ref_A_to_F.rda create mode 100644 data/FOCUS_2006_SFO_ref_A_to_F.rda delete mode 100644 inst/unitTests/runit.mkinmod.R create mode 100644 man/FOCUS_2006_DFOP_ref_A_to_B.Rd create mode 100644 man/FOCUS_2006_FOMC_ref_A_to_F.Rd create mode 100644 man/FOCUS_2006_HS_ref_A_to_F.Rd create mode 100644 man/FOCUS_2006_SFO_ref_A_to_F.Rd diff --git a/R/mkinfit.R b/R/mkinfit.R index cf58a7d..6e455e1 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -30,6 +30,7 @@ mkinfit <- function(mkinmod, observed, plot = FALSE, quiet = FALSE, err = NULL, weight = "none", scaleVar = FALSE, atol = 1e-6, n.outtimes = 100, + trace_parms = FALSE, ...) { # Get the names of the state variables in the model @@ -112,7 +113,7 @@ mkinfit <- function(mkinmod, observed, assign("calls", calls+1, inherits=TRUE) # Increase the model solution counter # Trace parameter values if quiet is off - if(!quiet) cat(P, "\n") + if(trace_parms) cat(P, "\n") # Time points at which observed data are available # Make sure we include time 0, so initial values for state variables are for time 0 @@ -216,10 +217,12 @@ mkinfit <- function(mkinmod, observed, } fit$errmin <- errmin - # Calculate dissipation times DT50 and DT90 from parameters + # Calculate dissipation times DT50 and DT90 and, if necessary, formation fractions + # from optimised parameters parms.all = backtransform_odeparms(c(fit$par, parms.fixed), mod_vars) fit$distimes <- data.frame(DT50 = rep(NA, length(obs_vars)), DT90 = rep(NA, length(obs_vars)), row.names = obs_vars) + fit$ff <- vector() fit$SFORB <- vector() for (obs_var in obs_vars) { type = names(mkinmod$map[[obs_var]])[1] @@ -230,7 +233,7 @@ mkinfit <- function(mkinmod, observed, DT90 = log(10)/k_tot for (k_name in k_names) { - fit$ff[[sub("^k_", "", k_name)]] = parms.all[[k_name]] / k_tot + fit$ff[[sub("k_", "", k_name)]] = parms.all[[k_name]] / k_tot } } if (type == "FOMC") { @@ -290,10 +293,12 @@ mkinfit <- function(mkinmod, observed, f_90 <- function(t) (SFORB_fraction(t) - 0.1)^2 DT90.o <- optimize(f_90, c(0.01, max_DT))$minimum if (abs(DT90.o - max_DT) < 0.01) DT90 = NA else DT90 = DT90.o + for (k_out_name in k_out_names) { - fit$ff[[sub("^k_", "", k_out_name)]] = parms.all[[k_out_name]] / k_1output + fit$ff[[sub("k_", "", k_out_name)]] = parms.all[[k_out_name]] / k_1output } + # Return the eigenvalues for comparison with DFOP rate constants fit$SFORB[[paste(obs_var, "b1", sep="_")]] = b1 fit$SFORB[[paste(obs_var, "b2", sep="_")]] = b2 @@ -310,6 +315,7 @@ mkinfit <- function(mkinmod, observed, fit$atol <- atol fit$parms.all <- parms.all # Return all backtransformed parameters for summary fit$odeparms.final <- parms.all[mkinmod$parms] # Return ode parameters for further fitting + fit$date <- date() class(fit) <- c("mkinfit", "modFit") return(fit) @@ -337,7 +343,12 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, ...) { param <- cbind(param, se) dimnames(param) <- list(pnames, c("Estimate", "Std. Error")) - ans <- list(residuals = object$residuals, + ans <- list( + version = as.character(packageVersion("mkin")), + Rversion = paste(R.version$major, R.version$minor, sep="."), + date.fit = object$date, + date.summary = date(), + residuals = object$residuals, residualVariance = resvar, sigma = sqrt(resvar), modVariance = modVariance, @@ -354,6 +365,7 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, ...) { ans$fixed <- object$fixed ans$errmin <- object$errmin ans$parms.all <- object$parms.all + ans$ff <- object$ff if(distimes) ans$distimes <- object$distimes if(length(object$SFORB) != 0) ans$SFORB <- object$SFORB class(ans) <- c("summary.mkinfit", "summary.modFit") @@ -362,6 +374,11 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, ...) { # Expanded from print.summary.modFit print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), ...) { + cat("mkin version: ", x$version, "\n") + cat("R version: ", x$Rversion, "\n") + cat("Date of fit: ", x$date.fit, "\n") + cat("Date of summary:", x$date.summary, "\n") + cat("\nEquations:\n") print(noquote(as.character(x[["diffs"]]))) df <- x$df @@ -393,6 +410,12 @@ print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), . print(x$distimes, digits=digits,...) } + printff <- !is.null(x$ff) + if(printff){ + cat("\nEstimated formation fractions:\n") + print(data.frame(ff = x$ff), digits=digits,...) + } + printSFORB <- !is.null(x$SFORB) if(printSFORB){ cat("\nEstimated Eigenvalues of SFORB model(s):\n") diff --git a/R/mkinpredict.R b/R/mkinpredict.R index 2b7e51d..be43b0e 100644 --- a/R/mkinpredict.R +++ b/R/mkinpredict.R @@ -1,3 +1,23 @@ +# $Id$ + +# Copyright (C) 2010-2012 Johannes Ranke +# Contact: jranke@uni-bremen.de + +# This file is part of the R package mkin + +# mkin is free software: you can redistribute it and/or modify it under the +# terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + mkinpredict <- function(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve", map_output = TRUE, atol = 1e-6, ...) { # Get the names of the state variables in the model @@ -35,7 +55,7 @@ mkinpredict <- function(mkinmod, odeparms, odeini, outtimes, solution_type = "de evalparse(parent.name), evalparse(paste("k", parent.name, "bound", sep="_")), evalparse(paste("k", sub("free", "bound", parent.name), "free", sep="_")), - evalparse(paste("k", parent.name, sep="_"))) + evalparse(paste("k", parent.name, "sink", sep="_"))) ) out <- cbind(outtimes, o) dimnames(out) <- list(outtimes, c("time", sub("_free", "", parent.name))) diff --git a/TODO b/TODO index a49957d..a7503bd 100644 --- a/TODO +++ b/TODO @@ -1,10 +1,9 @@ Must have: - Fix remaining problem with the schaefer complex test data (test.R) -- Fix parent only SFORB model (see vignette) -- Fix unit tests for mkinmod - Adapt mkinplot function Nice to have: +- Make unit tests for mkinpredict, comparing different solution types - Calculate confidence intervals for parameters assuming normal distribution - Calculate confidence intervals for DT50 and DT90 values when only one parameter is involved - Add unit tests for mkinfit diff --git a/data/FOCUS_2006_DFOP_ref_A_to_B.rda b/data/FOCUS_2006_DFOP_ref_A_to_B.rda new file mode 100644 index 0000000..8b9dc9f Binary files /dev/null and b/data/FOCUS_2006_DFOP_ref_A_to_B.rda differ diff --git a/data/FOCUS_2006_FOMC_ref_A_to_F.rda b/data/FOCUS_2006_FOMC_ref_A_to_F.rda new file mode 100644 index 0000000..246a53f Binary files /dev/null and b/data/FOCUS_2006_FOMC_ref_A_to_F.rda differ diff --git a/data/FOCUS_2006_HS_ref_A_to_F.rda b/data/FOCUS_2006_HS_ref_A_to_F.rda new file mode 100644 index 0000000..1e3b386 Binary files /dev/null and b/data/FOCUS_2006_HS_ref_A_to_F.rda differ diff --git a/data/FOCUS_2006_SFO_ref_A_to_F.rda b/data/FOCUS_2006_SFO_ref_A_to_F.rda new file mode 100644 index 0000000..411c536 Binary files /dev/null and b/data/FOCUS_2006_SFO_ref_A_to_F.rda differ diff --git a/inst/unitTests/runit.mkinfit.R b/inst/unitTests/runit.mkinfit.R index 2a026ce..a06e4ff 100644 --- a/inst/unitTests/runit.mkinfit.R +++ b/inst/unitTests/runit.mkinfit.R @@ -18,36 +18,243 @@ # You should have received a copy of the GNU General Public License along with # this program. If not, see +# Test SFO model to a relative tolerance of 1% # {{{ +test.FOCUS_2006_SFO <- function() +{ + SFO.1 <- mkinmod(parent = list(type = "SFO")) + SFO.2 <- mkinmod(parent = list(type = "SFO"), use_of_ff = "max") + + fit.A.SFO.1 <- mkinfit(SFO.1, FOCUS_2006_A, quiet=TRUE) + fit.A.SFO.2 <- mkinfit(SFO.2, FOCUS_2006_A, quiet=TRUE) + + median.A.SFO <- as.numeric(lapply(subset(FOCUS_2006_SFO_ref_A_to_F, dataset == "A", + c(M0, k, DT50, DT90)), "median")) + + fit.A.SFO.1.r <- as.numeric(c(fit.A.SFO.1$parms.all, fit.A.SFO.1$distimes)) + dev.A.SFO.1 <- abs(round(100 * ((median.A.SFO - fit.A.SFO.1.r)/median.A.SFO), digits=1)) + checkIdentical(dev.A.SFO.1 < 1, rep(TRUE, length(dev.A.SFO.1))) + + fit.A.SFO.2.r <- as.numeric(c(fit.A.SFO.2$parms.all, fit.A.SFO.2$distimes)) + dev.A.SFO.2 <- abs(round(100 * ((median.A.SFO - fit.A.SFO.2.r)/median.A.SFO), digits=1)) + checkIdentical(dev.A.SFO.2 < 1, rep(TRUE, length(dev.A.SFO.2))) + + fit.C.SFO.1 <- mkinfit(SFO.1, FOCUS_2006_C, quiet=TRUE) + fit.C.SFO.2 <- mkinfit(SFO.2, FOCUS_2006_C, quiet=TRUE) + + median.C.SFO <- as.numeric(lapply(subset(FOCUS_2006_SFO_ref_A_to_F, dataset == "C", + c(M0, k, DT50, DT90)), "median")) + + fit.C.SFO.1.r <- as.numeric(c(fit.C.SFO.1$parms.all, fit.C.SFO.1$distimes)) + dev.C.SFO.1 <- abs(round(100 * ((median.C.SFO - fit.C.SFO.1.r)/median.C.SFO), digits=1)) + checkIdentical(dev.C.SFO.1 < 1, rep(TRUE, length(dev.C.SFO.1))) + + fit.C.SFO.2.r <- as.numeric(c(fit.C.SFO.2$parms.all, fit.C.SFO.2$distimes)) + dev.C.SFO.2 <- abs(round(100 * ((median.C.SFO - fit.C.SFO.2.r)/median.C.SFO), digits=1)) + checkIdentical(dev.C.SFO.2 < 1, rep(TRUE, length(dev.C.SFO.2))) +} # }}} + +# Test FOMC model to a relative tolerance of 1% {{{ +# See kinfit vignette for a discussion of FOMC fits to FOCUS_2006_A +# In this case, only M0, DT50 and DT90 are checked +test.FOCUS_2006_FOMC <- function() +{ + FOMC <- mkinmod(parent = list(type = "FOMC")) + + # FOCUS_2006_A (compare kinfit vignette for discussion) + fit.A.FOMC <- mkinfit(FOMC, FOCUS_2006_A, quiet=TRUE) + + median.A.FOMC <- as.numeric(lapply(subset(FOCUS_2006_FOMC_ref_A_to_F, dataset == "A", + c(M0, alpha, beta, DT50, DT90)), "median")) + + fit.A.FOMC.r <- as.numeric(c(fit.A.FOMC$parms.all, fit.A.FOMC$distimes)) + dev.A.FOMC <- abs(round(100 * ((median.A.FOMC - fit.A.FOMC.r)/median.A.FOMC), digits=1)) + dev.A.FOMC <- dev.A.FOMC[c(1, 4, 5)] + checkIdentical(dev.A.FOMC < 1, rep(TRUE, length(dev.A.FOMC))) + + # FOCUS_2006_B + fit.B.FOMC <- mkinfit(FOMC, FOCUS_2006_B, quiet=TRUE) + + median.B.FOMC <- as.numeric(lapply(subset(FOCUS_2006_FOMC_ref_A_to_F, dataset == "B", + c(M0, alpha, beta, DT50, DT90)), "median")) + + fit.B.FOMC.r <- as.numeric(c(fit.B.FOMC$parms.all, fit.B.FOMC$distimes)) + dev.B.FOMC <- abs(round(100 * ((median.B.FOMC - fit.B.FOMC.r)/median.B.FOMC), digits=1)) + dev.B.FOMC <- dev.B.FOMC[c(1, 4, 5)] + checkIdentical(dev.B.FOMC < 1, rep(TRUE, length(dev.B.FOMC))) + + # FOCUS_2006_C + fit.C.FOMC <- mkinfit(FOMC, FOCUS_2006_C, quiet=TRUE) + + median.C.FOMC <- as.numeric(lapply(subset(FOCUS_2006_FOMC_ref_A_to_F, dataset == "C", + c(M0, alpha, beta, DT50, DT90)), "median")) + + fit.C.FOMC.r <- as.numeric(c(fit.C.FOMC$parms.all, fit.C.FOMC$distimes)) + dev.C.FOMC <- abs(round(100 * ((median.C.FOMC - fit.C.FOMC.r)/median.C.FOMC), digits=1)) + dev.C.FOMC <- dev.C.FOMC[c(1, 4, 5)] + checkIdentical(dev.C.FOMC < 1, rep(TRUE, length(dev.C.FOMC))) +} # }}} + +# Test DFOP model, tolerance of 1% with the exception of f parameter for A {{{ +test.FOCUS_2006_DFOP <- function() +{ + DFOP <- mkinmod(parent = list(type = "DFOP")) + + # FOCUS_2006_A + fit.A.DFOP <- mkinfit(DFOP, FOCUS_2006_A, quiet=TRUE) + fit.A.DFOP <- mkinfit(DFOP, FOCUS_2006_A, quiet=TRUE, plot=TRUE) + + median.A.DFOP <- as.numeric(lapply(subset(FOCUS_2006_DFOP_ref_A_to_B, dataset == "A", + c(M0, k1, k2, f, DT50, DT90)), "median")) + + fit.A.DFOP.r <- as.numeric(c(fit.A.DFOP$parms.all, fit.A.DFOP$distimes)) + dev.A.DFOP <- abs(round(100 * ((median.A.DFOP - fit.A.DFOP.r)/median.A.DFOP), digits=1)) + # about 6.7% deviation for parameter f, the others are < 0.1% + checkIdentical(dev.A.DFOP < c(1, 1, 1, 10, 1, 1), rep(TRUE, length(dev.A.DFOP))) + + # FOCUS_2006_B + fit.B.DFOP <- mkinfit(DFOP, FOCUS_2006_B, quiet=TRUE) + + median.B.DFOP <- as.numeric(lapply(subset(FOCUS_2006_DFOP_ref_A_to_B, dataset == "B", + c(M0, k1, k2, f, DT50, DT90)), "median")) + + fit.B.DFOP.r <- as.numeric(c(fit.B.DFOP$parms.all, fit.B.DFOP$distimes)) + dev.B.DFOP <- abs(round(100 * ((median.B.DFOP - fit.B.DFOP.r)/median.B.DFOP), digits=1)) + # about 0.6% deviation for parameter f, the others are <= 0.1% + checkIdentical(dev.B.DFOP < 1, rep(TRUE, length(dev.B.DFOP))) +} # }}} + +# Test HS model to a relative tolerance of 1% excluding Mathematica values {{{ +# as they are unreliable +test.FOCUS_2006_HS <- function() +{ + HS <- mkinmod(parent = list(type = "HS")) + + # FOCUS_2006_A + fit.A.HS <- mkinfit(HS, FOCUS_2006_A, quiet=TRUE) + + median.A.HS <- as.numeric(lapply(subset(FOCUS_2006_HS_ref_A_to_F, dataset == "A", + c(M0, k1, k2, tb, DT50, DT90)), "median")) + + fit.A.HS.r <- as.numeric(c(fit.A.HS$parms.all, fit.A.HS$distimes)) + dev.A.HS <- abs(round(100 * ((median.A.HS - fit.A.HS.r)/median.A.HS), digits=1)) + # about 6.7% deviation for parameter f, the others are < 0.1% + checkIdentical(dev.A.HS < 1, rep(TRUE, length(dev.A.HS))) + + # FOCUS_2006_B + fit.B.HS <- mkinfit(HS, FOCUS_2006_B, quiet=TRUE) + + median.B.HS <- as.numeric(lapply(subset(FOCUS_2006_HS_ref_A_to_F, dataset == "B", + c(M0, k1, k2, tb, DT50, DT90)), "median")) + + fit.B.HS.r <- as.numeric(c(fit.B.HS$parms.all, fit.B.HS$distimes)) + dev.B.HS <- abs(round(100 * ((median.B.HS - fit.B.HS.r)/median.B.HS), digits=1)) + # < 10% deviation for M0, k1, DT50 and DT90, others are problematic + dev.B.HS <- dev.B.HS[c(1, 2, 5, 6)] + checkIdentical(dev.B.HS < 10, rep(TRUE, length(dev.B.HS))) + + # FOCUS_2006_C + fit.C.HS <- mkinfit(HS, FOCUS_2006_C, quiet=TRUE) + + median.C.HS <- as.numeric(lapply(subset(FOCUS_2006_HS_ref_A_to_F, dataset == "C", + c(M0, k1, k2, tb, DT50, DT90)), "median")) + + fit.A.HS.r <- as.numeric(c(fit.A.HS$parms.all, fit.A.HS$distimes)) + dev.A.HS <- abs(round(100 * ((median.A.HS - fit.A.HS.r)/median.A.HS), digits=1)) + # deviation <= 0.1% + checkIdentical(dev.A.HS < 1, rep(TRUE, length(dev.A.HS))) +} # }}} + +# Test SFORB model against DFOP solutions to a relative tolerance of 1% # {{{ +test.FOCUS_2006_SFORB <- function() +{ + SFORB <- mkinmod(parent = list(type = "SFORB")) + + # FOCUS_2006_A + fit.A.SFORB.1 <- mkinfit(SFORB, FOCUS_2006_A, quiet=TRUE) + fit.A.SFORB.2 <- mkinfit(SFORB, FOCUS_2006_A, solution_type = "deSolve", quiet=TRUE) + + median.A.SFORB <- as.numeric(lapply(subset(FOCUS_2006_DFOP_ref_A_to_B, dataset == "A", + c(M0, k1, k2, DT50, DT90)), "median")) + + fit.A.SFORB.1.r <- as.numeric(c( + parent_0 = fit.A.SFORB.1$parms.all[[1]], + k1 = fit.A.SFORB.1$SFORB[[1]], + k2 = fit.A.SFORB.1$SFORB[[2]], + fit.A.SFORB.1$distimes)) + dev.A.SFORB.1 <- abs(round(100 * ((median.A.SFORB - fit.A.SFORB.1.r)/median.A.SFORB), digits=1)) + # The first Eigenvalue is a lot different from k1 in the DFOP fit + # The explanation is that the dataset is simply SFO + dev.A.SFORB.1 <- dev.A.SFORB.1[c(1, 3, 4, 5)] + checkIdentical(dev.A.SFORB.1 < 1, rep(TRUE, length(dev.A.SFORB.1))) + + fit.A.SFORB.2.r <- as.numeric(c( + parent_0 = fit.A.SFORB.2$parms.all[[1]], + k1 = fit.A.SFORB.2$SFORB[[1]], + k2 = fit.A.SFORB.2$SFORB[[2]], + fit.A.SFORB.2$distimes)) + dev.A.SFORB.2 <- abs(round(100 * ((median.A.SFORB - fit.A.SFORB.2.r)/median.A.SFORB), digits=1)) + # The first Eigenvalue is a lot different from k1 in the DFOP fit + # The explanation is that the dataset is simply SFO + dev.A.SFORB.2 <- dev.A.SFORB.2[c(1, 3, 4, 5)] + checkIdentical(dev.A.SFORB.2 < 1, rep(TRUE, length(dev.A.SFORB.2))) + + # FOCUS_2006_B + fit.B.SFORB.1 <- mkinfit(SFORB, FOCUS_2006_B, quiet=TRUE) + fit.B.SFORB.2 <- mkinfit(SFORB, FOCUS_2006_B, solution_type = "deSolve", quiet=TRUE) + + median.B.SFORB <- as.numeric(lapply(subset(FOCUS_2006_DFOP_ref_A_to_B, dataset == "B", + c(M0, k1, k2, DT50, DT90)), "median")) + + fit.B.SFORB.1.r <- as.numeric(c( + parent_0 = fit.B.SFORB.1$parms.all[[1]], + k1 = fit.B.SFORB.1$SFORB[[1]], + k2 = fit.B.SFORB.1$SFORB[[2]], + fit.B.SFORB.1$distimes)) + dev.B.SFORB.1 <- abs(round(100 * ((median.B.SFORB - fit.B.SFORB.1.r)/median.B.SFORB), digits=1)) + checkIdentical(dev.B.SFORB.1 < 1, rep(TRUE, length(dev.B.SFORB.1))) + + fit.B.SFORB.2.r <- as.numeric(c( + parent_0 = fit.B.SFORB.2$parms.all[[1]], + k1 = fit.B.SFORB.2$SFORB[[1]], + k2 = fit.B.SFORB.2$SFORB[[2]], + fit.B.SFORB.2$distimes)) + dev.B.SFORB.2 <- abs(round(100 * ((median.B.SFORB - fit.B.SFORB.2.r)/median.B.SFORB), digits=1)) + checkIdentical(dev.B.SFORB.2 < 1, rep(TRUE, length(dev.B.SFORB.2))) +} # }}} + +# Test eigenvalue based fit to Schaefer 2007 data against solution from conference paper {{{ test.mkinfit.schaefer07_complex_example <- function() { schaefer07_complex_model <- mkinmod( - parent = list(type = "SFO", to = c("A1", "B1", "C1")), + parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE), A1 = list(type = "SFO", to = "A2"), B1 = list(type = "SFO"), C1 = list(type = "SFO"), A2 = list(type = "SFO")) -# Commented out because it takes too much time and is currently not used (see below) -# fit <- mkinfit(schaefer07_complex_model, -# mkin_wide_to_long(schaefer07_complex_case, time = "time")) -# r <- schaefer07_complex_results -# r$mkin <- c( -# fit$parms.all["k_parent"], -# fit$distimes["parent", "DT50"], -# fit$parms.all["f_parent_to_A1"], -# fit$parms.all["k_A1"], -# fit$distimes["A1", "DT50"], -# fit$parms.all["f_parent_to_B1"], -# fit$parms.all["k_B1"], -# fit$distimes["B1", "DT50"], -# fit$parms.all["f_parent_to_C1"], -# fit$parms.all["k_C1"], -# fit$distimes["C1", "DT50"], -# fit$parms.all["f_A1_to_A2"], -# fit$parms.all["k_A2"], -# fit$distimes["A2", "DT50"]) -# r$means <- (r$KinGUI + r$ModelMaker)/2 -# r$mkin.deviation <- abs(round(100 * ((r$mkin - r$means)/r$means), digits=1)) - # Commented out the check as mkin is fitting a different model - #checkIdentical(r$mkin.deviation < 10, rep(TRUE, length(r$mkin.deviation))) -} + fit <- mkinfit(schaefer07_complex_model, + mkin_wide_to_long(schaefer07_complex_case, time = "time")) + s <- summary(fit) + r <- schaefer07_complex_results + attach(as.list(fit$parms.all)) + k_parent <- sum(k_parent_A1, k_parent_B1, k_parent_C1) + r$mkin <- c( + k_parent, + s$distimes["parent", "DT50"], + s$ff["parent_A1"], + sum(k_A1_sink, k_A1_A2), + s$distimes["A1", "DT50"], + s$ff["parent_B1"], + k_B1_sink, + s$distimes["B1", "DT50"], + s$ff["parent_C1"], + k_C1_sink, + s$distimes["C1", "DT50"], + s$ff["A1_A2"], + k_A2_sink, + s$distimes["A2", "DT50"]) + r$means <- (r$KinGUI + r$ModelMaker)/2 + r$mkin.deviation <- abs(round(100 * ((r$mkin - r$means)/r$means), digits=1)) + checkIdentical(r$mkin.deviation < 10, rep(TRUE, length(r$mkin.deviation))) +} # }}} +# vim: set foldmethod=marker ts=2 sw=2 expandtab: diff --git a/inst/unitTests/runit.mkinmod.R b/inst/unitTests/runit.mkinmod.R deleted file mode 100644 index 38b07cd..0000000 --- a/inst/unitTests/runit.mkinmod.R +++ /dev/null @@ -1,134 +0,0 @@ -# $Id: runit.mkinmod.R 64 2010-09-01 13:33:51Z jranke $ - -# Copyright (C) 2010-2012 Johannes Ranke -# Contact: jranke@uni-bremen.de - -# This file is part of the R package mkin - -# mkin is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -test.mkinmod.SFO <- function() -{ - SFO.diffs <- c( - parent = "d_parent = - k_parent * parent" - ) - SFO.parms <- c("k_parent") - SFO.map <- list(parent = c(SFO = "parent")) - SFO.coefmat <- matrix("- k_parent", dimnames = list("parent", "parent")) - SFO <- list(diffs = SFO.diffs, parms = SFO.parms, map = SFO.map, - coefmat = SFO.coefmat) - class(SFO) <- "mkinmod" - SFO.mkinmod <- mkinmod( - parent = list(type = "SFO") - ) - checkIdentical(SFO, SFO.mkinmod) -} - -test.mkinmod.SFORB <- function() -{ - SFORB.diffs <- c( - parent_free = paste( - "d_parent_free = - k_parent_free * parent_free", - "- k_parent_free_bound * parent_free", - "+ k_parent_bound_free * parent_bound"), - parent_bound = paste( - "d_parent_bound =", - "+ k_parent_free_bound * parent_free", - "- k_parent_bound_free * parent_bound") - ) - SFORB.parms <- c("k_parent_free", "k_parent_free_bound", "k_parent_bound_free") - SFORB.map <- list(parent = c(SFORB = "parent_free", SFORB = "parent_bound")) - vars <- paste("parent", c("free", "bound"), sep="_") - SFORB.coefmat <- matrix( - c("- k_parent_free - k_parent_free_bound", "k_parent_bound_free", - "k_parent_free_bound", "- k_parent_bound_free"), nrow=2, byrow=TRUE, - dimnames=list(vars, vars)) - SFORB <- list(diffs = SFORB.diffs, parms = SFORB.parms, - map = SFORB.map, coefmat = SFORB.coefmat) - class(SFORB) <- "mkinmod" - SFORB.mkinmod <- mkinmod( - parent = list(type = "SFORB") - ) - #checkIdentical(SFORB, SFORB.mkinmod) -} - -test.mkinmod.SFO_SFO <- function() -{ - SFO_SFO.diffs <- c( - parent = "d_parent = - k_parent * parent", - m1 = "d_m1 = + f_parent_to_m1 * k_parent * parent - k_m1 * m1" - ) - SFO_SFO.parms <- c("k_parent", "f_parent_to_m1", "k_m1") - SFO_SFO.map <- list(parent = c(SFO = "parent"), m1 = c(SFO = "m1")) - vars <- c("parent", "m1") - SFO_SFO.coefmat <- matrix(c("- k_parent", - "0", "f_parent_to_m1 * k_parent", "- k_m1"), nrow=2, byrow=TRUE, - dimnames=list(vars, vars)) - SFO_SFO <- list(diffs = SFO_SFO.diffs, parms = SFO_SFO.parms, - map = SFO_SFO.map, coefmat = SFO_SFO.coefmat) - class(SFO_SFO) <- "mkinmod" - SFO_SFO.mkinmod <- mkinmod( - parent = list(type = "SFO", to = "m1"), - m1 = list(type = "SFO", sink=TRUE) - ) - checkIdentical(SFO_SFO, SFO_SFO.mkinmod) -} - -test.mkinmod.SFO_SFO2 <- function() -{ - SFO_SFO2.diffs <- c( - parent = "d_parent = - k_parent * parent", - m1 = "d_m1 = + f_parent_to_m1 * k_parent * parent - k_m1 * m1", - m2 = "d_m2 = + f_parent_to_m2 * k_parent * parent - k_m2 * m2" - ) - SFO_SFO2.parms <- c("k_parent", "f_parent_to_m1", "f_parent_to_m2", "k_m1", "k_m2") - SFO_SFO2.map <- list(parent = c(SFO = "parent"), m1 = c(SFO = "m1"), m2 = c(SFO = "m2")) - vars <- c("parent", "m1", "m2") - SFO_SFO2.coefmat <- matrix( - c("- k_parent", "0", "0", - "f_parent_to_m1 * k_parent", "- k_m1", "0", - "f_parent_to_m2 * k_parent", "0", "- k_m2"), nrow=3, byrow=TRUE, - dimnames=list(vars, vars)) - SFO_SFO2 <- list(diffs = SFO_SFO2.diffs, parms = SFO_SFO2.parms, - map = SFO_SFO2.map, coefmat = SFO_SFO2.coefmat) - class(SFO_SFO2) <- "mkinmod" - SFO_SFO2.mkinmod <- mkinmod( - parent = list(type = "SFO", to = c("m1", "m2"), sink=TRUE), - m1 = list(type = "SFO", sink=TRUE), - m2 = list(type = "SFO", sink=TRUE) - ) - checkIdentical(SFO_SFO2, SFO_SFO2.mkinmod) -} - -test.mkinmod.FOMC_SFO2 <- function() -{ - FOMC_SFO2.diffs <- c( - parent = "d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent", - m1 = "d_m1 = + f_parent_to_m1 * (alpha/beta) * ((time/beta) + 1)^-1 * parent - k_m1 * m1", - m2 = "d_m2 = + f_parent_to_m2 * (alpha/beta) * ((time/beta) + 1)^-1 * parent - k_m2 * m2" - ) - FOMC_SFO2.parms <- c("alpha", "beta", "f_parent_to_m1", "f_parent_to_m2", "k_m1", "k_m2") - FOMC_SFO2.map <- list(parent = c(FOMC = "parent"), - m1 = c(SFO = "m1"), - m2 = c(SFO = "m2")) - FOMC_SFO2 <- list(diffs = FOMC_SFO2.diffs, parms = FOMC_SFO2.parms, - map = FOMC_SFO2.map) - class(FOMC_SFO2) <- "mkinmod" - FOMC_SFO2.mkinmod <- mkinmod( - parent = list(type = "FOMC", to = c("m1", "m2"), sink=TRUE), - m1 = list(type = "SFO"), - m2 = list(type = "SFO") - ) - checkIdentical(FOMC_SFO2, FOMC_SFO2.mkinmod) -} diff --git a/man/FOCUS_2006_DFOP_ref_A_to_B.Rd b/man/FOCUS_2006_DFOP_ref_A_to_B.Rd new file mode 100644 index 0000000..88bd4ac --- /dev/null +++ b/man/FOCUS_2006_DFOP_ref_A_to_B.Rd @@ -0,0 +1,39 @@ +\name{FOCUS_2006_DFOP_ref_A_to_B} +\Rdversion{1.1} +\alias{FOCUS_2006_DFOP_ref_A_to_B} +\docType{data} +\title{ +Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) +} +\description{ +A table with the fitted parameters and the resulting DT50 and DT90 values +generated with different software packages. Taken directly from FOCUS (2006). +The results from fitting the data with the Topfit software was removed, as +the initial concentration of the parent compound was fixed to a value of 100 +in this fit. +} +\usage{data(FOCUS_2006_DFOP_ref_A_to_B)} +\format{ + A data frame containing the following variables. + \describe{ + \item{\code{package}}{a factor giving the name of the software package} + \item{\code{M0}}{The fitted initial concentration of the parent compound} + \item{\code{f}}{The fitted f parameter} + \item{\code{k1}}{The fitted k1 parameter} + \item{\code{k2}}{The fitted k2 parameter} + \item{\code{DT50}}{The resulting half-life of the parent compound} + \item{\code{DT90}}{The resulting DT90 of the parent compound} + \item{\code{dataset}}{The FOCUS dataset that was used} + } +} +\source{ + 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://focus.jrc.ec.europa.eu/dk} +} +\examples{ +data(FOCUS_2006_DFOP_ref_A_to_B) +} +\keyword{datasets} diff --git a/man/FOCUS_2006_FOMC_ref_A_to_F.Rd b/man/FOCUS_2006_FOMC_ref_A_to_F.Rd new file mode 100644 index 0000000..2fcc2db --- /dev/null +++ b/man/FOCUS_2006_FOMC_ref_A_to_F.Rd @@ -0,0 +1,38 @@ +\name{FOCUS_2006_FOMC_ref_A_to_F} +\Rdversion{1.1} +\alias{FOCUS_2006_FOMC_ref_A_to_F} +\docType{data} +\title{ +Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) +} +\description{ +A table with the fitted parameters and the resulting DT50 and DT90 values +generated with different software packages. Taken directly from FOCUS (2006). +The results from fitting the data with the Topfit software was removed, as +the initial concentration of the parent compound was fixed to a value of 100 +in this fit. +} +\usage{data(FOCUS_2006_FOMC_ref_A_to_F)} +\format{ + A data frame containing the following variables. + \describe{ + \item{\code{package}}{a factor giving the name of the software package} + \item{\code{M0}}{The fitted initial concentration of the parent compound} + \item{\code{alpha}}{The fitted alpha parameter} + \item{\code{beta}}{The fitted beta parameter} + \item{\code{DT50}}{The resulting half-life of the parent compound} + \item{\code{DT90}}{The resulting DT90 of the parent compound} + \item{\code{dataset}}{The FOCUS dataset that was used} + } +} +\source{ + 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://focus.jrc.ec.europa.eu/dk} +} +\examples{ +data(FOCUS_2006_FOMC_ref_A_to_F) +} +\keyword{datasets} diff --git a/man/FOCUS_2006_HS_ref_A_to_F.Rd b/man/FOCUS_2006_HS_ref_A_to_F.Rd new file mode 100644 index 0000000..6fc9993 --- /dev/null +++ b/man/FOCUS_2006_HS_ref_A_to_F.Rd @@ -0,0 +1,39 @@ +\name{FOCUS_2006_HS_ref_A_to_F} +\Rdversion{1.1} +\alias{FOCUS_2006_HS_ref_A_to_F} +\docType{data} +\title{ +Results of fitting the HS model to Datasets A to F of FOCUS (2006) +} +\description{ +A table with the fitted parameters and the resulting DT50 and DT90 values +generated with different software packages. Taken directly from FOCUS (2006). +The results from fitting the data with the Topfit software was removed, as +the initial concentration of the parent compound was fixed to a value of 100 +in this fit. +} +\usage{data(FOCUS_2006_HS_ref_A_to_F)} +\format{ + A data frame containing the following variables. + \describe{ + \item{\code{package}}{a factor giving the name of the software package} + \item{\code{M0}}{The fitted initial concentration of the parent compound} + \item{\code{tb}}{The fitted tb parameter} + \item{\code{k1}}{The fitted k1 parameter} + \item{\code{k2}}{The fitted k2 parameter} + \item{\code{DT50}}{The resulting half-life of the parent compound} + \item{\code{DT90}}{The resulting DT90 of the parent compound} + \item{\code{dataset}}{The FOCUS dataset that was used} + } +} +\source{ + 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://focus.jrc.ec.europa.eu/dk} +} +\examples{ +data(FOCUS_2006_HS_ref_A_to_F) +} +\keyword{datasets} diff --git a/man/FOCUS_2006_SFO_ref_A_to_F.Rd b/man/FOCUS_2006_SFO_ref_A_to_F.Rd new file mode 100644 index 0000000..19650ed --- /dev/null +++ b/man/FOCUS_2006_SFO_ref_A_to_F.Rd @@ -0,0 +1,37 @@ +\name{FOCUS_2006_SFO_ref_A_to_F} +\Rdversion{1.1} +\alias{FOCUS_2006_SFO_ref_A_to_F} +\docType{data} +\title{ +Results of fitting the SFO model to Datasets A to F of FOCUS (2006) +} +\description{ +A table with the fitted parameters and the resulting DT50 and DT90 values +generated with different software packages. Taken directly from FOCUS (2006). +The results from fitting the data with the Topfit software was removed, as +the initial concentration of the parent compound was fixed to a value of 100 +in this fit. +} +\usage{data(FOCUS_2006_SFO_ref_A_to_F)} +\format{ + A data frame containing the following variables. + \describe{ + \item{\code{package}}{a factor giving the name of the software package} + \item{\code{M0}}{The fitted initial concentration of the parent compound} + \item{\code{k}}{The fitted first-order degradation rate constant} + \item{\code{DT50}}{The resulting half-life of the parent compound} + \item{\code{DT90}}{The resulting DT90 of the parent compound} + \item{\code{dataset}}{The FOCUS dataset that was used} + } +} +\source{ + 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://focus.jrc.ec.europa.eu/dk} +} +\examples{ +data(FOCUS_2006_SFO_ref_A_to_F) +} +\keyword{datasets} diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index 0c8e48f..5f70dae 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -17,7 +17,8 @@ mkinfit(mkinmod, observed, solution_type = "auto", plot = FALSE, quiet = FALSE, err = NULL, weight = "none", scaleVar = FALSE, - atol = 1e-6, n.outtimes, ...) + atol = 1e-6, n.outtimes, + trace_parms, ...) } \arguments{ \item{mkinmod}{ @@ -92,6 +93,9 @@ mkinfit(mkinmod, observed, the numerical solver if that is used (see \code{solution} argument. The default value is 100. } + \item{trace_parms}{ + Should a trace of the parameter values be listed? + } \item{\dots}{ Further arguments that will be passed to \code{\link{modFit}}. } @@ -101,7 +105,7 @@ mkinfit(mkinmod, observed, A summary can be obtained by \code{\link{summary.mkinfit}}. } \author{ - Johannes Ranke + Johannes Ranke } \examples{ # One parent compound, one metabolite, both single first order. diff --git a/vignettes/mkin.Rnw b/vignettes/mkin.Rnw index ee472ba..f674db7 100644 --- a/vignettes/mkin.Rnw +++ b/vignettes/mkin.Rnw @@ -147,8 +147,8 @@ on the fundamental system of the coefficient matrix, as proposed by <>= SFO.fit <- mkinfit(SFO, FOCUS_2006_C) summary(SFO.fit) -#SFORB.fit <- mkinfit(SFORB, FOCUS_2006_C) -#summary(SFORB.fit) +SFORB.fit <- mkinfit(SFORB, FOCUS_2006_C) +summary(SFORB.fit) SFO_SFO.fit <- mkinfit(SFO_SFO, FOCUS_2006_D, plot=TRUE) summary(SFO_SFO.fit, data=FALSE) SFORB_SFO.fit <- mkinfit(SFORB_SFO, FOCUS_2006_D, plot=TRUE) -- cgit v1.2.1