From 12934520d7ec3218ce1505787b6066334a24a562 Mon Sep 17 00:00:00 2001 From: jranke Date: Tue, 30 Mar 2010 19:49:44 +0000 Subject: Initial import of the kinfit package developed from 2008-07 to 2010-03 at Harlan Laboratories Ltd (former RCC Ltd). Supports fitting of parent data with the usual FOCUS kinetic models. git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/kinfit@2 edb9625f-4e0d-4859-8d74-9fd3b1da38cb --- DESCRIPTION | 11 + R/DFOP.R | 5 + R/FOMC.R | 4 + R/HS.R | 6 + R/SFO.R | 4 + R/kinerrmin.R | 21 + R/kinfit.R | 94 ++++ R/kinobject.R | 11 + R/kinobjects.R | 14 + R/kinplot.R | 66 +++ R/kinreport.R | 47 ++ R/kinresplot.R | 14 + R/kinresults.R | 74 +++ R/kinwrite.KinGUI.R | 11 + data/FOCUS_2006_A.rda | Bin 0 -> 229 bytes data/FOCUS_2006_A_SFO_ref.tex | 11 + data/FOCUS_2006_B.rda | Bin 0 -> 227 bytes data/FOCUS_2006_C.rda | Bin 0 -> 211 bytes data/FOCUS_2006_D.rda | Bin 0 -> 397 bytes data/FOCUS_2006_DFOP_ref_A_to_B.rda | Bin 0 -> 723 bytes data/FOCUS_2006_E.rda | Bin 0 -> 251 bytes data/FOCUS_2006_F.rda | Bin 0 -> 264 bytes data/FOCUS_2006_FOMC_ref_A_to_F.rda | Bin 0 -> 1266 bytes data/FOCUS_2006_HS_ref_A_to_F.rda | Bin 0 -> 1304 bytes data/FOCUS_2006_SFO_ref_A_to_F.rda | Bin 0 -> 1097 bytes inst/doc/FOCUS_2006_FOMC_F_total_ref.tex | 0 inst/doc/KinGUI/A_DFOP_report.txt | 63 +++ inst/doc/KinGUI/A_FOMC_report.txt | 61 ++ inst/doc/KinGUI/A_HS_report.txt | 63 +++ inst/doc/KinGUI/A_KinGUI.txt | 13 + inst/doc/KinGUI/A_SFO_report.txt | 59 ++ inst/doc/KinGUI/B_DFOP_report.txt | 63 +++ inst/doc/KinGUI/B_FOMC_report.txt | 61 ++ inst/doc/KinGUI/B_HS_report.txt | 63 +++ inst/doc/KinGUI/B_KinGUI.txt | 13 + inst/doc/KinGUI/B_SFO_report.txt | 59 ++ inst/doc/KinGUI/C_DFOP_report.txt | 64 +++ inst/doc/KinGUI/C_FOMC_report.txt | 62 ++ inst/doc/KinGUI/C_HS_report.txt | 64 +++ inst/doc/KinGUI/C_KinGUI.txt | 14 + inst/doc/KinGUI/C_SFO_report.txt | 60 ++ inst/doc/KinGUI/D_DFOP_report.txt | 77 +++ inst/doc/KinGUI/D_FOMC_report.txt | 75 +++ inst/doc/KinGUI/D_HS_report.txt | 77 +++ inst/doc/KinGUI/D_KinGUI.txt | 27 + inst/doc/KinGUI/D_SFO_report.txt | 73 +++ inst/doc/KinGUI/F_system_DFOP_report.txt | 64 +++ inst/doc/KinGUI/F_system_FOMC_report.txt | 62 ++ inst/doc/KinGUI/F_system_HS_report.txt | 64 +++ inst/doc/KinGUI/F_system_KinGUI.txt | 14 + inst/doc/KinGUI/F_system_SFO_report.txt | 60 ++ inst/doc/KinGUI/F_water_DFOP_report.txt | 64 +++ inst/doc/KinGUI/F_water_FOMC_report.txt | 62 ++ inst/doc/KinGUI/F_water_HS_report.txt | 64 +++ inst/doc/KinGUI/F_water_KinGUI.txt | 14 + inst/doc/KinGUI/F_water_SFO_report.txt | 60 ++ inst/doc/Rplots.pdf | 813 +++++++++++++++++++++++++++ inst/doc/header.tex | 31 + inst/doc/kinfit.Rnw | 933 +++++++++++++++++++++++++++++++ inst/doc/kinfit.pdf | Bin 0 -> 282336 bytes inst/doc/references.bib | 38 ++ inst/doc/run.bat | 5 + man/DFOP.Rd | 37 ++ man/FOCUS_2006_A.Rd | 29 + man/FOCUS_2006_B.Rd | 29 + man/FOCUS_2006_C.Rd | 30 + man/FOCUS_2006_D.Rd | 33 ++ man/FOCUS_2006_DFOP_ref_A_to_B.Rd | 43 ++ man/FOCUS_2006_E.Rd | 32 ++ man/FOCUS_2006_F.Rd | 32 ++ man/FOCUS_2006_FOMC_ref_A_to_F.Rd | 42 ++ man/FOCUS_2006_HS_ref_A_to_F.Rd | 43 ++ man/FOCUS_2006_SFO_ref_A_to_F.Rd | 41 ++ man/FOMC.Rd | 49 ++ man/HS.Rd | 35 ++ man/SFO.Rd | 30 + man/kinerrmin.Rd | 43 ++ man/kinfit.Rd | 77 +++ man/kinobject.Rd | 29 + man/kinobjects.Rd | 29 + man/kinplot.Rd | 50 ++ man/kinreport.Rd | 48 ++ man/kinresplot.Rd | 49 ++ man/kinresults.Rd | 45 ++ man/kinwrite.KinGUI.Rd | 47 ++ tests/test_FOCUS_2006_A.R | 25 + tests/test_FOCUS_2006_A.Rout.save | 79 +++ 87 files changed, 4878 insertions(+) create mode 100644 DESCRIPTION create mode 100644 R/DFOP.R create mode 100644 R/FOMC.R create mode 100644 R/HS.R create mode 100644 R/SFO.R create mode 100644 R/kinerrmin.R create mode 100644 R/kinfit.R create mode 100644 R/kinobject.R create mode 100644 R/kinobjects.R create mode 100644 R/kinplot.R create mode 100644 R/kinreport.R create mode 100644 R/kinresplot.R create mode 100644 R/kinresults.R create mode 100644 R/kinwrite.KinGUI.R create mode 100644 data/FOCUS_2006_A.rda create mode 100644 data/FOCUS_2006_A_SFO_ref.tex create mode 100644 data/FOCUS_2006_B.rda create mode 100644 data/FOCUS_2006_C.rda create mode 100644 data/FOCUS_2006_D.rda create mode 100644 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inst/doc/Rplots.pdf create mode 100644 inst/doc/header.tex create mode 100644 inst/doc/kinfit.Rnw create mode 100644 inst/doc/kinfit.pdf create mode 100644 inst/doc/references.bib create mode 100644 inst/doc/run.bat create mode 100644 man/DFOP.Rd create mode 100644 man/FOCUS_2006_A.Rd create mode 100644 man/FOCUS_2006_B.Rd create mode 100644 man/FOCUS_2006_C.Rd create mode 100644 man/FOCUS_2006_D.Rd create mode 100644 man/FOCUS_2006_DFOP_ref_A_to_B.Rd create mode 100644 man/FOCUS_2006_E.Rd create mode 100644 man/FOCUS_2006_F.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 create mode 100644 man/FOMC.Rd create mode 100644 man/HS.Rd create mode 100644 man/SFO.Rd create mode 100644 man/kinerrmin.Rd create mode 100644 man/kinfit.Rd create mode 100644 man/kinobject.Rd create mode 100644 man/kinobjects.Rd create mode 100644 man/kinplot.Rd create mode 100644 man/kinreport.Rd create mode 100644 man/kinresplot.Rd create mode 100644 man/kinresults.Rd create mode 100644 man/kinwrite.KinGUI.Rd create mode 100644 tests/test_FOCUS_2006_A.R create mode 100644 tests/test_FOCUS_2006_A.Rout.save diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000..da36b4f --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,11 @@ +Package: kinfit +Type: Package +Title: Routines for fitting kinetic models to chemical degradation data +Version: 1.0 +Date: 2009-10-05 +Author: Johannes Ranke +Maintainer: Johannes Ranke +Description: Simple calculation routines based on the FOCUS Kinetics + Report (2006) +License: GPL +LazyLoad: yes diff --git a/R/DFOP.R b/R/DFOP.R new file mode 100644 index 0000000..4cac735 --- /dev/null +++ b/R/DFOP.R @@ -0,0 +1,5 @@ +DFOP <- function(t, parent.0, k1, k2, g) +{ + parent = g * parent.0 * exp(-k1 * t) + + (1 - g) * parent.0 * exp(-k2 * t) +} diff --git a/R/FOMC.R b/R/FOMC.R new file mode 100644 index 0000000..9358bee --- /dev/null +++ b/R/FOMC.R @@ -0,0 +1,4 @@ +FOMC <- function(t, parent.0, alpha, beta) +{ + parent = parent.0 / (t/beta + 1)^alpha +} diff --git a/R/HS.R b/R/HS.R new file mode 100644 index 0000000..0755c90 --- /dev/null +++ b/R/HS.R @@ -0,0 +1,6 @@ +HS <- function(t, parent.0, k1, k2, tb) +{ + parent = ifelse(t <= tb, + parent.0 * exp(-k1 * t), + parent.0 * exp(-k1 * tb) * exp(-k2 * (t - tb))) +} diff --git a/R/SFO.R b/R/SFO.R new file mode 100644 index 0000000..a91625c --- /dev/null +++ b/R/SFO.R @@ -0,0 +1,4 @@ +SFO <- function(t, parent.0, k) +{ + parent = parent.0 * exp(-k * t) +} diff --git a/R/kinerrmin.R b/R/kinerrmin.R new file mode 100644 index 0000000..8ce30a3 --- /dev/null +++ b/R/kinerrmin.R @@ -0,0 +1,21 @@ +kinerrmin <- function(kinfits, kinmodel = "SFO", alpha = 0.05) +{ + m = kinfits[[kinmodel]] + + kindata <- data.frame(t = kinfits[[kinmodel]]$model$t, + parent = kinfits[[kinmodel]]$model$parent) + kindata.means <- aggregate(kindata, list(kindata$t), mean) + kindata.means.mean <- mean(kindata.means$parent, na.rm=TRUE) + + n.parms = length(coef(m)) + df = length(kindata.means$parent) - n.parms + kindata.means$est <- predict(m, kindata.means) + + f <- function(err) + { + (sum((kindata.means$parent - kindata.means$est)^2/((err*kindata.means.mean)^2)) - + qchisq(1 - alpha,df))^2 + } + err.min <- optimize(f, c(0.01,0.9))$minimum + return(err.min) +} diff --git a/R/kinfit.R b/R/kinfit.R new file mode 100644 index 0000000..42a6520 --- /dev/null +++ b/R/kinfit.R @@ -0,0 +1,94 @@ +kinfit <- function(kindata, kinmodels = c("SFO"), + parent.0.user = NA, + start.SFO = list(parent.0 = NA, k = NA), + start.FOMC = list(parent.0 = NA, alpha = NA, beta = NA), + start.DFOP = list(parent.0 = NA, k1 = NA, k2 = NA, g = NA), + start.HS = list(parent.0 = NA, k1 = NA, k2 = NA, tb = NA), + algorithm = "port") +{ + kindata <- subset(kindata, !is.na(kindata$parent)) + kinfits <- list() + + if (!is.na(parent.0.user)) { + start.SFO$parent.0 = parent.0.user + start.FOMC$parent.0 = parent.0.user + } + + lmlogged = lm(log(parent) ~ t, data = kindata) + + for (kinmodel in kinmodels) + { + + if (kinmodel == "SFO") { + if (is.na(start.SFO$parent.0)) { + start.SFO$parent.0 = max(kindata$parent) + } + if (is.na(start.SFO$k)) { + start.SFO$k = - coef(lmlogged)[["t"]] + } + kinfits[[kinmodel]] = try( + nls(parent ~ SFO(t, parent.0, k), + data = kindata, model = TRUE, + start = start.SFO, + algorithm = algorithm), silent=TRUE) + } + k.est = ifelse(is.na(coef(kinfits$SFO)[["k"]]), + -coef(lmlogged)[["t"]], + coef(kinfits$SFO)[["k"]]) + if (kinmodel == "FOMC") { + if (is.na(start.FOMC$parent.0)) { + start.FOMC$parent.0 = max(kindata$parent) + } + if (is.na(start.FOMC$alpha)) { + start.FOMC$alpha = 1 + } + if (is.na(start.FOMC$beta)) { + start.FOMC$beta = start.FOMC$alpha / k.est + } + kinfits[[kinmodel]] = try( + nls(parent ~ FOMC(t, parent.0, alpha, beta), + data = kindata, model = TRUE, + start = start.FOMC, + algorithm = algorithm), silent=TRUE) + } + if (kinmodel == "DFOP") { + if (is.na(start.DFOP$parent.0)) { + start.DFOP$parent.0 = max(kindata$parent) + } + if (is.na(start.DFOP$k1)) { + start.DFOP$k1 = k.est * 2 + } + if (is.na(start.DFOP$k2)) { + start.DFOP$k2 = k.est / 2 + } + if (is.na(start.DFOP$g)) { + start.DFOP$g = 0.5 + } + kinfits[[kinmodel]] = try( + nls(parent ~ DFOP(t, parent.0, k1, k2, g), + data = kindata, model = TRUE, + start = start.DFOP, + algorithm = algorithm), silent=TRUE) + } + if (kinmodel == "HS") { + if (is.na(start.HS$parent.0)) { + start.HS$parent.0 = max(kindata$parent) + } + if (is.na(start.HS$k1)) { + start.HS$k1 = k.est + } + if (is.na(start.HS$k2)) { + start.HS$k2 = k.est / 10 + } + if (is.na(start.HS$tb)) { + start.HS$tb = 0.05 * max(kindata$t) + } + kinfits[[kinmodel]] = try( + nls(parent ~ HS(t, parent.0, k1, k2, tb), + data = kindata, model = TRUE, + start = start.HS, + algorithm = algorithm), silent=TRUE) + } + } + return(kinfits) +} diff --git a/R/kinobject.R b/R/kinobject.R new file mode 100644 index 0000000..de6f6af --- /dev/null +++ b/R/kinobject.R @@ -0,0 +1,11 @@ +kinobject <- function(parent, type, system, + layers = NA, sampling_times = NA) +{ + kinobject <- list(parent = parent, + type = type, system = system) + if (!is.na(layers[1])) kinobject$layers = layers + if (!is.na(sampling_times[1])) { + kinobject$sampling_times = layers + } + return(kinobject) +} diff --git a/R/kinobjects.R b/R/kinobjects.R new file mode 100644 index 0000000..a767cea --- /dev/null +++ b/R/kinobjects.R @@ -0,0 +1,14 @@ +kinobjects<- function(parent, type, systems, + layers = NA, sampling_times = NA) +{ + kinobjects <- list() + for (system in systems) { + kinobjects[[system]] <- kinobject(parent = parent, + type = type, system = system) + if (!is.na(layers[1])) kinobjects[[system]]$layers = layers + if (!is.na(sampling_times[1])) { + kinobjects[[system]]$sampling_times = layers + } + } + return(kinobjects) +} diff --git a/R/kinplot.R b/R/kinplot.R new file mode 100644 index 0000000..ace1270 --- /dev/null +++ b/R/kinplot.R @@ -0,0 +1,66 @@ +kinplot <- function(kinobject, + xlab = "Time [days]", ylab = "Parent [% of applied radioactivity]", + ylim = c("auto", "auto"), + lpos = "topright") +{ + kindata <- na.omit(kinobject$data) + kinfits <- kinobject$fits + if (ylim[1] == "auto") ylim[1] <- 0 + if (ylim[2] == "auto") ylim[2] <- max(kindata$parent) + ylim <- as.numeric(ylim) + + plot(kindata$t, kindata$parent, + xlab = xlab, + ylab = ylab, + ylim = ylim + ) + n.m <- length(kinfits) + colors <- ltys <- 1:n.m + names(colors) <- names(ltys) <- names(kinfits) + ltext <- paste(kinobject$parent, "measured") + for (kinmodel in names(kinfits)) + { + m = kinfits[[kinmodel]] + if(class(m) == "nls") { + switch(kinmodel, + SFO = curve(SFO(x, + coef(m)[["parent.0"]], + coef(m)[["k"]]), + from = min(kindata$t), to = max(kindata$t), add=TRUE, + col = colors[[kinmodel]], + lty = ltys[[kinmodel]]), + FOMC = curve(FOMC(x, + coef(m)[["parent.0"]], + coef(m)[["alpha"]], + coef(m)[["beta"]]), + from = min(kindata$t), to = max(kindata$t), add=TRUE, + col = colors[[kinmodel]], + lty = ltys[[kinmodel]]), + HS = curve(HS(x, + coef(m)[["parent.0"]], + coef(m)[["k1"]], + coef(m)[["k2"]], + coef(m)[["tb"]]), + from = min(kindata$t), to = max(kindata$t), add=TRUE, + col = colors[[kinmodel]], + lty = ltys[[kinmodel]]), + DFOP = curve(DFOP(x, + coef(m)[["parent.0"]], + coef(m)[["k1"]], + coef(m)[["k2"]], + coef(m)[["g"]]), + from = min(kindata$t), to = max(kindata$t), add=TRUE, + col = colors[[kinmodel]], + lty = ltys[[kinmodel]])) + ltext <- c(ltext, paste("Fitted", kinmodel, "model")) + } else { + ltext <- c(ltext, paste(kinmodel, "model failed")) + ltys[[kinmodel]] <- NA + } + } + legend(lpos, bty="n", inset = 0.05, + legend = ltext, + pch = c(1, rep(NA, n.m)), + lty = c(NA, ltys), + col = c(1, colors)) +} diff --git a/R/kinreport.R b/R/kinreport.R new file mode 100644 index 0000000..4156803 --- /dev/null +++ b/R/kinreport.R @@ -0,0 +1,47 @@ +kinreport <- function(kinobject, file = NA, vcov = FALSE, endpoint.digits = 1) +{ + if (!is.na(file)) { + sink(file, split=TRUE) + } + + cat("Parent compound: ", kinobject$parent, "\n") + if (!is.null(kinobject$label)) cat("Label position:\t\t", kinobject$label, "\n") + cat("Study type: ", kinobject$type, "\n") + cat("System: ", kinobject$system, "\n") + if (!is.null(kinobject$source)) { + cat("Source: ", kinobject$source, "\n") + } + cat("\n") + fit.names <- names(kinobject$fits) + for (kinmodel in fit.names) + { + m <- kinobject$fits[[kinmodel]] + if (!(class(m) == "try-error")) { + cat("\n\n---\n") + cat("Nonlinear least squares fit of the", kinmodel, "model\n\n") + cat("Parameter estimation:\t") + s <- summary(m) + df <- s$df[2] + p <- 1 - pt(s$parameters[,3], df = df) + parms <- cbind(s$parameters[,c(1,2,3)], "Pr(>t)" = p) + cat("\n") + print(parms, digits=3) + cat("\n") + if(vcov) + { + cat("Variance-covariance matrix:\n") + print(vcov(m)) + cat("\n") + } + cat("Chi2 error estimation:\t", + round(100 * kinobject$results$stats[kinmodel, "err.min"], digits=2), + " %\n", sep="") + cat("\n") + } + } + cat("\n\n---\n") + cat("Endpoint estimates\n\n") + print(round(kinobject$results$results, digits=endpoint.digits)) + + if (!is.na(file)) sink() +} diff --git a/R/kinresplot.R b/R/kinresplot.R new file mode 100644 index 0000000..be0a85d --- /dev/null +++ b/R/kinresplot.R @@ -0,0 +1,14 @@ +kinresplot <- function(kinobject, kinmodel, + xlab = "Time [days]", ylab = "Residual [% of applied radioactivity]", + maxabs = "auto") +{ + m <- kinobject$fits[[kinmodel]] + t <- m$model$t + residuals <- residuals(m) + if (maxabs == "auto") maxabs = max(abs(residuals)) + plot(t, residuals, + xlab = xlab, + ylab = ylab, + ylim = c( -1.2 * maxabs, 1.2 * maxabs)) + title(paste("Residuals of", kinmodel, "fit"), font.main = 1) +} diff --git a/R/kinresults.R b/R/kinresults.R new file mode 100644 index 0000000..6bbff28 --- /dev/null +++ b/R/kinresults.R @@ -0,0 +1,74 @@ +kinresults <- function(kinfits, alpha = 0.05, SFORB=TRUE) +{ + kindata <- data.frame(t = kinfits[[1]]$model$t, parent = kinfits[[1]]$model$parent) + kindata.means <- aggregate(kindata, list(kindata$t), mean) + kindata.means.mean <- mean(kindata.means$parent, na.rm=TRUE) + n.times <- length(kindata.means$parent) + parms <- list() + df <- err.min <- RSS <- vector() + DT50 <- DT90 <- vector() + f <- list() + for (kinmodel in names(kinfits)) + { + m = kinfits[[kinmodel]] + if(class(m) == "nls") { + kindata.means$est <- predict(m, kindata.means) + parms[[kinmodel]] <- switch(kinmodel, + SFO = list(parent.0 = coef(m)[["parent.0"]], + k = coef(m)[["k"]]), + FOMC = list(parent.0 = coef(m)[["parent.0"]], + alpha = coef(m)[["alpha"]], + beta = coef(m)[["beta"]]), + HS = list(parent.0 = coef(m)[["parent.0"]], + k1 = coef(m)[["k1"]], + k2 = coef(m)[["k2"]], + tb = coef(m)[["tb"]]), + DFOP = list(parent.0 = coef(m)[["parent.0"]], + k1 = coef(m)[["k1"]], + k2 = coef(m)[["k2"]], + g = coef(m)[["g"]])) + if(kinmodel == "DFOP" & SFORB) { + k1 = coef(m)[["k1"]] + k2 = coef(m)[["k2"]] + g = coef(m)[["g"]] + parms[["SFORB"]] = + list(parent.0 = coef(m)[["parent.0"]], + k1out = g * k1 + (1 - g) * k2, + k21 = k1 * k2 / (g * k1 + (1 - g) * k2), + k12 = (g * (1 - g) * (k1 - k2)^2) / (g * k1 + (1 - g) * k2)) + } + n.parms = length(coef(m)) + f[[kinmodel]] = switch(kinmodel, + HS = function(t, x) { + (HS(t, coef(m)[["parent.0"]], + coef(m)[["k1"]], coef(m)[["k2"]], coef(m)[["tb"]]) - + (1 - x/100) * coef(m)[["parent.0"]])^2 + }, + DFOP = function(t, x) { + (DFOP(t, coef(m)[["parent.0"]], + coef(m)[["k1"]], coef(m)[["k2"]], coef(m)[["g"]]) - + (1 - x/100) * coef(m)[["parent.0"]])^2 + } + ) + coef(m) + + df[[kinmodel]] = n.times - n.parms + RSS[[kinmodel]] = sum(summary(m)$residuals^2) + DT50[[kinmodel]] = switch(kinmodel, + SFO = log(2)/coef(m)[["k"]], + FOMC = coef(m)[["beta"]] * (2^(1/coef(m)[["alpha"]]) - 1), + HS = optimize(f[[kinmodel]], c(0, max(kindata$t)), x=50)$minimum, + DFOP = optimize(f[[kinmodel]], c(0, max(kindata$t)), x=50)$minimum) + DT90[[kinmodel]] = switch(kinmodel, + SFO = log(10)/coef(m)[["k"]], + FOMC = coef(m)[["beta"]] * (10^(1/coef(m)[["alpha"]]) - 1), + HS = optimize(f[[kinmodel]], c(0, max(kindata$t)), x=90)$minimum, + DFOP = optimize(f[[kinmodel]], c(0, max(kindata$t)), x=90)$minimum) + err.min[[kinmodel]] <- kinerrmin(kinfits, kinmodel) + } + } + stats <- data.frame(n.times = n.times, df = df, mean.means = kindata.means.mean, + RSS = RSS, err.min = err.min) + results <- data.frame(DT50 = DT50, DT90 = DT90) + list(parms = parms, stats = stats, results = results) +} diff --git a/R/kinwrite.KinGUI.R b/R/kinwrite.KinGUI.R new file mode 100644 index 0000000..bf94f49 --- /dev/null +++ b/R/kinwrite.KinGUI.R @@ -0,0 +1,11 @@ +kinwrite.KinGUI <- function(kinobject, file, comment=NA) +{ + sink(file) + cat("Version:\t1.1\n") + cat("Project:\t", kinobject$parent, "\n", sep = "") + cat("Testsystem:\t", kinobject$type, "\n", sep = "") + cat("Comment:\t", comment, "\n", sep = "") + write.table(kinobject$data, sep = "\t", na = "NaN", + quote = FALSE, row.names = FALSE) + sink() +} diff --git a/data/FOCUS_2006_A.rda b/data/FOCUS_2006_A.rda new file mode 100644 index 0000000..c9498f6 Binary files /dev/null and b/data/FOCUS_2006_A.rda differ diff --git a/data/FOCUS_2006_A_SFO_ref.tex b/data/FOCUS_2006_A_SFO_ref.tex new file mode 100644 index 0000000..a63cf65 --- /dev/null +++ b/data/FOCUS_2006_A_SFO_ref.tex @@ -0,0 +1,11 @@ +ACSL & 109.20 & 0.0372 & 18.63 & 61.90 & A \\ +Excel & 109.15 & 0.0372 & 18.62 & 61.87 & A \\ +Kinetica & 109.11 & 0.0371 & 18.66 & 62.00 & A \\ +Madonna & 109.20 & 0.0372 & 18.63 & 61.90 & A \\ +Mathematica & 109.15 & 0.0372 & 18.62 & 61.87 & A \\ +MatLab & 109.15 & 0.0372 & 18.63 & 61.87 & A \\ +ModelMaker & 109.10 & 0.0371 & 18.68 & 62.06 & A \\ +ModelManager & 109.15 & 0.0372 & 18.62 & 61.86 & A \\ +PRISM & 109.20 & 0.0372 & 18.63 & 61.90 & A \\ +Statistica & 109.15 & 0.0372 & 18.63 & 61.90 & A \\ +Tablecurve & 109.15 & 0.0372 & 18.62 & 61.87 & A \\ diff --git a/data/FOCUS_2006_B.rda b/data/FOCUS_2006_B.rda new file mode 100644 index 0000000..79a475a Binary files /dev/null and b/data/FOCUS_2006_B.rda differ diff --git a/data/FOCUS_2006_C.rda b/data/FOCUS_2006_C.rda new file mode 100644 index 0000000..1344bf3 Binary files /dev/null and b/data/FOCUS_2006_C.rda differ diff --git a/data/FOCUS_2006_D.rda b/data/FOCUS_2006_D.rda new file mode 100644 index 0000000..c0fbebd Binary files /dev/null and b/data/FOCUS_2006_D.rda differ 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_E.rda b/data/FOCUS_2006_E.rda new file mode 100644 index 0000000..e90baed Binary files /dev/null and b/data/FOCUS_2006_E.rda differ diff --git a/data/FOCUS_2006_F.rda b/data/FOCUS_2006_F.rda new file mode 100644 index 0000000..be28c57 Binary files /dev/null and b/data/FOCUS_2006_F.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..c0ff69d 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..b50a5fc 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/doc/FOCUS_2006_FOMC_F_total_ref.tex b/inst/doc/FOCUS_2006_FOMC_F_total_ref.tex new file mode 100644 index 0000000..e69de29 diff --git a/inst/doc/KinGUI/A_DFOP_report.txt b/inst/doc/KinGUI/A_DFOP_report.txt new file mode 100644 index 0000000..b887a46 --- /dev/null +++ b/inst/doc/KinGUI/A_DFOP_report.txt @@ -0,0 +1,63 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\A_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_k1: 0.1000 0.0000 Inf + Parent_k2: 0.0100 0.0000 Inf + Parent_g: 0.5000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 9.6600 NaN + Kinetic Model: dfop sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_k1 0.0373 185.8206 0.4999 + Parent_k2 0.0372 160.9856 0.4999 + Parent_g 0.4780 >1000.0000 0.5000 + Parent_FFS 1.0000 + Parent_M(0) 109.2019 6.5416 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 18.6130 NaN + DT90: 61.8309 NaN + Kinetic model: dfop sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 101.2400 109.2019 -7.9619 NaN 0.0000 NaN + 3.0 99.2700 97.6587 1.6113 NaN 11.5432 NaN + 7.0 90.1100 84.1431 5.9669 NaN 25.0589 NaN + 14.0 72.1900 64.8345 7.3555 NaN 44.3674 NaN + 30.0 29.7100 35.7303 -6.0203 NaN 73.4716 NaN + 62.0 5.9800 10.8517 -4.8717 NaN 98.3502 NaN + 90.0 1.5400 3.8252 -2.2852 NaN 105.3768 NaN + 118.0 0.3900 1.3483 -0.9583 NaN 107.8536 NaN + diff --git a/inst/doc/KinGUI/A_FOMC_report.txt b/inst/doc/KinGUI/A_FOMC_report.txt new file mode 100644 index 0000000..dbd9182 --- /dev/null +++ b/inst/doc/KinGUI/A_FOMC_report.txt @@ -0,0 +1,61 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\A_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_alpha: 1.0000 0.0000 Inf + Parent_beta: 10.0000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 9.3116 NaN + Kinetic Model: fomc sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_alpha 28.4585 227.8602 0.4527 + Parent_beta 746.2785 >1000.0000 0.4539 + Parent_FFS 1.0000 + Parent_M(0) 109.4378 5.5762 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 18.3999 NaN + DT90: 62.8917 NaN + Kinetic model: fomc sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 101.2400 109.4378 -8.1978 NaN 0.0000 NaN + 3.0 99.2700 97.6300 1.6400 NaN 11.8079 NaN + 7.0 90.1100 83.9032 6.2068 NaN 25.5346 NaN + 14.0 72.1900 64.4848 7.7052 NaN 44.9531 NaN + 30.0 29.7100 35.6496 -5.9396 NaN 73.7882 NaN + 62.0 5.9800 11.2926 -5.3126 NaN 98.1452 NaN + 90.0 1.5400 4.2845 -2.7445 NaN 105.1534 NaN + 118.0 0.3900 1.6783 -1.2883 NaN 107.7596 NaN + diff --git a/inst/doc/KinGUI/A_HS_report.txt b/inst/doc/KinGUI/A_HS_report.txt new file mode 100644 index 0000000..00c5fef --- /dev/null +++ b/inst/doc/KinGUI/A_HS_report.txt @@ -0,0 +1,63 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\A_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_k1: 0.1000 0.0000 Inf + Parent_k2: 0.0100 0.0000 Inf + Parent_tb: 3.0000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 4.1106 NaN + Kinetic Model: hs sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_k1 0.0057 0.0149 0.3610 + Parent_k2 0.0462 0.0037 1.2e-004 + Parent_tb 5.8616 2.3515 0.0336 + Parent_FFS 1.0000 + Parent_M(0) 101.1190 3.1688 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 20.1455 NaN + DT90: 54.9884 NaN + Kinetic model: hs sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 101.2400 101.1190 0.1210 NaN 0.0000 NaN + 3.0 99.2700 99.4072 -0.1372 NaN 1.7118 NaN + 7.0 90.1100 92.7915 -2.6815 NaN 8.3275 NaN + 14.0 72.1900 67.1559 5.0341 NaN 33.9631 NaN + 30.0 29.7100 32.0712 -2.3612 NaN 69.0478 NaN + 62.0 5.9800 7.3144 -1.3344 NaN 93.8047 NaN + 90.0 1.5400 2.0067 -0.4667 NaN 99.1123 NaN + 118.0 0.3900 0.5505 -0.1605 NaN 100.5685 NaN + diff --git a/inst/doc/KinGUI/A_KinGUI.txt b/inst/doc/KinGUI/A_KinGUI.txt new file mode 100644 index 0000000..419b0dc --- /dev/null +++ b/inst/doc/KinGUI/A_KinGUI.txt @@ -0,0 +1,13 @@ +Version: 1.1 +Project: +Testsystem: +Comment: NA +t parent +0 101.24 +3 99.27 +7 90.11 +14 72.19 +30 29.71 +62 5.98 +90 1.54 +118 0.39 diff --git a/inst/doc/KinGUI/A_SFO_report.txt b/inst/doc/KinGUI/A_SFO_report.txt new file mode 100644 index 0000000..8ee2968 --- /dev/null +++ b/inst/doc/KinGUI/A_SFO_report.txt @@ -0,0 +1,59 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\A_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_k: 0.1000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 8.3852 NaN + Kinetic Model: sfo sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_k 0.0372 0.0043 6.5e-005 + Parent_FFS 1.0000 + Parent_M(0) 109.1513 4.3906 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 18.6257 NaN + DT90: 61.8733 NaN + Kinetic model: sfo sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 101.2400 109.1513 -7.9113 NaN 0.0000 NaN + 3.0 99.2700 97.6209 1.6491 NaN 11.5304 NaN + 7.0 90.1100 84.1191 5.9909 NaN 25.0322 NaN + 14.0 72.1900 64.8276 7.3624 NaN 44.3237 NaN + 30.0 29.7100 35.7411 -6.0311 NaN 73.4102 NaN + 62.0 5.9800 10.8638 -4.8838 NaN 98.2875 NaN + 90.0 1.5400 3.8322 -2.2922 NaN 105.3191 NaN + 118.0 0.3900 1.3518 -0.9618 NaN 107.7995 NaN + diff --git a/inst/doc/KinGUI/B_DFOP_report.txt b/inst/doc/KinGUI/B_DFOP_report.txt new file mode 100644 index 0000000..0ee160b --- /dev/null +++ b/inst/doc/KinGUI/B_DFOP_report.txt @@ -0,0 +1,63 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\B_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_k1: 0.1000 0.0000 Inf + Parent_k2: 0.0100 0.0000 Inf + Parent_g: 0.5000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 4.9562 NaN + Kinetic Model: dfop sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_k1 0.1045 0.2272 0.3347 + Parent_k2 0.0594 0.1224 0.3266 + Parent_g 0.5024 3.6431 0.4485 + Parent_FFS 1.0000 + Parent_M(0) 99.6663 2.5554 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 8.6800 NaN + DT90: 30.8040 NaN + Kinetic model: dfop sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 98.6200 99.6663 -1.0463 NaN 0.0000 NaN + 3.0 81.4300 78.0971 3.3329 NaN 21.5692 NaN + 7.0 53.1800 56.8198 -3.6398 NaN 42.8465 NaN + 14.0 34.8900 33.1902 1.6998 NaN 66.4761 NaN + 30.0 10.0900 10.5315 -0.4415 NaN 89.1348 NaN + 62.0 1.5000 1.3268 0.1732 NaN 98.3395 NaN + 90.0 0.3300 0.2412 0.0888 NaN 99.4251 NaN + 118.0 0.0800 0.0452 0.0348 NaN 99.6211 NaN + diff --git a/inst/doc/KinGUI/B_FOMC_report.txt b/inst/doc/KinGUI/B_FOMC_report.txt new file mode 100644 index 0000000..1a1db57 --- /dev/null +++ b/inst/doc/KinGUI/B_FOMC_report.txt @@ -0,0 +1,61 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\B_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_alpha: 1.0000 0.0000 Inf + Parent_beta: 10.0000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 4.6641 NaN + Kinetic Model: fomc sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_alpha 38.9958 202.8246 0.4276 + Parent_beta 491.1490 >1000.0000 0.4287 + Parent_FFS 1.0000 + Parent_M(0) 99.3410 2.2382 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 8.8082 NaN + DT90: 29.8742 NaN + Kinetic model: fomc sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 98.6200 99.3410 -0.7210 NaN 0.0000 NaN + 3.0 81.4300 78.3426 3.0874 NaN 20.9984 NaN + 7.0 53.1800 57.2085 -4.0285 NaN 42.1325 NaN + 14.0 34.8900 33.1999 1.6901 NaN 66.1411 NaN + 30.0 10.0900 9.8410 0.2490 NaN 89.5000 NaN + 62.0 1.5000 0.9634 0.5366 NaN 98.3776 NaN + 90.0 0.3300 0.1405 0.1895 NaN 99.2005 NaN + 118.0 0.0800 0.0224 0.0576 NaN 99.3186 NaN + diff --git a/inst/doc/KinGUI/B_HS_report.txt b/inst/doc/KinGUI/B_HS_report.txt new file mode 100644 index 0000000..18bb818 --- /dev/null +++ b/inst/doc/KinGUI/B_HS_report.txt @@ -0,0 +1,63 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\B_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_k1: 0.1000 0.0000 Inf + Parent_k2: 0.0100 0.0000 Inf + Parent_tb: 3.0000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 4.4535 NaN + Kinetic Model: hs sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_k1 0.0840 0.0068 1.3e-004 + Parent_k2 0.0704 0.0136 0.0033 + Parent_tb 7.0665 7.2051 0.1911 + Parent_FFS 1.0000 + Parent_M(0) 100.2115 2.2443 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 8.4848 NaN + DT90: 31.3565 NaN + Kinetic model: hs sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 98.6200 100.2115 -1.5915 NaN 0.0000 NaN + 3.0 81.4300 77.8968 3.5332 NaN 22.3146 NaN + 7.0 53.1800 55.6745 -2.4945 NaN 44.5370 NaN + 14.0 34.8900 33.9891 0.9009 NaN 66.2224 NaN + 30.0 10.0900 11.0248 -0.9348 NaN 89.1866 NaN + 62.0 1.5000 1.1599 0.3401 NaN 99.0515 NaN + 90.0 0.3300 0.1617 0.1683 NaN 100.0497 NaN + 118.0 0.0800 0.0225 0.0575 NaN 100.1889 NaN + diff --git a/inst/doc/KinGUI/B_KinGUI.txt b/inst/doc/KinGUI/B_KinGUI.txt new file mode 100644 index 0000000..f48e076 --- /dev/null +++ b/inst/doc/KinGUI/B_KinGUI.txt @@ -0,0 +1,13 @@ +Version: 1.1 +Project: +Testsystem: +Comment: NA +t parent +0 98.62 +3 81.43 +7 53.18 +14 34.89 +30 10.09 +62 1.5 +90 0.33 +118 0.08 diff --git a/inst/doc/KinGUI/B_SFO_report.txt b/inst/doc/KinGUI/B_SFO_report.txt new file mode 100644 index 0000000..d3856fe --- /dev/null +++ b/inst/doc/KinGUI/B_SFO_report.txt @@ -0,0 +1,59 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\B_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_k: 0.1000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 4.4562 NaN + Kinetic Model: sfo sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_k 0.0782 0.0039 4.7e-007 + Parent_FFS 1.0000 + Parent_M(0) 99.1740 1.9239 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 8.8686 NaN + DT90: 29.4608 NaN + Kinetic model: sfo sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 98.6200 99.1740 -0.5540 NaN 0.0000 NaN + 3.0 81.4300 78.4455 2.9845 NaN 20.7286 NaN + 7.0 53.1800 57.3845 -4.2045 NaN 41.7896 NaN + 14.0 34.8900 33.2040 1.6860 NaN 65.9700 NaN + 30.0 10.0900 9.5082 0.5818 NaN 89.6659 NaN + 62.0 1.5000 0.7797 0.7203 NaN 98.3944 NaN + 90.0 0.3300 0.0874 0.2426 NaN 99.0866 NaN + 118.0 0.0800 0.0098 0.0702 NaN 99.1642 NaN + diff --git a/inst/doc/KinGUI/C_DFOP_report.txt b/inst/doc/KinGUI/C_DFOP_report.txt new file mode 100644 index 0000000..65b8f29 --- /dev/null +++ b/inst/doc/KinGUI/C_DFOP_report.txt @@ -0,0 +1,64 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\C_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_k1: 0.1000 0.0000 Inf + Parent_k2: 0.0100 0.0000 Inf + Parent_g: 0.5000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 2.6613 NaN + Kinetic Model: dfop sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_k1 0.4596 0.0204 1.6e-006 + Parent_k2 0.0179 0.0030 0.0010 + Parent_g 0.8539 0.0134 9.1e-009 + Parent_FFS 1.0000 + Parent_M(0) 85.0044 0.8907 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 1.8869 NaN + DT90: 21.2535 NaN + Kinetic model: dfop sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 85.1000 85.0044 0.0956 NaN 0.0000 NaN + 1.0 57.9000 58.0394 -0.1394 NaN 26.9651 NaN + 3.0 29.9000 30.0534 -0.1534 NaN 54.9510 NaN + 7.0 14.6000 13.8668 0.7332 NaN 71.1376 NaN + 14.0 9.7000 9.7875 -0.0875 NaN 75.2170 NaN + 28.0 6.6000 7.5324 -0.9324 NaN 77.4720 NaN + 63.0 4.0000 4.0324 -0.0324 NaN 80.9721 NaN + 91.0 3.9000 2.4461 1.4539 NaN 82.5583 NaN + 119.0 0.6000 1.4838 -0.8838 NaN 83.5206 NaN + diff --git a/inst/doc/KinGUI/C_FOMC_report.txt b/inst/doc/KinGUI/C_FOMC_report.txt new file mode 100644 index 0000000..3d74181 --- /dev/null +++ b/inst/doc/KinGUI/C_FOMC_report.txt @@ -0,0 +1,62 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\C_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_alpha: 1.0000 0.0000 Inf + Parent_beta: 10.0000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 6.6574 NaN + Kinetic Model: fomc sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_alpha 1.0564 0.1700 4.0e-004 + Parent_beta 1.9260 0.5402 0.0059 + Parent_FFS 1.0000 + Parent_M(0) 85.8766 2.2459 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 1.7860 NaN + DT90: 15.1052 NaN + Kinetic model: fomc sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 85.1000 85.8766 -0.7766 NaN 0.0000 NaN + 1.0 57.9000 55.2088 2.6912 NaN 30.6678 NaN + 3.0 29.9000 31.8437 -1.9437 NaN 54.0329 NaN + 7.0 14.6000 16.9940 -2.3940 NaN 68.8827 NaN + 14.0 9.7000 9.2184 0.4816 NaN 76.6582 NaN + 28.0 6.6000 4.7343 1.8657 NaN 81.1423 NaN + 63.0 4.0000 2.0889 1.9111 NaN 83.7877 NaN + 91.0 3.9000 1.4302 2.4698 NaN 84.4464 NaN + 119.0 0.6000 1.0829 -0.4829 NaN 84.7938 NaN + diff --git a/inst/doc/KinGUI/C_HS_report.txt b/inst/doc/KinGUI/C_HS_report.txt new file mode 100644 index 0000000..ca137d4 --- /dev/null +++ b/inst/doc/KinGUI/C_HS_report.txt @@ -0,0 +1,64 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\C_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_k1: 0.1000 0.0000 Inf + Parent_k2: 0.0100 0.0000 Inf + Parent_tb: 3.0000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 4.6963 NaN + Kinetic Model: hs sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_k1 0.3560 0.0185 3.5e-006 + Parent_k2 0.0227 0.0057 0.0052 + Parent_tb 5.1551 0.3719 1.8e-005 + Parent_FFS 1.0000 + Parent_M(0) 84.4829 1.5377 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 1.9472 NaN + DT90: 25.7931 NaN + Kinetic model: hs sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 85.1000 84.4829 0.6171 NaN 0.0000 NaN + 1.0 57.9000 59.1796 -1.2796 NaN 25.3034 NaN + 3.0 29.9000 29.0387 0.8613 NaN 55.4442 NaN + 7.0 14.6000 12.9316 1.6684 NaN 71.5514 NaN + 14.0 9.7000 11.0354 -1.3354 NaN 73.4476 NaN + 28.0 6.6000 8.0363 -1.4363 NaN 76.4466 NaN + 63.0 4.0000 3.6369 0.3631 NaN 80.8460 NaN + 91.0 3.9000 1.9287 1.9713 NaN 82.5542 NaN + 119.0 0.6000 1.0229 -0.4229 NaN 83.4601 NaN + diff --git a/inst/doc/KinGUI/C_KinGUI.txt b/inst/doc/KinGUI/C_KinGUI.txt new file mode 100644 index 0000000..87f3191 --- /dev/null +++ b/inst/doc/KinGUI/C_KinGUI.txt @@ -0,0 +1,14 @@ +Version: 1.1 +Project: +Testsystem: +Comment: NA +t parent +0 85.1 +1 57.9 +3 29.9 +7 14.6 +14 9.7 +28 6.6 +63 4 +91 3.9 +119 0.6 diff --git a/inst/doc/KinGUI/C_SFO_report.txt b/inst/doc/KinGUI/C_SFO_report.txt new file mode 100644 index 0000000..5e32b0b --- /dev/null +++ b/inst/doc/KinGUI/C_SFO_report.txt @@ -0,0 +1,60 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\C_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_k: 0.1000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 15.8456 NaN + Kinetic Model: sfo sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_k 0.3060 0.0459 1.4e-004 + Parent_FFS 1.0000 + Parent_M(0) 82.4894 4.7401 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 2.2651 NaN + DT90: 7.5245 NaN + Kinetic model: sfo sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 85.1000 82.4894 2.6106 NaN 0.0000 NaN + 1.0 57.9000 60.7434 -2.8434 NaN 21.7460 NaN + 3.0 29.9000 32.9383 -3.0383 NaN 49.5511 NaN + 7.0 14.6000 9.6851 4.9149 NaN 72.8043 NaN + 14.0 9.7000 1.1371 8.5629 NaN 81.3522 NaN + 28.0 6.6000 0.0157 6.5843 NaN 82.4737 NaN + 63.0 4.0000 0.0000 4.0000 NaN 82.4894 NaN + 91.0 3.9000 0.0000 3.9000 NaN 82.4894 NaN + 119.0 0.6000 0.0000 0.6000 NaN 82.4894 NaN + diff --git a/inst/doc/KinGUI/D_DFOP_report.txt b/inst/doc/KinGUI/D_DFOP_report.txt new file mode 100644 index 0000000..31ab25d --- /dev/null +++ b/inst/doc/KinGUI/D_DFOP_report.txt @@ -0,0 +1,77 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\D_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_k1: 0.1000 0.0000 Inf + Parent_k2: 0.0100 0.0000 Inf + Parent_g: 0.5000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 7.2751 NaN + Kinetic Model: dfop sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_k1 0.0982 >1000.0000 0.5000 + Parent_k2 0.0976 >1000.0000 0.5000 + Parent_g 0.5525 >1000.0000 0.5000 + Parent_FFS 1.0000 + Parent_M(0) 99.4468 2.1924 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 7.0773 NaN + DT90: 23.5106 NaN + Kinetic model: dfop sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 99.4600 99.4468 0.0132 NaN 0.0000 NaN + 0.0 102.0400 99.4468 2.5932 NaN 0.0000 NaN + 1.0 93.5000 90.1688 3.3312 NaN 9.2780 NaN + 1.0 92.5000 90.1688 2.3312 NaN 9.2780 NaN + 3.0 63.2300 74.1289 -10.8989 NaN 25.3179 NaN + 3.0 68.9900 74.1289 -5.1389 NaN 25.3179 NaN + 7.0 52.3200 50.1015 2.2185 NaN 49.3454 NaN + 7.0 55.1300 50.1015 5.0285 NaN 49.3454 NaN + 14.0 27.2700 25.2413 2.0287 NaN 74.2055 NaN + 14.0 26.6400 25.2413 1.3987 NaN 74.2055 NaN + 21.0 11.5000 12.7167 -1.2167 NaN 86.7301 NaN + 21.0 11.6400 12.7167 -1.0767 NaN 86.7301 NaN + 35.0 2.8500 3.2278 -0.3778 NaN 96.2190 NaN + 35.0 2.9100 3.2278 -0.3178 NaN 96.2190 NaN + 50.0 0.6900 0.7429 -0.0529 NaN 98.7040 NaN + 50.0 0.6300 0.7429 -0.1129 NaN 98.7040 NaN + 75.0 0.0500 0.0642 -0.0142 NaN 99.3826 NaN + 75.0 0.0600 0.0642 -0.0042 NaN 99.3826 NaN + 100.0 NaN 0.0056 NaN NaN 99.4413 NaN + 100.0 NaN 0.0056 NaN NaN 99.4413 NaN + 120.0 NaN 0.0008 NaN NaN 99.4461 NaN + 120.0 NaN 0.0008 NaN NaN 99.4461 NaN + diff --git a/inst/doc/KinGUI/D_FOMC_report.txt b/inst/doc/KinGUI/D_FOMC_report.txt new file mode 100644 index 0000000..a2a60f9 --- /dev/null +++ b/inst/doc/KinGUI/D_FOMC_report.txt @@ -0,0 +1,75 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\D_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_alpha: 1.0000 0.0000 Inf + Parent_beta: 10.0000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 6.8080 NaN + Kinetic Model: fomc sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_alpha 10.5446 13.6880 0.2265 + Parent_beta 100.3104 139.0853 0.2409 + Parent_FFS 1.0000 + Parent_M(0) 100.1958 2.1103 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 6.8154 NaN + DT90: 24.4801 NaN + Kinetic model: fomc sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 99.4600 100.1958 -0.7358 NaN 0.0000 NaN + 0.0 102.0400 100.1958 1.8442 NaN 0.0000 NaN + 1.0 93.5000 90.2449 3.2551 NaN 9.9509 NaN + 1.0 92.5000 90.2449 2.2551 NaN 9.9509 NaN + 3.0 63.2300 73.4343 -10.2043 NaN 26.7615 NaN + 3.0 68.9900 73.4343 -4.4443 NaN 26.7615 NaN + 7.0 52.3200 49.1968 3.1232 NaN 50.9990 NaN + 7.0 55.1300 49.1968 5.9332 NaN 50.9990 NaN + 14.0 27.2700 25.2669 2.0031 NaN 74.9289 NaN + 14.0 26.6400 25.2669 1.3731 NaN 74.9289 NaN + 21.0 11.5000 13.5012 -2.0012 NaN 86.6946 NaN + 21.0 11.6400 13.5012 -1.8612 NaN 86.6946 NaN + 35.0 2.8500 4.2679 -1.4179 NaN 95.9279 NaN + 35.0 2.9100 4.2679 -1.3579 NaN 95.9279 NaN + 50.0 0.6900 1.4085 -0.7185 NaN 98.7872 NaN + 50.0 0.6300 1.4085 -0.7785 NaN 98.7872 NaN + 75.0 0.0500 0.2781 -0.2281 NaN 99.9177 NaN + 75.0 0.0600 0.2781 -0.2181 NaN 99.9177 NaN + 100.0 NaN 0.0682 NaN NaN 100.1276 NaN + 100.0 NaN 0.0682 NaN NaN 100.1276 NaN + 120.0 NaN 0.0250 NaN NaN 100.1708 NaN + 120.0 NaN 0.0250 NaN NaN 100.1708 NaN + diff --git a/inst/doc/KinGUI/D_HS_report.txt b/inst/doc/KinGUI/D_HS_report.txt new file mode 100644 index 0000000..92186cd --- /dev/null +++ b/inst/doc/KinGUI/D_HS_report.txt @@ -0,0 +1,77 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\D_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_k1: 0.1000 0.0000 Inf + Parent_k2: 0.0100 0.0000 Inf + Parent_tb: 3.0000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 5.8196 NaN + Kinetic Model: hs sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_k1 0.1213 0.0130 1.1e-007 + Parent_k2 0.0879 0.0083 2.2e-008 + Parent_tb 3.0000 5.3734 0.2927 + Parent_FFS 1.0000 + Parent_M(0) 100.9303 1.9766 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 6.7461 NaN + DT90: 25.0545 NaN + Kinetic model: hs sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 99.4600 100.9303 -1.4703 NaN 0.0000 NaN + 0.0 102.0400 100.9303 1.1097 NaN 0.0000 NaN + 1.0 93.5000 89.4028 4.0972 NaN 11.5275 NaN + 1.0 92.5000 89.4028 3.0972 NaN 11.5275 NaN + 3.0 63.2300 70.1471 -6.9171 NaN 30.7832 NaN + 3.0 68.9900 70.1471 -1.1571 NaN 30.7832 NaN + 7.0 52.3200 49.3513 2.9687 NaN 51.5789 NaN + 7.0 55.1300 49.3513 5.7787 NaN 51.5789 NaN + 14.0 27.2700 26.6720 0.5980 NaN 74.2583 NaN + 14.0 26.6400 26.6720 -0.0320 NaN 74.2583 NaN + 21.0 11.5000 14.4149 -2.9149 NaN 86.5154 NaN + 21.0 11.6400 14.4149 -2.7749 NaN 86.5154 NaN + 35.0 2.8500 4.2104 -1.3604 NaN 96.7199 NaN + 35.0 2.9100 4.2104 -1.3004 NaN 96.7199 NaN + 50.0 0.6900 1.1263 -0.4363 NaN 99.8040 NaN + 50.0 0.6300 1.1263 -0.4963 NaN 99.8040 NaN + 75.0 0.0500 0.1251 -0.0751 NaN 100.8052 NaN + 75.0 0.0600 0.1251 -0.0651 NaN 100.8052 NaN + 100.0 NaN 0.0139 NaN NaN 100.9164 NaN + 100.0 NaN 0.0139 NaN NaN 100.9164 NaN + 120.0 NaN 0.0024 NaN NaN 100.9279 NaN + 120.0 NaN 0.0024 NaN NaN 100.9279 NaN + diff --git a/inst/doc/KinGUI/D_KinGUI.txt b/inst/doc/KinGUI/D_KinGUI.txt new file mode 100644 index 0000000..a79ee5e --- /dev/null +++ b/inst/doc/KinGUI/D_KinGUI.txt @@ -0,0 +1,27 @@ +Version: 1.1 +Project: +Testsystem: +Comment: NA +t parent m1 +0 99.46 0 +0 102.04 0 +1 93.5 4.84 +1 92.5 5.64 +3 63.23 12.91 +3 68.99 12.96 +7 52.32 22.97 +7 55.13 24.47 +14 27.27 41.69 +14 26.64 33.21 +21 11.5 44.37 +21 11.64 46.44 +35 2.85 41.22 +35 2.91 37.95 +50 0.69 41.19 +50 0.63 40.01 +75 0.05 40.09 +75 0.06 33.85 +100 NaN 31.04 +100 NaN 33.13 +120 NaN 25.15 +120 NaN 33.31 diff --git a/inst/doc/KinGUI/D_SFO_report.txt b/inst/doc/KinGUI/D_SFO_report.txt new file mode 100644 index 0000000..902decf --- /dev/null +++ b/inst/doc/KinGUI/D_SFO_report.txt @@ -0,0 +1,73 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\D_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_k: 0.1000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 6.4539 NaN + Kinetic Model: sfo sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_k 0.0979 0.0048 3.8e-013 + Parent_FFS 1.0000 + Parent_M(0) 99.4443 1.8316 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 7.0776 NaN + DT90: 23.5111 NaN + Kinetic model: sfo sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 99.4600 99.4443 0.0157 NaN 0.0000 NaN + 0.0 102.0400 99.4443 2.5957 NaN 0.0000 NaN + 1.0 93.5000 90.1668 3.3332 NaN 9.2775 NaN + 1.0 92.5000 90.1668 2.3332 NaN 9.2775 NaN + 3.0 63.2300 74.1277 -10.8977 NaN 25.3165 NaN + 3.0 68.9900 74.1277 -5.1377 NaN 25.3165 NaN + 7.0 52.3200 50.1013 2.2187 NaN 49.3430 NaN + 7.0 55.1300 50.1013 5.0287 NaN 49.3430 NaN + 14.0 27.2700 25.2416 2.0284 NaN 74.2026 NaN + 14.0 26.6400 25.2416 1.3984 NaN 74.2026 NaN + 21.0 11.5000 12.7171 -1.2171 NaN 86.7272 NaN + 21.0 11.6400 12.7171 -1.0771 NaN 86.7272 NaN + 35.0 2.8500 3.2279 -0.3779 NaN 96.2163 NaN + 35.0 2.9100 3.2279 -0.3179 NaN 96.2163 NaN + 50.0 0.6900 0.7429 -0.0529 NaN 98.7014 NaN + 50.0 0.6300 0.7429 -0.1129 NaN 98.7014 NaN + 75.0 0.0500 0.0642 -0.0142 NaN 99.3801 NaN + 75.0 0.0600 0.0642 -0.0042 NaN 99.3801 NaN + 100.0 NaN 0.0055 NaN NaN 99.4387 NaN + 100.0 NaN 0.0055 NaN NaN 99.4387 NaN + 120.0 NaN 0.0008 NaN NaN 99.4435 NaN + 120.0 NaN 0.0008 NaN NaN 99.4435 NaN + diff --git a/inst/doc/KinGUI/F_system_DFOP_report.txt b/inst/doc/KinGUI/F_system_DFOP_report.txt new file mode 100644 index 0000000..9ec5931 --- /dev/null +++ b/inst/doc/KinGUI/F_system_DFOP_report.txt @@ -0,0 +1,64 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\F_system_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_k1: 0.1000 0.0000 Inf + Parent_k2: 0.0100 0.0000 Inf + Parent_g: 0.5000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 14.1524 NaN + Kinetic Model: dfop sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_k1 0.0397 547.5131 0.5000 + Parent_k2 0.0396 >1000.0000 0.5000 + Parent_g 0.6827 >1000.0000 0.5000 + Parent_FFS 1.0000 + Parent_M(0) 103.7338 7.5788 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 17.4895 NaN + DT90: 58.0989 NaN + Kinetic model: dfop sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 95.6000 103.7338 -8.1338 NaN 0.0000 NaN + 3.0 91.9000 92.1051 -0.2051 NaN 11.6286 NaN + 7.0 86.5000 78.6024 7.8976 NaN 25.1314 NaN + 14.0 72.9000 59.5595 13.3405 NaN 44.1742 NaN + 28.0 29.6000 34.1966 -4.5966 NaN 69.5372 NaN + 43.0 10.0000 18.8713 -8.8713 NaN 84.8624 NaN + 56.0 6.8000 11.2732 -4.4732 NaN 92.4606 NaN + 70.0 3.5000 6.4726 -2.9726 NaN 97.2612 NaN + 100.0 4.2000 1.9711 2.2289 NaN 101.7626 NaN + diff --git a/inst/doc/KinGUI/F_system_FOMC_report.txt b/inst/doc/KinGUI/F_system_FOMC_report.txt new file mode 100644 index 0000000..9eb0651 --- /dev/null +++ b/inst/doc/KinGUI/F_system_FOMC_report.txt @@ -0,0 +1,62 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\F_system_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_alpha: 1.0000 0.0000 Inf + Parent_beta: 10.0000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 13.4533 NaN + Kinetic Model: fomc sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_alpha 53.4222 992.5119 0.4794 + Parent_beta >1000.0000 >1000.0000 0.4797 + Parent_FFS 1.0000 + Parent_M(0) 104.6197 7.0437 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 17.2240 NaN + DT90: 58.0894 NaN + Kinetic model: fomc sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 95.6000 104.6197 -9.0197 NaN 0.0000 NaN + 3.0 91.9000 92.6616 -0.7616 NaN 11.9581 NaN + 7.0 86.5000 78.8498 7.6502 NaN 25.7699 NaN + 14.0 72.9000 59.5161 13.3839 NaN 45.1036 NaN + 28.0 29.6000 34.0577 -4.4577 NaN 70.5620 NaN + 43.0 10.0000 18.8478 -8.8478 NaN 85.7719 NaN + 56.0 6.8000 11.3461 -4.5461 NaN 93.2736 NaN + 70.0 3.5000 6.6038 -3.1038 NaN 98.0159 NaN + 100.0 4.2000 2.1086 2.0914 NaN 102.5111 NaN + diff --git a/inst/doc/KinGUI/F_system_HS_report.txt b/inst/doc/KinGUI/F_system_HS_report.txt new file mode 100644 index 0000000..81546c7 --- /dev/null +++ b/inst/doc/KinGUI/F_system_HS_report.txt @@ -0,0 +1,64 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\F_system_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_k1: 0.1000 0.0000 Inf + Parent_k2: 0.0100 0.0000 Inf + Parent_tb: 3.0000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 3.2178 NaN + Kinetic Model: hs sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_k1 0.0142 0.0047 0.0151 + Parent_k2 0.0635 0.0039 8.1e-006 + Parent_tb 12.4685 1.3021 1.1e-004 + Parent_FFS 1.0000 + Parent_M(0) 95.6835 1.9092 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 20.5934 NaN + DT90: 45.9498 NaN + Kinetic model: hs sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 95.6000 95.6835 -0.0835 NaN 0.0000 NaN + 3.0 91.9000 91.6844 0.2156 NaN 3.9991 NaN + 7.0 86.5000 86.6111 -0.1111 NaN 9.0724 NaN + 14.0 72.9000 72.7042 0.1958 NaN 22.9793 NaN + 28.0 29.6000 29.8977 -0.2977 NaN 65.7858 NaN + 43.0 10.0000 11.5385 -1.5385 NaN 84.1450 NaN + 56.0 6.8000 5.0559 1.7441 NaN 90.6277 NaN + 70.0 3.5000 2.0791 1.4209 NaN 93.6044 NaN + 100.0 4.2000 0.3097 3.8903 NaN 95.3738 NaN + diff --git a/inst/doc/KinGUI/F_system_KinGUI.txt b/inst/doc/KinGUI/F_system_KinGUI.txt new file mode 100644 index 0000000..ba130e0 --- /dev/null +++ b/inst/doc/KinGUI/F_system_KinGUI.txt @@ -0,0 +1,14 @@ +Version: 1.1 +Project: +Testsystem: +Comment: NA +t parent +0 95.6 +3 91.9 +7 86.5 +14 72.9 +28 29.6 +43 10 +56 6.8 +70 3.5 +100 4.2 diff --git a/inst/doc/KinGUI/F_system_SFO_report.txt b/inst/doc/KinGUI/F_system_SFO_report.txt new file mode 100644 index 0000000..7dffe34 --- /dev/null +++ b/inst/doc/KinGUI/F_system_SFO_report.txt @@ -0,0 +1,60 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\F_system_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_k: 0.1000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 12.5386 NaN + Kinetic Model: sfo sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_k 0.0400 0.0053 6.4e-005 + Parent_FFS 1.0000 + Parent_M(0) 104.4774 5.6578 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 17.3489 NaN + DT90: 57.6318 NaN + Kinetic model: sfo sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 95.6000 104.4774 -8.8774 NaN 0.0000 NaN + 3.0 91.9000 92.6761 -0.7761 NaN 11.8013 NaN + 7.0 86.5000 78.9881 7.5119 NaN 25.4893 NaN + 14.0 72.9000 59.7174 13.1826 NaN 44.7600 NaN + 28.0 29.6000 34.1334 -4.5334 NaN 70.3440 NaN + 43.0 10.0000 18.7459 -8.7459 NaN 85.7315 NaN + 56.0 6.8000 11.1516 -4.3516 NaN 93.3258 NaN + 70.0 3.5000 6.3740 -2.8740 NaN 98.1034 NaN + 100.0 4.2000 1.9225 2.2775 NaN 102.5549 NaN + diff --git a/inst/doc/KinGUI/F_water_DFOP_report.txt b/inst/doc/KinGUI/F_water_DFOP_report.txt new file mode 100644 index 0000000..c8275d9 --- /dev/null +++ b/inst/doc/KinGUI/F_water_DFOP_report.txt @@ -0,0 +1,64 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\F_water_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_k1: 0.1000 0.0000 Inf + Parent_k2: 0.0100 0.0000 Inf + Parent_g: 0.5000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 12.1821 NaN + Kinetic Model: dfop sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_k1 0.0551 >1000.0000 0.5000 + Parent_k2 0.0551 >1000.0000 0.5000 + Parent_g 0.6959 >1000.0000 0.5000 + Parent_FFS 1.0000 + Parent_M(0) 100.5778 6.1529 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 12.5797 NaN + DT90: 41.7890 NaN + Kinetic model: dfop sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 95.6000 100.5778 -4.9778 NaN 0.0000 NaN + 3.0 84.7000 85.2536 -0.5536 NaN 15.3242 NaN + 7.0 74.6000 68.3902 6.2098 NaN 32.1876 NaN + 14.0 54.1000 46.5035 7.5965 NaN 54.0742 NaN + 28.0 13.5000 21.5015 -8.0015 NaN 79.0762 NaN + 43.0 4.3000 9.4086 -5.1086 NaN 91.1692 NaN + 56.0 2.0000 4.5966 -2.5966 NaN 95.9812 NaN + 70.0 0.5000 2.1253 -1.6253 NaN 98.4525 NaN + 100.0 0.8000 0.4069 0.3931 NaN 100.1708 NaN + diff --git a/inst/doc/KinGUI/F_water_FOMC_report.txt b/inst/doc/KinGUI/F_water_FOMC_report.txt new file mode 100644 index 0000000..6604e72 --- /dev/null +++ b/inst/doc/KinGUI/F_water_FOMC_report.txt @@ -0,0 +1,62 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\F_water_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_alpha: 1.0000 0.0000 Inf + Parent_beta: 10.0000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 11.6682 NaN + Kinetic Model: fomc sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_alpha 60.1183 907.7673 0.4747 + Parent_beta >1000.0000 >1000.0000 0.4750 + Parent_FFS 1.0000 + Parent_M(0) 100.6891 5.3413 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 12.4948 NaN + DT90: 42.0685 NaN + Kinetic model: fomc sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 95.6000 100.6891 -5.0891 NaN 0.0000 NaN + 3.0 84.7000 85.1898 -0.4898 NaN 15.4992 NaN + 7.0 74.6000 68.2194 6.3806 NaN 32.4696 NaN + 14.0 54.1000 46.3363 7.7637 NaN 54.3527 NaN + 28.0 13.5000 21.5356 -8.0356 NaN 79.1535 NaN + 43.0 4.3000 9.5778 -5.2778 NaN 91.1112 NaN + 56.0 2.0000 4.7873 -2.7873 NaN 95.9018 NaN + 70.0 0.5000 2.2886 -1.7886 NaN 98.4004 NaN + 100.0 0.8000 0.4850 0.3150 NaN 100.2041 NaN + diff --git a/inst/doc/KinGUI/F_water_HS_report.txt b/inst/doc/KinGUI/F_water_HS_report.txt new file mode 100644 index 0000000..3cda8e3 --- /dev/null +++ b/inst/doc/KinGUI/F_water_HS_report.txt @@ -0,0 +1,64 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\F_water_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_k1: 0.1000 0.0000 Inf + Parent_k2: 0.0100 0.0000 Inf + Parent_tb: 3.0000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 1.6558 NaN + Kinetic Model: hs sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_k1 0.0356 0.0022 8.3e-006 + Parent_k2 0.0955 0.0041 1.4e-006 + Parent_tb 12.8509 0.6443 2.9e-006 + Parent_FFS 1.0000 + Parent_M(0) 95.1656 0.8209 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 15.3239 NaN + DT90: 32.1824 NaN + Kinetic model: hs sink + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 95.6000 95.1656 0.4344 NaN 0.0000 NaN + 3.0 84.7000 85.5346 -0.8346 NaN 9.6310 NaN + 7.0 74.6000 74.1920 0.4080 NaN 20.9736 NaN + 14.0 54.1000 53.9934 0.1066 NaN 41.1723 NaN + 28.0 13.5000 14.1869 -0.6869 NaN 80.9788 NaN + 43.0 4.3000 3.3882 0.9118 NaN 91.7774 NaN + 56.0 2.0000 0.9794 1.0206 NaN 94.1862 NaN + 70.0 0.5000 0.2574 0.2426 NaN 94.9083 NaN + 100.0 0.8000 0.0147 0.7853 NaN 95.1510 NaN + diff --git a/inst/doc/KinGUI/F_water_KinGUI.txt b/inst/doc/KinGUI/F_water_KinGUI.txt new file mode 100644 index 0000000..bd80f86 --- /dev/null +++ b/inst/doc/KinGUI/F_water_KinGUI.txt @@ -0,0 +1,14 @@ +Version: 1.1 +Project: +Testsystem: +Comment: NA +t parent +0 95.6 +3 84.7 +7 74.6 +14 54.1 +28 13.5 +43 4.3 +56 2 +70 0.5 +100 0.8 diff --git a/inst/doc/KinGUI/F_water_SFO_report.txt b/inst/doc/KinGUI/F_water_SFO_report.txt new file mode 100644 index 0000000..9927133 --- /dev/null +++ b/inst/doc/KinGUI/F_water_SFO_report.txt @@ -0,0 +1,60 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\F_water_KinGUI.txt + +# ================================= +# Results of the kinetic evaluation +# ================================= + +# --------------------------------- +# Initial values +# --------------------------------- + Initial Value Lower Bound Upper Bound + Parent_M(0): 100.0000 0.0000 Inf + Parent_k: 0.1000 0.0000 Inf + Sink_M(0): 0.0000 0.0000 Inf + +# --------------------------------- +# Chi2 error estimation +# --------------------------------- + Parent Sink + Chi2Err%: 10.8069 NaN + Kinetic Model: sfo sink + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Parameter Estimate St.Dev Prob > t + Parent_k 0.0551 0.0059 1.7e-005 + Parent_FFS 1.0000 + Parent_M(0) 100.5476 4.3549 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 12.5846 NaN + DT90: 41.8052 NaN + Kinetic model: sfo sink + +# --------------------------------- +# Measured vs. predicted values +# 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+\usepackage{booktabs} +\usepackage{amsfonts} +\usepackage{latexsym} +\usepackage{amsmath} +\usepackage{amssymb} +\usepackage{graphicx} +\usepackage{parskip} +\usepackage[round]{natbib} +\usepackage{amstext} +\usepackage{hyperref} +\usepackage[latin1]{inputenc} + +\newcommand{\Rpackage}[1]{{\normalfont\fontseries{b}\selectfont #1}} +\newcommand{\Robject}[1]{\texttt{#1}} +\newcommand{\Rclass}[1]{\textit{#1}} +\newcommand{\Rcmd}[1]{\texttt{#1}} + +\newcommand{\RR}{\textsf{R}} + +\RequirePackage[T1]{fontenc} +\RequirePackage{graphicx,ae,fancyvrb} +\IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} +\usepackage{relsize} + +\DefineVerbatimEnvironment{Sinput}{Verbatim}{baselinestretch=1.05} +\DefineVerbatimEnvironment{Soutput}{Verbatim}{fontfamily=courier, + baselinestretch=1.05, + fontshape=it, + fontsize=\relsize{-1}} +\DefineVerbatimEnvironment{Scode}{Verbatim}{} +\newenvironment{Schunk}{}{} diff --git a/inst/doc/kinfit.Rnw b/inst/doc/kinfit.Rnw new file mode 100644 index 0000000..7a590d5 --- /dev/null +++ b/inst/doc/kinfit.Rnw @@ -0,0 +1,933 @@ +%%\VignetteIndexEntry{Routines for fitting kinetic models to chemical degradation data} +%%VignetteDepends{nls} +%%\usepackage{Sweave} +\documentclass[12pt,a4paper]{article} +\usepackage{a4wide} +%%\usepackage[lists,heads]{endfloat} +\input{header} +\hypersetup{ + pdftitle = {kinfit - Routines for fitting kinetic models to chemical degradation data}, + pdfsubject = {Manuscript}, + pdfauthor = {Johannes Ranke}, + colorlinks = {true}, + linkcolor = {blue}, + citecolor = {blue}, + urlcolor = {red}, + hyperindex = {true}, + linktocpage = {true}, +} +\SweaveOpts{engine=R, eps=FALSE, keep.source = TRUE} +<>= +options(prompt = "R> ") +options(SweaveHooks = list( + cex = function() par(cex.lab = 1.3, cex.axis = 1.3))) +@ +\begin{document} +\title{kinfit -\\ +Routines for fitting kinetic models to chemical degradation +data\footnote{This is a preprint of an article published in +The R Journal, Volume 1, Number ?, ?--?. available online +\url{http://journal.r-project.org}.}} +\author{\textbf{Johannes Ranke} \\ +%EndAName +Product Safety \\ +Harlan Laboratories Ltd. \\ +Zelgliweg 1, CH--4452 Itingen, Switzerland} +\maketitle + +\begin{abstract} +In the regulatory evaluation of chemical substances like plant protection +products (pesticides), biocides and other chemicals, degradation data play an +important role. For the evaluation of pesticide degradation experiments, +detailed guidance has been developed, based on nonlinear regression. +The \RR{} add-on package \Rpackage{kinfit} implements fitting the models +recommended in this guidance from within R and calculates the +recommended statistical measures for data series within one compartment +without metabolite data. +\end{abstract} + + +\thispagestyle{empty} \setcounter{page}{0} + +\clearpage + +\tableofcontents + +\textbf{Key words}: Kinetics, FOCUS, nonlinear fitting + +\section{Introduction} +\label{intro} + +Many approaches are possible regarding the evaluation of chemical degradation +data. The \Rpackage{kinfit} package \citep{pkg:kinfit} in \RR{} +\citep{rcore2009} implements the approach recommended in the kinetics report +provided by the FOrum for Co-ordination of pesticide fate models and their +USe \citep{FOCUS2006} for simple data series for one parent compound in one +compartment. + +\section{Example} +\label{exam} + +In the following, requirements for data formatting are explained. Then the +procedure for fitting the four kinetic models recommended by the FOCUS group +to an example dataset given in the FOCUS kinetics report is illustrated. +The explanations are kept rather verbose in order to lower the barrier for +\RR{} newcomers. + +\subsection{Data format} + +The following listing shows example dataset C from the FOCUS kinetics +report as distributed with the \Rpackage{kinfit} package + +<>= +library("kinfit") +data("FOCUS_2006_C", package = "kinfit") +print(FOCUS_2006_C) +@ + +Note that the data needs to be in the format of a data frame containing +a variable \Robject{t} containing sampling times and a variable +\Robject{parent} containing the measured data. Replicate measurements are +not recorded in extra columns but simply appended, leading to multiple +occurrences of the sampling times \Robject{t}. + +Small to medium size dataset can be conveniently entered directly as \RR{} code +as shown in the following listing + +<>= +kindata_example <- data.frame( + t = c(0, 1, 3, 7, 14, 28, 63, 91, 119), + parent = c(85.1, 57.9, 29.9, 14.6, 9.7, 6.6, 4, 3.9, 0.6) +) +@ + + +\subsection{Fitting the kinetic models} + +The user can choose for which kinetic models the \Robject{kinfit} function +will try to find optimised parameters. This is achieved by the argument +\Robject{kinmodels} to the function, as shown below. The models currently +implemented are abbreviated \Robject{SFO} (Single First-Order), \Robject{FOMC} +(First-Order Multi-Compartment), \Robject{DFOP} (Double First-Order in Parallel) +and \Robject{HS} (Hockey-Stick) as defined by the \cite{FOCUS2006}. From the +DFOP model, corresponding parameters in the notation of the SFORB model (Single +First-Order Reversible Binding) are additionally calculated. + +<>= +kinfits.C <- kinfit(FOCUS_2006_C, kinmodels = c("SFO", "FOMC", "DFOP", "HS")) +@ + +The results of the fitting procedure are returned by the function, and can +then be inspected by the function \Robject{kinresults}. + +<>= +kinresults(kinfits.C) +@ + +The higher level functions \Robject{kinplot} and \Robject{kinreport} +work on lists called \Robject{kinobject}. They contain the fitted models, +optionally the data used for fitting the models, and the name of the parent +compound as well as the test system type used for generating the data, +as well as some more optional entries. The construction of such an +object is shown below. + +<>= +kinobject.C <- kinobject <- list( + parent = "Compound XY", + type = "Degradation in the environment", + system = "System 1", + source = "Synthetic example data from FOCUS kinetics", + data = FOCUS_2006_C, + fits = kinfits.C, + results = kinresults(kinfits.C)) +@ + +The plotting and reporting functions then work on this object. The example +below outputs the report to the console, because no \Robject{file} argument +is specified. If a filename is specified, the report will be written to +a text file. + +<>= +kinreport(kinobject.C) +@ + +Plotting is done on an on-screen device. Graphics files in vector based +formats can be obtained using the \RR{} devices \Robject{pdf}, \Robject{eps}, +or, subject to platform restrictions, \Robject{windows.metafile}. + +\setkeys{Gin}{width=0.6\textwidth} +\begin{figure}[t] +\begin{center} +<>= +kinfits.C <- kinfit(FOCUS_2006_C, kinmodels = c("SFO", "FOMC", "DFOP", "HS")) +kinplot(kinobject.C) +title("FOCUS dataset C") +@ +\caption{Fits of standard models to FOCUS dataset C.} +\label{fig:FOCUS_2006_C} +\end{center} +\end{figure} + +A residual plot can be obtained with the function \Robject{kinresplot} as +shown in Figure \ref{fig:FOCUS_2006_C_res}. + +\setkeys{Gin}{width=0.6\textwidth} +\begin{figure}[t] +\begin{center} +<>= +kinresplot(kinobject.C, "SFO") +@ +\caption{Residual plot for fitting the SFO model to FOCUS dataset C.} +\label{fig:FOCUS_2006_C_res} +\end{center} +\end{figure} + +\section{Validation} +\label{vali} + +In the following comparisons, the results for fitting the four recommended +kinetic models to FOCUS datasets A to F with \Rpackage{kinfit} were +obtained. + +<>= +datasets <- LETTERS[1:4] +data(list=paste("FOCUS_2006_", datasets, sep=""), package = "kinfit") +kinobjects <- list() +for (dataset in datasets) +{ + kinobjects[[dataset]] <- list() + kinobjects[[dataset]]$data <- get(paste("FOCUS_2006_", dataset, sep="")) + kinobjects[[dataset]]$fits <- + kinfit(kinobjects[[dataset]]$data, + kinmodels = c("SFO", "FOMC", "DFOP", "HS")) + kinobjects[[dataset]]$results <- + kinresults(kinobjects[[dataset]]$fits) +} + +data(FOCUS_2006_F, package = "kinfit") +# Set the initial concentration in the sediment to zero +FOCUS_2006_F[1, "parent.sediment"] <- 0 +# Calculate total system values for the parent compound +FOCUS_2006_F = transform(FOCUS_2006_F, + parent.system = parent.water + parent.sediment) + +subsets <- c("system", "water") +for (subset in subsets) +{ + index <- paste("F", subset, sep=" ") + kinobjects[[index]] <- list() + kinobjects[[index]]$data <- data.frame( + t = FOCUS_2006_F$t, + parent = FOCUS_2006_F[[paste("parent", subset, sep=".")]]) + kinobjects[[index]]$fits <- + kinfit(kinobjects[[index]]$data, + kinmodels = c("SFO", "FOMC", "DFOP", "HS")) + kinobjects[[index]]$results <- + kinresults(kinobjects[[index]]$fits) +} +@ + +\subsection{Single First Order Model} + +In Tables \ref{tab:vali.SFO.A} to \ref{tab:vali.SFO.F_water}, +the results from fitting the SFO model to FOCUS example datasets with +various software packages as given in the report by the \cite{FOCUS2006} are +compared with the results obtained with \Rpackage{kinfit}. + +<>= +data("FOCUS_2006_SFO_ref_A_to_F", package = "kinfit") +kinmodel = "SFO" +refs <- list() +for (kinobjectname in names(kinobjects)) +{ + ref <- subset(FOCUS_2006_SFO_ref_A_to_F, dataset == kinobjectname) + ref <- ref[-6] + texfile <- paste("FOCUS_2006_", kinmodel, "_", + gsub(" ", "_", kinobjectname), "_ref.tex", sep="") + write.table(format(ref, nsmall=2), + file = texfile, + sep=" & ", quote=FALSE, + row.names=FALSE, col.names=FALSE, eol = " \\\\ \n") + refs[[kinobjectname]] <- ref +} +@ + +\begin{table} +\caption{Results of fitting the SFO model to the example dataset A +\citep{FOCUS2006}, as given in the report, in comparison to the results +obtained by \Rpackage{kinfit}. \label{tab:vali.SFO.A}} +\begin{center} +\vspace{0.5cm} +\begin{tabular}{lcccc} +\toprule +Package & $M_0$ & $k$ & DT$_{50}$ & DT$_{90}$ \\ +\midrule +\input{FOCUS_2006_SFO_A_ref} +\midrule +Median & +\Sexpr{format(median(refs$A$M0), nsmall=2)} & +\Sexpr{format(median(refs$A$k), nsmall=4)} & +\Sexpr{format(median(refs$A$DT50), nsmall=2)} & +\Sexpr{format(median(refs$A$DT90), nsmall=2)} \\ +\midrule +\Rpackage{kinfit} & +\Sexpr{round(kinobjects$A$results$parms$SFO$parent.0, 2)} & +\Sexpr{round(kinobjects$A$results$parms$SFO$k, 4)} & +\Sexpr{round(kinobjects$A$results$results[["SFO", "DT50"]], 2)} & +\Sexpr{round(kinobjects$A$results$results[["SFO", "DT90"]], 2)} \\ +\bottomrule +\end{tabular} +\end{center} +\end{table} + +\begin{table} +\caption{Results of fitting the SFO model to the example dataset B +\citep{FOCUS2006}, as given in the report, in comparison to the results +obtained by \Rpackage{kinfit}. \label{tab:vali.SFO.B}} +\begin{center} +\vspace{0.5cm} +\begin{tabular}{lcccc} +\toprule +Package & $M_0$ & $k$ & DT$_{50}$ & DT$_{90}$ \\ +\midrule +\input{FOCUS_2006_SFO_B_ref} +\midrule +Median & +\Sexpr{format(median(refs$B$M0), nsmall=2)} & +\Sexpr{format(median(refs$B$k), nsmall=4)} & +\Sexpr{format(median(refs$B$DT50), nsmall=2)} & +\Sexpr{format(median(refs$B$DT90), nsmall=2)} \\ +\midrule +\Rpackage{kinfit} & +\Sexpr{round(kinobjects$B$results$parms$SFO$parent.0, 2)} & +\Sexpr{round(kinobjects$B$results$parms$SFO$k, 4)} & +\Sexpr{round(kinobjects$B$results$results[["SFO", "DT50"]], 2)} & +\Sexpr{round(kinobjects$B$results$results[["SFO", "DT90"]], 2)} \\ +\bottomrule +\end{tabular} +\end{center} +\end{table} + +\begin{table} +\caption{Results of fitting the SFO model to the example dataset C +\citep{FOCUS2006}, as given in the report, in comparison to the results +obtained by \Rpackage{kinfit}. \label{tab:vali.SFO.C}} +\begin{center} +\vspace{0.5cm} +\begin{tabular}{lcccc} +\toprule +Package & $M_0$ & $k$ & DT$_{50}$ & DT$_{90}$ \\ +\midrule +\input{FOCUS_2006_SFO_C_ref} +\midrule +Median & +\Sexpr{format(median(refs$C$M0), nsmall=2)} & +\Sexpr{format(median(refs$C$k), nsmall=4)} & +\Sexpr{format(median(refs$C$DT50), nsmall=2)} & +\Sexpr{format(median(refs$C$DT90), nsmall=2)} \\ +\midrule +\Rpackage{kinfit} & +\Sexpr{round(kinobjects$C$results$parms$SFO$parent.0, 2)} & +\Sexpr{round(kinobjects$C$results$parms$SFO$k, 4)} & +\Sexpr{round(kinobjects$C$results$results[["SFO", "DT50"]], 2)} & +\Sexpr{round(kinobjects$C$results$results[["SFO", "DT90"]], 2)} \\ +\bottomrule +\end{tabular} +\end{center} +\end{table} + +\begin{table} +\caption{Results of fitting the SFO model to the example dataset D +\citep{FOCUS2006}, as given in the report, in comparison to the results +obtained by \Rpackage{kinfit}. \label{tab:vali.SFO.D}} +\begin{center} +\vspace{0.5cm} +\begin{tabular}{lcccc} +\toprule +Package & $M_0$ & $k$ & DT$_{50}$ & DT$_{90}$ \\ +\midrule +\input{FOCUS_2006_SFO_D_ref} +\midrule +Median & +\Sexpr{format(median(refs$D$M0), nsmall=2)} & +\Sexpr{format(median(refs$D$k), nsmall=4)} & +\Sexpr{format(median(refs$D$DT50), nsmall=2)} & +\Sexpr{format(median(refs$D$DT90), nsmall=2)} \\ +\midrule +\Rpackage{kinfit} & +\Sexpr{round(kinobjects$D$results$parms$SFO$parent.0, 2)} & +\Sexpr{round(kinobjects$D$results$parms$SFO$k, 4)} & +\Sexpr{round(kinobjects$D$results$results[["SFO", "DT50"]], 2)} & +\Sexpr{round(kinobjects$D$results$results[["SFO", "DT90"]], 2)} \\ +\bottomrule +\end{tabular} +\end{center} +\end{table} + +\begin{table} +\caption{Results of fitting the SFO model to the total system data from +example dataset F \citep{FOCUS2006}, as given in the report, in comparison to +the results obtained by \Rpackage{kinfit}. \label{tab:vali.SFO.F_system}} +\begin{center} +\vspace{0.5cm} +\begin{tabular}{lcccc} +\toprule +Package & $M_0$ & $k$ & DT$_{50}$ & DT$_{90}$ \\ +\midrule +\input{FOCUS_2006_SFO_F_system_ref} +\midrule +Median & +\Sexpr{format(median(refs[["F system"]]$M0), nsmall=2)} & +\Sexpr{format(median(refs[["F system"]]$k), nsmall=4)} & +\Sexpr{format(median(refs[["F system"]]$DT50), nsmall=2)} & +\Sexpr{format(median(refs[["F system"]]$DT90), nsmall=2)} \\ +\midrule +\Rpackage{kinfit} & +\Sexpr{round(kinobjects[["F system"]]$results$parms$SFO$parent.0, 2)} & +\Sexpr{round(kinobjects[["F system"]]$results$parms$SFO$k, 4)} & +\Sexpr{round(kinobjects[["F system"]]$results$results[["SFO", "DT50"]], 2)} & +\Sexpr{round(kinobjects[["F system"]]$results$results[["SFO", "DT90"]], 2)} \\ +\bottomrule +\end{tabular} +\end{center} +\end{table} + +\begin{table} +\caption{Results of fitting the SFO model to the water phase data from +example dataset F \citep{FOCUS2006}, as given in the report, in comparison to +the results obtained by \Rpackage{kinfit}. \label{tab:vali.SFO.F_water}} +\begin{center} +\vspace{0.5cm} +\begin{tabular}{lcccc} +\toprule +Package & $M_0$ & $k$ & DT$_{50}$ & DT$_{90}$ \\ +\midrule +\input{FOCUS_2006_SFO_F_water_ref} +\midrule +Median & +\Sexpr{format(median(refs[["F water"]]$M0), nsmall=2)} & +\Sexpr{format(median(refs[["F water"]]$k), nsmall=4)} & +\Sexpr{format(median(refs[["F water"]]$DT50), nsmall=2)} & +\Sexpr{format(median(refs[["F water"]]$DT90), nsmall=2)} \\ +\midrule +\Rpackage{kinfit} & +\Sexpr{round(kinobjects[["F water"]]$results$parms$SFO$parent.0, 2)} & +\Sexpr{round(kinobjects[["F water"]]$results$parms$SFO$k, 4)} & +\Sexpr{round(kinobjects[["F water"]]$results$results[["SFO", "DT50"]], 2)} & +\Sexpr{format(kinobjects[["F water"]]$results$results[["SFO", "DT90"]], digits=4, nsmall=2)} \\ +\bottomrule +\end{tabular} +\end{center} +\end{table} + +The comparisons show that all packages evaluated in the FOCUS report give +very similar results for the SFO model. The results obtained with +\Rpackage{kinfit} are very close to the median of the results reported for +the other packages. + +\subsection{First Order Multi Compartment Model} + +<>= +data("FOCUS_2006_FOMC_ref_A_to_F", package = "kinfit") +kinmodel = "FOMC" +refs <- list() +for (kinobjectname in names(kinobjects)[c(1:3, 5:6)]) +{ + ref <- subset(FOCUS_2006_FOMC_ref_A_to_F, dataset == kinobjectname) + ref$package <- gsub("#", "$^a$", ref$package) + ref <- ref[-7] + texfile <- paste("FOCUS_2006_", kinmodel, "_", + gsub(" ", "_", kinobjectname), "_ref.tex", sep="") + write.table(format(ref, nsmall=2), + file = texfile, + sep=" & ", quote=FALSE, + row.names=FALSE, col.names=FALSE, eol = " \\\\ \n") + refs[[kinobjectname]] <- ref +} +@ + +\begin{table} +\caption{Results of fitting the FOMC model to the example dataset A +\citep{FOCUS2006}, as given in the report, in comparison to the results +obtained by \Rpackage{kinfit}. \label{tab:vali.FOMC.A}} +\begin{center} +\vspace{0.5cm} +\begin{tabular}{lccccc} +\toprule +Package & $M_0$ & $\alpha$ & $\beta$ & DT$_{50}$ & DT$_{90}$ \\ +\midrule +\input{FOCUS_2006_FOMC_A_ref} +\midrule +Median & +\Sexpr{format(median(refs$A$M0), nsmall=2)} & +\Sexpr{format(median(refs$A$alpha), scientific=TRUE)} & +\Sexpr{format(median(as.numeric(refs$A$beta)), nsmall=0)} & +\Sexpr{format(median(refs$A$DT50), nsmall=2)} & +\Sexpr{format(median(refs$A$DT90), nsmall=2)} \\ +\midrule +\Rpackage{kinfit} & +no fit \\ +\bottomrule +\end{tabular} +\end{center} +\end{table} + +\begin{table} +\caption{Results of fitting the FOMC model to the example dataset B +\citep{FOCUS2006}, as given in the report, in comparison to the results +obtained by \Rpackage{kinfit}. \label{tab:vali.FOMC.B}} +\begin{center} +\vspace{0.5cm} +\begin{tabular}{lccccc} +\toprule +Package & $M_0$ & $\alpha$ & $\beta$ & DT$_{50}$ & DT$_{90}$ \\ +\midrule +\input{FOCUS_2006_FOMC_B_ref} +\midrule +Median & +\Sexpr{format(median(refs$B$M0), digits=4, nsmall=2)} & +\Sexpr{format(median(refs$B$alpha), scientific=TRUE)} & +\Sexpr{format(median(as.numeric(refs$B$beta)), nsmall=0)} & +\Sexpr{format(median(refs$B$DT50), nsmall=2)} & +\Sexpr{format(median(refs$B$DT90), digits=4, nsmall=2)} \\ +\midrule +\Rpackage{kinfit} & +\Sexpr{round(kinobjects$B$results$parms$FOMC$parent.0, 2)} & +\Sexpr{round(kinobjects$B$results$parms$FOMC$alpha, 4)} & +\Sexpr{round(kinobjects$B$results$parms$FOMC$beta, 4)} & +\Sexpr{round(kinobjects$B$results$results[["FOMC", "DT50"]], 2)} & +\Sexpr{format(kinobjects$B$results$results[["FOMC", "DT90"]], digits=4, nsmall=2)} \\ +\bottomrule +\end{tabular} +\end{center} +\end{table} + + +\begin{table} +\caption{Results of fitting the FOMC model to the example dataset C +\citep{FOCUS2006}, as given in the report, in comparison to the results +obtained by \Rpackage{kinfit}. \label{tab:vali.FOMC.C}} +\begin{center} +\vspace{0.5cm} +\begin{tabular}{lccccc} +\toprule +Package & $M_0$ & $\alpha$ & $\beta$ & DT$_{50}$ & DT$_{90}$ \\ +\midrule +\input{FOCUS_2006_FOMC_C_ref} +\midrule +Median & +\Sexpr{format(median(refs$C$M0), nsmall=2)} & +\Sexpr{format(median(refs$C$alpha), nsmall=2)} & +\Sexpr{format(median(as.numeric(refs$C$beta)), nsmall=2)} & +\Sexpr{format(median(refs$C$DT50), nsmall=2)} & +\Sexpr{format(median(refs$C$DT90), nsmall=2)} \\ +\midrule +\Rpackage{kinfit} & +\Sexpr{round(kinobjects$C$results$parms$FOMC$parent.0, 2)} & +\Sexpr{round(kinobjects$C$results$parms$FOMC$alpha, 4)} & +\Sexpr{round(kinobjects$C$results$parms$FOMC$beta, 4)} & +\Sexpr{round(kinobjects$C$results$results[["FOMC", "DT50"]], 2)} & +\Sexpr{format(kinobjects$C$results$results[["FOMC", "DT90"]], digits=4, nsmall=2)} \\ +\bottomrule +\end{tabular} +\end{center} +\end{table} + +\begin{table} +\caption{Results of fitting the FOMC model to the total system data from +example dataset F \citep{FOCUS2006}, as given in the report, in comparison to +the results obtained by \Rpackage{kinfit}. \label{tab:vali.FOMC.F_system}} +\begin{center} +\vspace{0.5cm} +\begin{tabular}{lccccc} +\toprule +Package & $M_0$ & $\alpha$ & $\beta$ & DT$_{50}$ & DT$_{90}$ \\ +\midrule +\input{FOCUS_2006_FOMC_F_system_ref} +\midrule +Median & +\Sexpr{format(median(refs[["F system"]]$M0), nsmall=2)} & +\Sexpr{format(median(refs[["F system"]]$alpha), nsmall=4)} & +\Sexpr{format(median(refs[["F system"]]$beta), nsmall=4)} & +\Sexpr{format(median(refs[["F system"]]$DT50), nsmall=2)} & +\Sexpr{format(median(refs[["F system"]]$DT90), nsmall=2)} \\ +\midrule +\Rpackage{kinfit} & +no fit \\ +\bottomrule +\end{tabular} +\end{center} +\end{table} + +\begin{table} +\caption{Results of fitting the FOMC model to the water phase data from +example dataset F \citep{FOCUS2006}, as given in the report, in comparison to +the results obtained by \Rpackage{kinfit}. \label{tab:vali.FOMC.F_water}} +\begin{center} +\vspace{0.5cm} +\begin{tabular}{lccccc} +\toprule +Package & $M_0$ & $\alpha$ & $\beta$ & DT$_{50}$ & DT$_{90}$ \\ +\midrule +\input{FOCUS_2006_FOMC_F_water_ref} +\midrule +Median & +\Sexpr{format(median(refs[["F water"]]$M0), nsmall=2)} & +\Sexpr{format(median(refs[["F water"]]$alpha), nsmall=4)} & +\Sexpr{format(median(refs[["F water"]]$beta), nsmall=4)} & +\Sexpr{format(median(refs[["F water"]]$DT50), nsmall=2)} & +\Sexpr{format(median(refs[["F water"]]$DT90), nsmall=2)} \\ +\midrule +\Rpackage{kinfit} & +no fit \\ +\bottomrule +\end{tabular} +\end{center} +\end{table} + +The comparison of the results obtained for the FOMC model show much more +variability between software packages. For dataset A, results for the +\Robject{alpha} and \Robject{beta} parameters differ over several +orders of magnitude between the different packages. The method used +by the \Robject{kinfit} routine does not converge for this dataset. +The same applies to the total system and water phase only data for +example dataset F and the FOMC model. + +For datasets B and C, the \Rpackage{kinfit} function produces results +which are very close to the median of the results obtained by the +other packages. + +\subsection{Dual First Order in Parallel Model} + +<>= +data("FOCUS_2006_DFOP_ref_A_to_B", package = "kinfit") +kinmodel = "DFOP" +refs <- list() +for (kinobjectname in names(kinobjects)[1:2]) +{ + ref <- subset(FOCUS_2006_DFOP_ref_A_to_B, dataset == kinobjectname) + ref <- ref[-8] + texfile <- paste("FOCUS_2006_", kinmodel, "_", + gsub(" ", "_", kinobjectname), "_ref.tex", sep="") + write.table(format(ref, nsmall=2), + file = texfile, + sep=" & ", quote=FALSE, + row.names=FALSE, col.names=FALSE, eol = " \\\\ \n") + refs[[kinobjectname]] <- ref +} +@ + +\begin{table} +\caption{Results of fitting the DFOP model to the example dataset A +\citep{FOCUS2006}, as given in the report, in comparison to the results +obtained by \Rpackage{kinfit}. \label{tab:vali.DFOP.A}} +\begin{center} +\vspace{0.5cm} +\begin{tabular}{lcccccc} +\toprule +Package & $M_0$ & $f$ & $k_1$ & $k_2$ & DT$_{50}$ & DT$_{90}$ \\ +\midrule +\input{FOCUS_2006_DFOP_A_ref} +\midrule +Median & +\Sexpr{format(median(refs$A$M0), nsmall=2)} & +\Sexpr{format(median(refs$A$f), nsmall=2)} & +\Sexpr{format(median(refs$A$k1), nsmall=4)} & +\Sexpr{format(median(refs$A$k2), nsmall=4)} & +\Sexpr{format(median(refs$A$DT50), nsmall=2)} & +\Sexpr{format(median(refs$A$DT90), nsmall=2)} \\ +\midrule +\Rpackage{kinfit} & +no fit \\ +\bottomrule +\end{tabular} +\end{center} +\end{table} + +\begin{table} +\caption{Results of fitting the DFOP model to the example dataset B +\citep{FOCUS2006}, as given in the report, in comparison to the results +obtained by \Rpackage{kinfit}. \label{tab:vali.DFOP.B}} +\begin{center} +\vspace{0.5cm} +\begin{tabular}{lcccccc} +\toprule +Package & $M_0$ & $f$ & $k_1$ & $k_2$ & DT$_{50}$ & DT$_{90}$ \\ +\midrule +\input{FOCUS_2006_DFOP_B_ref} +\midrule +Median & +\Sexpr{format(median(refs$B$M0), nsmall=2)} & +\Sexpr{format(median(refs$B$f), nsmall=2)} & +\Sexpr{format(median(refs$B$k1), nsmall=4)} & +\Sexpr{format(median(refs$B$k2), nsmall=4)} & +\Sexpr{format(median(refs$B$DT50), nsmall=2)} & +\Sexpr{format(median(refs$B$DT90), digits=4, nsmall=2)} \\ +\midrule +\Rpackage{kinfit} & +\Sexpr{round(kinobjects$B$results$parms$DFOP$parent.0, 2)} & +\Sexpr{round(kinobjects$B$results$parms$DFOP$g, 2)} & +\Sexpr{round(kinobjects$B$results$parms$DFOP$k1, 4)} & +\Sexpr{round(kinobjects$B$results$parms$DFOP$k2, 4)} & +\Sexpr{round(kinobjects$B$results$results[["DFOP", "DT50"]], 2)} & +\Sexpr{format(kinobjects$B$results$results[["DFOP", "DT90"]], digits=4, nsmall=2)} \\ +\bottomrule +\end{tabular} +\end{center} +\end{table} + +Regarding fitting the DFOP model to FOCUS example dataset A, it is already +indicated in the report that it is not a good example dataset for fitting +this particular model, as the two kinetic constants postulated by the DFOP +model are hardly distinguishable. As a consequence, the software packages +strongly disagree especially on the model parameter $f$ specifying the +distribution between the kinetic domains that are characterised by the +two kinetic constants. Again, the \Rpackage{kinfit} routine does not +show conversion for this model and this dataset (Table \ref{tab:vali.DFOP.A}). + +Fitting the DFOP model with \Rpackage{kinfit} to dataset B yields results +that are very close to the median of the results obtained by other packages, +as illustrated in Table \ref{tab:vali.DFOP.B}. + +\subsection{Hockey Stick Model} + +Analysis of dataset A shows basically two different parameter sets +generated by the 8 packages reported in the FOCUS report \citep{FOCUS2006}. +The \Rpackage{kinfit} package does not show conversion with the standard +paramater defaults, but can reproduce the two parameter sets when given +the respective paramter values as starting values, as shown in the last +two lines in Table \ref{tab:vali.HS.A}. + +<>= +data("FOCUS_2006_HS_ref_A_to_F", package = "kinfit") +kinmodel = "HS" +refs <- list() +for (kinobjectname in names(kinobjects)[c(1:3, 5:6)]) +{ + ref <- subset(FOCUS_2006_HS_ref_A_to_F, dataset == kinobjectname) + ref$package <- gsub("\\*", "$^a$", ref$package) + ref <- ref[-8] + texfile <- paste("FOCUS_2006_", kinmodel, "_", + gsub(" ", "_", kinobjectname), "_ref.tex", sep="") + write.table(format(ref, nsmall=2), + file = texfile, + sep=" & ", quote=FALSE, + row.names=FALSE, col.names=FALSE, eol = " \\\\ \n") + refs[[kinobjectname]] <- ref +} +@ + +<>= +kinobjects$A$fits.2 <- kinfit(kinobjects$A$data, + kinmodels = c("HS"), + start.HS = list(parent.0 = 100, tb = 5, k1 = 0.017, k2 = 0.05)) +kinobjects$A$results.2 <- kinresults(kinobjects$A$fits.2) + +kinobjects$A$fits.3 <- kinfit(kinobjects$A$data, + kinmodels = c("HS"), + start.HS = list(parent.0 = 100, tb = 11, k1 = 0.017, k2 = 0.05)) +kinobjects$A$results.3 <- kinresults(kinobjects$A$fits.3) +@ + +\begin{table} +\caption{Results of fitting the HS model to the example dataset A +\citep{FOCUS2006}, as given in the report, in comparison to the results +obtained by \Rpackage{kinfit}. \label{tab:vali.HS.A}} +\begin{center} +\vspace{0.5cm} +\begin{tabular}{lcccccc} +\toprule +Package & $M_0$ & $t_b$ & $k_1$ & $k_2$ & DT$_{50}$ & DT$_{90}$ \\ +\midrule +\input{FOCUS_2006_HS_A_ref} +\midrule +Median & +\Sexpr{format(median(refs$A$M0), nsmall=2)} & +\Sexpr{format(median(refs$A$tb), nsmall=2)} & +\Sexpr{format(median(refs$A$k1), nsmall=4)} & +\Sexpr{format(median(refs$A$k2), nsmall=4)} & +\Sexpr{format(median(refs$A$DT50), nsmall=2)} & +\Sexpr{format(median(refs$A$DT90), digits=4, nsmall=2)} \\ +\midrule +\Rpackage{kinfit} & no fit \\ +\Rpackage{kinfit} & +\Sexpr{round(kinobjects$A$results.2$parms$HS$parent.0, 2)} & +\Sexpr{round(kinobjects$A$results.2$parms$HS$tb, 2)} & +\Sexpr{round(kinobjects$A$results.2$parms$HS$k1, 4)} & +\Sexpr{round(kinobjects$A$results.2$parms$HS$k2, 4)} & +\Sexpr{round(kinobjects$A$results.2$results[["HS", "DT50"]], 2)} & +\Sexpr{format(kinobjects$A$results.2$results[["HS", "DT90"]], digits=4, nsmall=2)} \\ +\Rpackage{kinfit} & +\Sexpr{round(kinobjects$A$results.3$parms$HS$parent.0, 2)} & +\Sexpr{round(kinobjects$A$results.3$parms$HS$tb, 2)} & +\Sexpr{round(kinobjects$A$results.3$parms$HS$k1, 4)} & +\Sexpr{round(kinobjects$A$results.3$parms$HS$k2, 4)} & +\Sexpr{round(kinobjects$A$results.3$results[["HS", "DT50"]], 2)} & +\Sexpr{format(kinobjects$A$results.3$results[["HS", "DT90"]], digits=4, nsmall=2)} \\ +\bottomrule +\end{tabular} +\end{center} +\end{table} + +\begin{table} +\caption{Results of fitting the HS model to the example dataset B +\citep{FOCUS2006}, as given in the report, in comparison to the results +obtained by \Rpackage{kinfit}. \label{tab:vali.HS.B}} +\begin{center} +\vspace{0.5cm} +\begin{tabular}{lcccccc} +\toprule +Package & $M_0$ & $t_b$ & $k_1$ & $k_2$ & DT$_{50}$ & DT$_{90}$ \\ +\midrule +\input{FOCUS_2006_HS_B_ref} +\midrule +Median & +\Sexpr{format(median(refs$B$M0), nsmall=2)} & +\Sexpr{format(median(refs$B$tb), nsmall=2)} & +\Sexpr{format(median(refs$B$k1), nsmall=4)} & +\Sexpr{format(median(refs$B$k2), nsmall=4)} & +\Sexpr{format(median(refs$B$DT50), nsmall=2)} & +\Sexpr{format(median(refs$B$DT90), digits=4, nsmall=2)} \\ +\midrule +\Rpackage{kinfit} & no fit \\ +\bottomrule +\end{tabular} +\end{center} +\end{table} + +\begin{table} +\caption{Results of fitting the HS model to the example dataset C +\citep{FOCUS2006}, as given in the report, in comparison to the results +obtained by \Rpackage{kinfit}. \label{tab:vali.HS.C}} +\begin{center} +\vspace{0.5cm} +\begin{tabular}{lcccccc} +\toprule +Package & $M_0$ & $t_b$ & $k_1$ & $k_2$ & DT$_{50}$ & DT$_{90}$ \\ +\midrule +\input{FOCUS_2006_HS_C_ref} +\midrule +Median & +\Sexpr{format(median(refs$C$M0), nsmall=2)} & +\Sexpr{format(median(refs$C$tb), nsmall=2)} & +\Sexpr{format(median(refs$C$k1), nsmall=4)} & +\Sexpr{format(median(as.numeric(refs$C$k2)), nsmall=4)} & +\Sexpr{format(median(refs$C$DT50), nsmall=2)} & +\Sexpr{format(median(refs$C$DT90), digits=4, nsmall=2)} \\ +\midrule +\Rpackage{kinfit} & +\Sexpr{round(kinobjects$C$results$parms$HS$parent.0, 2)} & +\Sexpr{round(kinobjects$C$results$parms$HS$tb, 2)} & +\Sexpr{round(kinobjects$C$results$parms$HS$k1, 4)} & +\Sexpr{round(kinobjects$C$results$parms$HS$k2, 4)} & +\Sexpr{round(kinobjects$C$results$results[["HS", "DT50"]], 2)} & +\Sexpr{format(kinobjects$C$results$results[["HS", "DT90"]], digits=4, nsmall=2)} \\ +\bottomrule +\end{tabular} +\end{center} +\end{table} + +The HS fit did not converge for dataset B with \Rpackage{kinfit}. Again, this +should be viewed in the light of the vastly differing results produced by +the other software packages as listed in Table \ref{tab:vali.HS.B}. + +The results from fitting the HS model to dataset C with \Rpackage{kinfit} +agree nicely with the median of the results obtained with the other packages, +as shown in Table \ref{tab:vali.HS.C}. + +\subsection{$\chi^2$ statistics} + +As no values for the minimum error rate that has to be assumed for the +model to agree with the data ($\chi^2$ statistics) are reported for +the FOCUS datasets A to F, the respective values calculated by +\Rpackage{kinfit} are compared to the $\chi^2$ values calculated by +the KinGUI package \citep{schaefer2007} as shown in Table +\ref{tab:vali.chi2}. + +For this, the possibility to write KinGUI input files using the function +\Robject{kinwrite.KinGUI} from \Rpackage{kinfit} was used. + +<>= +chi2.SFO.kinfit <- chi2.FOMC.kinfit <- array(dim = length(kinobjects), + dimnames = list(names(kinobjects))) +chi2.DFOP.kinfit <- chi2.HS.kinfit <- array(dim = length(kinobjects), + dimnames = list(names(kinobjects))) +for (kinobjectname in names(kinobjects)) +{ + outname <- paste("KinGUI/", gsub(" ", "_", kinobjectname), "_KinGUI.txt", + sep="") + kinwrite.KinGUI(kinobjects[[kinobjectname]], outname) + chi2.SFO.kinfit[[kinobjectname]] <- + kinobjects[[kinobjectname]]$results$stats[["SFO", "err.min"]] + chi2.FOMC.kinfit[[kinobjectname]] <- + ifelse(class(kinobjects[[kinobjectname]]$fits$FOMC) == "try-error", + NA, kinobjects[[kinobjectname]]$results$stats[["FOMC", "err.min"]]) + chi2.DFOP.kinfit[[kinobjectname]] <- + ifelse(class(kinobjects[[kinobjectname]]$fits$DFOP) == "try-error", + NA, kinobjects[[kinobjectname]]$results$stats[["DFOP", "err.min"]]) + chi2.HS.kinfit[[kinobjectname]] <- + ifelse(class(kinobjects[[kinobjectname]]$fits$HS) == "try-error", + NA, kinobjects[[kinobjectname]]$results$stats[["HS", "err.min"]]) +} + +chi2.SFO.KinGUI <- c(8.3852, 4.4562, 15.8456, 6.4539, 12.5386, 10.8069) +chi2.FOMC.KinGUI <- c(9.3116, 4.6641, 6.6574, 6.8080, 13.4533, 11.6682) +chi2.DFOP.KinGUI <- c(9.6600, 4.9562, 2.6613, 7.2751, 14.1524, 12.1821) +chi2.HS.KinGUI <- c(4.1106, 4.4535, 4.6963, 5.8196, 3.2178, 1.6558) +names(chi2.SFO.KinGUI) <- names(chi2.FOMC.KinGUI) <- names(kinobjects) +names(chi2.DFOP.KinGUI) <- names(chi2.HS.KinGUI) <- names(kinobjects) + +chi2 <- data.frame( + SFO.KinGUI = chi2.SFO.KinGUI, + SFO.kinfit = round(100 * chi2.SFO.kinfit, 4), + FOMC.KinGUI = chi2.FOMC.KinGUI, + FOMC.kinfit = round(100 * chi2.FOMC.kinfit, 4), + DFOP.KinGUI = chi2.DFOP.KinGUI, + DFOP.kinfit = round(100 * chi2.DFOP.kinfit, 4), + HS.KinGUI = chi2.HS.KinGUI, + HS.kinfit = round(100 * chi2.HS.kinfit, 4) +) +write.table(chi2, + file = "chi2_comparison.tex", + sep=" & ", quote=FALSE, na="", + row.names=TRUE, col.names=FALSE, eol = " \\\\ \n") +@ + +\begin{table} +\caption{Comparison of $\chi^2$ error levels in percent calculated for model +fits by the KinGUI and \Rpackage{kinfit} packages. \label{tab:vali.chi2}} +\vspace{0.5cm} +\begin{tabular}{lcccccccc} +\toprule + & \multicolumn{2}{c}{SFO} & +\multicolumn{2}{c}{FOMC} & +\multicolumn{2}{c}{DFOP} & +\multicolumn{2}{c}{HS} \\ +Dataset & KinGUI & \Rpackage{kinfit} & KinGUI & \Rpackage{kinfit} & +KinGUI & \Rpackage{kinfit} & KinGUI & \Rpackage{kinfit} \\ +\midrule +\input{chi2_comparison} +\bottomrule +\end{tabular} +\end{table} + +The comparison shows that whenever a minimum error level $\chi^2$ was +calculated using the \Rpackage{kinfit} package, it was very close to +the value generated by KinGUI. + +\section{Conclusion} + +The \Rpackage{kinfit} package for \RR{} gives access to the possibility to +fit the kinetic models recommended by the FOCUS group \citep{FOCUS2006} +from within \RR. Comparison with the results obtained with other +software packages shows that \Rpackage{kinfit} produces kinetic endpoints that +are within the variability and even very close to the median of results obtained +with other packages, except for some cases where \Rpackage{kinfit} does not +produce results and the results obtained with other software packages are +strongly divergent. + +\bibliographystyle{plainnat} +\bibliography{references} + +\end{document} +% vim: set foldmethod=marker: diff --git a/inst/doc/kinfit.pdf b/inst/doc/kinfit.pdf new file mode 100644 index 0000000..e54106c Binary files /dev/null and b/inst/doc/kinfit.pdf differ diff --git a/inst/doc/references.bib b/inst/doc/references.bib new file mode 100644 index 0000000..53e3bea --- /dev/null +++ b/inst/doc/references.bib @@ -0,0 +1,38 @@ +@Manual{pkg:kinfit, + title = {kinfit: {R}outines for fitting kinetic models to chemical degradation data}, + author = {kinfit}, + year = {2009}, + note = {R package version 1.0-0}, + url = {http://CRAN.R-project.org} +} + +@Manual{ rcore2009, + title = {\textsf{R}: A Language and Environment for Statistical + Computing}, + author = {{R Development Core Team}}, + organization = {R Foundation for Statistical Computing}, + address = {Vienna, Austria}, + year = 2009, + note = {{ISBN} 3-900051-07-0}, + url = {http://www.R-project.org} +} + +@Manual{ FOCUS2006, + title = {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}, + note = {EC Document Reference Sanco/10058/2005 version 2.0}, + author = {{FOCUS Work Group on Degradation Kinetics}}, + year = {2006}, + url = {http://focus.jrc.ec.europa.eu/dk} +} + +@Inproceedings{ schaefer2007, + title = {{KinGUI}: a new kinetic software tool for evaluations according to FOCUS degradation kinetics}, + author = {D. Sch\"{a}fer and M. Kikolasch and P. Rainbird and B. Harvey}, + booktitle = {Proceedings of the XIII Symposium Pesticide Chemistry}, + editor = {Del Re A. A. M. and Capri E. and Fragoulis G. and Trevisan M.}, + year = {2007}, + address = {Piacenza}, + pages = {916--923} +} diff --git a/inst/doc/run.bat b/inst/doc/run.bat new file mode 100644 index 0000000..530c31e --- /dev/null +++ b/inst/doc/run.bat @@ -0,0 +1,5 @@ +R.exe -e "Sweave('kinfit.Rnw', stylepath=FALSE)" +pdflatex.exe kinfit +bibtex.exe kinfit +pdflatex.exe kinfit +pdflatex.exe kinfit diff --git a/man/DFOP.Rd b/man/DFOP.Rd new file mode 100644 index 0000000..129b3b1 --- /dev/null +++ b/man/DFOP.Rd @@ -0,0 +1,37 @@ +\name{DFOP} +\Rdversion{1.1} +\alias{DFOP} +\title{ +Dual First-Order in Parallel kinetics +} +\description{ + Function describing decline from a defined starting value using the sum + of two exponential decline functions. +} +\usage{ +DFOP(t, parent.0, k1, k2, g) +} +\arguments{ + \item{t}{ Time. } + \item{parent.0}{ Starting value for the response variable at time zero. } + \item{k1}{ First kinetic constant. } + \item{k2}{ Second kinetic constant. } + \item{g}{ Fraction of the starting value declining according to the + first kinetic constant. + } +} +\value{ + The value of the response variable at time \code{t}. +} +\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://focus.jrc.ec.europa.eu/dk} +} +\author{ Johannes Ranke } +\examples{ + \dontrun{plot(function(x) DFOP(x, 100, 5, 0.5, 0.3), 0, 4, ylim=c(0,100))} +} +\keyword{ manip } diff --git a/man/FOCUS_2006_A.Rd b/man/FOCUS_2006_A.Rd new file mode 100644 index 0000000..218004e --- /dev/null +++ b/man/FOCUS_2006_A.Rd @@ -0,0 +1,29 @@ +\name{FOCUS_2006_A} +\Rdversion{1.1} +\alias{FOCUS_2006_A} +\docType{data} +\title{ +Dataset A from the FOCUS Kinetics report from 2006 +} +\description{ +Data generated using a model and assuming some variability. +} +\usage{data(FOCUS_2006_A)} +\format{ + A data frame with 8 observations on the following 2 variables. + \describe{ + \item{\code{t}}{a numeric vector containing time points} + \item{\code{parent}}{a numeric vector containing parent concentrations in percent of applied radioactivity} + } +} +\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_A) +} +\keyword{datasets} diff --git a/man/FOCUS_2006_B.Rd b/man/FOCUS_2006_B.Rd new file mode 100644 index 0000000..112056a --- /dev/null +++ b/man/FOCUS_2006_B.Rd @@ -0,0 +1,29 @@ +\name{FOCUS_2006_B} +\Rdversion{1.1} +\alias{FOCUS_2006_B} +\docType{data} +\title{ +Dataset B from the FOCUS Kinetics report from 2006 +} +\description{ +Data generated using a model and assuming some variability. +} +\usage{data(FOCUS_2006_B)} +\format{ + A data frame with 8 observations on the following 2 variables. + \describe{ + \item{\code{t}}{a numeric vector containing time points} + \item{\code{parent}}{a numeric vector containing parent concentrations in percent of applied radioactivity} + } +} +\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_B) +} +\keyword{datasets} diff --git a/man/FOCUS_2006_C.Rd b/man/FOCUS_2006_C.Rd new file mode 100644 index 0000000..a20bc82 --- /dev/null +++ b/man/FOCUS_2006_C.Rd @@ -0,0 +1,30 @@ +\name{FOCUS_2006_C} +\Rdversion{1.1} +\alias{FOCUS_2006_C} +\docType{data} +\title{ +Dataset C from the FOCUS Kinetics report from 2006 +} +\description{ +Data taken from an \dQuote{existing dataset}. +} +\usage{data(FOCUS_2006_C)} +\format{ + A data frame with 9 observations on the following 2 variables. + \describe{ + \item{\code{t}}{a numeric vector containing time points} + \item{\code{parent}}{a numeric vector containing parent concentrations in percent of applied radioactivity} + } +} +\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} +} +\note{ This dataset is just a subset of \code{\link{FOCUS_2006_E}}. } +\examples{ +data(FOCUS_2006_C) +} +\keyword{datasets} diff --git a/man/FOCUS_2006_D.Rd b/man/FOCUS_2006_D.Rd new file mode 100644 index 0000000..c548f8d --- /dev/null +++ b/man/FOCUS_2006_D.Rd @@ -0,0 +1,33 @@ +\name{FOCUS_2006_D} +\Rdversion{1.1} +\alias{FOCUS_2006_D} +\docType{data} +\title{ +Dataset D from the FOCUS Kinetics report from 2006 +} +\description{ +Data taken from an \dQuote{existing dataset}. At each time point two data +points were generated, as the experiment was performed in duplicate. +} +\usage{data(FOCUS_2006_D)} +\format{ + A data frame with 10 observations on the following 2 variables. + \describe{ + \item{\code{t}}{a numeric vector containing time points} + \item{\code{parent}}{a numeric vector containing parent concentrations + in percent of applied radioactivity} + \item{\code{m1}}{a numeric vector containing concentrations of metabolite 1 + in percent of applied radioactivity} + } +} +\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_D) +} +\keyword{datasets} 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..b0b01d7 --- /dev/null +++ b/man/FOCUS_2006_DFOP_ref_A_to_B.Rd @@ -0,0 +1,43 @@ +\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} + } +} +\note{ + The comparison of these results with the results obtained with the + current version of \code{kinfit} can be found in the package vignette. +} +\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_E.Rd b/man/FOCUS_2006_E.Rd new file mode 100644 index 0000000..7ae905b --- /dev/null +++ b/man/FOCUS_2006_E.Rd @@ -0,0 +1,32 @@ +\name{FOCUS_2006_E} +\Rdversion{1.1} +\alias{FOCUS_2006_E} +\docType{data} +\title{ +Dataset E from the FOCUS Kinetics report from 2006 +} +\description{ +Data taken from an \dQuote{existing dataset}. +} +\usage{data(FOCUS_2006_E)} +\format{ + A data frame with 9 observations on the following 3 variables. + \describe{ + \item{\code{t}}{a numeric vector containing time points} + \item{\code{parent}}{a numeric vector containing parent concentrations + in percent of applied radioactivity} + \item{\code{m1}}{a numeric vector containing concentrations of metabolite 1 + in percent of applied radioactivity} + } +} +\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_E) +} +\keyword{datasets} diff --git a/man/FOCUS_2006_F.Rd b/man/FOCUS_2006_F.Rd new file mode 100644 index 0000000..87bd1af --- /dev/null +++ b/man/FOCUS_2006_F.Rd @@ -0,0 +1,32 @@ +\name{FOCUS_2006_F} +\Rdversion{1.1} +\alias{FOCUS_2006_F} +\docType{data} +\title{ +Water sediment study dataset F from the FOCUS Kinetics report from 2006 +} +\description{ +Data taken from an \dQuote{existing dataset}. +} +\usage{data(FOCUS_2006_F)} +\format{ + A data frame with 9 observations on the following 3 variables. + \describe{ + \item{\code{t}}{a numeric vector containing time points} + \item{\code{parent.water}}{a numeric vector containing parent + concentrations in water in percent of applied radioactivity} + \item{\code{parent.sediment}}{a numeric vector containing parent + concentrations in water in percent of applied radioactivity} + } +} +\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_F) +} +\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..8710046 --- /dev/null +++ b/man/FOCUS_2006_FOMC_ref_A_to_F.Rd @@ -0,0 +1,42 @@ +\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} + } +} +\note{ + The comparison of these results with the results obtained with the + current version of \code{kinfit} can be found in the package vignette. +} +\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..4ed8555 --- /dev/null +++ b/man/FOCUS_2006_HS_ref_A_to_F.Rd @@ -0,0 +1,43 @@ +\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} + } +} +\note{ + The comparison of these results with the results obtained with the + current version of \code{kinfit} can be found in the package vignette. +} +\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..fb6b304 --- /dev/null +++ b/man/FOCUS_2006_SFO_ref_A_to_F.Rd @@ -0,0 +1,41 @@ +\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} + } +} +\note{ + The comparison of these results with the results obtained with the + current version of \code{kinfit} can be found in the package vignette. +} +\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/FOMC.Rd b/man/FOMC.Rd new file mode 100644 index 0000000..7228b1b --- /dev/null +++ b/man/FOMC.Rd @@ -0,0 +1,49 @@ +\name{FOMC} +\Rdversion{1.1} +\alias{FOMC} +\title{ First-Order Multi-Compartment kinetics } +\description{ + Function describing exponential decline from a defined starting value, with + a decreasing rate constant. + + The form given here differs slightly from the original reference by Gustafson + and Holden (1990). The parameter \code{beta} corresponds to 1/beta in the + original equation. +} +\usage{ +FOMC(t, parent.0, alpha, beta) +} +\arguments{ + \item{t}{ Time. } + \item{parent.0}{ Starting value for the response variable at time zero. } + \item{alpha}{ + Shape parameter determined by coefficient of variation of rate constant + values. } + \item{beta}{ + Location parameter. +} +} +\note{ + The FOMC kinetic model reduces to the \code{\link{SFO}} kinetic model for + large values of \code{alpha} and \code{beta} with + \eqn{k = \frac{\beta}{\alpha}}{k = beta/alpha}. +} +\value{ + The value of the response variable at time \code{t}. +} +\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://focus.jrc.ec.europa.eu/dk} + + Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: A + new model based on spatial variability. \emph{Environmental Science and + Technology} \bold{24}, 1032-1038 +} +\author{ Johannes Ranke } +\examples{ + \dontrun{plot(function(x) FOMC(x, 100, 10, 2), 0, 2)} +} +\keyword{ manip } diff --git a/man/HS.Rd b/man/HS.Rd new file mode 100644 index 0000000..9adbd18 --- /dev/null +++ b/man/HS.Rd @@ -0,0 +1,35 @@ +\name{HS} +\Rdversion{1.1} +\alias{HS} +\title{ Hockey-Stick kinetics } +\description{ + Function describing two exponential decline functions with a break point + between them. +} +\usage{ +HS(t, parent.0, k1, k2, tb) +} +\arguments{ + \item{t}{ Time. } + \item{parent.0}{ Starting value for the response variable at time zero. } + \item{k1}{ First kinetic constant. } + \item{k2}{ Second kinetic constant. } + \item{tb}{ Break point. Before this time, exponential decline according + to \code{k1} is calculated, after this time, exponential decline proceeds + according to \code{k2}. } +} +\value{ + The value of the response variable at time \code{t}. +} +\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://focus.jrc.ec.europa.eu/dk} +} +\author{ Johannes Ranke } +\examples{ + \dontrun{plot(function(x) HS(x, 100, 2, 0.3, 0.5), 0, 2, ylim=c(0,100))} +} +\keyword{ manip } diff --git a/man/SFO.Rd b/man/SFO.Rd new file mode 100644 index 0000000..e4986da --- /dev/null +++ b/man/SFO.Rd @@ -0,0 +1,30 @@ +\name{SFO} +\Rdversion{1.1} +\alias{SFO} +\title{ Single First-Order kinetics } +\description{ + Function describing exponential decline from a defined starting value. +} +\usage{ + SFO(t, parent.0, k) +} +\arguments{ + \item{t}{ Time. } + \item{parent.0}{ Starting value for the response variable at time zero. } + \item{k}{ Kinetic constant. } +} +\value{ + The value of the response variable at time \code{t}. +} +\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://focus.jrc.ec.europa.eu/dk} +} +\author{ Johannes Ranke } +\examples{ + \dontrun{plot(function(x) SFO(x, 100, 3), 0, 2)} +} +\keyword{ manip } diff --git a/man/kinerrmin.Rd b/man/kinerrmin.Rd new file mode 100644 index 0000000..1afddf0 --- /dev/null +++ b/man/kinerrmin.Rd @@ -0,0 +1,43 @@ +\name{kinerrmin} +\Rdversion{1.1} +\alias{kinerrmin} +\title{ +Calculate the minimum error to assume in order to pass the variance test +} +\description{ +This function uses \code{\link{optimize}} in order to iteratively find the +smallest relative error still resulting in passing the chi-squared test +as defined in the FOCUS kinetics report from 2006. +} +\usage{ +kinerrmin(kinfits, kinmodel = "SFO", alpha = 0.05) +} +\arguments{ + \item{kinfits}{ +The list of kinetic model(s) from which to select. Usually this will have been +generated by \code{\link{kinfit}}. +} + \item{kinmodel}{ +The kinetic model to be checked. Should be one of the names of the kinetic models used for generating \code{kinfits}. +} + \item{alpha}{ +The confidence level chosen for the chi-squared test. +} +} +\value{ +The relative error, expressed as a fraction. +} +\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://focus.jrc.ec.europa.eu/dk} +} +\author{ Johannes Ranke } +\examples{ +data(FOCUS_2006_A) +kinfits <- kinfit(FOCUS_2006_A) +kinerrmin(kinfits) +} +\keyword{ manip } diff --git a/man/kinfit.Rd b/man/kinfit.Rd new file mode 100644 index 0000000..f0301fd --- /dev/null +++ b/man/kinfit.Rd @@ -0,0 +1,77 @@ +\name{kinfit} +\Rdversion{1.1} +\alias{kinfit} +\title{ +Fit kinetic models to chemical degradation data +} +\description{ + A selection of kinetic models as defined in the FOCUS kinetics report from + 2006 are fitted to a given dataframe of chemical degradation data. +} +\usage{ +kinfit(kindata, kinmodels = c("SFO"), parent.0.user = NA, + start.SFO = list(parent.0 = NA, k = NA), + start.FOMC = list(parent.0 = NA, alpha = NA, beta = NA), + start.DFOP = list(parent.0 = NA, k1 = NA, k2 = NA, g = NA), + start.HS = list(parent.0 = NA, k1 = NA, k2 = NA, tb = NA), + algorithm = "port") +} +\arguments{ + \item{kindata}{ + A data frame containing a time variable named \code{t} and concentration + data for the parent compound named \code{parent}. + } + \item{kinmodels}{ + An array of character strings which are names of the models to be fit. + Possible names are \code{\link{SFO}}, \code{\link{FOMC}}, \code{\link{DFOP}} + and \code{\link{HS}}. + } + \item{parent.0.user}{ + The user can give a starting estimate for parent.0 here, overriding other + potential sources for starting values as specified below. + } + \item{start.SFO}{ + A list of starting parameters for fitting the \code{\link{SFO}} model, + containing \code{parent.0} and \code{k}. + } + \item{start.FOMC}{ + A list of starting parameters for fitting the \code{\link{FOMC}} model, + containing \code{parent.0}, \code{alpha} and \code{beta}. + } + \item{start.DFOP}{ + A list of starting parameters for fitting the \code{\link{DFOP}} model, + containing \code{parent.0}, \code{k1}, \code{k2} and \code{g}. + } + \item{start.HS}{ + A list of starting parameters for fitting the \code{\link{HS}} model, + containing \code{parent.0}, \code{k1}, \code{k2} and \code{tb}. + } + \item{algorithm}{ + The algorithm to use for the calls to \code{\link{nls}}. + } +} +\details{ + Per default all starting parameters are \code{NA} and the function tries to + find suitable starting parameters on its own. +} +\value{ + A list of models of class \code{nls} representing the models that were + fitted successfully. +} +\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://focus.jrc.ec.europa.eu/dk} +} +\author{ Johannes Ranke } +\examples{ +data(FOCUS_2006_A) +(kinfits <- kinfit(FOCUS_2006_A)) +data(FOCUS_2006_B) +(kinfits <- kinfit(FOCUS_2006_B, kinmodels=c("SFO","FOMC"))) +} +\keyword{ models } +\keyword{ regression } +\keyword{ nonlinear } diff --git a/man/kinobject.Rd b/man/kinobject.Rd new file mode 100644 index 0000000..cd6f0ca --- /dev/null +++ b/man/kinobject.Rd @@ -0,0 +1,29 @@ +\name{kinobject} +\Rdversion{1.1} +\alias{kinobject} +\title{ +Creates list representing a kinetic experiment or trial +} +\description{ +Function to initialise an object representing a kinetic experiment or trial. +} +\usage{ + kinobject(parent, type, system, layers = NA, sampling_times = NA) +} +\arguments{ + \item{parent}{ The name of the parent compound } + \item{type}{ The type of experiment or trial, optionally with an ID } + \item{system}{ System name. Important if several systems were used, e.g. several soils. } + \item{layers}{ Optional specification of the layer names in a field trial. } + \item{sampling_times}{ Optional specification of the sampling time pionts. } +} +\value{ + A list containing the specified information. +} +\author{ Johannes Ranke } +\examples{ +ko <- kinobject("Compound XY", + "Degradation in the environment", + "System 1") +} +\keyword{ manip } diff --git a/man/kinobjects.Rd b/man/kinobjects.Rd new file mode 100644 index 0000000..7c960f3 --- /dev/null +++ b/man/kinobjects.Rd @@ -0,0 +1,29 @@ +\name{kinobjects} +\Rdversion{1.1} +\alias{kinobjects} +\title{ +Creates list of objects, each representing a kinetic experiment or trial +} +\description{ +Function to initialise several objects representing a kinetic experiment or trial at once. +} +\usage{ + kinobjects(parent, type, systems, layers = NA, sampling_times = NA) +} +\arguments{ + \item{parent}{ The name of the parent compound } + \item{type}{ The type of experiment or trial, optionally with an ID } + \item{systems}{ An array of the system names } + \item{layers}{ Optional specification of the layer names in a field trial. } + \item{sampling_times}{ Optional specification of the sampling time pionts. } +} +\value{ + A list of lists containing the specified information. +} +\author{ Johannes Ranke } +\examples{ +ko <- kinobjects("Compound XY", + "Degradation in the environment", + c("System 1", "System 2", "System 3")) +} +\keyword{ manip } diff --git a/man/kinplot.Rd b/man/kinplot.Rd new file mode 100644 index 0000000..9e684b7 --- /dev/null +++ b/man/kinplot.Rd @@ -0,0 +1,50 @@ +\name{kinplot} +\Rdversion{1.1} +\alias{kinplot} +\title{ +Creates a plot of the kinetic fits +} +\description{ +Function to create a plot for a set of fitted models +} +\usage{ +kinplot(kinobject, xlab = "Time [days]", ylab = "Parent [\% of applied radioactivity]", ylim = c("auto", "auto"), lpos = "topright") +} +\arguments{ + \item{kinobject}{ + A list containing the following elements: + The name of the parent compound to be output (\code{parent}), + the type of the test system (\code{type}), + the name of the specific test system used for generating this dataset + (\code{system}), + the list of fitted kinetic models (\code{fits}), as returned by + \code{\link{kinfit}}, and the list of results (\code{results}) + as returned by \code{\link{kinresults}}. + Optionally also + the label position of the test compound (\code{label}) and + the source of the data (\code{source}). } + \item{xlab}{ Label for the x axis. } + \item{ylab}{ Label for the y axis. } + \item{ylim}{ An array of length two holding the range for values on the y axis or "auto". } + \item{lpos}{ Where should the legend be placed? Will be passed on to + \code{\link{legend}}. } +} +\value{ +The function is called for its side effect, namely creating a plot with +the fitted model. +} +\author{ Johannes Ranke } +\examples{ +data(FOCUS_2006_C) +kinfits <- kinfit(FOCUS_2006_C, kinmodels = c("SFO", "FOMC", "DFOP")) +kinobject <- list( + parent = "Compound XY", + type = "Degradation in the environment", + system = "System 1", + source = "Synthetic example data from FOCUS kinetics", + data = FOCUS_2006_C, + fits = kinfits, + results = kinresults(kinfits)) +\dontrun{kinplot(kinobject)} +} +\keyword{ hplot } diff --git a/man/kinreport.Rd b/man/kinreport.Rd new file mode 100644 index 0000000..de7e632 --- /dev/null +++ b/man/kinreport.Rd @@ -0,0 +1,48 @@ +\name{kinreport} +\Rdversion{1.1} +\alias{kinreport} +\title{ +Creates a report of the kinetic fits +} +\description{ +Function to create a report for a set of fitted models, passing it to the +console as well as to a file, if specified. +} +\usage{ +kinreport(kinobject, file = NA, vcov = FALSE, endpoint.digits = 1) +} +\arguments{ + \item{kinobject}{ + A list containing the following elements: + The name of the parent compound to be output (\code{parent}), + the type of the test system (\code{type}), + the name of the specific test system used for generating this dataset + (\code{system}), + the list of fitted kinetic models (\code{fits}), as returned by + \code{\link{kinfit}}, and the list of results (\code{results}) + as returned by \code{\link{kinresults}}. + Optionally also + the label position of the test compound (\code{label}) and + the source of the data (\code{source}). } + \item{file}{ The name of the file to which to write. } + \item{vcov}{ Should the variance-covariance matrix/matrices be reported? } + \item{endpoint.digits}{ How many digits should be reported for DT50 and DT90 values? } +} +\value{ +The function is called for its side effect, namely the report being passed +to the R console as well as to a text file. +} +\author{ Johannes Ranke } +\examples{ +data(FOCUS_2006_A) +kinfits <- kinfit(FOCUS_2006_A) +kinobject <- list( + parent = "Compound XY", + type = "Degradation in the environment", + system = "System 1", + source = "Synthetic example data from FOCUS kinetics", + fits = kinfits, + results = kinresults(kinfits)) +kinreport(kinobject) +} +\keyword{ manip } diff --git a/man/kinresplot.Rd b/man/kinresplot.Rd new file mode 100644 index 0000000..85ec333 --- /dev/null +++ b/man/kinresplot.Rd @@ -0,0 +1,49 @@ +\name{kinresplot} +\Rdversion{1.1} +\alias{kinresplot} +\title{ +Creates a plot of the residual for specified kinetic fits +} +\description{ +Function to create a residual plot for a specified fitted model +} +\usage{ +kinresplot(kinobject, kinmodel, xlab = "Time [days]", ylab = "Residual [\% of applied radioactivity]", maxabs = "auto") +} +\arguments{ + \item{kinobject}{ + A list containing the following elements: + The name of the parent compound to be output (\code{parent}), + the type of the test system (\code{type}), + the name of the specific test system used for generating this dataset + (\code{system}), + the list of fitted kinetic models (\code{fits}), as returned by + \code{\link{kinfit}}, and optionally the list of results + (\code{results}) as returned by \code{\link{kinresults}}. + Also optional is the label position of the test compound (\code{label}) + and the source of the data (\code{source}). } + \item{kinmodel}{ The fitted model for which the residuals should be plotted. } + \item{xlab}{ Label for the x axis. } + \item{ylab}{ Label for the y axis. } + \item{maxabs}{ Maximum value of the absolute residuals, will be calculated + from the residuals if not specified otherwise. } +} +\value{ +The function is called for its side effect, namely creating a residual plot +for the specified fit. +} +\author{ Johannes Ranke } +\examples{ +data(FOCUS_2006_C) +kinfits <- kinfit(FOCUS_2006_C) +kinobject <- list( + parent = "Compound XY", + type = "Degradation in the environment", + system = "System 1", + source = "Synthetic example data from FOCUS kinetics", + data = FOCUS_2006_C, + fits = kinfits, + results = kinresults(kinfits)) +\dontrun{kinresplot(kinobject, "SFO")} +} +\keyword{ hplot } diff --git a/man/kinresults.Rd b/man/kinresults.Rd new file mode 100644 index 0000000..6ab93a7 --- /dev/null +++ b/man/kinresults.Rd @@ -0,0 +1,45 @@ +\name{kinresults} +\Rdversion{1.1} +\alias{kinresults} +\title{ +Function to collect useful results for a set of fitted kinetic models +} +\description{ +This function collects the parameters and some statistics for the fitted kinetic +models. It also generates DT50 and DT90 estimates. +} +\usage{ +kinresults(kinfits, alpha = 0.05, SFORB = TRUE) +} +\arguments{ + \item{kinfits}{ +The list of kinetic model(s) for which to collect results. Usually this will +have been generated by \code{\link{kinfit}}. +} + \item{alpha}{ +The confidence level chosen for the chi-squared test used in the call to +\code{\link{kinerrmin}}. +} + \item{SFORB}{ +Should the results of the \code{\link{DFOP}} model be presented as parameters +to the Single First-Order Reversible Binding (SFORB) model? } +} +\value{ +A list containing a list of the parameters fitted by the models, a dataframe +containing some statistics for each of the fitted models, and a dataframe with +the resulting DT50 and DT90 values. +} +\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://focus.jrc.ec.europa.eu/dk} +} +\author{ Johannes Ranke } +\examples{ +data(FOCUS_2006_A) +kinfits <- kinfit(FOCUS_2006_A) +kinresults(kinfits) +} +\keyword{ manip } diff --git a/man/kinwrite.KinGUI.Rd b/man/kinwrite.KinGUI.Rd new file mode 100644 index 0000000..f5a5ddc --- /dev/null +++ b/man/kinwrite.KinGUI.Rd @@ -0,0 +1,47 @@ +\name{kinwrite.KinGUI} +\Rdversion{1.1} +\alias{kinwrite.KinGUI} +\encoding{latin1} +\title{ +Function to write KinGUI input files from kinetic data +} +\description{ +This function takes an R object as used by the \code{kinfit} package +and tries to write a text file which is compatible with the KinGUI +software tool. +} +\usage{ +kinwrite.KinGUI(kinobject, file, comment=NA) +} +\arguments{ + \item{kinobject}{ + A list containing the following elements: + The name of the parent compound to be output (\code{parent}), + the type of the test system (\code{type}), + the name of the specific test system used for generating this dataset + (\code{system}), + a data frame containing the raw data (\code{data}), + which should be in the same form as required by + by \code{\link{kinfit}}. +} + \item{file}{ +The filename, potentially including the full path, specifying where the output whould be written. +} + \item{comment}{ +An optional comment that will be integrated in the header of the KinGUI input file. +} +} +\value{ +The function is called for its side effect, namely the generation of a text file. +} +\references{ +Schäfer D, Kikolasch M, Rainbird P and Harvey B (2007). KinGUI: a new kinetic software tool for evaluations according to FOCUS degradation kinetics. In: Del Re AAM, Capri E, Fragoulis G and Trevisan M (Eds.). Proceedings of the XIII Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923. +} +\note{ +The KinGUI software tool was announced to be freely available on CD from the main author of the paper cited above, Dieter Schäfer . +} +\author{ +Johannes Ranke +} + +\keyword{ IO } diff --git a/tests/test_FOCUS_2006_A.R b/tests/test_FOCUS_2006_A.R new file mode 100644 index 0000000..2077315 --- /dev/null +++ b/tests/test_FOCUS_2006_A.R @@ -0,0 +1,25 @@ +library(kinfit) +data(FOCUS_2006_A) +fits <- kinfit(FOCUS_2006_A, kinmodels = c("SFO", "HS")) +print(kinresults(fits)$results, digits=5) +print(kinresults(fits)$stats, digits=5) + +data(FOCUS_2006_B) +fits <- kinfit(FOCUS_2006_B, kinmodels = c("SFO", "FOMC", "DFOP")) +print(kinresults(fits)$results, digits=5) +print(kinresults(fits)$stats, digits=5) + +data(FOCUS_2006_C) +fits <- kinfit(FOCUS_2006_C, kinmodels = c("SFO", "FOMC", "DFOP")) +print(kinresults(fits)$results, digits=5) +print(kinresults(fits)$stats, digits=5) + +data(FOCUS_2006_D) +fits <- kinfit(FOCUS_2006_D, kinmodels = c("SFO", "FOMC")) +print(kinresults(fits)$results, digits=5) +print(kinresults(fits)$stats, digits=5) + +data(FOCUS_2006_E) +fits <- kinfit(FOCUS_2006_E, kinmodels = c("SFO", "FOMC", "DFOP")) +print(kinresults(fits)$results, digits=5) +print(kinresults(fits)$stats, digits=5) diff --git a/tests/test_FOCUS_2006_A.Rout.save b/tests/test_FOCUS_2006_A.Rout.save new file mode 100644 index 0000000..a26b701 --- /dev/null +++ b/tests/test_FOCUS_2006_A.Rout.save @@ -0,0 +1,79 @@ + +R version 2.10.0 (2009-10-26) +Copyright (C) 2009 The R Foundation for Statistical Computing +ISBN 3-900051-07-0 + +R is free software and comes with ABSOLUTELY NO WARRANTY. +You are welcome to redistribute it under certain conditions. +Type 'license()' or 'licence()' for distribution details. + +R is a collaborative project with many contributors. +Type 'contributors()' for more information and +'citation()' on how to cite R or R packages in publications. + +Type 'demo()' for some demos, 'help()' for on-line help, or +'help.start()' for an HTML browser interface to help. +Type 'q()' to quit R. + +> library(kinfit) +> data(FOCUS_2006_A) +> fits <- kinfit(FOCUS_2006_A, kinmodels = c("SFO", "HS")) +> print(kinresults(fits)$results, digits=5) + DT50 DT90 +SFO 18.624 61.868 +HS 20.294 49.854 +> print(kinresults(fits)$stats, digits=5) + n.times df mean.means RSS err.min +SFO 8 6 50.054 221.8078 0.083848 +HS 8 4 50.054 6.6927 0.016766 +> +> data(FOCUS_2006_B) +> fits <- kinfit(FOCUS_2006_B, kinmodels = c("SFO", "FOMC", "DFOP")) +> print(kinresults(fits)$results, digits=5) + DT50 DT90 +SFO 8.8686 29.461 +FOMC 8.6834 30.754 +DFOP 8.6829 30.789 +> print(kinresults(fits)$stats, digits=5) + n.times df mean.means RSS err.min +SFO 8 6 35.015 30.656 0.044555 +FOMC 8 5 35.015 28.583 0.045886 +DFOP 8 4 35.015 28.550 0.049527 +> +> data(FOCUS_2006_C) +> fits <- kinfit(FOCUS_2006_C, kinmodels = c("SFO", "FOMC", "DFOP")) +> print(kinresults(fits)$results, digits=5) + DT50 DT90 +SFO 2.2647 7.5232 +FOMC 1.7852 15.1479 +DFOP 1.8869 21.2507 +> print(kinresults(fits)$stats, digits=5) + n.times df mean.means RSS err.min +SFO 9 7 23.589 196.5334 0.158440 +FOMC 9 6 23.589 31.0509 0.066568 +DFOP 9 5 23.589 4.3627 0.026621 +> +> data(FOCUS_2006_D) +> fits <- kinfit(FOCUS_2006_D, kinmodels = c("SFO", "FOMC")) +> print(kinresults(fits)$results, digits=5) + DT50 DT90 +SFO 7.0776 23.511 +FOMC 6.9350 24.044 +> print(kinresults(fits)$stats, digits=5) + n.times df mean.means RSS err.min +SFO 9 7 39.523 207.63 0.064524 +FOMC 9 6 39.523 205.45 0.067802 +> +> data(FOCUS_2006_E) +> fits <- kinfit(FOCUS_2006_E, kinmodels = c("SFO", "FOMC", "DFOP")) +> print(kinresults(fits)$results, digits=5) + DT50 DT90 +SFO 2.2647 7.5232 +FOMC 1.7852 15.1479 +DFOP 1.8869 21.2507 +> print(kinresults(fits)$stats, digits=5) + n.times df mean.means RSS err.min +SFO 9 7 23.589 196.5334 0.158440 +FOMC 9 6 23.589 31.0509 0.066568 +DFOP 9 5 23.589 4.3627 0.026621 +> -- cgit v1.2.1