From 3a6b9f52c74d6ef88a8d32c50e42864b3f251719 Mon Sep 17 00:00:00 2001 From: jranke Date: Thu, 15 Mar 2012 15:54:14 +0000 Subject: Update kinfit and mkin to the latest version published on BerliOS. git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/kinfit@17 edb9625f-4e0d-4859-8d74-9fd3b1da38cb --- DESCRIPTION | 15 ++- NAMESPACE | 5 + R/kinerrmin.R | 20 ++++ R/kinfit.R | 115 +++++++++++++++---- R/kinobject.R | 20 ++++ R/kinobjects.R | 20 ++++ R/kinplot.R | 128 ++++++++++++++------- R/kinreport.R | 97 +++++++++++----- R/kinresplot.R | 23 +++- R/kinresults.R | 175 ++++++++++++++++++++--------- R/kinwrite.KinGUI.R | 20 ++++ inst/doc/KinGUI/A_DFOP_report_detailed.txt | 86 ++++++++++++++ inst/doc/KinGUI/A_FOMC_report_detailed.txt | 83 ++++++++++++++ inst/doc/KinGUI/A_HS_report_detailed.txt | 86 ++++++++++++++ inst/doc/KinGUI/A_KinGUI.txt | 26 ++--- inst/doc/KinGUI/A_SFO_report_detailed.txt | 80 +++++++++++++ inst/doc/KinGUI/B_DFOP_report_detailed.txt | 86 ++++++++++++++ inst/doc/KinGUI/B_FOMC_report_detailed.txt | 83 ++++++++++++++ inst/doc/KinGUI/B_HS_report_detailed.txt | 86 ++++++++++++++ inst/doc/KinGUI/B_KinGUI.txt | 26 ++--- inst/doc/KinGUI/B_SFO_report_detailed.txt | 80 +++++++++++++ inst/doc/KinGUI/C_DFOP_report_detailed.txt | 87 ++++++++++++++ inst/doc/KinGUI/C_FOMC_report_detailed.txt | 84 ++++++++++++++ inst/doc/KinGUI/C_HS_report_detailed.txt | 87 ++++++++++++++ inst/doc/KinGUI/C_KinGUI.txt | 28 ++--- inst/doc/KinGUI/C_SFO_report_detailed.txt | 81 +++++++++++++ inst/doc/KinGUI/D_DFOP_report_detailed.txt | 100 +++++++++++++++++ inst/doc/KinGUI/D_FOMC_report_detailed.txt | 97 ++++++++++++++++ inst/doc/KinGUI/D_HS_report_detailed.txt | 100 +++++++++++++++++ inst/doc/KinGUI/D_KinGUI.txt | 54 ++++----- inst/doc/KinGUI/D_SFO_report_detailed.txt | 94 ++++++++++++++++ inst/doc/KinGUI/F_system_KinGUI.txt | 28 ++--- inst/doc/KinGUI/F_water_KinGUI.txt | 28 ++--- inst/doc/kinfit.Rnw | 83 +++++++++++++- inst/doc/kinfit.pdf | Bin 177393 -> 264306 bytes inst/doc/references.bib | 4 +- man/kinfit.Rd | 8 +- man/kinobject.Rd | 2 +- man/kinobjects.Rd | 2 +- man/kinplot.Rd | 4 +- man/kinreport.Rd | 11 +- man/kinresplot.Rd | 2 +- man/kinresults.Rd | 9 +- man/kinwrite.KinGUI.Rd | 2 +- tests/test_FOCUS_2006_A.R | 20 ++++ tests/test_FOCUS_2006_A.Rout.save | 65 +++++++---- 46 files changed, 2164 insertions(+), 276 deletions(-) create mode 100644 NAMESPACE create mode 100644 inst/doc/KinGUI/A_DFOP_report_detailed.txt create mode 100644 inst/doc/KinGUI/A_FOMC_report_detailed.txt create mode 100644 inst/doc/KinGUI/A_HS_report_detailed.txt create mode 100644 inst/doc/KinGUI/A_SFO_report_detailed.txt create mode 100644 inst/doc/KinGUI/B_DFOP_report_detailed.txt create mode 100644 inst/doc/KinGUI/B_FOMC_report_detailed.txt create mode 100644 inst/doc/KinGUI/B_HS_report_detailed.txt create mode 100644 inst/doc/KinGUI/B_SFO_report_detailed.txt create mode 100644 inst/doc/KinGUI/C_DFOP_report_detailed.txt create mode 100644 inst/doc/KinGUI/C_FOMC_report_detailed.txt create mode 100644 inst/doc/KinGUI/C_HS_report_detailed.txt create mode 100644 inst/doc/KinGUI/C_SFO_report_detailed.txt create mode 100644 inst/doc/KinGUI/D_DFOP_report_detailed.txt create mode 100644 inst/doc/KinGUI/D_FOMC_report_detailed.txt create mode 100644 inst/doc/KinGUI/D_HS_report_detailed.txt create mode 100644 inst/doc/KinGUI/D_SFO_report_detailed.txt diff --git a/DESCRIPTION b/DESCRIPTION index 11dced9..622a9a0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,11 +1,16 @@ Package: kinfit Type: Package Title: Routines for fitting kinetic models to chemical degradation data -Version: 1.0.2 -Date: 2010-05-20 -Author: Johannes Ranke -Maintainer: Johannes Ranke +Version: 1.1.06 +Date: 2011-11-09 +Author: Johannes Ranke and Katrin Lindenberger +Maintainer: Johannes Ranke Description: Simple calculation routines based on the FOCUS Kinetics - Report (2006) + Report (2006). Only kinetic models for parent only datasets are + included (no metabolite formation/decline or multicompartment kinetics). + Please note that no warranty is implied for correctness of results or + fitness for a particular purpose. License: GPL LazyLoad: yes +LazyData: yes +URL: http://cran.r-project.org, http://developer.berlios.de/projects/mkin/ diff --git a/NAMESPACE b/NAMESPACE new file mode 100644 index 0000000..cd24e63 --- /dev/null +++ b/NAMESPACE @@ -0,0 +1,5 @@ +# Default NAMESPACE created by R +# Remove the previous line if you edit this file + +# Export all names +exportPattern(".") diff --git a/R/kinerrmin.R b/R/kinerrmin.R index 8ce30a3..dbd64b3 100644 --- a/R/kinerrmin.R +++ b/R/kinerrmin.R @@ -1,3 +1,23 @@ +# $Id: kinerrmin.R 59 2010-07-28 12:29:15Z jranke $ + +# Copyright (C) 2008-2010 Johannes Ranke +# Contact: mkin-devel@lists.berlios.de + +# This file is part of the R package kinfit + +# kinfit is free software: you can redistribute it and/or modify it under the +# terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + kinerrmin <- function(kinfits, kinmodel = "SFO", alpha = 0.05) { m = kinfits[[kinmodel]] diff --git a/R/kinfit.R b/R/kinfit.R index 42a6520..d55180e 100644 --- a/R/kinfit.R +++ b/R/kinfit.R @@ -1,43 +1,76 @@ +# $Id: kinfit.R 116 2011-06-14 08:46:47Z kati $ + +# Copyright (C) 2008-2010 Johannes Ranke +# Contact: mkin-devel@lists.berlios.de + +# This file is part of the R package kinfit + +# kinfit is free software: you can redistribute it and/or modify it under the +# terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + kinfit <- function(kindata, kinmodels = c("SFO"), parent.0.user = NA, + parent.0.fixed = FALSE, 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") + algorithm = "default") { + kindata <- subset(kindata, !is.na(kindata$parent)) kinfits <- list() if (!is.na(parent.0.user)) { start.SFO$parent.0 = parent.0.user start.FOMC$parent.0 = parent.0.user + start.DFOP$parent.0 = parent.0.user + start.HS$parent.0 = parent.0.user } lmlogged = lm(log(parent) ~ t, data = kindata) + k.est = -coef(lmlogged)[["t"]] for (kinmodel in kinmodels) { if (kinmodel == "SFO") { if (is.na(start.SFO$parent.0)) { - start.SFO$parent.0 = max(kindata$parent) + 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) + if (parent.0.fixed) + { + start.SFO = start.SFO[-1] + kinfits[[kinmodel]] = try( + nls(parent ~ SFO(t, parent.0.user, k), + data = kindata, model = TRUE, + start = start.SFO, + algorithm = algorithm), silent=TRUE) + } else { + kinfits[[kinmodel]] = try( + nls(parent ~ SFO(t, parent.0, k), + data = kindata, model = TRUE, + start = start.SFO, + algorithm = algorithm), silent=TRUE) + } + k.est = coef(kinfits$SFO)[["k"]] } - k.est = ifelse(is.na(coef(kinfits$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) + start.FOMC$parent.0 = max(kindata$parent) } if (is.na(start.FOMC$alpha)) { start.FOMC$alpha = 1 @@ -45,15 +78,29 @@ kinfit <- function(kindata, kinmodels = c("SFO"), if (is.na(start.FOMC$beta)) { start.FOMC$beta = start.FOMC$alpha / k.est } - kinfits[[kinmodel]] = try( - nls(parent ~ FOMC(t, parent.0, alpha, beta), - data = kindata, model = TRUE, - start = start.FOMC, - algorithm = algorithm), silent=TRUE) + + if (parent.0.fixed) + { + start.FOMC = list(alpha = start.FOMC$alpha, beta = start.FOMC$beta) + + kinfits[[kinmodel]] = try( + nls(parent ~ FOMC(t, parent.0.user, alpha, beta), + data = kindata, model = TRUE, + start = start.FOMC, + algorithm = algorithm), silent=TRUE) + + } else { + kinfits[[kinmodel]] = try( + nls(parent ~ FOMC(t, parent.0, alpha, beta), + data = kindata, model = TRUE, + start = start.FOMC, + algorithm = algorithm), silent=TRUE) + + } } if (kinmodel == "DFOP") { if (is.na(start.DFOP$parent.0)) { - start.DFOP$parent.0 = max(kindata$parent) + start.DFOP$parent.0 = max(kindata$parent) } if (is.na(start.DFOP$k1)) { start.DFOP$k1 = k.est * 2 @@ -64,15 +111,26 @@ kinfit <- function(kindata, kinmodels = c("SFO"), if (is.na(start.DFOP$g)) { start.DFOP$g = 0.5 } - kinfits[[kinmodel]] = try( + if (parent.0.fixed) + { + start.DFOP = list(k1 = start.DFOP$k1, k2 = start.DFOP$k2, g = start.DFOP$g) + + kinfits[[kinmodel]] = try( + nls(parent ~ DFOP(t, parent.0.user, k1, k2, g), + data = kindata, model = TRUE, + start = start.DFOP, + algorithm = algorithm), silent=TRUE) + }else{ + kinfits[[kinmodel]] = try( nls(parent ~ DFOP(t, parent.0, k1, k2, g), data = kindata, model = TRUE, start = start.DFOP, - algorithm = algorithm), silent=TRUE) + algorithm = algorithm), silent=TRUE) + } } if (kinmodel == "HS") { if (is.na(start.HS$parent.0)) { - start.HS$parent.0 = max(kindata$parent) + start.HS$parent.0 = max(kindata$parent) } if (is.na(start.HS$k1)) { start.HS$k1 = k.est @@ -83,11 +141,24 @@ kinfit <- function(kindata, kinmodels = c("SFO"), if (is.na(start.HS$tb)) { start.HS$tb = 0.05 * max(kindata$t) } - kinfits[[kinmodel]] = try( + + if (parent.0.fixed) + { + + start.HS = list(k1 = start.HS$k1, k2 = start.HS$k2, tb = start.HS$tb) + + kinfits[[kinmodel]] = try( + nls(parent ~ HS(t, parent.0.user, k1, k2, tb), + data = kindata, model = TRUE, + start = start.HS, + algorithm = algorithm), silent=TRUE) + }else{ + kinfits[[kinmodel]] = try( nls(parent ~ HS(t, parent.0, k1, k2, tb), data = kindata, model = TRUE, start = start.HS, - algorithm = algorithm), silent=TRUE) + algorithm = algorithm), silent=TRUE) + } } } return(kinfits) diff --git a/R/kinobject.R b/R/kinobject.R index de6f6af..2ecc962 100644 --- a/R/kinobject.R +++ b/R/kinobject.R @@ -1,3 +1,23 @@ +# $Id: kinobject.R 59 2010-07-28 12:29:15Z jranke $ + +# Copyright (C) 2008-2010 Johannes Ranke +# Contact: mkin-devel@lists.berlios.de + +# This file is part of the R package kinfit + +# kinfit is free software: you can redistribute it and/or modify it under the +# terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + kinobject <- function(parent, type, system, layers = NA, sampling_times = NA) { diff --git a/R/kinobjects.R b/R/kinobjects.R index a767cea..33abe61 100644 --- a/R/kinobjects.R +++ b/R/kinobjects.R @@ -1,3 +1,23 @@ +# $Id: kinobjects.R 59 2010-07-28 12:29:15Z jranke $ + +# Copyright (C) 2008-2010 Johannes Ranke +# Contact: mkin-devel@lists.berlios.de + +# This file is part of the R package kinfit + +# kinfit is free software: you can redistribute it and/or modify it under the +# terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + kinobjects<- function(parent, type, systems, layers = NA, sampling_times = NA) { diff --git a/R/kinplot.R b/R/kinplot.R index ace1270..394e271 100644 --- a/R/kinplot.R +++ b/R/kinplot.R @@ -1,61 +1,113 @@ +# $Id: kinplot.R 117 2011-06-14 08:52:14Z kati $ + +# Copyright (C) 2008-2010 Johannes Ranke +# Contact: mkin-devel@lists.berlios.de + +# This file is part of the R package kinfit + +# kinfit is free software: you can redistribute it and/or modify it under the +# terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + kinplot <- function(kinobject, + main = "", 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$parent) - ylim <- as.numeric(ylim) + if (ylim[1] == "auto") ylim[1] <- 0 + if (ylim[2] == "auto") ylim[2] <- max(kindata$parent) + ylim <- as.numeric(ylim) plot(kindata$t, kindata$parent, + main = main, xlab = xlab, ylab = ylab, ylim = ylim - ) + ) n.m <- length(kinfits) colors <- ltys <- 1:n.m names(colors) <- names(ltys) <- names(kinfits) - ltext <- paste(kinobject$parent, "measured") + ltext <- paste(kinobject$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")) + if (!"parent.0" %in% names(coef(m))) { + switch(kinmodel, + SFO = lines( + t <- seq(min(kindata$t), max(kindata$t), length.out=500), + predict(m, + newdata = data.frame(t)), + col = colors[[kinmodel]], + lty = ltys[[kinmodel]]), + FOMC = lines( + t <- seq(min(kindata$t), max(kindata$t), length.out=500), + predict(m, + newdata = data.frame(t)), + col = colors[[kinmodel]], + lty = ltys[[kinmodel]]), + HS = lines( + t <- seq(min(kindata$t), max(kindata$t), length.out=500), + predict(m, + newdata = data.frame(t)), + col = colors[[kinmodel]], + lty = ltys[[kinmodel]]), + DFOP = lines( + t <- seq(min(kindata$t), max(kindata$t), length.out=500), + predict(m, + newdata = data.frame(t)), + col = colors[[kinmodel]], + lty = ltys[[kinmodel]]) + ) + ltext <- c(ltext, paste("Fitted", kinmodel, "model")) + } else { + 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 + ltext <- c(ltext, paste(kinmodel, "model failed")) + ltys[[kinmodel]] <- NA } } legend(lpos, bty="n", inset = 0.05, diff --git a/R/kinreport.R b/R/kinreport.R index 4156803..d405b8e 100644 --- a/R/kinreport.R +++ b/R/kinreport.R @@ -1,43 +1,86 @@ -kinreport <- function(kinobject, file = NA, vcov = FALSE, endpoint.digits = 1) +# $Id: kinreport.R 123 2011-11-01 12:26:41Z jranke $ + +# Copyright (C) 2008-2010 Johannes Ranke +# Contact: mkin-devel@lists.berlios.de + +# This file is part of the R package kinfit + +# kinfit is free software: you can redistribute it and/or modify it under the +# terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + +kinreport <- function(kinobject, file = NA, data = TRUE, R2 = FALSE, 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$label, "\n") + if (!is.null(kinobject$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$source, "\n") - } + cat("Source: ", kinobject$source, "\n") + } + cat("kinfit version: ", as.character(packageVersion("kinfit")), "\n") + cat("R version: ", paste(R.version$major, R.version$minor, sep="."), "\n") + cat("Report generated:", date(), "\n") cat("\n") + if (data) { + cat("Data:\n") + print(kinobject$data) + cat("\n") + } fit.names <- names(kinobject$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") - } + m <- kinobject$fits[[kinmodel]] + if (!(class(m) == "try-error")) { + cat("\n\n---\n") + cat("Nonlinear least squares fit of the", kinmodel, "model\n") + if (!"parent.0" %in% names(coef(m))) { + cat(paste("Initial value of parent fixed to ", m$model$parent.0.user, "\n", sep="")) + } + cat("\n") + cat("Parameter estimation:\t") + s <- summary(m) + df <- s$df[2] + p <- 1 - pt(s$parameters[,3], df = df) + parms <- matrix(nrow = nrow(s$parameters), ncol=4) + dimnames(parms) = list(rownames(s$parameters), + c("Estimate", "Std. Error", "t value", "Pr(>t)")) + parms[, c(1,2,3)] <- s$parameters[,c(1,2,3)] + parms[, 4] <- 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: ", + round(100 * kinobject$results$stats[kinmodel, "err.min"], digits=2), + " %\n", sep="") + cat("\n") + if(R2) + { + cat("Coefficient of determination R2: ", + round(kinobject$results$stats[kinmodel, "R2"], digits=3), "\n") + } + } } cat("\n\n---\n") cat("Endpoint estimates\n\n") diff --git a/R/kinresplot.R b/R/kinresplot.R index be0a85d..36eb55a 100644 --- a/R/kinresplot.R +++ b/R/kinresplot.R @@ -1,3 +1,23 @@ +# $Id: kinresplot.R 106 2011-05-12 10:55:37Z jranke $ + +# Copyright (C) 2008-2010 Johannes Ranke +# Contact: mkin-devel@lists.berlios.de + +# This file is part of the R package kinfit + +# kinfit is free software: you can redistribute it and/or modify it under the +# terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + kinresplot <- function(kinobject, kinmodel, xlab = "Time [days]", ylab = "Residual [% of applied radioactivity]", maxabs = "auto") @@ -5,10 +25,11 @@ kinresplot <- function(kinobject, kinmodel, m <- kinobject$fits[[kinmodel]] t <- m$model$t residuals <- residuals(m) - if (maxabs == "auto") maxabs = max(abs(residuals)) + if (maxabs == "auto") maxabs = max(abs(residuals), na.rm = TRUE) plot(t, residuals, xlab = xlab, ylab = ylab, ylim = c( -1.2 * maxabs, 1.2 * maxabs)) + abline(h=0, lty=2) title(paste("Residuals of", kinmodel, "fit"), font.main = 1) } diff --git a/R/kinresults.R b/R/kinresults.R index 6bbff28..27bdafb 100644 --- a/R/kinresults.R +++ b/R/kinresults.R @@ -1,74 +1,145 @@ -kinresults <- function(kinfits, alpha = 0.05, SFORB=TRUE) +# $Id: kinresults.R 124 2011-11-09 10:58:27Z jranke $ + +# Copyright (C) 2008-2011 Johannes Ranke +# Contact: mkin-devel@lists.berlios.de + +# This file is part of the R package kinfit + +# kinfit is free software: you can redistribute it and/or modify it under the +# terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + +kinresults <- function(kinfits, alpha = 0.05, DTmax = 1000, SFORB=TRUE) { - kindata <- data.frame(t = kinfits[[1]]$model$t, parent = kinfits[[1]]$model$parent) - kindata.means <- aggregate(kindata, list(kindata$t), mean) + kindata <- data.frame( + t = kinfits[[1]]$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() + df <- err.min <- R2 <- RSS <- TSS <- RSS.means <- TSS.means <- 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)) + + if (!"parent.0" %in% names(coef(m))) { + + parms[[kinmodel]] <- switch(kinmodel, + SFO = list(k = coef(m)[["k"]]), + FOMC = list(alpha = coef(m)[["alpha"]], + beta = coef(m)[["beta"]]), + HS = list(k1 = coef(m)[["k1"]], + k2 = coef(m)[["k2"]], + tb = coef(m)[["tb"]]), + DFOP= list(k1 = coef(m)[["k1"]], + k2 = coef(m)[["k2"]], + g = coef(m)[["g"]])) + } else { + 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)) + if (!"parent.0" %in% names(coef(m))) { + + f[[kinmodel]] = switch(kinmodel, + HS = function(t, x) { + (HS(t, kinfits[[kinmodel]]$model[["parent.0.user"]], + coef(m)[["k1"]], coef(m)[["k2"]], coef(m)[["tb"]]) - + (1 - x/100) * kinfits[[kinmodel]]$model[["parent.0.user"]])^2 + }, + DFOP = function(t, x) { + (DFOP(t, kinfits[[kinmodel]]$model[["parent.0.user"]], + coef(m)[["k1"]], coef(m)[["k2"]], coef(m)[["g"]]) - + (1 - x/100) * kinfits[[kinmodel]]$model[["parent.0.user"]])^2 + } + ) + }else{ + f[[kinmodel]] = switch(kinmodel, + HS = function(t, x) { + (HS(t, coef(m)[["parent.0"]], + coef(m)[["k1"]], coef(m)[["k2"]], coef(m)[["tb"]]) - + (1 - x/100) * coef(m)[["parent.0"]])^2 + }, + DFOP = function(t, x) { + (DFOP(t, coef(m)[["parent.0"]], + coef(m)[["k1"]], coef(m)[["k2"]], coef(m)[["g"]]) - + (1 - x/100) * coef(m)[["parent.0"]])^2 + } + ) } - n.parms = length(coef(m)) - f[[kinmodel]] = switch(kinmodel, - HS = function(t, x) { - (HS(t, coef(m)[["parent.0"]], - coef(m)[["k1"]], coef(m)[["k2"]], coef(m)[["tb"]]) - - (1 - x/100) * coef(m)[["parent.0"]])^2 - }, - DFOP = function(t, x) { - (DFOP(t, coef(m)[["parent.0"]], - coef(m)[["k1"]], coef(m)[["k2"]], coef(m)[["g"]]) - - (1 - x/100) * coef(m)[["parent.0"]])^2 - } - ) + coef(m) df[[kinmodel]] = n.times - n.parms RSS[[kinmodel]] = sum(summary(m)$residuals^2) - DT50[[kinmodel]] = switch(kinmodel, - SFO = log(2)/coef(m)[["k"]], + TSS[[kinmodel]] = sum((m$model$parent - mean(m$model$parent))^2) + + DT50.o = 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) + HS = optimize(f[[kinmodel]], c(0, DTmax), x=50)$minimum, + DFOP = optimize(f[[kinmodel]], c(0, DTmax), x=50)$minimum) + + + DT50[[kinmodel]] = ifelse(abs(DT50.o - DTmax) < 0.1, NA, DT50.o) + DT90.o = switch(kinmodel, + SFO = log(10)/coef(m)[["k"]], + FOMC = coef(m)[["beta"]] * (10^(1/coef(m)[["alpha"]]) - 1), + HS = optimize(f[[kinmodel]], c(0, DTmax), x=90)$minimum, + DFOP = optimize(f[[kinmodel]], c(0, DTmax), x=90)$minimum) + DT90[[kinmodel]] = ifelse(abs(DT90.o - DTmax) < 0.1, NA, DT90.o) + + # Chi2 error level as defined in FOCUS kinetics (see ?kinerrmin) + err.min[[kinmodel]] <- kinerrmin(kinfits, kinmodel) + + # Coefficient of determination calculated from residual sum of squares and totals sum of squares + # so this r2 is what is called model efficiency in FOCUS kinetics (2006), p. 99 + R2[[kinmodel]] = 1 - RSS[[kinmodel]]/TSS[[kinmodel]] + } } - stats <- data.frame(n.times = n.times, df = df, mean.means = kindata.means.mean, - RSS = RSS, err.min = err.min) + + stats <- data.frame(n.times = n.times, df = df, + mean.means = kindata.means.mean, + RSS = RSS, err.min = err.min, R2 = R2) 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 index bf94f49..2445685 100644 --- a/R/kinwrite.KinGUI.R +++ b/R/kinwrite.KinGUI.R @@ -1,3 +1,23 @@ +# $Id: kinwrite.KinGUI.R 59 2010-07-28 12:29:15Z jranke $ + +# Copyright (C) 2008-2010 Johannes Ranke +# Contact: mkin-devel@lists.berlios.de + +# This file is part of the R package kinfit + +# kinfit is free software: you can redistribute it and/or modify it under the +# terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + kinwrite.KinGUI <- function(kinobject, file, comment=NA) { sink(file) diff --git a/inst/doc/KinGUI/A_DFOP_report_detailed.txt b/inst/doc/KinGUI/A_DFOP_report_detailed.txt new file mode 100644 index 0000000..242c1e7 --- /dev/null +++ b/inst/doc/KinGUI/A_DFOP_report_detailed.txt @@ -0,0 +1,86 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\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 All + Number of data sets: 8 0 8 + Number of parameters: 4 0 4 + Degrees of Freedom: 4 0 4 + + Parent Sink All + + RMSE: 7.4470 NaN 7.4470 + Chi2Sigma: 4.8354 NaN 4.8354 + Chi2Err%: 9.6603 NaN 9.6603 + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Degrees of Freedom: 4 + Parameter Estimate Lower CI Upper CI St.Dev Prob > t + Parent_k1 0.0371<-1000.0000 >1000.0000 799.1761 0.5000 + Parent_k2 0.0372<-1000.0000 >1000.0000 736.5327 0.5000 + Parent_g 0.4787<-1000.0000 >1000.0000 >1000.0000 0.5000 + Parent_FFS 1.0000 + Parent_M(0) 109.0548 91.3583 126.7513 6.3738 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 18.6534 NaN + DT90: 61.9654 NaN + Kinetic model: dfop sink + +# --------------------------------- +# Additional Statistics +# --------------------------------- +# Correlation and R-square of predicted vs. measured data + Parent Sink All + EF: 0.9845 NaN 0.9845 + R-square: 0.9857 NaN 0.9857 + +# Correlation matrix of parameters + Parent_k1 Parent_k2 Parent_g Parent_M + Parent_k1 1.0000 1.0000 1.0000 0.3572 + Parent_k2 1.0000 1.0000 1.0000 0.3605 + Parent_g 1.0000 1.0000 1.0000 0.3588 + Parent_M 0.3572 0.3605 0.3588 1.0000 + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 101.2400 109.0548 -7.8148 NaN 0.0000 NaN + 3.0 99.2700 97.5507 1.7193 NaN 11.5041 NaN + 7.0 90.1100 84.0772 6.0328 NaN 24.9776 NaN + 14.0 72.1900 64.8204 7.3696 NaN 44.2344 NaN + 30.0 29.7100 35.7686 -6.0586 NaN 73.2862 NaN + 62.0 5.9800 10.8915 -4.9115 NaN 98.1634 NaN + 90.0 1.5400 3.8479 -2.3079 NaN 105.2069 NaN + 118.0 0.3900 1.3594 -0.9694 NaN 107.6954 NaN + diff --git a/inst/doc/KinGUI/A_FOMC_report_detailed.txt b/inst/doc/KinGUI/A_FOMC_report_detailed.txt new file mode 100644 index 0000000..2b14a22 --- /dev/null +++ b/inst/doc/KinGUI/A_FOMC_report_detailed.txt @@ -0,0 +1,83 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\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 All + Number of data sets: 8 0 8 + Number of parameters: 3 0 3 + Degrees of Freedom: 5 0 5 + + Parent Sink All + + RMSE: 6.9610 NaN 6.9610 + Chi2Sigma: 4.6781 NaN 4.6781 + Chi2Err%: 9.3462 NaN 9.3462 + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Degrees of Freedom: 5 + Parameter Estimate Lower CI Upper CI St.Dev Prob > t + Parent_alpha 26.0717 -467.3094 519.4528 191.9336 0.4486 + Parent_beta 682.1168<-1000.0000 >1000.0000 >1000.0000 0.4500 + Parent_FFS 1.0000 + Parent_M(0) 109.4699 95.0742 123.8656 5.6002 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 18.3781 NaN + DT90: 62.9832 NaN + Kinetic model: fomc sink + +# --------------------------------- +# Additional Statistics +# --------------------------------- +# Correlation and R-square of predicted vs. measured data + Parent Sink All + EF: 0.9831 NaN 0.9831 + R-square: 0.9845 NaN 0.9845 + +# Correlation matrix of parameters + Parent_alpha Parent_beta Parent_M + Parent_alpha 1.0000 0.9998 -0.4272 + Parent_beta 0.9998 1.0000 -0.4364 + Parent_M -0.4272 -0.4364 1.0000 + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 101.2400 109.4699 -8.2299 NaN 0.0000 NaN + 3.0 99.2700 97.6350 1.6350 NaN 11.8349 NaN + 7.0 90.1100 83.8862 6.2238 NaN 25.5837 NaN + 14.0 72.1900 64.4547 7.7353 NaN 45.0152 NaN + 30.0 29.7100 35.6410 -5.9310 NaN 73.8288 NaN + 62.0 5.9800 11.3304 -5.3504 NaN 98.1395 NaN + 90.0 1.5400 4.3252 -2.7852 NaN 105.1447 NaN + 118.0 0.3900 1.7087 -1.3187 NaN 107.7612 NaN + diff --git a/inst/doc/KinGUI/A_HS_report_detailed.txt b/inst/doc/KinGUI/A_HS_report_detailed.txt new file mode 100644 index 0000000..9cc5aee --- /dev/null +++ b/inst/doc/KinGUI/A_HS_report_detailed.txt @@ -0,0 +1,86 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\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 All + Number of data sets: 8 0 8 + Number of parameters: 4 0 4 + Degrees of Freedom: 4 0 4 + + Parent Sink All + + RMSE: 3.1728 NaN 3.1728 + Chi2Sigma: 2.0601 NaN 2.0601 + Chi2Err%: 4.1158 NaN 4.1158 + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Degrees of Freedom: 4 + Parameter Estimate Lower CI Upper CI St.Dev Prob > t + Parent_k1 0.0049 -0.0365 0.0464 0.0149 0.3785 + Parent_k2 0.0461 0.0357 0.0565 0.0037 1.2e-004 + Parent_tb 5.7617 -0.4681 11.9916 2.2438 0.0311 + Parent_FFS 1.0000 + Parent_M(0) 100.9820 92.1729 109.7910 3.1728 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 20.1783 NaN + DT90: 55.0878 NaN + Kinetic model: hs sink + +# --------------------------------- +# Additional Statistics +# --------------------------------- +# Correlation and R-square of predicted vs. measured data + Parent Sink All + EF: 0.9972 NaN 0.9972 + R-square: 0.9973 NaN 0.9973 + +# Correlation matrix of parameters + Parent_k1 Parent_k2 Parent_tb Parent_M + Parent_k1 1.0000 0.0024 0.8460 0.7018 + Parent_k2 0.0024 1.0000 0.2691 0.0013 + Parent_tb 0.8460 0.2691 1.0000 0.3820 + Parent_M 0.7018 0.0013 0.3820 1.0000 + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 101.2400 100.9820 0.2580 NaN 0.0000 NaN + 3.0 99.2700 99.4947 -0.2247 NaN 1.4873 NaN + 7.0 90.1100 92.6989 -2.5889 NaN 8.2831 NaN + 14.0 72.1900 67.1302 5.0598 NaN 33.8518 NaN + 30.0 29.7100 32.1041 -2.3941 NaN 68.8779 NaN + 62.0 5.9800 7.3425 -1.3625 NaN 93.6394 NaN + 90.0 1.5400 2.0194 -0.4794 NaN 98.9626 NaN + 118.0 0.3900 0.5554 -0.1654 NaN 100.4266 NaN + diff --git a/inst/doc/KinGUI/A_KinGUI.txt b/inst/doc/KinGUI/A_KinGUI.txt index f42b72c..419b0dc 100644 --- a/inst/doc/KinGUI/A_KinGUI.txt +++ b/inst/doc/KinGUI/A_KinGUI.txt @@ -1,13 +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 +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_detailed.txt b/inst/doc/KinGUI/A_SFO_report_detailed.txt new file mode 100644 index 0000000..98e5979 --- /dev/null +++ b/inst/doc/KinGUI/A_SFO_report_detailed.txt @@ -0,0 +1,80 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\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 All + Number of data sets: 8 0 8 + Number of parameters: 2 0 2 + Degrees of Freedom: 6 0 6 + + Parent Sink All + + RMSE: 6.0801 NaN 6.0801 + Chi2Sigma: 4.1971 NaN 4.1971 + Chi2Err%: 8.3852 NaN 8.3852 + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Degrees of Freedom: 6 + Parameter Estimate Lower CI Upper CI St.Dev Prob > t + Parent_k 0.0372 0.0267 0.0477 0.0043 6.5e-005 + Parent_FFS 1.0000 + Parent_M(0) 109.1513 98.4079 119.8947 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 + +# --------------------------------- +# Additional Statistics +# --------------------------------- +# Correlation and R-square of predicted vs. measured data + Parent Sink All + EF: 0.9845 NaN 0.9845 + R-square: 0.9856 NaN 0.9856 + +# Correlation matrix of parameters + Parent_k Parent_M + Parent_k 1.0000 0.5750 + Parent_M 0.5750 1.0000 + +# --------------------------------- +# 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_detailed.txt b/inst/doc/KinGUI/B_DFOP_report_detailed.txt new file mode 100644 index 0000000..e30f7b1 --- /dev/null +++ b/inst/doc/KinGUI/B_DFOP_report_detailed.txt @@ -0,0 +1,86 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\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 All + Number of data sets: 8 0 8 + Number of parameters: 4 0 4 + Degrees of Freedom: 4 0 4 + + Parent Sink All + + RMSE: 2.6723 NaN 2.6723 + Chi2Sigma: 1.7351 NaN 1.7351 + Chi2Err%: 4.9554 NaN 4.9554 + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Degrees of Freedom: 4 + Parameter Estimate Lower CI Upper CI St.Dev Prob > t + Parent_k1 0.1024 -0.4603 0.6650 0.2027 0.3200 + Parent_k2 0.0580 -0.2942 0.4102 0.1268 0.3355 + Parent_g 0.5406 -9.3329 10.4141 3.5562 0.4433 + Parent_FFS 1.0000 + Parent_M(0) 99.6744 92.5981 106.7508 2.5487 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 8.6786 NaN + DT90: 30.8006 NaN + Kinetic model: dfop sink + +# --------------------------------- +# Additional Statistics +# --------------------------------- +# Correlation and R-square of predicted vs. measured data + Parent Sink All + EF: 0.9973 NaN 0.9973 + R-square: 0.9973 NaN 0.9973 + +# Correlation matrix of parameters + Parent_k1 Parent_k2 Parent_g Parent_M + Parent_k1 1.0000 0.9674 -0.9908 0.3017 + Parent_k2 0.9674 1.0000 -0.9919 0.2094 + Parent_g -0.9908 -0.9919 1.0000 -0.2409 + Parent_M 0.3017 0.2094 -0.2409 1.0000 + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 98.6200 99.6744 -1.0544 NaN 0.0000 NaN + 3.0 81.4300 78.1107 3.3193 NaN 21.5637 NaN + 7.0 53.1800 56.8237 -3.6437 NaN 42.8507 NaN + 14.0 34.8900 33.1764 1.7136 NaN 66.4981 NaN + 30.0 10.0900 10.5286 -0.4386 NaN 89.1458 NaN + 62.0 1.5000 1.3480 0.1520 NaN 98.3264 NaN + 90.0 0.3300 0.2522 0.0778 NaN 99.4222 NaN + 118.0 0.0800 0.0489 0.0311 NaN 99.6255 NaN + diff --git a/inst/doc/KinGUI/B_FOMC_report_detailed.txt b/inst/doc/KinGUI/B_FOMC_report_detailed.txt new file mode 100644 index 0000000..449ab34 --- /dev/null +++ b/inst/doc/KinGUI/B_FOMC_report_detailed.txt @@ -0,0 +1,83 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\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 All + Number of data sets: 8 0 8 + Number of parameters: 3 0 3 + Degrees of Freedom: 5 0 5 + + Parent Sink All + + RMSE: 2.4135 NaN 2.4135 + Chi2Sigma: 1.6220 NaN 1.6220 + Chi2Err%: 4.6322 NaN 4.6322 + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Degrees of Freedom: 5 + Parameter Estimate Lower CI Upper CI St.Dev Prob > t + Parent_alpha 8.5369 -15.5894 32.6631 9.3855 0.2024 + Parent_beta 101.4875 -206.6864 409.6614 119.8849 0.2179 + Parent_FFS 1.0000 + Parent_M(0) 99.9273 94.1784 105.6762 2.2364 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 8.5840 NaN + DT90: 31.4206 NaN + Kinetic model: fomc sink + +# --------------------------------- +# Additional Statistics +# --------------------------------- +# Correlation and R-square of predicted vs. measured data + Parent Sink All + EF: 0.9973 NaN 0.9973 + R-square: 0.9973 NaN 0.9973 + +# Correlation matrix of parameters + Parent_alpha Parent_beta Parent_M + Parent_alpha 1.0000 0.9989 -0.3574 + Parent_beta 0.9989 1.0000 -0.3825 + Parent_M -0.3574 -0.3825 1.0000 + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 98.6200 99.9273 -1.3073 NaN 0.0000 NaN + 3.0 81.4300 77.9251 3.5049 NaN 22.0022 NaN + 7.0 53.1800 56.5452 -3.3652 NaN 43.3822 NaN + 14.0 34.8900 33.1569 1.7331 NaN 66.7704 NaN + 30.0 10.0900 10.9528 -0.8628 NaN 88.9745 NaN + 62.0 1.5000 1.7058 -0.2058 NaN 98.2215 NaN + 90.0 0.3300 0.4424 -0.1124 NaN 99.4849 NaN + 118.0 0.0800 0.1380 -0.0580 NaN 99.7893 NaN + diff --git a/inst/doc/KinGUI/B_HS_report_detailed.txt b/inst/doc/KinGUI/B_HS_report_detailed.txt new file mode 100644 index 0000000..f723ea4 --- /dev/null +++ b/inst/doc/KinGUI/B_HS_report_detailed.txt @@ -0,0 +1,86 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\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 All + Number of data sets: 8 0 8 + Number of parameters: 4 0 4 + Degrees of Freedom: 4 0 4 + + Parent Sink All + + RMSE: 2.7291 NaN 2.7291 + Chi2Sigma: 1.7720 NaN 1.7720 + Chi2Err%: 5.0608 NaN 5.0608 + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Degrees of Freedom: 4 + Parameter Estimate Lower CI Upper CI St.Dev Prob > t + Parent_k1 0.0747 0.0369 0.1124 0.0136 0.0027 + Parent_k2 0.0799 0.0614 0.0984 0.0067 1.4e-004 + Parent_tb 3.0662 NaN NaN NaN NaN + Parent_FFS 1.0000 + Parent_M(0) 99.0235 91.4501 106.5970 2.7277 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 8.8792 NaN + DT90: 29.0329 NaN + Kinetic model: hs sink + +# --------------------------------- +# Additional Statistics +# --------------------------------- +# Correlation and R-square of predicted vs. measured data + Parent Sink All + EF: 0.9972 NaN 0.9972 + R-square: 0.9973 NaN 0.9973 + +# Correlation matrix of parameters + Parent_k1 Parent_k2 Parent_tb Parent_M + Parent_k1 1.0000 -0.4395 NaN 0.6629 + Parent_k2 -0.4395 1.0000 NaN -0.0336 + Parent_tb NaN NaN NaN NaN + Parent_M 0.6629 -0.0336 NaN 1.0000 + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 98.6200 99.0235 -0.4035 NaN 0.0000 NaN + 3.0 81.4300 79.1517 2.2783 NaN 19.8719 NaN + 7.0 53.1800 57.5283 -4.3483 NaN 41.4952 NaN + 14.0 34.8900 32.8934 1.9966 NaN 66.1302 NaN + 30.0 10.0900 9.1664 0.9236 NaN 89.8572 NaN + 62.0 1.5000 0.7118 0.7882 NaN 98.3117 NaN + 90.0 0.3300 0.0761 0.2539 NaN 98.9475 NaN + 118.0 0.0800 0.0081 0.0719 NaN 99.0154 NaN + diff --git a/inst/doc/KinGUI/B_KinGUI.txt b/inst/doc/KinGUI/B_KinGUI.txt index 6a589b2..f48e076 100644 --- a/inst/doc/KinGUI/B_KinGUI.txt +++ b/inst/doc/KinGUI/B_KinGUI.txt @@ -1,13 +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 +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_detailed.txt b/inst/doc/KinGUI/B_SFO_report_detailed.txt new file mode 100644 index 0000000..ff6e9c8 --- /dev/null +++ b/inst/doc/KinGUI/B_SFO_report_detailed.txt @@ -0,0 +1,80 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\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 All + Number of data sets: 8 0 8 + Number of parameters: 2 0 2 + Degrees of Freedom: 6 0 6 + + Parent Sink All + + RMSE: 2.2604 NaN 2.2604 + Chi2Sigma: 1.5603 NaN 1.5603 + Chi2Err%: 4.4562 NaN 4.4562 + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Degrees of Freedom: 6 + Parameter Estimate Lower CI Upper CI St.Dev Prob > t + Parent_k 0.0782 0.0687 0.0876 0.0039 4.7e-007 + Parent_FFS 1.0000 + Parent_M(0) 99.1741 94.4666 103.8816 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 + +# --------------------------------- +# Additional Statistics +# --------------------------------- +# Correlation and R-square of predicted vs. measured data + Parent Sink All + EF: 0.9971 NaN 0.9971 + R-square: 0.9972 NaN 0.9972 + +# Correlation matrix of parameters + Parent_k Parent_M + Parent_k 1.0000 0.5804 + Parent_M 0.5804 1.0000 + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 98.6200 99.1741 -0.5541 NaN 0.0000 NaN + 3.0 81.4300 78.4455 2.9845 NaN 20.7286 NaN + 7.0 53.1800 57.3844 -4.2044 NaN 41.7897 NaN + 14.0 34.8900 33.2040 1.6860 NaN 65.9701 NaN + 30.0 10.0900 9.5081 0.5819 NaN 89.6660 NaN + 62.0 1.5000 0.7797 0.7203 NaN 98.3944 NaN + 90.0 0.3300 0.0874 0.2426 NaN 99.0867 NaN + 118.0 0.0800 0.0098 0.0702 NaN 99.1643 NaN + diff --git a/inst/doc/KinGUI/C_DFOP_report_detailed.txt b/inst/doc/KinGUI/C_DFOP_report_detailed.txt new file mode 100644 index 0000000..b26c063 --- /dev/null +++ b/inst/doc/KinGUI/C_DFOP_report_detailed.txt @@ -0,0 +1,87 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\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 All + Number of data sets: 9 0 9 + Number of parameters: 4 0 4 + Degrees of Freedom: 5 0 5 + + Parent Sink All + + RMSE: 0.9341 NaN 0.9341 + Chi2Sigma: 0.6278 NaN 0.6278 + Chi2Err%: 2.6613 NaN 2.6613 + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Degrees of Freedom: 5 + Parameter Estimate Lower CI Upper CI St.Dev Prob > t + Parent_k1 0.4594 0.4071 0.5117 0.0204 1.6e-006 + Parent_k2 0.0178 0.0100 0.0256 0.0030 0.0010 + Parent_g 0.8540 0.8194 0.8885 0.0134 9.1e-009 + Parent_FFS 1.0000 + Parent_M(0) 84.9867 82.6972 87.2762 0.8907 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 1.8876 NaN + DT90: 21.2511 NaN + Kinetic model: dfop sink + +# --------------------------------- +# Additional Statistics +# --------------------------------- +# Correlation and R-square of predicted vs. measured data + Parent Sink All + EF: 0.9994 NaN 0.9994 + R-square: 0.9994 NaN 0.9994 + +# Correlation matrix of parameters + Parent_k1 Parent_k2 Parent_g Parent_M + Parent_k1 1.0000 0.4657 -0.6601 0.4339 + Parent_k2 0.4657 1.0000 -0.7418 0.0793 + Parent_g -0.6601 -0.7418 1.0000 -0.0190 + Parent_M 0.4339 0.0793 -0.0190 1.0000 + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 85.1000 84.9867 0.1133 NaN 0.0000 NaN + 1.0 57.9000 58.0356 -0.1356 NaN 26.9512 NaN + 3.0 29.9000 30.0560 -0.1560 NaN 54.9308 NaN + 7.0 14.6000 13.8653 0.7347 NaN 71.1214 NaN + 14.0 9.7000 9.7841 -0.0841 NaN 75.2026 NaN + 28.0 6.6000 7.5314 -0.9314 NaN 77.4553 NaN + 63.0 4.0000 4.0343 -0.0343 NaN 80.9524 NaN + 91.0 3.9000 2.4485 1.4515 NaN 82.5382 NaN + 119.0 0.6000 1.4860 -0.8860 NaN 83.5007 NaN + diff --git a/inst/doc/KinGUI/C_FOMC_report_detailed.txt b/inst/doc/KinGUI/C_FOMC_report_detailed.txt new file mode 100644 index 0000000..f19484c --- /dev/null +++ b/inst/doc/KinGUI/C_FOMC_report_detailed.txt @@ -0,0 +1,84 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\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 All + Number of data sets: 9 0 9 + Number of parameters: 3 0 3 + Degrees of Freedom: 6 0 6 + + Parent Sink All + + RMSE: 2.2749 NaN 2.2749 + Chi2Sigma: 1.5704 NaN 1.5704 + Chi2Err%: 6.6572 NaN 6.6572 + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Degrees of Freedom: 6 + Parameter Estimate Lower CI Upper CI St.Dev Prob > t + Parent_alpha 1.0540 0.6398 1.4681 0.1693 4.0e-004 + Parent_beta 1.9192 0.6033 3.2352 0.5378 0.0059 + Parent_FFS 1.0000 + Parent_M(0) 85.8774 80.3817 91.3731 2.2460 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 1.7854 NaN + DT90: 15.1385 NaN + Kinetic model: fomc sink + +# --------------------------------- +# Additional Statistics +# --------------------------------- +# Correlation and R-square of predicted vs. measured data + Parent Sink All + EF: 0.9955 NaN 0.9955 + R-square: 0.9959 NaN 0.9959 + +# Correlation matrix of parameters + Parent_alpha Parent_beta Parent_M + Parent_alpha 1.0000 0.9547 -0.2034 + Parent_beta 0.9547 1.0000 -0.3624 + Parent_M -0.2034 -0.3624 1.0000 + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 85.1000 85.8774 -0.7774 NaN 0.0000 NaN + 1.0 57.9000 55.1960 2.7040 NaN 30.6813 NaN + 3.0 29.9000 31.8455 -1.9455 NaN 54.0318 NaN + 7.0 14.6000 17.0087 -2.4087 NaN 68.8687 NaN + 14.0 9.7000 9.2363 0.4637 NaN 76.6411 NaN + 28.0 6.6000 4.7498 1.8502 NaN 81.1275 NaN + 63.0 4.0000 2.0994 1.9006 NaN 83.7779 NaN + 91.0 3.9000 1.4387 2.4613 NaN 84.4387 NaN + 119.0 0.6000 1.0899 -0.4899 NaN 84.7874 NaN + diff --git a/inst/doc/KinGUI/C_HS_report_detailed.txt b/inst/doc/KinGUI/C_HS_report_detailed.txt new file mode 100644 index 0000000..b8a5753 --- /dev/null +++ b/inst/doc/KinGUI/C_HS_report_detailed.txt @@ -0,0 +1,87 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\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 All + Number of data sets: 9 0 9 + Number of parameters: 4 0 4 + Degrees of Freedom: 5 0 5 + + Parent Sink All + + RMSE: 1.6484 NaN 1.6484 + Chi2Sigma: 1.1078 NaN 1.1078 + Chi2Err%: 4.6963 NaN 4.6963 + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Degrees of Freedom: 5 + Parameter Estimate Lower CI Upper CI St.Dev Prob > t + Parent_k1 0.3560 0.3084 0.4036 0.0185 3.5e-006 + Parent_k2 0.0227 0.0081 0.0372 0.0057 0.0052 + Parent_tb 5.1547 4.0767 6.2327 0.4193 3.2e-005 + Parent_FFS 1.0000 + Parent_M(0) 84.4914 80.5387 88.4441 1.5377 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 1.9470 NaN + DT90: 25.7899 NaN + Kinetic model: hs sink + +# --------------------------------- +# Additional Statistics +# --------------------------------- +# Correlation and R-square of predicted vs. measured data + Parent Sink All + EF: 0.9980 NaN 0.9980 + R-square: 0.9980 NaN 0.9980 + +# Correlation matrix of parameters + Parent_k1 Parent_k2 Parent_tb Parent_M + Parent_k1 1.0000 -0.0002 -0.5436 0.5345 + Parent_k2 -0.0002 1.0000 -0.4781 -0.0001 + Parent_tb -0.5436 -0.4781 1.0000 -0.1210 + Parent_M 0.5345 -0.0001 -0.1210 1.0000 + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 85.1000 84.4914 0.6086 NaN 0.0000 NaN + 1.0 57.9000 59.1836 -1.2836 NaN 25.3078 NaN + 3.0 29.9000 29.0389 0.8611 NaN 55.4525 NaN + 7.0 14.6000 12.9326 1.6674 NaN 71.5588 NaN + 14.0 9.7000 11.0360 -1.3360 NaN 73.4553 NaN + 28.0 6.6000 8.0365 -1.4365 NaN 76.4548 NaN + 63.0 4.0000 3.6367 0.3633 NaN 80.8547 NaN + 91.0 3.9000 1.9285 1.9715 NaN 82.5629 NaN + 119.0 0.6000 1.0226 -0.4226 NaN 83.4687 NaN + diff --git a/inst/doc/KinGUI/C_KinGUI.txt b/inst/doc/KinGUI/C_KinGUI.txt index 1e0e3d8..87f3191 100644 --- a/inst/doc/KinGUI/C_KinGUI.txt +++ b/inst/doc/KinGUI/C_KinGUI.txt @@ -1,14 +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 +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_detailed.txt b/inst/doc/KinGUI/C_SFO_report_detailed.txt new file mode 100644 index 0000000..512e10e --- /dev/null +++ b/inst/doc/KinGUI/C_SFO_report_detailed.txt @@ -0,0 +1,81 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\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 All + Number of data sets: 9 0 9 + Number of parameters: 2 0 2 + Degrees of Freedom: 7 0 7 + + Parent Sink All + + RMSE: 5.2987 NaN 5.2987 + Chi2Sigma: 3.7378 NaN 3.7378 + Chi2Err%: 15.8456 NaN 15.8456 + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Degrees of Freedom: 7 + Parameter Estimate Lower CI Upper CI St.Dev Prob > t + Parent_k 0.3060 0.1975 0.4146 0.0459 1.4e-004 + Parent_FFS 1.0000 + Parent_M(0) 82.4905 71.2818 93.6992 4.7402 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 2.2649 NaN + DT90: 7.5240 NaN + Kinetic model: sfo sink + +# --------------------------------- +# Additional Statistics +# --------------------------------- +# Correlation and R-square of predicted vs. measured data + Parent Sink All + EF: 0.9714 NaN 0.9714 + R-square: 0.9869 NaN 0.9869 + +# Correlation matrix of parameters + Parent_k Parent_M + Parent_k 1.0000 0.5212 + Parent_M 0.5212 1.0000 + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 85.1000 82.4905 2.6095 NaN 0.0000 NaN + 1.0 57.9000 60.7429 -2.8429 NaN 21.7476 NaN + 3.0 29.9000 32.9366 -3.0366 NaN 49.5539 NaN + 7.0 14.6000 9.6838 4.9162 NaN 72.8067 NaN + 14.0 9.7000 1.1368 8.5632 NaN 81.3537 NaN + 28.0 6.6000 0.0157 6.5843 NaN 82.4749 NaN + 63.0 4.0000 0.0000 4.0000 NaN 82.4905 NaN + 91.0 3.9000 0.0000 3.9000 NaN 82.4905 NaN + 119.0 0.6000 0.0000 0.6000 NaN 82.4905 NaN + diff --git a/inst/doc/KinGUI/D_DFOP_report_detailed.txt b/inst/doc/KinGUI/D_DFOP_report_detailed.txt new file mode 100644 index 0000000..8326b6b --- /dev/null +++ b/inst/doc/KinGUI/D_DFOP_report_detailed.txt @@ -0,0 +1,100 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\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 All + Number of data sets: 9 0 9 + Number of parameters: 4 0 4 + Degrees of Freedom: 5 0 5 + + Parent Sink All + + RMSE: 4.2785 NaN 4.2785 + Chi2Sigma: 2.8753 NaN 2.8753 + Chi2Err%: 7.2751 NaN 7.2751 + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Degrees of Freedom: 14 + Parameter Estimate Lower CI Upper CI St.Dev Prob > t + Parent_k1 0.0982<-1000.0000 >1000.0000 696.9952 0.4999 + Parent_k2 0.0976<-1000.0000 >1000.0000 852.9518 0.5000 + Parent_g 0.5524<-1000.0000 >1000.0000 >1000.0000 0.5000 + Parent_FFS 1.0000 + Parent_M(0) 99.4470 93.8860 105.0081 2.5928 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 7.0773 NaN + DT90: 23.5106 NaN + Kinetic model: dfop sink + +# --------------------------------- +# Additional Statistics +# --------------------------------- +# Correlation and R-square of predicted vs. measured data + Parent Sink All + EF: 0.9919 NaN 0.9919 + R-square: 0.9919 NaN 0.9919 + +# Correlation matrix of parameters + Parent_k1 Parent_k2 Parent_g Parent_M + Parent_k1 1.0000 1.0000 -1.0000 0.5546 + Parent_k2 1.0000 1.0000 -1.0000 0.5530 + Parent_g -1.0000 -1.0000 1.0000 -0.5538 + Parent_M 0.5546 0.5530 -0.5538 1.0000 + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 99.4600 99.4470 0.0130 NaN 0.0000 NaN + 0.0 102.0400 99.4470 2.5930 NaN 0.0000 NaN + 1.0 93.5000 90.1690 3.3310 NaN 9.2780 NaN + 1.0 92.5000 90.1690 2.3310 NaN 9.2780 NaN + 3.0 63.2300 74.1290 -10.8990 NaN 25.3180 NaN + 3.0 68.9900 74.1290 -5.1390 NaN 25.3180 NaN + 7.0 52.3200 50.1015 2.2185 NaN 49.3456 NaN + 7.0 55.1300 50.1015 5.0285 NaN 49.3456 NaN + 14.0 27.2700 25.2413 2.0287 NaN 74.2057 NaN + 14.0 26.6400 25.2413 1.3987 NaN 74.2057 NaN + 21.0 11.5000 12.7167 -1.2167 NaN 86.7303 NaN + 21.0 11.6400 12.7167 -1.0767 NaN 86.7303 NaN + 35.0 2.8500 3.2278 -0.3778 NaN 96.2192 NaN + 35.0 2.9100 3.2278 -0.3178 NaN 96.2192 NaN + 50.0 0.6900 0.7429 -0.0529 NaN 98.7042 NaN + 50.0 0.6300 0.7429 -0.1129 NaN 98.7042 NaN + 75.0 0.0500 0.0642 -0.0142 NaN 99.3828 NaN + 75.0 0.0600 0.0642 -0.0042 NaN 99.3828 NaN + 100.0 NaN 0.0056 NaN NaN 99.4415 NaN + 100.0 NaN 0.0056 NaN NaN 99.4415 NaN + 120.0 NaN 0.0008 NaN NaN 99.4463 NaN + 120.0 NaN 0.0008 NaN NaN 99.4463 NaN + diff --git a/inst/doc/KinGUI/D_FOMC_report_detailed.txt b/inst/doc/KinGUI/D_FOMC_report_detailed.txt new file mode 100644 index 0000000..a3ff6cc --- /dev/null +++ b/inst/doc/KinGUI/D_FOMC_report_detailed.txt @@ -0,0 +1,97 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\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 All + Number of data sets: 9 0 9 + Number of parameters: 3 0 3 + Degrees of Freedom: 6 0 6 + + Parent Sink All + + RMSE: 3.8927 NaN 3.8927 + Chi2Sigma: 2.6871 NaN 2.6871 + Chi2Err%: 6.7989 NaN 6.7989 + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Degrees of Freedom: 15 + Parameter Estimate Lower CI Upper CI St.Dev Prob > t + Parent_alpha 11.4924 -23.1706 46.1555 16.2627 0.2453 + Parent_beta 109.9914 -242.4545 462.4373 165.3550 0.2580 + Parent_FFS 1.0000 + Parent_M(0) 100.1262 95.6389 104.6136 2.1053 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 6.8381 NaN + DT90: 24.4003 NaN + Kinetic model: fomc sink + +# --------------------------------- +# Additional Statistics +# --------------------------------- +# Correlation and R-square of predicted vs. measured data + Parent Sink All + EF: 0.9920 NaN 0.9920 + R-square: 0.9921 NaN 0.9921 + +# Correlation matrix of parameters + Parent_alpha Parent_beta Parent_M + Parent_alpha 1.0000 0.9994 -0.4135 + Parent_beta 0.9994 1.0000 -0.4306 + Parent_M -0.4135 -0.4306 1.0000 + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 99.4600 100.1262 -0.6662 NaN 0.0000 NaN + 0.0 102.0400 100.1262 1.9138 NaN 0.0000 NaN + 1.0 93.5000 90.2352 3.2648 NaN 9.8911 NaN + 1.0 92.5000 90.2352 2.2648 NaN 9.8911 NaN + 3.0 63.2300 73.4920 -10.2620 NaN 26.6343 NaN + 3.0 68.9900 73.4920 -4.5020 NaN 26.6343 NaN + 7.0 52.3200 49.2726 3.0474 NaN 50.8536 NaN + 7.0 55.1300 49.2726 5.8574 NaN 50.8536 NaN + 14.0 27.2700 25.2676 2.0024 NaN 74.8586 NaN + 14.0 26.6400 25.2676 1.3724 NaN 74.8586 NaN + 21.0 11.5000 13.4417 -1.9417 NaN 86.6845 NaN + 21.0 11.6400 13.4417 -1.8017 NaN 86.6845 NaN + 35.0 2.8500 4.1845 -1.3345 NaN 95.9417 NaN + 35.0 2.9100 4.1845 -1.2745 NaN 95.9417 NaN + 50.0 0.6900 1.3499 -0.6599 NaN 98.7764 NaN + 50.0 0.6300 1.3499 -0.7199 NaN 98.7764 NaN + 75.0 0.0500 0.2545 -0.2045 NaN 99.8718 NaN + 75.0 0.0600 0.2545 -0.1945 NaN 99.8718 NaN + 100.0 NaN 0.0593 NaN NaN 100.0670 NaN + 100.0 NaN 0.0593 NaN NaN 100.0670 NaN + 120.0 NaN 0.0208 NaN NaN 100.1054 NaN + 120.0 NaN 0.0208 NaN NaN 100.1054 NaN + diff --git a/inst/doc/KinGUI/D_HS_report_detailed.txt b/inst/doc/KinGUI/D_HS_report_detailed.txt new file mode 100644 index 0000000..6f9030e --- /dev/null +++ b/inst/doc/KinGUI/D_HS_report_detailed.txt @@ -0,0 +1,100 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\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 All + Number of data sets: 9 0 9 + Number of parameters: 4 0 4 + Degrees of Freedom: 5 0 5 + + Parent Sink All + + RMSE: 3.4039 NaN 3.4039 + Chi2Sigma: 2.2876 NaN 2.2876 + Chi2Err%: 5.7881 NaN 5.7881 + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Degrees of Freedom: 14 + Parameter Estimate Lower CI Upper CI St.Dev Prob > t + Parent_k1 0.1219 0.0502 0.1935 0.0334 0.0013 + Parent_k2 0.0879 0.0757 0.1001 0.0057 1.7e-010 + Parent_tb 2.9984 1.1617 4.8350 0.8563 0.0018 + Parent_FFS 1.0000 + Parent_M(0) 101.1066 96.3031 105.9101 2.2396 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 6.7257 NaN + DT90: 25.0308 NaN + Kinetic model: hs sink + +# --------------------------------- +# Additional Statistics +# --------------------------------- +# Correlation and R-square of predicted vs. measured data + Parent Sink All + EF: 0.9945 NaN 0.9945 + R-square: 0.9948 NaN 0.9948 + +# Correlation matrix of parameters + Parent_k1 Parent_k2 Parent_tb Parent_M + Parent_k1 1.0000 0.0001 0.9101 0.6628 + Parent_k2 0.0001 1.0000 0.1728 0.0000 + Parent_tb 0.9101 0.1728 1.0000 0.4166 + Parent_M 0.6628 0.0000 0.4166 1.0000 + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 99.4600 101.1066 -1.6466 NaN 0.0000 NaN + 0.0 102.0400 101.1066 0.9334 NaN 0.0000 NaN + 1.0 93.5000 89.5056 3.9944 NaN 11.6010 NaN + 1.0 92.5000 89.5056 2.9944 NaN 11.6010 NaN + 3.0 63.2300 70.1481 -6.9181 NaN 30.9585 NaN + 3.0 68.9900 70.1481 -1.1581 NaN 30.9585 NaN + 7.0 52.3200 49.3489 2.9711 NaN 51.7577 NaN + 7.0 55.1300 49.3489 5.7811 NaN 51.7577 NaN + 14.0 27.2700 26.6677 0.6023 NaN 74.4389 NaN + 14.0 26.6400 26.6677 -0.0277 NaN 74.4389 NaN + 21.0 11.5000 14.4109 -2.9109 NaN 86.6956 NaN + 21.0 11.6400 14.4109 -2.7709 NaN 86.6956 NaN + 35.0 2.8500 4.2083 -1.3583 NaN 96.8983 NaN + 35.0 2.9100 4.2083 -1.2983 NaN 96.8983 NaN + 50.0 0.6900 1.1255 -0.4355 NaN 99.9811 NaN + 50.0 0.6300 1.1255 -0.4955 NaN 99.9811 NaN + 75.0 0.0500 0.1249 -0.0749 NaN 100.9816 NaN + 75.0 0.0600 0.1249 -0.0649 NaN 100.9816 NaN + 100.0 NaN 0.0139 NaN NaN 101.0927 NaN + 100.0 NaN 0.0139 NaN NaN 101.0927 NaN + 120.0 NaN 0.0024 NaN NaN 101.1042 NaN + 120.0 NaN 0.0024 NaN NaN 101.1042 NaN + diff --git a/inst/doc/KinGUI/D_KinGUI.txt b/inst/doc/KinGUI/D_KinGUI.txt index f1c53e9..a79ee5e 100644 --- a/inst/doc/KinGUI/D_KinGUI.txt +++ b/inst/doc/KinGUI/D_KinGUI.txt @@ -1,27 +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 +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_detailed.txt b/inst/doc/KinGUI/D_SFO_report_detailed.txt new file mode 100644 index 0000000..24ace5f --- /dev/null +++ b/inst/doc/KinGUI/D_SFO_report_detailed.txt @@ -0,0 +1,94 @@ +Project: +Testsystem: +Comment: NA + +KinGUI Version: 1.1 + +Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\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 All + Number of data sets: 9 0 9 + Number of parameters: 2 0 2 + Degrees of Freedom: 7 0 7 + + Parent Sink All + + RMSE: 3.6160 NaN 3.6160 + Chi2Sigma: 2.5508 NaN 2.5508 + Chi2Err%: 6.4539 NaN 6.4539 + +# --------------------------------- +# Parameter estimation +# --------------------------------- + + Degrees of Freedom: 16 + Parameter Estimate Lower CI Upper CI St.Dev Prob > t + Parent_k 0.0979 0.0877 0.1082 0.0048 3.8e-013 + Parent_FFS 1.0000 + Parent_M(0) 99.4442 95.5614 103.3271 1.8316 + Sink_M(0) 0.0000 + +# --------------------------------- +# DT50 and DT90 values +# --------------------------------- + Parent Sink + DT50: 7.0776 NaN + DT90: 23.5112 NaN + Kinetic model: sfo sink + +# --------------------------------- +# Additional Statistics +# --------------------------------- +# Correlation and R-square of predicted vs. measured data + Parent Sink All + EF: 0.9919 NaN 0.9919 + R-square: 0.9919 NaN 0.9919 + +# Correlation matrix of parameters + Parent_k Parent_M + Parent_k 1.0000 0.5360 + Parent_M 0.5360 1.0000 + +# --------------------------------- +# Measured vs. predicted values +# --------------------------------- + Time Compartment Parent Compartment Sink + measured predicted residual measured predicted residual + 0.0 99.4600 99.4442 0.0158 NaN 0.0000 NaN + 0.0 102.0400 99.4442 2.5958 NaN 0.0000 NaN + 1.0 93.5000 90.1668 3.3332 NaN 9.2774 NaN + 1.0 92.5000 90.1668 2.3332 NaN 9.2774 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 25.2417 2.0283 NaN 74.2026 NaN + 14.0 26.6400 25.2417 1.3983 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 98.7013 NaN + 50.0 0.6300 0.7429 -0.1129 NaN 98.7013 NaN + 75.0 0.0500 0.0642 -0.0142 NaN 99.3800 NaN + 75.0 0.0600 0.0642 -0.0042 NaN 99.3800 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_KinGUI.txt b/inst/doc/KinGUI/F_system_KinGUI.txt index 92bd722..ba130e0 100644 --- a/inst/doc/KinGUI/F_system_KinGUI.txt +++ b/inst/doc/KinGUI/F_system_KinGUI.txt @@ -1,14 +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 +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_water_KinGUI.txt b/inst/doc/KinGUI/F_water_KinGUI.txt index ce3611d..bd80f86 100644 --- a/inst/doc/KinGUI/F_water_KinGUI.txt +++ b/inst/doc/KinGUI/F_water_KinGUI.txt @@ -1,14 +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 +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/kinfit.Rnw b/inst/doc/kinfit.Rnw index a433e44..3292fd1 100644 --- a/inst/doc/kinfit.Rnw +++ b/inst/doc/kinfit.Rnw @@ -1,3 +1,4 @@ +% $Id: kinfit.Rnw 125 2011-11-10 07:19:59Z jranke $ %%\VignetteIndexEntry{Routines for fitting kinetic models to chemical degradation data} %%VignetteDepends{nls} %%\usepackage{Sweave} @@ -680,7 +681,7 @@ 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}). +show convergence 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, @@ -912,6 +913,86 @@ 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. +\subsection{$R^2$ value} + +In a similar manner, the coefficient of determination calculated by kinfit +according to the formula + +\begin{equation} +R^2 = 1 - RSS / TSS +\end{equation} + +where RSS is the sum of squares of the residuals and TSS is the sum of squares +of the deviations from the mean value is compared to the model efficiency EF +calculated by KinGUI based on the same formula (FOCUS 2006, p. 99) as shown +in Table \ref{tab:vali.R2}. This exercise was done for FOCUS datasets A to D +only. + +<>= +R2.SFO.kinfit <- R2.FOMC.kinfit <- array(dim = 4, + dimnames = list(names(kinobjects[1:4]))) +R2.DFOP.kinfit <- R2.HS.kinfit <- array(dim = 4, + dimnames = list(names(kinobjects[1:4]))) +for (kinobjectname in names(kinobjects[1:4])) +{ + R2.SFO.kinfit[[kinobjectname]] <- + kinobjects[[kinobjectname]]$results$stats[["SFO", "R2"]] + R2.FOMC.kinfit[[kinobjectname]] <- + ifelse(class(kinobjects[[kinobjectname]]$fits$FOMC) == "try-error", + NA, kinobjects[[kinobjectname]]$results$stats[["FOMC", "R2"]]) + R2.DFOP.kinfit[[kinobjectname]] <- + ifelse(class(kinobjects[[kinobjectname]]$fits$DFOP) == "try-error", + NA, kinobjects[[kinobjectname]]$results$stats[["DFOP", "R2"]]) + R2.HS.kinfit[[kinobjectname]] <- + ifelse(class(kinobjects[[kinobjectname]]$fits$HS) == "try-error", + NA, kinobjects[[kinobjectname]]$results$stats[["HS", "R2"]]) +} + +EF.SFO.KinGUI <- c(0.9845, 0.9971, 0.9714, 0.9919) +EF.FOMC.KinGUI <- c(0.9831, 0.9973, 0.9955, 0.9920) +EF.HS.KinGUI <- c(0.9972, 0.9972, 0.9980, 0.9945) +EF.DFOP.KinGUI <- c(0.9845, 0.9973, 0.9994, 0.9919) +names(EF.SFO.KinGUI) <- names(EF.FOMC.KinGUI) <- names(kinobjects[1:4]) +names(EF.DFOP.KinGUI) <- names(EF.HS.KinGUI) <- names(kinobjects[1:4]) + +R2 <- data.frame( + SFO.KinGUI = EF.SFO.KinGUI, + SFO.kinfit = round(R2.SFO.kinfit, 4), + FOMC.KinGUI = EF.FOMC.KinGUI, + FOMC.kinfit = round(R2.FOMC.kinfit, 4), + DFOP.KinGUI = EF.DFOP.KinGUI, + DFOP.kinfit = round(R2.DFOP.kinfit, 4), + HS.KinGUI = EF.HS.KinGUI, + HS.kinfit = round(R2.HS.kinfit, 4) +) +write.table(R2, + file = "R2_comparison.tex", + sep=" & ", quote=FALSE, na="", + row.names=TRUE, col.names=FALSE, eol = " \\\\ \n") +@ + +\begin{table} +\caption{Comparison of model efficiency (EF) values calculated +by KinGUI and $R^2$ values calculated by \Rpackage{kinfit}. \label{tab:vali.R2}} +\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{R2_comparison} +\bottomrule +\end{tabular} +\end{table} + +The comparison shows that whenever the comparison was possible, the $R^2$ +value calculated by the \Rpackage{kinfit} package was equal to the model +efficiency calculated by KinGUI, both rounded to four digits. + \section{Conclusion} The \Rpackage{kinfit} package for \RR{} gives access to the possibility to diff --git a/inst/doc/kinfit.pdf b/inst/doc/kinfit.pdf index 2945545..d57b999 100644 Binary files a/inst/doc/kinfit.pdf and b/inst/doc/kinfit.pdf differ diff --git a/inst/doc/references.bib b/inst/doc/references.bib index 53e3bea..8cde4bd 100644 --- a/inst/doc/references.bib +++ b/inst/doc/references.bib @@ -28,8 +28,8 @@ } @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}, + title = {{KinGUI}: a new kinetic software tool for evaluations according to {FOCUS} degradation kinetics}, + author = {D. Sch\"{a}fer and M. Mikolasch 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}, diff --git a/man/kinfit.Rd b/man/kinfit.Rd index f0301fd..2e2ceb2 100644 --- a/man/kinfit.Rd +++ b/man/kinfit.Rd @@ -9,12 +9,12 @@ Fit kinetic models to chemical degradation data 2006 are fitted to a given dataframe of chemical degradation data. } \usage{ -kinfit(kindata, kinmodels = c("SFO"), parent.0.user = NA, +kinfit(kindata, kinmodels = c("SFO"), parent.0.user = NA, parent.0.fixed = FALSE, 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") + algorithm = "default") } \arguments{ \item{kindata}{ @@ -30,6 +30,10 @@ kinfit(kindata, kinmodels = c("SFO"), parent.0.user = NA, The user can give a starting estimate for parent.0 here, overriding other potential sources for starting values as specified below. } + \item{parent.0.fixed}{ + If TRUE, the initial value for the observed value will be fixed to the + value specified by \code{parent.0.user}. + } \item{start.SFO}{ A list of starting parameters for fitting the \code{\link{SFO}} model, containing \code{parent.0} and \code{k}. diff --git a/man/kinobject.Rd b/man/kinobject.Rd index cd6f0ca..c5c5f77 100644 --- a/man/kinobject.Rd +++ b/man/kinobject.Rd @@ -15,7 +15,7 @@ Function to initialise an object representing a kinetic experiment or trial. \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. } + \item{sampling_times}{ Optional specification of the sampling time points. } } \value{ A list containing the specified information. diff --git a/man/kinobjects.Rd b/man/kinobjects.Rd index 7c960f3..cbc46aa 100644 --- a/man/kinobjects.Rd +++ b/man/kinobjects.Rd @@ -15,7 +15,7 @@ Function to initialise several objects representing a kinetic experiment or tria \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. } + \item{sampling_times}{ Optional specification of the sampling time points. } } \value{ A list of lists containing the specified information. diff --git a/man/kinplot.Rd b/man/kinplot.Rd index b6974ee..eb6363a 100644 --- a/man/kinplot.Rd +++ b/man/kinplot.Rd @@ -8,7 +8,7 @@ Creates a plot of the kinetic fits 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") +kinplot(kinobject, main = "", xlab = "Time [days]", ylab = "Parent [\% of applied radioactivity]", ylim = c("auto", "auto"), lpos = "topright") } \arguments{ \item{kinobject}{ @@ -17,6 +17,7 @@ kinplot(kinobject, xlab = "Time [days]", ylab = "Parent [\% of applied radioacti the type of the test system (\code{type}), the name of the specific test system used for generating this dataset (\code{system}), + the input dataset (\code{data}), 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}}. @@ -25,6 +26,7 @@ kinplot(kinobject, xlab = "Time [days]", ylab = "Parent [\% of applied radioacti Optionally also the label position of the test compound (\code{label}) and the source of the data (\code{source}). } + \item{main}{ Title. } \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". } diff --git a/man/kinreport.Rd b/man/kinreport.Rd index de7e632..f1b8111 100644 --- a/man/kinreport.Rd +++ b/man/kinreport.Rd @@ -9,7 +9,7 @@ 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) +kinreport(kinobject, file = NA, data = TRUE, R2 = FALSE, vcov = FALSE, endpoint.digits = 1) } \arguments{ \item{kinobject}{ @@ -18,6 +18,7 @@ kinreport(kinobject, file = NA, vcov = FALSE, endpoint.digits = 1) the type of the test system (\code{type}), the name of the specific test system used for generating this dataset (\code{system}), + the input dataset (\code{data}), 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}}. @@ -25,12 +26,17 @@ kinreport(kinobject, file = NA, vcov = FALSE, endpoint.digits = 1) 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{data}{ Boolean specifying if the input data should be printed? } + \item{R2}{ Boolean specifying if the coefficient of determination R2 should + be printed. R2 is calculated from all values (not mean values) as 1 - RSS/TSS where + RSS is the sum of squares of residuals, and TSS ist the total sum of squares, i.e. + the sum of squares of the difference of each observation from the overall mean. } \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. +to the R console as well as to a text file if a filename is specified. } \author{ Johannes Ranke } \examples{ @@ -40,6 +46,7 @@ kinobject <- list( parent = "Compound XY", type = "Degradation in the environment", system = "System 1", + data = FOCUS_2006_A, source = "Synthetic example data from FOCUS kinetics", fits = kinfits, results = kinresults(kinfits)) diff --git a/man/kinresplot.Rd b/man/kinresplot.Rd index 85ec333..fcf0561 100644 --- a/man/kinresplot.Rd +++ b/man/kinresplot.Rd @@ -8,7 +8,7 @@ Creates a plot of the residual for specified kinetic fits 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") + kinresplot(kinobject, kinmodel, xlab = "Time [days]", ylab = "Residual [\% of applied radioactivity]", maxabs = "auto") } \arguments{ \item{kinobject}{ diff --git a/man/kinresults.Rd b/man/kinresults.Rd index 6ab93a7..9e5bc43 100644 --- a/man/kinresults.Rd +++ b/man/kinresults.Rd @@ -9,7 +9,7 @@ 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) +kinresults(kinfits, alpha = 0.05, DTmax = 1000, SFORB = TRUE) } \arguments{ \item{kinfits}{ @@ -19,6 +19,13 @@ 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{DTmax}{ +Upper end of the time interval that will be checked for the iterative determination +of DT50 and DT90 values for the FOMC and the DFOP model. If the DT50 or the +DT90 value is less than 0.1 different from \code{DTmax}, which will generally +be the case if the optimization routine hits the upper end, the respective DT50 or +DT90 value will be reported as \code{NA}. } \item{SFORB}{ Should the results of the \code{\link{DFOP}} model be presented as parameters diff --git a/man/kinwrite.KinGUI.Rd b/man/kinwrite.KinGUI.Rd index f5a5ddc..c0910cf 100644 --- a/man/kinwrite.KinGUI.Rd +++ b/man/kinwrite.KinGUI.Rd @@ -35,7 +35,7 @@ An optional comment that will be integrated in the header of the KinGUI input fi 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. +Schäfer D, Mikolasch 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 . diff --git a/tests/test_FOCUS_2006_A.R b/tests/test_FOCUS_2006_A.R index 2077315..ff55174 100644 --- a/tests/test_FOCUS_2006_A.R +++ b/tests/test_FOCUS_2006_A.R @@ -1,3 +1,23 @@ +# $Id: test_FOCUS_2006_A.R 59 2010-07-28 12:29:15Z jranke $ + +# Copyright (C) 2008-2010 Johannes Ranke +# Contact: mkin-devel@lists.berlios.de + +# This file is part of the R package kinfit + +# kinfit is free software: you can redistribute it and/or modify it under the +# terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + library(kinfit) data(FOCUS_2006_A) fits <- kinfit(FOCUS_2006_A, kinmodels = c("SFO", "HS")) diff --git a/tests/test_FOCUS_2006_A.Rout.save b/tests/test_FOCUS_2006_A.Rout.save index a26b701..d209084 100644 --- a/tests/test_FOCUS_2006_A.Rout.save +++ b/tests/test_FOCUS_2006_A.Rout.save @@ -1,7 +1,8 @@ -R version 2.10.0 (2009-10-26) -Copyright (C) 2009 The R Foundation for Statistical Computing +R version 2.14.0 (2011-10-31) +Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 +Platform: i386-pc-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. @@ -15,17 +16,35 @@ 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. +> # $Id: test_FOCUS_2006_A.R 59 2010-07-28 12:29:15Z jranke $ +> +> # Copyright (C) 2008-2010 Johannes Ranke +> # Contact: mkin-devel@lists.berlios.de +> +> # This file is part of the R package kinfit +> +> # kinfit is free software: you can redistribute it and/or modify it under the +> # terms of the GNU General Public License as published by the Free Software +> # Foundation, either version 3 of the License, or (at your option) any later +> # version. +> +> # This program is distributed in the hope that it will be useful, but WITHOUT +> # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +> # FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +> # details. +> +> # You should have received a copy of the GNU General Public License along with +> # this program. If not, see +> > 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 + n.times df mean.means RSS err.min R2 +SFO 8 6 50.054 221.81 0.083848 0.9845 > > data(FOCUS_2006_B) > fits <- kinfit(FOCUS_2006_B, kinmodels = c("SFO", "FOMC", "DFOP")) @@ -35,23 +54,23 @@ SFO 8.8686 29.461 FOMC 8.6834 30.754 DFOP 8.6829 30.789 > print(kinresults(fits)$stats, digits=5) - n.times df mean.means RSS err.min -SFO 8 6 35.015 30.656 0.044555 -FOMC 8 5 35.015 28.583 0.045886 -DFOP 8 4 35.015 28.550 0.049527 + n.times df mean.means RSS err.min R2 +SFO 8 6 35.015 30.656 0.044555 0.99713 +FOMC 8 5 35.015 28.583 0.045886 0.99733 +DFOP 8 4 35.015 28.550 0.049527 0.99733 > > data(FOCUS_2006_C) > fits <- kinfit(FOCUS_2006_C, kinmodels = c("SFO", "FOMC", "DFOP")) > print(kinresults(fits)$results, digits=5) DT50 DT90 -SFO 2.2647 7.5232 +SFO 2.2647 7.5233 FOMC 1.7852 15.1479 DFOP 1.8869 21.2507 > print(kinresults(fits)$stats, digits=5) - n.times df mean.means RSS err.min -SFO 9 7 23.589 196.5334 0.158440 -FOMC 9 6 23.589 31.0509 0.066568 -DFOP 9 5 23.589 4.3627 0.026621 + n.times df mean.means RSS err.min R2 +SFO 9 7 23.589 196.5334 0.158440 0.97136 +FOMC 9 6 23.589 31.0509 0.066568 0.99548 +DFOP 9 5 23.589 4.3627 0.026621 0.99936 > > data(FOCUS_2006_D) > fits <- kinfit(FOCUS_2006_D, kinmodels = c("SFO", "FOMC")) @@ -60,20 +79,20 @@ DFOP 9 5 23.589 4.3627 0.026621 SFO 7.0776 23.511 FOMC 6.9350 24.044 > print(kinresults(fits)$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 + n.times df mean.means RSS err.min R2 +SFO 9 7 39.523 207.63 0.064524 0.99194 +FOMC 9 6 39.523 205.45 0.067802 0.99202 > > data(FOCUS_2006_E) > fits <- kinfit(FOCUS_2006_E, kinmodels = c("SFO", "FOMC", "DFOP")) > print(kinresults(fits)$results, digits=5) DT50 DT90 -SFO 2.2647 7.5232 +SFO 2.2647 7.5233 FOMC 1.7852 15.1479 DFOP 1.8869 21.2507 > print(kinresults(fits)$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 + n.times df mean.means RSS err.min R2 +SFO 9 7 23.589 196.5334 0.158440 0.97136 +FOMC 9 6 23.589 31.0509 0.066568 0.99548 +DFOP 9 5 23.589 4.3627 0.026621 0.99936 > -- cgit v1.2.1