# $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 <http://www.gnu.org/licenses/>
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$label, "\n")
}
cat("Study type: ", kinobject$type, "\n")
cat("System: ", kinobject$system, "\n")
if (!is.null(kinobject$source)) {
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")
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$stats[kinmodel, "R2"], digits=3), "\n")
}
}
}
cat("\n\n---\n")
cat("Endpoint estimates\n\n")
print(round(kinobject$results$results, digits=endpoint.digits))
if (!is.na(file)) sink()
}
