diff options
Diffstat (limited to 'R/kinreport.R')
| -rw-r--r-- | R/kinreport.R | 97 |
1 files changed, 70 insertions, 27 deletions
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 <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$label, "\n")
+ if (!is.null(kinobject$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")
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