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authorjranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>2012-11-26 23:03:19 +0000
committerjranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>2012-11-26 23:03:19 +0000
commitdf916b91c90f80e2c68f3e136a7b6e07b8c6bae1 (patch)
tree4b54b46c68a0b5866aa6bf15131b55b34668af08 /R
parentd267b8c116f78ee9b7b4d76c9ddb7b8950a127b4 (diff)
- Added an S3 plot method for mkinfit models
- Fixed a bug in the mkinfit summary method which crashed on missing covariance matrices git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@58 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Diffstat (limited to 'R')
-rw-r--r--R/mkinfit.R2
-rw-r--r--R/mkinplot.R38
-rw-r--r--R/plot.mkinfit.R45
3 files changed, 48 insertions, 37 deletions
diff --git a/R/mkinfit.R b/R/mkinfit.R
index 02155966..3649b204 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -317,7 +317,7 @@ print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), .
print(x$SFORB, digits=digits,...)
}
- printcor <- !is.null(x$cov.unscaled)
+ printcor <- is.numeric(x$cov.unscaled)
if (printcor){
Corr <- cov2cor(x$cov.unscaled)
rownames(Corr) <- colnames(Corr) <- rownames(x$par)
diff --git a/R/mkinplot.R b/R/mkinplot.R
index 546c5061..b9becfdf 100644
--- a/R/mkinplot.R
+++ b/R/mkinplot.R
@@ -1,38 +1,4 @@
-mkinplot <- function(fit, xlab = "Time", ylab = "Observed", xlim = range(fit$data$time), ylim = range(fit$data$observed, na.rm = TRUE), legend = TRUE, ...)
+mkinplot <- function(fit, ...)
{
- solution_type = fit$solution_type
- fixed <- fit$fixed$value
- names(fixed) <- rownames(fit$fixed)
- parms.all <- c(fit$parms.all, fixed)
- ininames <- c(
- rownames(subset(fit$start, type == "state")),
- rownames(subset(fit$fixed, type == "state")))
- odeini <- parms.all[ininames]
- names(odeini) <- names(fit$mkinmod$diffs)
-
- outtimes <- seq(xlim[1], xlim[2], length.out=100)
-
- odenames <- c(
- rownames(subset(fit$start, type == "deparm")),
- rownames(subset(fit$fixed, type == "deparm")))
- odeparms <- parms.all[odenames]
-
- out <- mkinpredict(fit$mkinmod, odeparms, odeini, outtimes,
- solution_type = solution_type, atol = fit$atol, rtol = fit$rtol, ...)
-
- # Plot the data and model output
- plot(0, type="n",
- xlim = xlim, ylim = ylim,
- xlab = xlab, ylab = ylab, ...)
- col_obs <- pch_obs <- lty_obs <- 1:length(fit$mkinmod$map)
- names(col_obs) <- names(pch_obs) <- names(lty_obs) <- names(fit$mkinmod$map)
- for (obs_var in names(fit$mkinmod$map)) {
- points(subset(fit$data, variable == obs_var, c(time, observed)),
- pch = pch_obs[obs_var], col = col_obs[obs_var])
- }
- matlines(out$time, out[-1])
- if (legend == TRUE) {
- legend("topright", inset=c(0.05, 0.05), legend=names(fit$mkinmod$map),
- col=col_obs, pch=pch_obs, lty=lty_obs)
- }
+ plot(fit, ...)
}
diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R
new file mode 100644
index 00000000..1858aa8a
--- /dev/null
+++ b/R/plot.mkinfit.R
@@ -0,0 +1,45 @@
+plot.mkinfit <- function(x, fit = x,
+ xlab = "Time", ylab = "Observed",
+ xlim = range(fit$data$time), ylim = range(fit$data$observed, na.rm = TRUE),
+ col_obs = 1:length(fit$mkinmod$map),
+ pch_obs = col_obs, lty_obs = rep(1, length(fit$mkinmod$map)),
+ add = FALSE, legend = !add, ...)
+{
+ solution_type = fit$solution_type
+ fixed <- fit$fixed$value
+ names(fixed) <- rownames(fit$fixed)
+ parms.all <- c(fit$parms.all, fixed)
+ ininames <- c(
+ rownames(subset(fit$start, type == "state")),
+ rownames(subset(fit$fixed, type == "state")))
+ odeini <- parms.all[ininames]
+ names(odeini) <- names(fit$mkinmod$diffs)
+
+ outtimes <- seq(xlim[1], xlim[2], length.out=100)
+
+ odenames <- c(
+ rownames(subset(fit$start, type == "deparm")),
+ rownames(subset(fit$fixed, type == "deparm")))
+ odeparms <- parms.all[odenames]
+
+ out <- mkinpredict(fit$mkinmod, odeparms, odeini, outtimes,
+ solution_type = solution_type, atol = fit$atol, rtol = fit$rtol, ...)
+
+ # Set up the plot if not to be added to an existing plot
+ if (add == FALSE) {
+ plot(0, type="n",
+ xlim = xlim, ylim = ylim,
+ xlab = xlab, ylab = ylab, ...)
+ }
+ # Plot the data and model output
+ names(col_obs) <- names(pch_obs) <- names(lty_obs) <- names(fit$mkinmod$map)
+ for (obs_var in names(fit$mkinmod$map)) {
+ points(subset(fit$data, variable == obs_var, c(time, observed)),
+ pch = pch_obs[obs_var], col = col_obs[obs_var])
+ }
+ matlines(out$time, out[-1], col = col_obs, lty = lty_obs)
+ if (legend == TRUE) {
+ legend("topright", inset=c(0.05, 0.05), legend=names(fit$mkinmod$map),
+ col=col_obs, pch=pch_obs, lty=lty_obs)
+ }
+}

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