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-rw-r--r--R/plot.mkinfit.R16
-rw-r--r--man/plot.mkinfit.Rd5
2 files changed, 8 insertions, 13 deletions
diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R
index 2b85977..80cf45f 100644
--- a/R/plot.mkinfit.R
+++ b/R/plot.mkinfit.R
@@ -18,7 +18,7 @@
if(getRversion() >= '2.15.1') utils::globalVariables(c("type", "variable", "observed"))
plot.mkinfit <- function(x, fit = x,
- obs_vars = vector(),
+ obs_vars = names(fit$mkinmod$map),
xlab = "Time", ylab = "Observed",
xlim = range(fit$data$time),
ylim = c(0, max(subset(fit$data, variable %in% obs_vars)$observed, na.rm = TRUE)),
@@ -31,12 +31,6 @@ plot.mkinfit <- function(x, fit = x,
solution_type = fit$solution_type
parms.all <- c(fit$bparms.optim, fit$bparms.fixed)
- obs_vars_all <- names(fit$mkinmod$map)
-
- if (length(obs_vars) > 0){
- vars <- intersect(obs_vars_all, obs_vars)
- } else vars <- obs_vars_all
-
ininames <- c(
rownames(subset(fit$start, type == "state")),
rownames(subset(fit$fixed, type == "state")))
@@ -64,13 +58,13 @@ plot.mkinfit <- function(x, fit = x,
}
# Plot the data and model output
names(col_obs) <- names(pch_obs) <- names(lty_obs) <- names(fit$mkinmod$map)
- for (obs_var in vars) {
+ for (obs_var in obs_vars) {
points(subset(fit$data, variable == obs_var, c(time, observed)),
pch = pch_obs[obs_var], col = col_obs[obs_var])
}
- matlines(out$time, out[vars], col = col_obs[vars], lty = lty_obs[vars])
+ matlines(out$time, out[obs_vars], col = col_obs[obs_vars], lty = lty_obs[obs_vars])
if (legend == TRUE) {
- legend(lpos, inset= inset, legend = vars,
- col = col_obs[vars], pch = pch_obs[vars], lty = lty_obs[vars])
+ legend(lpos, inset= inset, legend = obs_vars,
+ col = col_obs[obs_vars], pch = pch_obs[obs_vars], lty = lty_obs[obs_vars])
}
}
diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd
index 41682ad..4ae82a5 100644
--- a/man/plot.mkinfit.Rd
+++ b/man/plot.mkinfit.Rd
@@ -10,7 +10,7 @@
}
\usage{
\method{plot}{mkinfit}(x, fit = x,
- obs_vars = vector(),
+ obs_vars = names(fit$mkinmod$map),
xlab = "Time", ylab = "Observed",
xlim = range(fit$data$time), ylim = c(0, max(fit$data$observed, na.rm = TRUE)),
col_obs = 1:length(fit$mkinmod$map), pch_obs = col_obs,
@@ -26,7 +26,8 @@
}
\item{obs_vars}{
A character vector of names of the observed variables for which the
- data and the model should be plotted.
+ data and the model should be plotted. Defauls to all observed variables
+ in the model.
}
\item{xlab}{
label for the x axis.

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