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authorJohannes Ranke <jranke@uni-bremen.de>2014-04-26 03:04:12 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2014-04-26 03:04:12 +0200
commitd619711839afb6776f003c990e1a77c8fedf1a6a (patch)
treea906918522894be5f7ed10d2ab88ee68b2129c12 /R/plot.mkinfit.R
parent59e2c3b5ce470ace53b93ad5e6e7d9acbfe86f21 (diff)
Enable selection of observed variables to plot
Diffstat (limited to 'R/plot.mkinfit.R')
-rw-r--r--R/plot.mkinfit.R25
1 files changed, 14 insertions, 11 deletions
diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R
index d4ad6c4..2b85977 100644
--- a/R/plot.mkinfit.R
+++ b/R/plot.mkinfit.R
@@ -1,10 +1,5 @@
-# $Id: $
-
-# Copyright (C) 2010-2013 Johannes Ranke
+# Copyright (C) 2010-2014 Johannes Ranke
# Contact: jranke@uni-bremen.de
-# The summary function is an adapted and extended version of summary.modFit
-# from the FME package, v 1.1 by Soetart and Petzoldt, which was in turn
-# inspired by summary.nls.lm
# This file is part of the R package mkin
@@ -23,8 +18,10 @@
if(getRversion() >= '2.15.1') utils::globalVariables(c("type", "variable", "observed"))
plot.mkinfit <- function(x, fit = x,
+ obs_vars = vector(),
xlab = "Time", ylab = "Observed",
- xlim = range(fit$data$time), ylim = c(0, max(fit$data$observed, na.rm = TRUE)),
+ xlim = range(fit$data$time),
+ ylim = c(0, max(subset(fit$data, variable %in% obs_vars)$observed, na.rm = TRUE)),
col_obs = 1:length(fit$mkinmod$map),
pch_obs = col_obs,
lty_obs = rep(1, length(fit$mkinmod$map)),
@@ -34,6 +31,12 @@ 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$fixed, type == "state")))
@@ -61,13 +64,13 @@ plot.mkinfit <- function(x, fit = x,
}
# Plot the data and model output
names(col_obs) <- names(pch_obs) <- names(lty_obs) <- names(fit$mkinmod$map)
- for (obs_var in names(fit$mkinmod$map)) {
+ for (obs_var in vars) {
points(subset(fit$data, variable == obs_var, c(time, observed)),
pch = pch_obs[obs_var], col = col_obs[obs_var])
}
- matlines(out$time, out[-1], col = col_obs, lty = lty_obs)
+ matlines(out$time, out[vars], col = col_obs[vars], lty = lty_obs[vars])
if (legend == TRUE) {
- legend(lpos, inset= inset, legend=names(fit$mkinmod$map),
- col=col_obs, pch=pch_obs, lty=lty_obs)
+ legend(lpos, inset= inset, legend = vars,
+ col = col_obs[vars], pch = pch_obs[vars], lty = lty_obs[vars])
}
}

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