diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/plot.mkinfit.R | 25 |
1 files changed, 14 insertions, 11 deletions
diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R index d4ad6c42..2b85977e 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]) } } |