From 448fd5ede69121c9f4c693ed72ade98d6b9b83e0 Mon Sep 17 00:00:00 2001 From: jranke Date: Thu, 28 Jun 2012 04:59:12 +0000 Subject: - Formatting improvement of mkinmod - Small fix in mkinplot git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@45 edb9625f-4e0d-4859-8d74-9fd3b1da38cb --- R/mkinmod.R | 29 +++++++++++++++-------------- R/mkinplot.R | 8 ++++---- 2 files changed, 19 insertions(+), 18 deletions(-) diff --git a/R/mkinmod.R b/R/mkinmod.R index c7f11d9..1a1c55c 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -1,6 +1,6 @@ # $Id$ -# Copyright (C) 2010-2012 Johannes Ranke#{{{ +# Copyright (C) 2010-2012 Johannes Ranke {{{ # Contact: jranke@uni-bremen.de # This file is part of the R package mkin @@ -16,7 +16,7 @@ # details. # You should have received a copy of the GNU General Public License along with -# this program. If not, see #}}} +# this program. If not, see }}} mkinmod <- function(..., use_of_ff = "min") { @@ -47,11 +47,11 @@ mkinmod <- function(..., use_of_ff = "min") } else message <- "ok" } else mat = TRUE#}}} - # Establish list of differential equations as well as map from observed#{{{ + # Establish list of differential equations as well as map from observed {{{ # compartments to differential equations for (varname in obs_vars) { - # Check the type component of the compartment specification#{{{ + # Check the type component of the compartment specification {{{ if(is.null(spec[[varname]]$type)) stop( "Every part of the model specification must be a list containing a type component") if(!spec[[varname]]$type %in% c("SFO", "FOMC", "DFOP", "HS", "SFORB")) stop( @@ -59,8 +59,8 @@ mkinmod <- function(..., use_of_ff = "min") if(spec[[varname]]$type %in% c("FOMC", "DFOP", "HS") & match(varname, obs_vars) != 1) { stop(paste("Types FOMC, DFOP and HS are only implemented for the first compartment,", "which is assumed to be the source compartment")) - }#}}} - # New (sub)compartments (boxes) needed for the model type#{{{ + } #}}} + # New (sub)compartments (boxes) needed for the model type {{{ new_boxes <- switch(spec[[varname]]$type, SFO = varname, FOMC = varname, @@ -69,22 +69,23 @@ mkinmod <- function(..., use_of_ff = "min") SFORB = paste(varname, c("free", "bound"), sep="_") ) map[[varname]] <- new_boxes - names(map[[varname]]) <- rep(spec[[varname]]$type, length(new_boxes))#}}} - # Start a new differential equation for each new box#{{{ + names(map[[varname]]) <- rep(spec[[varname]]$type, length(new_boxes)) #}}} + # Start a new differential equation for each new box {{{ new_diffs <- paste("d_", new_boxes, " =", sep="") names(new_diffs) <- new_boxes - diffs <- c(diffs, new_diffs)#}}} - }#}}} + diffs <- c(diffs, new_diffs) #}}} + } #}}} - # Create content of differential equations and build parameter list#{{{ + # Create content of differential equations and build parameter list {{{ for (varname in obs_vars) { # Get the name of the box(es) we are working on for the decline term(s) box_1 = map[[varname]][[1]] # This is the only box unless type is SFORB if(spec[[varname]]$type %in% c("SFO", "SFORB")) { # {{{ Add SFO or SFORB decline term if (use_of_ff == "min") { # Minimum use of formation fractions - # Turn on sink if this is not explicitly excluded by the user by specifying sink=FALSE - if(is.null(spec[[varname]]$sink)) spec[[varname]]$sink <- TRUE + # Turn on sink if this is not explicitly excluded by the user by + # specifying sink=FALSE + if(is.null(spec[[varname]]$sink)) spec[[varname]]$sink <- TRUE if(spec[[varname]]$sink) { # If sink is required, add first-order sink term @@ -170,7 +171,7 @@ mkinmod <- function(..., use_of_ff = "min") } } } #}}} - }#}}} + } #}}} model <- list(diffs = diffs, parms = parms, map = map, use_of_ff = use_of_ff) diff --git a/R/mkinplot.R b/R/mkinplot.R index 789a6f9..7641d26 100644 --- a/R/mkinplot.R +++ b/R/mkinplot.R @@ -24,15 +24,15 @@ mkinplot <- function(fit, xlab = "Time", ylab = "Observed", xlim = range(fit$dat plot(0, type="n", xlim = xlim, ylim = ylim, xlab = xlab, ylab = ylab, ...) - col_obs <- pch_obs <- 1:length(fit$mkinmod$map) - names(col_obs) <- names(pch_obs) <- names(fit$mkinmod$map) + col_obs <- pch_obs <- lty_obs <- 1:length(fit$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]) + 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=1:length(pch_obs)) + col=col_obs, pch=pch_obs, lty=lty_obs) } } -- cgit v1.2.1