diff options
Diffstat (limited to 'CakeNullPlot.R')
| -rw-r--r-- | CakeNullPlot.R | 17 |
1 files changed, 12 insertions, 5 deletions
diff --git a/CakeNullPlot.R b/CakeNullPlot.R index 3eacd67..f5484b4 100644 --- a/CakeNullPlot.R +++ b/CakeNullPlot.R @@ -1,4 +1,4 @@ -#$Id: CakeNullPlot.R 216 2011-07-05 14:35:03Z nelr $ +#$Id$ # Generates model curves so the GUI can plot them. Used when all params are fixed so there was no fit # The CAKE R modules are based on mkin # Based on code in IRLSkinfit @@ -19,7 +19,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>.” -CakeNullPlot <- function(model, parms.ini, state.ini, observed, xlim = range(observed$time), digits = max(3, getOption("digits") - 3), ...) +CakeNullPlot <- function(model, parms.ini, state.ini, observed, xlim = range(observed$time), digits = max(3, getOption("digits") - 3), sannMaxIter = 10000, ...) { # Print the fixed values fixed <- data.frame(value = c(state.ini, parms.ini)) @@ -31,13 +31,20 @@ CakeNullPlot <- function(model, parms.ini, state.ini, observed, xlim = range(obs obs_vars = unique(as.character(observed$name)) distimes <- data.frame(DT50 = rep(NA, length(obs_vars)), DT90 = rep(NA, length(obs_vars)), row.names = obs_vars) + extraDT50<- data.frame(DT50 = rep(NA, 2), row.names = c("k1", "k2")) + for (obs_var in obs_vars) { type = names(model$map[[obs_var]])[1] if(exists("DT50")) distimes[obs_var, ] = c(DT50, DT90) - distimes[obs_var, ] = CakeDT(type,obs_var,parms.ini) + distimes[obs_var, ] = CakeDT(type,obs_var,parms.ini,sannMaxIter) } + cat("\nEstimated disappearance times:\n") print(distimes, digits=digits,...) + + extraDT50[ ,c("DT50")] = CakeExtraDT(type,parms.ini) + cat("\nHalf Lives for Extra k values:\n") + print(extraDT50, digits=digits,...) # Plot the model @@ -45,7 +52,7 @@ CakeNullPlot <- function(model, parms.ini, state.ini, observed, xlim = range(obs odeini <- state.ini odenames <- model$parms - odeparms <- params.ini + odeparms <- parms.ini # Solve the system evalparse <- function(string) @@ -86,7 +93,7 @@ CakeNullPlot <- function(model, parms.ini, state.ini, observed, xlim = range(obs predicted_long <- mkin_wide_to_long(out_transformed,time="time") # Calculate chi2 error levels according to FOCUS (2006) - errmin<-CakeChi2(observed, predicted_long, obs_vars, c(), c()) + errmin<-CakeChi2(model, observed, predicted_long, obs_vars, c("auto"), c(), state.ini, c("auto")) cat("\nChi2 error levels in percent:\n") errmin$err.min <- 100 * errmin$err.min print(errmin, digits=digits,...) |