- See ChangeLog entry for today (2 small bugfixes and lots of GUI progress)

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@117 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

5 files changed, 120 insertions, 32 deletions

diff --git a/ChangeLog b/ChangeLog
index a53ea241..d87fa0d9 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,9 @@
+2013-10-17  Johannes Ranke <jranke@stiller> for mkin (0.9-22)

+

+	* Fix plot.mkinfit as it passed graphical arguments like main to the solver

+	* Do not use plot=TRUE in mkinfit example

+	* The first successful fits in the not so simple GUI

+

 2013-10-16  Johannes Ranke<jranke@uni-bremen.de> for mkin (0.9-22)

 

 	* Unify naming of initial values of state variables

@@ -12,10 +18,9 @@
 

 2013-10-09  Johannes Ranke <jranke@uni-bremen.de> for mkin (0.9-22)

 

-  * Do not use 0 values at time zero for chi2 error level calculations.

-    This is the way it is done in KinGUII and it makes sense

-

+	* Do not use 0 values at time zero for chi2 error level calculations.

+	  This is the way it is done in KinGUII and it makes sense

 

 Changes performed in earlier versions are documented in the subversion log

 files on R-Forge http://www.r-forge.r-project.org/scm/?group_id=615

-vim: set expandtab ts=2 sw=2:

+vim: set noexpandtab ts=2 sw=2:

diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R
index 5e2db394..a07ddea1 100644
--- a/R/plot.mkinfit.R
+++ b/R/plot.mkinfit.R
@@ -48,7 +48,7 @@ plot.mkinfit <- function(x, fit = x,
   odeparms <- parms.all[odenames]
 
   out <- mkinpredict(fit$mkinmod, odeparms, odeini, outtimes, 
-          solution_type = solution_type, atol = fit$atol, rtol = fit$rtol, ...)
+          solution_type = solution_type, atol = fit$atol, rtol = fit$rtol)
 
   # Set up the plot if not to be added to an existing plot
   if (add == FALSE) {
diff --git a/inst/GUI/TODO b/inst/GUI/TODO
index ea875cea..e9089eda 100644
--- a/inst/GUI/TODO
+++ b/inst/GUI/TODO
@@ -1 +1,4 @@
-- Write the model editor
+- Import of csv files
+- Create widgets for model configuration only once per dataset, it takes too much time
+- Make summary text file accessible
+- Make plot of fit and residuals accessible
diff --git a/inst/GUI/simple.R b/inst/GUI/simple.R
index f5eafb62..f53b064d 100644
--- a/inst/GUI/simple.R
+++ b/inst/GUI/simple.R
@@ -38,8 +38,8 @@ studies.df <- data.frame(Index = as.integer(1),
 # Initial datasets {{{2

 ds <- list()

 observed.all <- vector()

-for (i in 1:5) {

-  ds.letter = LETTERS[i]

+for (i in 1:2) {

+  ds.letter = LETTERS[i + 2]

   ds.index <- as.character(i)

   ds.name = paste0("FOCUS_2006_", ds.letter)

   ds[[ds.index]] <- list(

@@ -74,15 +74,13 @@ override <- function(d) {
              value = ifelse(is.na(d$override), d$value, d$override),

              err = d$err)

 }

-f <- s <- f.gg <- f.gg.rows <- list()

-f.gg.ini <- f.gg.fixed <- f.gg.optim <- list()

+f <- s <- f.gg <- list()

+f.gg.parms <- f.gg.opts <- list()

 for (ds.i in 1:length(ds)) {

   f[[as.character(ds.i)]] <- list()

   f.gg[[as.character(ds.i)]] <- list()

-  f.gg.rows[[as.character(ds.i)]] <- list()

-  f.gg.ini[[as.character(ds.i)]] <- list()

-  f.gg.fixed[[as.character(ds.i)]] <- list()

-  f.gg.optim[[as.character(ds.i)]] <- list()

+  f.gg.parms[[as.character(ds.i)]] <- list()

+  f.gg.opts[[as.character(ds.i)]] <- list()

   s[[as.character(ds.i)]] <- list()

 }

 # Data frames with datasets, models and fits to be continuosly updated {{{1

@@ -220,30 +218,112 @@ size(m.gtable) <- list(columnWidths = c(40, 200))
 

 # Section for selecting datasets and model {{{2

 dsmsel <- gvbox(cont = dsm)

+show_plot <- function(ds.i, m.i, type) {

+  ow <- options("warn")

+  options(warn = -1)

+  Parameters <- f.gg.parms[[ds.i]][[m.i]][,]

+  Parameters.de <- subset(Parameters, Type == "deparm", type)

+  stateparms <- subset(Parameters, Type == "state")[[type]]

+  deparms <- as.numeric(Parameters.de[[type]])

+  names(deparms) <- rownames(Parameters.de)

+  if (type == "Initial") {

+    f[[ds.i]][[m.i]] <<- mkinfit(m[[m.i]], override(ds[[ds.i]]$data),

+                                 state.ini = stateparms,

+                                 parms.ini = deparms,

+                                 err = "err", control.modFit = list(maxiter = 0))

+  }

+  options(ow)

+  ftmp <- f[[ds.i]][[m.i]]

+  f <- get_tempfile(ext=".svg")

+  svg(f, width = 7, height = 5)

+  plot(ftmp, main = ds[[ds.i]]$title,

+       xlab = ifelse(ds[[ds.i]]$time_unit == "", "Time", 

+                     paste("Time in", ds[[ds.i]]$time_unit)),

+       ylab = ifelse(ds[[ds.i]]$unit == "", "Observed", 

+                     paste("Observed in", ds[[ds.i]]$unit)))

+  dev.off()

+  svalue(plots[[ds.i]]) <<- f

+}

+get_Parameters <- function(stmp, optimised)

+{

+  pars <- rbind(stmp$start[1:2], stmp$fixed)

+

+  pars$fixed <- c(rep(FALSE, length(stmp$start$value)),

+                  rep(TRUE, length(stmp$fixed$value)))

+  pars$name <- rownames(pars)

+  Parameters <- data.frame(Name = pars$name,

+                           Type = pars$type,

+                           Initial = pars$value,

+                           Fixed = pars$fixed,

+                           Optimised = as.numeric(NA))

+  Parameters <- rbind(subset(Parameters, Type == "state"),

+                      subset(Parameters, Type == "deparm"))

+  rownames(Parameters) <- Parameters$Name

+  if (optimised) {

+    Parameters[rownames(stmp$bpar), "Optimised"] <- stmp$bpar[, "Estimate"]

+  }

+  return(Parameters)

+}

+run_fit <- function(ds.i, m.i) {

+  Parameters <- f.gg.parms[[ds.i]][[m.i]][,]

+  Parameters.de <- subset(Parameters, Type == "deparm")

+  deparms <- Parameters.de$Initial

+  names(deparms) <- rownames(Parameters.de)

+  f[[ds.i]][[m.i]] <<- mkinfit(m[[m.i]], override(ds[[ds.i]]$data),

+                               state.ini = subset(Parameters,

+                                                  Type == "state")$Initial,

+                               parms.ini = deparms, 

+                               err = "err")

+  s[[ds.i]][[m.i]] <<- summary(f[[ds.i]][[m.i]])

+

+  f.gg.parms[[ds.i]][[m.i]][,] <- get_Parameters(s[[ds.i]][[m.i]], TRUE)

+

+  show_plot(ds.i, m.i, "Optimised")

+}

+show_fit_config <- function(ds.i, m.i) {

+  ftmp <- f[[ds.i]][[m.i]]

+  stmp <- summary(ftmp)

+  Parameters <- get_Parameters(stmp, FALSE)

+

+  f.gg.parms[[ds.i]][[m.i]] <<- gdf(Parameters, 

+                                    width = 420, height = 300,

+                                    cont = f.gg[[ds.i]][[m.i]],

+                                    do_add_remove_buttons = FALSE)

+  f.gg.parms[[ds.i]][[m.i]]$set_column_width(1, 200)

+  f.gg.parms[[ds.i]][[m.i]]$set_column_width(2, 50)

+  f.gg.parms[[ds.i]][[m.i]]$set_column_width(3, 60)

+  f.gg.parms[[ds.i]][[m.i]]$set_column_width(4, 50)

+  f.gg.parms[[ds.i]][[m.i]]$set_column_width(5, 60)

+

+  f.gg.rest <- gvbox(cont = f.gg[[ds.i]][[m.i]])

+  f.gg.buttons <- ggroup(cont = f.gg.rest)

+  gbutton("Show initial", handler = function(h, ...) show_plot(ds.i, m.i, "Initial"),

+          cont = f.gg.buttons)

+  gbutton("Run", handler = function(h, ...) run_fit(ds.i, m.i),

+          cont = f.gg.buttons)

+  f.gg.opts[[ds.i]][[m.i]] <<- gformlayout(cont = f.gg.rest)

+  solution_types <- character()

+  if (length(ftmp$mkinmod$map) == 1) solution_types <- "analytical"

+  if (is.matrix(ftmp$mkinmod$coefmat)) solution_types <- c(solution_types, "eigen")

+  solution_types <- c(solution_types, "deSolve")

+

+  gcombobox(solution_types, selected = 1, label = "solution_type", 

+            cont = f.gg.opts[[ds.i]][[m.i]])

+}

 configure_fits_handler <- function(h, ...) {

   ds.sel <- as.character(svalue(ds.gtable))

   m.sel <- as.character(svalue(m.gtable))

+  ow <- options("warn")

+  options("warn" = -1)

   for (ds.i in ds.sel) {

     for (m.i in m.sel) {

       f.gg[[ds.i]][[m.i]] <<- ggroup(cont = f.gn[[ds.i]], label = m[[m.i]]$name)

-      f.gg.parms <- gvbox(cont = f.gg[[ds.i]][[m.i]])

-      f.gg.rows[[ds.i]][[m.i]] <<- list()

-      f.gg.ini[[ds.i]][[m.i]] <<- list()

-      f[[ds.i]][[m.i]] <- ftmp <- mkinfit(m[[m.i]], override(ds[[ds.i]]$data), 

+      f[[ds.i]][[m.i]] <<- mkinfit(m[[m.i]], override(ds[[ds.i]]$data), 

                                   err = "err", control.modFit = list(maxiter = 0))

-      s[[ds.i]][[m.i]] <- stmp <- summary(ftmp)

-      pars <- rbind(stmp$start[1:2], stmp$fixed)

-      pars$fixed <- c(rep(FALSE, length(stmp$start$value)),

-                      rep(TRUE, length(stmp$fixed$value)))

-

-      for (parm in c(paste0(names(ftmp$mkinmod$map), "_0"), names(ftmp$bparms.ode))) {

-        f.gg.rows[[ds.i]][[m.i]][[parm]] <- ggroup(cont = f.gg.parms)

-        glabel(parm, cont = f.gg.rows[[ds.i]][[m.i]][[parm]])

-        f.gg.ini[[ds.i]][[m.i]][[parm]] <- gedit(pars[parm, "value"], 

-                                             cont = f.gg.rows[[ds.i]][[m.i]][[parm]])

-      }

+      show_fit_config(ds.i, m.i)

     }

   }

+  options(ow)

 }

 dsconfig <- gbutton("Configure fits for selections", cont = dsmsel, 

                   handler = configure_fits_handler)

@@ -262,7 +342,7 @@ copy_dataset_handler <- function(h, ...) {
   ds.gtable[,] <- ds.df

   prows[[ds.cur]] <<- ggroup(cont = pfv)

   plots[[ds.cur]] <<- gsvg(svg_plot(ds.cur), 

-                        container=prows[[ds.cur]], 

+                        container = prows[[ds.cur]], 

                         width = 490, height = 350)

 }

  

@@ -560,7 +640,7 @@ for (ds.i in 1:length(ds)) {
   plots[[ds.plot]] <- gsvg(svg_plot(ds.plot), 

                         container=prows[[ds.plot]], 

                         width = 490, height = 350)

-  f.gn[[ds.plot]] <- gnotebook(cont = prows[[ds.plot]], width = 600,

+  f.gn[[ds.plot]] <- gnotebook(cont = prows[[ds.plot]], width = 750,

                          handler = function(h, ...) galert("test", parent = w))

 }

 

diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 750c3468..c15c0843 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -198,7 +198,7 @@ SFORB_SFO <- mkinmod(
 fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D)
 # Use starting parameters from parent only SFORB fit (not really needed in this case)
 fit.SFORB = mkinfit(SFORB, FOCUS_2006_D)
-fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode, plot=TRUE)
+fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode)
 
 # Weighted fits, including IRLS
 SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"),