Now working with mkin >= 0.9.49.6

5 files changed, 51 insertions, 34 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index f8765e0..9316135 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: gmkin
 Type: Package
 Title: Graphical User Interface for Fitting Kinetic Models to Chemical Degradation Data
 Version: 0.6.10
-Date: 2019-07-05
+Date: 2019-07-08
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), 
                     email = "jranke@uni-bremen.de"),
              person("Stefan", "Meinecke", role = "ctb"),
@@ -10,7 +10,7 @@ Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
 Description: Browser based graphical user interface for R package mkin, based
   on the gWidgetsWWW2 package. Both gmkin and gWidgetsWWW2 are developed on
   GitHub, but are also available from the R-Forge repository.
-Depends: mkin (>= 0.9.47.3), gWidgetsWWW2 (>= 0.4-7)
+Depends: mkin (>= 0.9.49.6), gWidgetsWWW2 (>= 0.4-7)
 Imports: R6, markdown, plyr, devEMF
 Suggests: knitr, rmarkdown
 License: GPL
@@ -19,6 +19,5 @@ LazyData: yes
 Encoding: UTF-8
 VignetteBuilder: knitr
 BugReports: http://github.com/jranke/gmkin/issues
-URL: http://kinfit.r-forge.r-project.org/gmkin_static,
-     http://pkgdown.jrwb.de/gmkin
+URL: http://pkgdown.jrwb.de/gmkin
 RoxygenNote: 6.1.1
diff --git a/NEWS.md b/NEWS.md
index f9c771f..a6aea8d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,11 +1,13 @@
 # NEWS for package 'gmkin'
 
-## gmkin 0.6-10 (2019-07-06)
+## gmkin 0.6-10 (2019-07-08)
 
-- Adapt to mkin 0.9.49.1
+- Adapt to mkin 0.9.49.6
 
 - Use devEMF for better vector graphics export for Windows
 
+- Manual weighting is not possible as this functionality is currently not present in mkin versions > 0.9.48.1
+
 ## gmkin 0.6-9 (2018-09-13)
 
 - Enable fits with the two-component error model during iterative reweighting (IRLS)
diff --git a/README.md b/README.md
index 7c0f7ea..19f3980 100644
--- a/README.md
+++ b/README.md
@@ -15,8 +15,7 @@ For running gmkin you need a system running a recent version of R (version
 (Firefox/Iceweasel and Chrome work for me) with JavaScript enabled.
 
 It should be possible to run gmkin on most laptop or desktop computers running
-Linux, Mac OS X, Windows XP or Windows 7. It is frequently checked under Linux and
-Windows 7.
+Linux, Mac OS X, Windows 7 or Windows 10. 
 
 To view the complete set of widgets in the browser window without resizing
 anything, it needs a screen space of 1366x740 pixels.
@@ -168,3 +167,6 @@ Agency ([Umweltbundesamt](http://www.umweltbundesamt.de)) in two projects in
 gratefully acknowledged. In particular, Stefan Meinecke contributed with a lot
 of user feedback and suggestions for improvement in that time.
 
+The adaptation to mkin versions > 0.9.49.6 that can do fits using a two-component
+error model was supported by another project by the Umweltbundesamt in 2018/2019.
+
diff --git a/inst/GUI/gmkin.R b/inst/GUI/gmkin.R
index b7ddc13..1320da0 100644
--- a/inst/GUI/gmkin.R
+++ b/inst/GUI/gmkin.R
@@ -299,17 +299,25 @@ c.ds <- glabel(empty_conf_labels[1], cont = c.gf, ext.args = list(margin = "0 0
 c.m <- glabel(empty_conf_labels[2], cont = c.gf, ext.args = list(margin = "0 0 0 5"))

 

 update_f_conf <- function() { # {{{3

-  stmp <<- summary(ftmp)

+  stmp <<- suppressWarnings(summary(ftmp))

   svalue(f.gg.opts.st) <<- ftmp$solution_type

   svalue(f.gg.opts.atol) <<- ftmp$atol

   svalue(f.gg.opts.rtol) <<- ftmp$rtol

   svalue(f.gg.opts.transform_rates) <<- ftmp$transform_rates

   svalue(f.gg.opts.transform_fractions) <<- ftmp$transform_fractions

-  svalue(f.gg.opts.error_model) <<- ftmp$error_model

-  svalue(f.gg.opts.error_model_algorithm) <<- ftmp$error_model_algorithm

+  if (!is.null(ftmp$error_model_algorithm)) {

+    svalue(f.gg.opts.error_model_algorithm) <<- ftmp$error_model_algorithm

+    if (ftmp$error_model_algorithm == "OLS") {

+      svalue(f.gg.opts.error_model) <<- "const"

+    } else {

+      svalue(f.gg.opts.error_model) <<- ftmp$error_model

+    }

+  }

   svalue(f.gg.opts.reweight.tol) <<- ftmp$reweight.tol

   svalue(f.gg.opts.reweight.max.iter) <<- ftmp$reweight.max.iter

-  svalue(f.gg.opts.maxit) <<- ftmp$maxit

+  if (!is.null(ftmp$maxit)) {

+    svalue(f.gg.opts.maxit) <<- ftmp$maxit

+  }

   show_fit_option_widgets(TRUE)

   update_plot_obssel()

   f.gg.parms[,] <- get_Parameters(stmp, ftmp$optimised)

@@ -369,7 +377,6 @@ configure_fit_handler <- function(h, ...) { # Configure fit button {{{3
     update_f_conf()

 

     f.run$call_Ext("enable")

-    print("test")

     svalue(f.running.label) <- "Fit configured and ready to run"

   } else {

     svalue(f.running.label) <- paste("No fit configured:",

@@ -977,13 +984,6 @@ run_fit_handler <- function(h, ...) { #{{{3
       iniparms <- Parameters.ini$Initial

       names(iniparms) <- sub("_0", "", Parameters.ini$Name)

       inifixed <- names(iniparms[Parameters.ini$Fixed])

-      weight <- svalue(f.gg.opts.weight)

-      if (weight == "manual") {

-        err = "err"

-      } else {

-        err = NULL

-      }

-      reweight.method <- svalue(f.gg.opts.reweight.method)

       if (svalue(f.gg.opts.plot)) {

         if (.Platform$OS.type == "windows") {

           # When on windows, check for an active windows device. If not present,

@@ -991,7 +991,6 @@ run_fit_handler <- function(h, ...) { #{{{3
           if (attr(dev.cur(), "names") != "windows") windows()

         }

       }

-      if (reweight.method == "none") reweight.method = NULL

       ftmp <<- mkinfit(m.cur, override(ds.cur$data),

                        state.ini = iniparms,

                        fixed_initials = inifixed,

@@ -1022,7 +1021,6 @@ run_fit_handler <- function(h, ...) { #{{{3
       f.keep$call_Ext("enable")

       show.initial.gb.o$call_Ext("enable")

       svalue(f.gg.opts.st) <- ftmp$solution_type

-      svalue(f.gg.opts.weight) <- ftmp$weight.ini

 

       svalue(f.running.label) <- "Terminated"

       update_f_results()

@@ -1089,7 +1087,8 @@ get_Parameters <- function(stmp, optimised) # {{{3
                            Fixed = pars$fixed,

                            Optimised = as.numeric(NA))

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

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

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

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

   rownames(Parameters) <- Parameters$Name

   if (optimised) {

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

@@ -1154,13 +1153,13 @@ f.gg.opts.error_model <- gcombobox(error_models, selected = 1,
                                    label = "error_model",

                                    width = 160,

                                    cont = f.gg.opts.1)

-error_model_algorithms <- c("d_3", "direct", "threestep", "IRLS")

-f.gg.opts.error_model_algorithm <- gcombobox(error_model_algorithms, selected = 1,

+error_model_algorithms <- c("d_3", "direct", "threestep", "IRLS", "OLS")

+f.gg.opts.error_model_algorithm <- gcombobox(error_model_algorithms, selected = 5,

                                    label = "error_model_algorithm",

                                    width = 160,

                                    cont = f.gg.opts.1)

-f.gg.opts.maxit <- gedit("auto", label = "maxit",

-                                 width = 20, cont = f.gg.opts.1)

+f.gg.opts.maxit <- gedit(200, label = "maxit",

+                         width = 20, cont = f.gg.opts.1)

 

 # Second group {{{4

 f.gg.opts.2 <- gformlayout(cont = f.gg.opts.g)

@@ -1169,12 +1168,6 @@ f.gg.opts.transform_rates <- gcheckbox("transform_rates",
 f.gg.opts.transform_fractions <- gcheckbox("transform_fractions",

                          cont = f.gg.opts.2, checked = TRUE)

 weights <- c("manual", "none", "std", "mean")

-f.gg.opts.weight <- gcombobox(weights, selected = 1, label = "weight",

-                              width = 180, cont = f.gg.opts.2)

-f.gg.opts.reweight.method <- gcombobox(c("none", "obs", "tc"), selected = 1,

-                                       label = "IRLS",

-                                       width = 180,

-                                       cont = f.gg.opts.2)

 f.gg.opts.reweight.tol <- gedit(1e-8, label = "reweight.tol",

                                  width = 20, cont = f.gg.opts.2)

 f.gg.opts.reweight.max.iter <- gedit(10, label = "reweight.max.iter",

@@ -1421,7 +1414,7 @@ plot_ftmp_save <- function(filename) {
   switch(plot_format,

          png = png(filename, width = 400, height = 400),

          pdf = pdf(filename),

-         wmf = win.metafile(filename))

+         emf = devEMF::emf(filename))

   plot_ftmp()

   dev.off()

   svalue(sb) <- paste("Saved plot to", filename, "in working directory", getwd())

diff --git a/test.R b/test.R
new file mode 100644
index 0000000..eb61a1a
--- /dev/null
+++ b/test.R
@@ -0,0 +1,21 @@
+library(gmkin)
+
+app <- gmkin(script = "~/git/gmkin/inst/GUI/gmkin.R")
+s <- gmkin:::get_current_session(app)
+
+s$show_fit_option_widgets(TRUE)
+s$f.run$call_Ext("enable")
+
+names(s)
+s$ftmp$reweight.max.iter
+s$ftmp$maxit
+names(s$ftmp)
+
+s$ws$ftmp$maxit
+s$f.run$call_Ext("enable")
+s$f.gg.parms[,]
+s$show_fit_option_widgets
+svalue(s$f.gg.opts.reweight.tol) <-
+svalue(s$f.gg.opts.error_model)
+svalue(s$f.gg.opts.error_model_algorithm)
+visible(s$f.gg.opts.g) <- TRUE