Format of gmkin workspace files, copyright, updates

- Change the format of the workspace files of gmkin so they can be
  distributed in the mkin package
- Add gmkin workspace datasets FOCUS_2006_gmkin and FOCUS_2006_Z_gmkin
- Restrict the unit test with the Schaefer data to parent and primary
  metabolites as formation fraction and DT50 for A2 are higly correlated
  and passing the test is platform dependent. For example, the test
  fails in 1 out of 14 platforms on CRAN as of today
- Add Eurofins Regulatory AG copyright notices
- Import FME and deSolve instead of depending on them to have cleaner
  startup

2 files changed, 60 insertions, 33 deletions

diff --git a/inst/GUI/gmkin.R b/inst/GUI/gmkin.R
index 07f892e0..6de4de2e 100644
--- a/inst/GUI/gmkin.R
+++ b/inst/GUI/gmkin.R
@@ -1,9 +1,8 @@
-# $Id: mkinGUI.R 122 2013-10-21 20:19:57Z jranke $ {{{1

+# gWidgetsWWW2 GUI for mkin {{{1

 

-# gWidgetsWWW2 GUI for mkin

-

-# Copyright (C) 2013 Johannes Ranke

-# Contact: jranke@uni-bremen.de, johannesranke@eurofins.com

+# Copyright (C) 2013,2014 Johannes Ranke

+# Portions of this file are copyright (C) 2013 Eurofins Regulatory AG, Switzerland

+# Contact: jranke@uni-bremen.de

 

 # This file is part of the R package mkin

 

@@ -19,10 +18,11 @@
 

 # You should have received a copy of the GNU General Public License along with

 # this program. If not, see <http://www.gnu.org/licenses/>

+

 require(mkin) # {{{1

 # Set the GUI title and create the basic widget layout {{{1

-w      <- gwindow("Browser based GUI for kinetic evaluations using mkin")

-sb     <- gstatusbar("Powered by gWidgetsWWW2 and Rook", cont = w)

+w      <- gwindow("gmkin - Browser based GUI for kinetic evaluations using mkin")

+sb     <- gstatusbar(paste("Powered by gWidgetsWWW2, ExtJS, Rook, FME, deSolve and minpack.lm --- Working directory is", getwd()), cont = w)

 pg     <- gpanedgroup(cont = w, default.size = 300)

 center <- gnotebook(cont = pg)

 left   <- gvbox(cont = pg)

@@ -35,7 +35,8 @@ override <- function(d) {
 }

 # Set default values for project data {{{1

 # Initial project file name {{{2

-project_file <- "mkin_FOCUS_2006.RData"

+project_name <- "mkin_FOCUS_2006"

+project_file <- paste0(project_name, ".RData")

 # Initial studies {{{2

 studies.df <- data.frame(Index = as.integer(1), 

                          Citation = "FOCUS (2006) Guidance on degradation kinetics",

@@ -133,53 +134,79 @@ upload_file_handler <- function(h, ...)
 {

   # General

   tmpfile <- normalizePath(svalue(h$obj), winslash = "/")

-  try(load(tmpfile))

   project_file <<- pr.gf$filename

-  svalue(pr.ge) <- project_file

+  project_name <<- try(load(tmpfile))

+  if (inherits(project_name, "try-error")) {

+    galert(paste("Failed to load", project_file, "from", getwd()), parent = w)

+  } 

+

+  svalue(sb) <- paste("Loaded project file", project_file, "from working directory", getwd())

+  svalue(pr.ge) <- project_name

+  workspace <- get(project_name)

 

   # Studies

-  studies.gdf[,] <- studies.df 

+  studies.gdf[,] <- studies.df <- workspace$studies.df

 

   # Datasets

-  ds.cur <<- ds.cur

-  ds <<- ds

+  ds.cur <<- workspace$ds.cur

+  ds <<- workspace$ds

   update_ds.df()

   ds.gtable[,] <- ds.df

   update_ds_editor()

 

   # Models

-  m.cur <<- ds.cur

-  m <<- m

+  m.cur <<- workspace$m.cur

+  m <<- workspace$m

   update_m.df()

   m.gtable[,] <- m.df

   update_m_editor()

 

   # Fits

-  f.cur <<- f.cur

-  f <<- f

-  s <<- s

-  if (length(f) > 0) update_f.df()

-  else f.df <- f.df.empty

+  f.cur <<- workspace$f.cur

+  f <<- workspace$f

+  s <<- workspace$s

+  if (length(f) > 0) {

+    update_f.df()

+    ftmp <<- f[[f.cur]]

+    stmp <<- s[[f.cur]]

+    ds.i <<- ds.cur

+    update_plotting_and_fitting()

+  } else {

+    f.df <<- f.df.empty

+    update_ds_editor()

+    svalue(center) <- 1

+  }

   f.gtable[,] <- f.df

-  ftmp <<- f[[f.cur]]

-  stmp <<- s[[f.cur]]

-  ds.i <<- ds.cur

-  update_plotting_and_fitting()

 }

 save_to_file_handler <- function(h, ...)

 {

-   studies.df <- data.frame(studies.gdf[,], stringsAsFactors = FALSE)

-   save(studies.df, ds, ds.cur, m, m.cur, f, s, f.cur, file = project_file)

-   galert(paste("Saved project contents to", project_file), parent = w)

+  studies.df <- data.frame(studies.gdf[,], stringsAsFactors = FALSE)

+  workspace <- list(

+                    studies.df = studies.df,

+

+                    ds = ds,

+                    ds.cur = ds.cur,

+

+                    m = m,

+                    m.cur = m.cur,

+

+                    f = f,

+                    f.cur = f.cur,

+

+                    s = s)

+  assign(project_name, workspace)

+  save(list = project_name, file = project_file)

+  svalue(sb) <- paste("Saved project contents to", project_file, "in working directory", getwd())

 }

-change_project_file_handler = function(h, ...) {

-  project_file <<- as.character(svalue(h$obj))

+change_project_name_handler = function(h, ...) {

+  project_name <<- as.character(svalue(h$obj))

+  project_file <<- paste0(project_name, ".RData")

 }

 # Project data management GUI elements {{{2

 pr.gf <- gfile(text = "Select project file", cont = prg,

                handler = upload_file_handler)

-pr.ge <- gedit(project_file, cont = prg, 

-               handler = change_project_file_handler)

+pr.ge <- gedit(project_name, cont = prg, label = "Project", width = 240,

+               handler = change_project_name_handler)

 # The save button is always visible {{{1

 gbutton("Save current project contents", cont = left,

         handler = save_to_file_handler)

diff --git a/inst/unitTests/runit.mkinfit.R b/inst/unitTests/runit.mkinfit.R
index 89f4daf9..9a6bd722 100644
--- a/inst/unitTests/runit.mkinfit.R
+++ b/inst/unitTests/runit.mkinfit.R
@@ -1,6 +1,6 @@
 # $Id: runit.mkinfit.R 68 2010-09-09 22:40:04Z jranke $

 

-# Copyright (C) 2010-2012 Johannes Ranke

+# Copyright (C) 2010-2013 Johannes Ranke

 # Contact: jranke@uni-bremen.de

 

 # This file is part of the R package mkin

@@ -288,7 +288,7 @@ test.mkinfit.schaefer07_complex_example <- function()
     s$distimes["A2", "DT50"])

   r$means <- (r$KinGUI + r$ModelMaker)/2

   r$mkin.deviation <- abs(round(100 * ((r$mkin - r$means)/r$means), digits=1))

-  checkIdentical(r$mkin.deviation < 10, rep(TRUE, length(r$mkin.deviation)))

+  checkIdentical(r$mkin.deviation[1:11] < 10, rep(TRUE, 11))

 } # }}}

 

 # vim: set foldmethod=marker ts=2 sw=2 expandtab: