From 34452dfa5c069dc0f0a58681a35719fbb8cca158 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 7 May 2014 15:01:50 +0200 Subject: Fork the GUI into package gmkin. See ChangeLog for details --- ChangeLog | 9 +- DESCRIPTION | 4 +- R/gmkin.R | 11 - README.md | 36 +- TODO | 11 +- data/FOCUS_2006_Z_gmkin.RData | Bin 63994 -> 0 bytes data/FOCUS_2006_gmkin.RData | Bin 5451 -> 0 bytes gmkin_screenshot.png | Bin 185559 -> 0 bytes inst/GUI/README | 1 - inst/GUI/TODO | 1 - inst/GUI/gmkin.R | 928 ------------------------------------------ man/FOCUS_2006_Z_gmkin.Rd | 27 -- man/FOCUS_2006_gmkin.Rd | 28 -- man/gmkin.Rd | 22 - 14 files changed, 14 insertions(+), 1064 deletions(-) delete mode 100644 R/gmkin.R delete mode 100644 data/FOCUS_2006_Z_gmkin.RData delete mode 100644 data/FOCUS_2006_gmkin.RData delete mode 100644 gmkin_screenshot.png delete mode 100644 inst/GUI/README delete mode 100644 inst/GUI/TODO delete mode 100644 inst/GUI/gmkin.R delete mode 100644 man/FOCUS_2006_Z_gmkin.Rd delete mode 100644 man/FOCUS_2006_gmkin.Rd delete mode 100644 man/gmkin.Rd diff --git a/ChangeLog b/ChangeLog index 2bbc8573..c60caf5e 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,13 +1,12 @@ -2014-04-28 Johannes Ranke for mkin (0.9-26) +2014-05-07 Johannes Ranke for mkin (0.9-26) - * DESCRIPTION: Added copyright information and location of gWidgetsWWW2 + * Fork the GUI into a separate package gmkin + * DESCRIPTION, NAMESPACE, TODO: Adapt and add copyright information + * Remove files belonging to the GUI * Possibility to fit without parameter transformation * Add McCall 2,4,5-T dataset * Enable selection of observed variables in plotting * Add possibility to show residual plot in plot.mkinfit - * gmkin: New layout for plotting and fitting - * gmkin: Only use png plots, remove SVGTipsDevice from DESCRIPTION - * gmkin: Introduce plotting options allowing to select plotted variables 2014-02-27 Johannes Ranke for mkin (0.9-25) diff --git a/DESCRIPTION b/DESCRIPTION index 594d68c7..fe5977cf 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -15,11 +15,9 @@ Description: Calculation routines based on the FOCUS Kinetics Report (2006). and a choice of the optimisation methods made available by the FME package (default is a Levenberg-Marquardt variant). Please note that no warranty is implied for correctness of results or fitness for a particular purpose. - An experimental graphical user interface is included which is based - on the gWidgetsWWW2 package on GitHub (http://github.com/jverzani/gWidgetsWWW2/) Depends: minpack.lm, rootSolve Imports: FME, deSolve -Suggests: knitr, RUnit, gWidgetsWWW2 +Suggests: knitr, RUnit License: GPL LazyLoad: yes LazyData: yes diff --git a/R/gmkin.R b/R/gmkin.R deleted file mode 100644 index 912d31c2..00000000 --- a/R/gmkin.R +++ /dev/null @@ -1,11 +0,0 @@ -gmkin <- function() { - if (require(gWidgetsWWW2)) load_app(system.file("GUI/gmkin.R", package = "mkin")) - else { - message( - "\nYou need to install gWidgetsWWW2 in order to run the mkin GUI gmkin.\n", - "This package is not currently on CRAN but can be installed from github\n", - "using the devtools package:\n", - "library(devtools)\n", - "install_github('gWidgetsWWW2', 'jverzani')") - } -} diff --git a/README.md b/README.md index 98fc276a..41c03235 100644 --- a/README.md +++ b/README.md @@ -104,40 +104,10 @@ or the package vignettes referenced from the ## GUI -There is a graphical user interface that I consider useful for real work. It -depends on the gWidgetsWWW2 package from John Verzani which also lives on -github. Installing gWidgetsWWW2 yields a lot of warnings concerning overly -long path names. This is because the JavaScript library ExtJS is installed -along with it which has lots of files with long paths to be installed. +There is a graphical user interface that I consider useful for real work. +It is available from github in the separate package +[gmkin](http://github.com/jranke/gmkin). - -```s -require(devtools) -install_github("gWidgetsWWW2", "jverzani") -``` - -You start the GUI from your R terminal with latest mkin installed as shown below. -You may also want to adapt the browser that R starts (using -`options(browser="/usr/bin/firefox")` on linux, or setting the default browser -on Windows from the browser itself). Development was done with firefox. I also -did some testing with Chrome on Windows. Chrome sometimes hung when loading -the GUI and therefore ExtJS the first time, but when the GUI is loaded it appears -to work fine. - -```s -require(mkin) -gmkin() -``` - -The following screenshot is taken after loading the gmkin workspace with -an analysis of FOCUS dataset Z. It has to be saved as an .RData file -first, and can then be loaded to the GUI. - -```s -save(FOCUS_2006_Z_gmkin, file = "FOCUS_2006_gmkin_Z.RData") -``` - -![gmkin screenshot](gmkin_screenshot.png) ## Credits and historical remarks diff --git a/TODO b/TODO index 944ad57d..9ae762ea 100644 --- a/TODO +++ b/TODO @@ -1,13 +1,14 @@ TODO for version 1.0 - Think about what a user would expect from version 1.0 -- Support model definitions without pathway to sink in combination with formation fractions +- Support model definitions without pathway to sink in combination with + formation fractions - Complete the main package vignette named mkin to include a method description - Calculate pseudoDT50 values as recommended by FOCUS - Improve formatting of differential equations in the summary Nice to have: -- Calculate confidence intervals for DT50 and DT90 values when only one parameter is involved -- Calculate transformation only DT50 values (exclude pathways to sink) as additional information +- Calculate confidence intervals for DT50 and DT90 values when only one + parameter is involved +- Calculate transformation only DT50 values (exclude pathways to sink) as + additional information - Calculate DT50 values from smaller rate constant/eigenvalue of DFOP, HS and SFORB models -- Check possibility to include a stripped extJS in gWidgetsWWW2, or to publish a separate - R package for extJS diff --git a/data/FOCUS_2006_Z_gmkin.RData b/data/FOCUS_2006_Z_gmkin.RData deleted file mode 100644 index 3d87d5ac..00000000 Binary files a/data/FOCUS_2006_Z_gmkin.RData and /dev/null differ diff --git a/data/FOCUS_2006_gmkin.RData b/data/FOCUS_2006_gmkin.RData deleted file mode 100644 index a961f2ae..00000000 Binary files a/data/FOCUS_2006_gmkin.RData and /dev/null differ diff --git a/gmkin_screenshot.png b/gmkin_screenshot.png deleted file mode 100644 index 8fc23ab1..00000000 Binary files a/gmkin_screenshot.png and /dev/null differ diff --git a/inst/GUI/README b/inst/GUI/README deleted file mode 100644 index 89e37265..00000000 --- a/inst/GUI/README +++ /dev/null @@ -1 +0,0 @@ -These code fragments are still experimental, but some basic functionality works. diff --git a/inst/GUI/TODO b/inst/GUI/TODO deleted file mode 100644 index 1fbcca66..00000000 --- a/inst/GUI/TODO +++ /dev/null @@ -1 +0,0 @@ -- Make plot of fit and residuals configurable diff --git a/inst/GUI/gmkin.R b/inst/GUI/gmkin.R deleted file mode 100644 index ae9d88d1..00000000 --- a/inst/GUI/gmkin.R +++ /dev/null @@ -1,928 +0,0 @@ -# gWidgetsWWW2 GUI for mkin {{{1 - -# 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 - -# mkin is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -require(mkin) # {{{1 -# Set the GUI title and create the basic widget layout {{{1 -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 = 260) -center <- gnotebook(cont = pg) -left <- gvbox(cont = pg, use.scrollwindow = TRUE) -# Set initial values {{{1 -# Initial project workspace contents {{{2 -project_name <- "FOCUS_2006_gmkin" -project_file <- paste0(project_name, ".RData") -workspace <- get(project_name) # From dataset distributed with mkin -studies.df <- workspace$studies.df # dataframe containing study titles -ds <- workspace$ds # list of datasets -ds.cur <- workspace$ds.cur # current dataset index -m <- workspace$m # list with mkinmod models, amended with mkinmod$name -m.cur <- workspace$m.cur # m.cur current model index -f <- workspace$f # f list of fitted mkinfit objects -f.cur <- workspace$f.cur # current fit index -s <- workspace$s # list of summaries of the fitted mkinfit objects -# Initialise meta data objects so assignments within functions using <<- will {{{2 -# update them in the right environment -observed.all <- vector() # vector of names of observed variables in datasets -ds.df <- data.frame() -m.df <- data.frame() -f.df <- data.frame() -# Empty versions of meta data {{{2 -f.df.empty <- data.frame(Fit = "0", - Dataset = "", - Model = "", - stringsAsFactors = FALSE) -# Helper functions {{{1 -# Override function for making it possible to override original data in the GUI {{{2 -override <- function(d) { - data.frame(name = d$name, time = d$time, - value = ifelse(is.na(d$override), d$value, d$override), - err = d$err) -} -# Update dataframe with datasets for selection {{{2 -update_ds.df <- function() { - ds.n <- length(ds) - ds.df <<- data.frame(Index = 1:ds.n, - Title = character(ds.n), - Study = character(ds.n), - stringsAsFactors = FALSE) - for (i in 1:ds.n) - { - ds.index <- names(ds)[[i]] - ds.df[i, "Title"] <<- ds[[ds.index]]$title - ds.df[i, "Study"] <<- ds[[ds.index]]$study_nr - observed = as.character(unique(ds[[ds.index]]$data$name)) - observed.all <<- union(observed, observed.all) - } -} -# Update dataframe with models for selection {{{2 -update_m.df <- function() { - m.n <- length(m) - m.df <<- data.frame(Index = 1:m.n, - Name = character(m.n), - stringsAsFactors = FALSE) - for (i in 1:m.n) { - m.index <- names(m)[[i]] - m.df[i, "Name"] <<- m[[m.index]]$name - } -} -# Update dataframe with fits for selection {{{2 -update_f.df <- function() { - f.df <<- f.df.empty - f.count <- 0 - for (fit.index in names(f)) { - f.count <- f.count + 1 - ftmp <- f[[fit.index]] - f.df[f.count, ] <<- c(as.character(f.count), ftmp$ds.index, ftmp$mkinmod$name) - } -} -# Initialise meta data objects {{{1 -update_ds.df() -update_m.df() -update_f.df() -# Widgets and handlers for project data {{{1 -prg <- gexpandgroup("Project file management", cont = left, horizontal = FALSE) -# Project data management handler functions {{{2 -upload_file_handler <- function(h, ...) -{ - # General - tmpfile <- normalizePath(svalue(h$obj), winslash = "/") - project_file <<- pr.gf$filename - project_name <<- try(load(tmpfile)) - if (inherits(project_name, "try-error")) { - galert(paste("Failed to load", project_file), parent = w) - } - - svalue(sb) <- paste("Loaded project file", project_file) - svalue(pr.ge) <- project_name - workspace <- get(project_name) - - # Studies - studies.gdf[,] <- studies.df <- workspace$studies.df - - # Datasets - ds.cur <<- workspace$ds.cur - ds <<- workspace$ds - update_ds.df() - ds.gtable[,] <- ds.df - update_ds_editor() - - # Models - m.cur <<- workspace$m.cur - m <<- workspace$m - update_m.df() - m.gtable[,] <- m.df - update_m_editor() - - # Fits - f.cur <<- workspace$f.cur - f <<- workspace$f - s <<- workspace$s - if (length(f) > 0) { - update_f.df() - ftmp <<- f[[f.cur]] - stmp <<- s[[f.cur]] - ds.i <<- ds.cur - delete(f.gg.plotopts, f.gg.po.obssel) - f.gg.po.obssel <<- gcheckboxgroup(names(ftmp$mkinmod$spec), cont = f.gg.plotopts, - checked = TRUE) - update_plotting_and_fitting() - } else { - f.df <<- f.df.empty - update_ds_editor() - svalue(center) <- 1 - } - f.gtable[,] <- f.df -} -save_to_file_handler <- function(h, ...) -{ - studies.df <- data.frame(studies.gdf[,], stringsAsFactors = FALSE) - workspace <- list( - studies.df = studies.df, - - ds = ds, - ds.cur = ds.cur, - - m = m, - m.cur = m.cur, - - f = f, - f.cur = f.cur, - - s = s) - assign(project_name, workspace) - save(list = project_name, file = project_file) - svalue(sb) <- paste("Saved project contents to", project_file, "in working directory", getwd()) -} -change_project_name_handler = function(h, ...) { - project_name <<- as.character(svalue(h$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_name, cont = prg, label = "Project", - handler = change_project_name_handler) -# The save button is always visible {{{2 -gbutton("Save current project contents", cont = left, - handler = save_to_file_handler) - -# GUI widgets and a function for Studies {{{1 -stg <- gexpandgroup("Studies", cont = left) -visible(stg) <- FALSE -update_study_selector <- function(h, ...) { - delete(ds.e.1, ds.study.gc) - ds.study.gc <<- gcombobox(paste("Study", studies.gdf[,1]), cont = ds.e.1) - svalue(ds.study.gc, index = TRUE) <- ds[[ds.cur]]$study_nr -} -studies.gdf <- gdf(studies.df, name = "Edit studies in the project", - width = 235, - height = 180, cont = stg) -studies.gdf$set_column_width(1, 40) -addHandlerChanged(studies.gdf, update_study_selector) -# Datasets and models {{{1 -dsm <- gframe("Datasets and models", cont = left, horizontal = FALSE) -# Dataset table with handler {{{2 -ds.switcher <- function(h, ...) { - ds.cur <<- as.character(svalue(h$obj)) - update_ds_editor() - svalue(center) <- 1 -} -ds.gtable <- gtable(ds.df, cont = dsm) -addHandlerDoubleClick(ds.gtable, ds.switcher) -size(ds.gtable) <- list(columnWidths = c(40, 150, 30)) -ds.gtable$value <- 1 - -# Model table with handler {{{2 -m.switcher <- function(h, ...) { - m.cur <<- as.character(svalue(h$obj)) - update_m_editor() - svalue(center) <- 2 -} -m.gtable <- gtable(m.df, cont = dsm) -addHandlerDoubleClick(m.gtable, m.switcher) -m.gtable$set_column_width(1, 40) -m.gtable$value <- 1 - -# Button for setting up a fit for the selected dataset and model {{{2 -configure_fit_handler = function(h, ...) { - ds.i <<- as.character(svalue(ds.gtable)) - m.i <<- as.character(svalue(m.gtable)) - ftmp <<- suppressWarnings(mkinfit(m[[m.i]], - override(ds[[ds.i]]$data), - err = "err", - control.modFit = list(maxiter = 0))) - ftmp$ds.index <<- ds.i - ftmp$ds <<- ds[[ds.i]] - stmp <<- summary(ftmp) - svalue(pf) <- paste0("Dataset ", ds.i, ", Model ", m[[m.i]]$name) - svalue(f.gg.opts.st) <<- ftmp$solution_type - svalue(f.gg.opts.weight) <<- ftmp$weight - svalue(f.gg.opts.atol) <<- ftmp$atol - svalue(f.gg.opts.rtol) <<- ftmp$rtol - svalue(f.gg.opts.transform_rates) <<- ftmp$transform_rates - svalue(f.gg.opts.transform_fractions) <<- ftmp$transform_fractions - svalue(f.gg.opts.reweight.method) <<- ifelse( - is.null(ftmp$reweight.method), - "none", ftmp$reweight.method) - svalue(f.gg.opts.reweight.tol) <<- ftmp$reweight.tol - svalue(f.gg.opts.reweight.max.iter) <<- ftmp$reweight.max.iter - f.gg.parms[,] <- get_Parameters(stmp, FALSE) - delete(f.gg.plotopts, f.gg.po.obssel) - f.gg.po.obssel <<- gcheckboxgroup(names(ftmp$mkinmod$spec), cont = f.gg.plotopts, - checked = TRUE) - show_plot("Initial", default = TRUE) - oldwidth <<- options()$width - options(width = 90) - svalue(f.gg.summary) <- c("
", capture.output(stmp), "
") - options(width = oldwidth) - svalue(center) <- 3 -} -gbutton("Configure fit for selected model and dataset", cont = dsm, - handler = configure_fit_handler) - -# Fits {{{1 -f.gf <- gframe("Fits", cont = left, horizontal = FALSE) -f.switcher <- function(h, ...) { - if (svalue(h$obj) != "0") { - f.cur <<- svalue(h$obj) - ftmp <<- f[[f.cur]] - stmp <<- s[[f.cur]] - ds.i <<- ftmp$ds.index - update_plotting_and_fitting() - } - svalue(center) <- 3 -} -f.gtable <- gtable(f.df, cont = f.gf) -addHandlerDoubleClick(f.gtable, f.switcher) -f.gtable$set_column_width(1, 40) -f.gtable$set_column_width(2, 60) - -# Dataset editor {{{1 -ds.editor <- gframe("Dataset 1", horizontal = FALSE, cont = center, - label = "Dataset editor") -# Handler functions {{{3 -copy_dataset_handler <- function(h, ...) { - ds.old <- ds.cur - ds.cur <<- as.character(1 + length(ds)) - svalue(ds.editor) <- paste("Dataset", ds.cur) - ds[[ds.cur]] <<- ds[[ds.old]] - update_ds.df() - ds.gtable[,] <- ds.df -} - -delete_dataset_handler <- function(h, ...) { - ds[[ds.cur]] <<- NULL - names(ds) <<- as.character(1:length(ds)) - ds.cur <<- names(ds)[[1]] - update_ds.df() - ds.gtable[,] <- ds.df - update_ds_editor() -} - -new_dataset_handler <- function(h, ...) { - ds.cur <<- as.character(1 + length(ds)) - ds[[ds.cur]] <<- list( - study_nr = 1, - title = "", - sampling_times = c(0, 1), - time_unit = "", - observed = "parent", - unit = "", - replicates = 1, - data = data.frame( - name = "parent", - time = c(0, 1), - value = c(100, NA), - override = "NA", - err = 1, - stringsAsFactors = FALSE - ) - ) - update_ds.df() - ds.gtable[,] <- ds.df - update_ds_editor() -} - -load_text_file_with_data <- function(h, ...) { - tmptextfile <<- normalizePath(svalue(h$obj), winslash = "/") - tmptext <- readLines(tmptextfile, warn = FALSE) - tmptextskip <<- 0 - for (tmptextline in tmptext) { - if (grepl(":|#|/", tmptextline)) tmptextskip <<- tmptextskip + 1 - else break() - } - svalue(ds.e.up.skip) <- tmptextskip - if (svalue(ds.e.up.header)) { - tmptextheader <<- strsplit(tmptext[tmptextskip + 1], - " |\t|;|,")[[1]] - } - svalue(ds.e.up.wide.time) <- tmptextheader[[1]] - svalue(ds.e.up.long.time) <- tmptextheader[[2]] - svalue(ds.e.up.text) <- c("
", tmptext, "
") - svalue(ds.e.stack) <- 2 -} - -new_ds_from_csv_handler <- function(h, ...) { - tmpd <- try(read.table(tmptextfile, - skip = as.numeric(svalue(ds.e.up.skip)), - dec = svalue(ds.e.up.dec), - sep = switch(svalue(ds.e.up.sep), - whitespace = "", - ";" = ";", - "," = ","), - header = svalue(ds.e.up.header), - stringsAsFactors = FALSE)) - if(svalue(ds.e.up.widelong) == "wide") { - tmpdl <- mkin_wide_to_long(tmpd, time = as.character(svalue(ds.e.up.wide.time))) - } else { - tmpdl <- tmpd - } - if (class(tmpd) != "try-error") { - ds.cur <<- as.character(1 + length(ds)) - ds[[ds.cur]] <<- list( - study_nr = NA, - title = "New upload", - sampling_times = sort(unique(tmpd$t)), - time_unit = "", - observed = unique(tmpdl$name), - unit = "", - replicates = max(aggregate(tmpdl$time, - list(tmpdl$time, - tmpdl$name), - length)$x), - data = tmpdl) - ds[[ds.cur]]$data$override <<- as.numeric(NA) - ds[[ds.cur]]$data$err <<- 1 - update_ds.df() - ds.gtable[,] <- ds.df - update_ds_editor() - } else { - galert("Uploading failed", parent = "w") - } -} - -empty_grid_handler <- function(h, ...) { - obs <- strsplit(svalue(ds.e.obs), ", ")[[1]] - sampling_times <- strsplit(svalue(ds.e.st), ", ")[[1]] - replicates <- as.numeric(svalue(ds.e.rep)) - new.data = data.frame( - name = rep(obs, each = replicates * length(sampling_times)), - time = as.numeric(rep(sampling_times, each = replicates, times = length(obs))), - value = as.numeric(NA), - override = as.numeric(NA), - err = 1, - stringsAsFactors = FALSE - ) - ds.e.gdf[,] <- new.data -} - -keep_ds_changes_handler <- function(h, ...) { - ds[[ds.cur]]$title <<- svalue(ds.title.ge) - ds[[ds.cur]]$study_nr <<- as.numeric(gsub("Study ", "", svalue(ds.study.gc))) - update_ds.df() - ds.gtable[,] <- ds.df - tmpd <- ds.e.gdf[,] - ds[[ds.cur]]$data <<- tmpd - ds[[ds.cur]]$sampling_times <<- sort(unique(tmpd$time)) - ds[[ds.cur]]$time_unit <<- svalue(ds.e.stu) - ds[[ds.cur]]$observed <<- unique(tmpd$name) - ds[[ds.cur]]$unit <<- svalue(ds.e.obu) - ds[[ds.cur]]$replicates <<- max(aggregate(tmpd$time, - list(tmpd$time, tmpd$name), length)$x) - update_ds_editor() - observed.all <<- union(observed.all, ds[[ds.cur]]$observed) - update_m_editor() -} - -# Widget setup {{{3 -# Line 1 {{{4 -ds.e.1 <- ggroup(cont = ds.editor, horizontal = TRUE) -glabel("Title: ", cont = ds.e.1) -ds.title.ge <- gedit(ds[[ds.cur]]$title, cont = ds.e.1) -glabel(" from ", cont = ds.e.1) -ds.study.gc <- gcombobox(paste("Study", studies.gdf[,1]), cont = ds.e.1) - -# Line 2 {{{4 -ds.e.2 <- ggroup(cont = ds.editor, horizontal = TRUE) -ds.e.2a <- ggroup(cont = ds.e.2, horizontal = FALSE) -gbutton("Copy dataset", cont = ds.e.2a, handler = copy_dataset_handler) -gbutton("Delete dataset", cont = ds.e.2a, handler = delete_dataset_handler) -gbutton("New dataset", cont = ds.e.2a, handler = new_dataset_handler) - -ds.e.2b <- ggroup(cont = ds.e.2) -tmptextfile <- "" # Initialize file name for imported data -tmptextskip <- 0 # Initialize number of lines to be skipped -tmptexttime <- "V1" # Initialize name of time variable if no header row -upload_dataset.gf <- gfile(text = "Upload text file", cont = ds.e.2b, - handler = load_text_file_with_data) - -gbutton("Keep changes", cont = ds.e.2, handler = keep_ds_changes_handler) - -# Line 3 with forms or upload area {{{4 -ds.e.stack <- gstackwidget(cont = ds.editor) -# Forms for meta data {{{5 -ds.e.forms <- ggroup(cont = ds.e.stack, horizontal = TRUE) - -ds.e.3a <- gvbox(cont = ds.e.forms) -ds.e.3a.gfl <- gformlayout(cont = ds.e.3a) -ds.e.st <- gedit(paste(ds[[ds.cur]]$sampling_times, collapse = ", "), - width = 40, - label = "Sampling times", - cont = ds.e.3a.gfl) -ds.e.stu <- gedit(ds[[ds.cur]]$time_unit, - width = 20, - label = "Unit", cont = ds.e.3a.gfl) -ds.e.rep <- gedit(ds[[ds.cur]]$replicates, - width = 20, - label = "Replicates", cont = ds.e.3a.gfl) - -ds.e.3b <- gvbox(cont = ds.e.forms) -ds.e.3b.gfl <- gformlayout(cont = ds.e.3b) -ds.e.obs <- gedit(paste(ds[[ds.cur]]$observed, collapse = ", "), - width = 50, - label = "Observed", cont = ds.e.3b.gfl) -ds.e.obu <- gedit(ds[[ds.cur]]$unit, - width = 20, label = "Unit", - cont = ds.e.3b.gfl) -generate_grid.gb <- gbutton("Generate empty grid for kinetic data", cont = ds.e.3b, - handler = empty_grid_handler) -tooltip(generate_grid.gb) <- "Overwrites the kinetic data shown below" -# Data upload area {{{5 -ds.e.upload <- ggroup(cont = ds.e.stack, horizontal = TRUE) -ds.e.up.text <- ghtml("
", cont = ds.e.upload, width = 400, height = 400)
-ds.e.up.options <- ggroup(cont = ds.e.upload, horizontal = FALSE)
-ds.e.up.import <- gbutton("Import using options specified below", cont = ds.e.up.options,
-                          handler = new_ds_from_csv_handler)
-ds.e.up.skip <- gedit(tmptextskip, label = "Comment lines", cont = ds.e.up.options)
-ds.e.up.header <- gcheckbox(cont = ds.e.up.options, label = "Column names", 
-                            checked = TRUE)
-ds.e.up.sep <- gcombobox(c("whitespace", ";", ","), cont = ds.e.up.options,
-                         selected = 1, label = "Separator")
-ds.e.up.dec <- gcombobox(c(".", ","), cont = ds.e.up.options,
-                         selected = 1, label = "Decimal")
-ds.e.up.widelong <- gradio(c("wide", "long"), horizontal = TRUE, 
-                           label = "Format", cont = ds.e.up.options,
-                           handler = function(h, ...) {
-                             widelong = svalue(h$obj, index = TRUE)
-                             svalue(ds.e.up.wlstack) <- widelong
-                           })
-ds.e.up.wlstack <- gstackwidget(cont = ds.e.up.options)
-ds.e.up.wide <- ggroup(cont = ds.e.up.wlstack, horizontal = FALSE, width = 300)
-ds.e.up.wide.time <- gedit(tmptexttime, cont = ds.e.up.wide, label = "Time column")
-ds.e.up.long <- ggroup(cont = ds.e.up.wlstack, horizontal = FALSE, width = 300)
-ds.e.up.long.name <- gedit("name", cont = ds.e.up.long, label = "Observed variables")
-ds.e.up.long.time <- gedit(tmptexttime, cont = ds.e.up.long, label = "Time column")
-ds.e.up.long.value <- gedit("value", cont = ds.e.up.long, label = "Value column")
-ds.e.up.long.err <- gedit("err", cont = ds.e.up.long, label = "Relative errors")
-svalue(ds.e.up.wlstack) <- 1
-
-svalue(ds.e.stack) <- 1
-
-
-# Kinetic Data {{{4
-ds.e.gdf <- gdf(ds[[ds.cur]]$data, name = "Kinetic data", 
-                width = 500, height = 700, cont = ds.editor)
-ds.e.gdf$set_column_width(2, 70)
-
-# Update the dataset editor {{{3
-update_ds_editor <- function() {
-  svalue(ds.editor) <- paste("Dataset", ds.cur)
-  svalue(ds.title.ge) <- ds[[ds.cur]]$title
-  svalue(ds.study.gc, index = TRUE) <- ds[[ds.cur]]$study_nr
-
-  svalue(ds.e.st) <- paste(ds[[ds.cur]]$sampling_times, collapse = ", ")
-  svalue(ds.e.stu) <- ds[[ds.cur]]$time_unit
-  svalue(ds.e.obs) <- paste(ds[[ds.cur]]$observed, collapse = ", ")
-  svalue(ds.e.obu) <- ds[[ds.cur]]$unit
-  svalue(ds.e.rep) <- ds[[ds.cur]]$replicates
-  svalue(ds.e.stack) <- 1
-  ds.e.gdf[,] <- ds[[ds.cur]]$data
-}
-# Model editor {{{1
-m.editor <- gframe("Model 1", horizontal = FALSE, cont = center, label = "Model editor")
-# Handler functions {{{3
-copy_model_handler <- function(h, ...) {
-  m.old <- m.cur
-  m.cur <<- as.character(1 + length(m))
-  svalue(m.editor) <- paste("Model", m.cur)
-  m[[m.cur]] <<- m[[m.old]]
-  update_m.df()
-  m.gtable[,] <- m.df
-}
- 
-delete_model_handler <- function(h, ...) {
-  m[[m.cur]] <<- NULL
-  names(m) <<- as.character(1:length(m))
-  m.cur <<- "1"
-  update_m.df()
-  m.gtable[,] <- m.df
-  update_m_editor()
-}
-
-add_observed_handler <- function(h, ...) {
-  obs.i <- length(m.e.rows) + 1
-  m.e.rows[[obs.i]] <<- ggroup(cont = m.editor, horizontal = TRUE)
-  m.e.obs[[obs.i]] <<- gcombobox(observed.all, selected = obs.i, 
-                                cont = m.e.rows[[obs.i]])
-  m.e.type[[obs.i]] <<- gcombobox(c("SFO", "FOMC", "DFOP", "HS", "SFORB"),
-                                 cont = m.e.rows[[obs.i]])
-  svalue(m.e.type[[obs.i]]) <- "SFO"
-  glabel("to", cont = m.e.rows[[obs.i]]) 
-  m.e.to[[obs.i]] <<- gedit("", cont = m.e.rows[[obs.i]])
-  m.e.sink[[obs.i]] <<- gcheckbox("Path to sink", 
-                                  checked = TRUE, cont = m.e.rows[[obs.i]]) 
-  gbutton("Remove compound", handler = remove_compound_handler, 
-          action = obs.i, cont = m.e.rows[[obs.i]])
-}
-
-remove_compound_handler <- function(h, ...) {
-  m[[m.cur]]$spec[[h$action]] <<- NULL
-  update_m_editor()
-}
-
-keep_m_changes_handler <- function(h, ...) {
-  spec <- list()
-  for (obs.i in 1:length(m.e.rows)) {
-    to_vector = strsplit(svalue(m.e.to[[obs.i]]), ", ")[[1]]
-    if (length(to_vector) == 0) to_vector = ""
-    spec[[obs.i]] <- list(type = svalue(m.e.type[[obs.i]]),
-                          to = to_vector,
-                          sink = svalue(m.e.sink[[obs.i]]))
-    if(spec[[obs.i]]$to == "") spec[[obs.i]]$to = NULL
-    names(spec)[[obs.i]] <- svalue(m.e.obs[[obs.i]])
-  }
-  m[[m.cur]] <<- mkinmod(use_of_ff = svalue(m.ff.gc), 
-                         speclist = spec)
-  m[[m.cur]]$name <<- svalue(m.name.ge) 
-  update_m.df()
-  m.gtable[,] <- m.df
-}
- 
-# Widget setup {{{3
-m.e.0 <- ggroup(cont = m.editor, horizontal = TRUE)
-glabel("Model name: ", cont = m.e.0) 
-m.name.ge <- gedit(m[[m.cur]]$name, cont = m.e.0) 
-glabel("Use of formation fractions: ", cont = m.e.0) 
-m.ff.gc <- gcombobox(c("min", "max"), cont = m.e.0)
-svalue(m.ff.gc) <- m[[m.cur]]$use_of_ff
-
-# Model handling buttons {{{4
-m.e.b <- ggroup(cont = m.editor, horizontal = TRUE)
-gbutton("Copy model", cont = m.e.b, handler = copy_model_handler)
-gbutton("Delete model", cont = m.e.b, handler = delete_model_handler)
-gbutton("Add transformation product", cont = m.e.b, 
-        handler = add_observed_handler)
-gbutton("Keep changes", cont = m.e.b, handler = keep_m_changes_handler)
-
-
-m.observed <- names(m[[m.cur]]$spec)
-m.e.rows <- m.e.obs <- m.e.type <- m.e.to <- m.e.sink <- list()
-obs.to <- ""
-
-# Show the model specification {{{4
-show_m_spec <- function() {
-  for (obs.i in 1:length(m[[m.cur]]$spec)) {
-    obs.name <- names(m[[m.cur]]$spec)[[obs.i]]
-    m.e.rows[[obs.i]] <<- ggroup(cont = m.editor, horizontal = TRUE)
-    m.e.obs[[obs.i]] <<- gcombobox(observed.all, selected = 0, 
-                                  cont = m.e.rows[[obs.i]])
-    svalue(m.e.obs[[obs.i]]) <<- obs.name
-    m.e.type[[obs.i]] <<- gcombobox(c("SFO", "FOMC", "DFOP", "HS", "SFORB"),
-                                   cont = m.e.rows[[obs.i]])
-    svalue(m.e.type[[obs.i]]) <<- m[[m.cur]]$spec[[obs.i]]$type
-    glabel("to", cont = m.e.rows[[obs.i]]) 
-    obs.to <<- ifelse(is.null(m[[m.cur]]$spec[[obs.i]]$to), "",
-                 paste(m[[m.cur]]$spec[[obs.i]]$to, collapse = ", "))
-    m.e.to[[obs.i]] <<- gedit(obs.to, cont = m.e.rows[[obs.i]])
-    m.e.sink[[obs.i]] <<- gcheckbox("Path to sink", checked = m[[m.cur]]$spec[[obs.i]]$sink,
-              cont = m.e.rows[[obs.i]]) 
-    if (obs.i > 1) {
-      gbutton("Remove compound", handler = remove_compound_handler, 
-              action = obs.i, cont = m.e.rows[[obs.i]])
-    }
-  }
-}
-show_m_spec()
-
-# Update the model editor {{{3
-update_m_editor <- function() {
-  svalue(m.editor) <- paste("Model", m.cur)
-  svalue(m.name.ge) <- m[[m.cur]]$name
-  svalue(m.ff.gc) <- m[[m.cur]]$use_of_ff
-  for (oldrow.i in 1:length(m.e.rows)) {
-    delete(m.editor, m.e.rows[[oldrow.i]])
-  }
-  m.observed <<- names(m[[m.cur]]$spec)
-  m.e.rows <<- m.e.obs <<- m.e.type <<- m.e.to <<- m.e.sink <<- list()
-  show_m_spec()
-}
-
-# 3}}}
-# 2}}}
-# Plotting and fitting {{{1
-show_plot <- function(type, default = FALSE) {
-  Parameters <- f.gg.parms[,]
-  Parameters.de <- subset(Parameters, Type == "deparm", type)
-  stateparms <- subset(Parameters, Type == "state")[[type]]
-  deparms <- as.numeric(Parameters.de[[type]])
-  names(deparms) <- rownames(Parameters.de)
-  if (type == "Initial" & default == FALSE) {
-    ftmp <<- suppressWarnings(mkinfit(ftmp$mkinmod, 
-                                      override(ds[[ds.i]]$data),
-                                      parms.ini = deparms,
-                                      state.ini = stateparms, 
-                                      fixed_parms = names(deparms),
-                                      fixed_initials = names(stateparms),
-                                      err = "err", 
-                                      control.modFit = list(maxiter = 0)))
-    ftmp$ds.index <<- ds.i
-    ftmp$ds <<- ds[[ds.i]]
-  } 
-  svalue(plot.ftmp.gi) <<- plot_ftmp_png()
-  svalue(plot.confint.gi) <<- plot_confint_png()
-}
-get_Parameters <- function(stmp, optimised)
-{
-  pars <- rbind(stmp$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() {
-  Parameters <- f.gg.parms[,]
-  Parameters.de <- subset(Parameters, Type == "deparm")
-  deparms <- Parameters.de$Initial
-  names(deparms) <- Parameters.de$Name
-  defixed <- names(deparms[Parameters.de$Fixed])
-  Parameters.ini <- subset(Parameters, Type == "state")
-  iniparms <- Parameters.ini$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 (reweight.method == "none") reweight.method = NULL
-  ftmp <<- mkinfit(ftmp$mkinmod, override(ds[[ds.i]]$data),
-                   state.ini = iniparms,
-                   fixed_initials = inifixed,
-                   parms.ini = deparms, 
-                   fixed_parms = defixed,
-                   solution_type = svalue(f.gg.opts.st),
-                   atol = as.numeric(svalue(f.gg.opts.atol)),
-                   rtol = as.numeric(svalue(f.gg.opts.rtol)),
-                   transform_rates = svalue(f.gg.opts.transform_rates),
-                   transform_fractions = svalue(f.gg.opts.transform_fractions),
-                   weight = weight,
-                   err = err,
-                   reweight.method = reweight.method,
-                   reweight.tol = as.numeric(svalue(f.gg.opts.reweight.tol)),
-                   reweight.max.iter = as.numeric(svalue(f.gg.opts.reweight.max.iter))
-                   )
-  ftmp$ds.index <<- ds.i
-  ftmp$ds <<- ds[[ds.i]]
-  stmp <<- summary(ftmp)
-  show_plot("Optimised")
-  svalue(f.gg.opts.st) <- ftmp$solution_type
-  svalue(f.gg.opts.weight) <- ftmp$weight.ini
-  f.gg.parms[,] <- get_Parameters(stmp, TRUE)
-  svalue(f.gg.summary) <- c("
", capture.output(stmp), "
")
-}
-ds.i <- m.i <- "1"
-f.cur <- "0"
-
-# GUI widgets {{{2
-pf <- gframe("Dataset 1, Model SFO", horizontal = TRUE, 
-             cont = center, label = "Plotting and fitting")
-
-# Plot area to the left {{{3
-pf.p <- ggroup(cont = pf, horizontal = FALSE)
-ftmp <- suppressWarnings(mkinfit(m[[m.cur]], override(ds[[ds.i]]$data), 
-                                 err = "err", 
-                                 control.modFit = list(maxiter = 0)))
-ftmp$ds.index = ds.i
-ftmp$ds = ds[[ds.i]]
-stmp <- summary(ftmp)
-Parameters <- get_Parameters(stmp, FALSE)
-
-plot_ftmp_png <- function() {
-  tf <- get_tempfile(ext=".png")
-  if(exists("f.gg.po.obssel")) {
-    obs_vars_plot = svalue(f.gg.po.obssel)
-  } else {
-    obs_vars_plot = names(ftmp$mkinmod$spec)
-  }
-  png(tf, width = 400, height = 400)
-  plot(ftmp, main = ftmp$ds$title, obs_vars = obs_vars_plot,
-       xlab = ifelse(ftmp$ds$time_unit == "", "Time", 
-                     paste("Time in", ftmp$ds$time_unit)),
-       ylab = ifelse(ds[[ds.i]]$unit == "", "Observed", 
-                     paste("Observed in", ftmp$ds$unit)),
-       show_residuals = TRUE)
-  dev.off()
-  return(tf)
-}
-
-plot_confint_png <- function() {
-  tf <- get_tempfile(ext=".png")
-  png(tf, width = 400, height = 400)
-  mkinparplot(ftmp) 
-  dev.off()
-  return(tf)
-}
-
-plot.ftmp.gi <- gimage(plot_ftmp_png(), container = pf.p, width = 400, height = 400)
-plot.confint.gi <- gimage(plot_confint_png(), container = pf.p, width = 400, height = 400)
-
-# Buttons and notebook area to the right {{{3
-p.gg <- ggroup(cont = pf, horizontal = FALSE)
-# Row with buttons {{{4
-f.gg.buttons <- ggroup(cont = p.gg)
-run.fit.gb <- gbutton("Run", width = 100,
-                      handler = function(h, ...) run_fit(), cont =
-                      f.gg.buttons)
-tooltip(run.fit.gb) <- "Fit with current settings on the current dataset, with the original model"
-
-keep.fit.gb <- gbutton("Keep fit", 
-                       handler = function(h, ...) {
-                            f.cur <<- as.character(length(f) + 1)
-                            f[[f.cur]] <<- ftmp
-                            s[[f.cur]] <<- stmp
-                            update_f.df()
-                            f.gtable[,] <<- f.df
-                            delete(f.gg.plotopts, f.gg.po.obssel)
-                            f.gg.po.obssel <<- gcheckboxgroup(names(ftmp$mkinmod$spec), 
-                                                              cont = f.gg.plotopts, 
-                                                              checked = TRUE)
-                            delete(f.gg.buttons, get.initials.gc)
-                            get.initials.gc <<- gcombobox(paste("Fit", f.df$Fit), 
-                                                          cont = f.gg.buttons)
-                          }, cont = f.gg.buttons)
-tooltip(keep.fit.gb) <- "Store the optimised model with all settings and the current dataset in the fit list"
-
-delete.fit.gb <- gbutton("Delete fit", handler = function(h, ...) {
-          if (length(f) > 0) {
-            f[[f.cur]] <<- NULL
-            s[[f.cur]] <<- NULL
-          }
-          if (length(f) > 0) {
-            names(f) <<- as.character(1:length(f))
-            names(s) <<- as.character(1:length(f))
-            update_f.df()
-            f.cur <<- "1"
-            ftmp <<- f[[f.cur]]
-            stmp <<- s[[f.cur]]
-            ds.i <<- ftmp$ds.index
-            update_plotting_and_fitting()
-          } else {
-            f.df <<- f.df.empty
-            f.cur <<- "0"
-          }
-          f.gtable[,] <<- f.df
-        }, cont = f.gg.buttons)
-tooltip(delete.fit.gb) <- "Delete the currently loaded fit from the fit list"
-
-show.initial.gb <- gbutton("Show initial", 
-                           handler = function(h, ...) show_plot("Initial"),
-                           cont = f.gg.buttons)
-tooltip(show.initial.gb) <- "Show model with current inital settings for current dataset"
-
-get_initials_handler <- function(h, ...)
-{
-  f.i <- svalue(get.initials.gc, index = TRUE)
-  if (length(f) > 0) {
-    got_initials <- c(f[[f.i]]$bparms.fixed, f[[f.i]]$bparms.optim)
-    parnames <- f.gg.parms[,"Name"]
-    newparnames <- names(got_initials)
-    commonparnames <- intersect(parnames, newparnames)
-    f.gg.parms[commonparnames, "Initial"] <<- got_initials[commonparnames]
-  }
-}
-get.initials.gb <- gbutton("Get initials from", cont = f.gg.buttons,
-                           handler = get_initials_handler)
-get.initials.gc <- gcombobox(paste("Fit", f.df$Fit), cont = f.gg.buttons)
-
-# Notebook to the right {{{3
-f.gn <- gnotebook(cont = p.gg, width = 680, height = 790)
-# Dataframe with initial and optimised parameters {{{4
-f.gg.parms <- gdf(Parameters, cont = f.gn, 
-                 width = 670, height = 750,
-                 do_add_remove_buttons = FALSE, label = "Parameters")
-f.gg.parms$set_column_width(1, 200)
-f.gg.parms$set_column_width(2, 50)
-f.gg.parms$set_column_width(3, 60)
-f.gg.parms$set_column_width(4, 50)
-f.gg.parms$set_column_width(5, 60)
-
-# Fit options form {{{4
-f.gg.opts <- gformlayout(cont = f.gn, label = "Fit options")
-solution_types <- c("auto", "analytical", "eigen", "deSolve")
-f.gg.opts.st <- gcombobox(solution_types, selected = 1, 
-                          label = "solution_type", width = 200, 
-                          cont = f.gg.opts)
-f.gg.opts.atol <- gedit(ftmp$atol, label = "atol", width = 20, 
-                         cont = f.gg.opts)
-f.gg.opts.rtol <- gedit(ftmp$rtol, label = "rtol", width = 20, 
-                         cont = f.gg.opts)
-f.gg.opts.transform_rates <- gcheckbox("transform_rates",
-                         cont = f.gg.opts, checked = TRUE)
-f.gg.opts.transform_fractions <- gcheckbox("transform_fractions",
-                         cont = f.gg.opts, checked = TRUE)
-weights <- c("manual", "none", "std", "mean")
-f.gg.opts.weight <- gcombobox(weights, selected = 1, label = "weight", 
-                              width = 200, cont = f.gg.opts)
-f.gg.opts.reweight.method <- gcombobox(c("none", "obs"), selected = 1,
-                                       label = "reweight.method",
-                                       width = 200,
-                                       cont = f.gg.opts)
-f.gg.opts.reweight.tol <- gedit(1e-8, label = "reweight.tol",
-                                 width = 20, cont = f.gg.opts)
-f.gg.opts.reweight.max.iter <- gedit(10, label = "reweight.max.iter",
-                                 width = 20, cont = f.gg.opts)
-
-# Summary {{{3
-oldwidth <- options()$width
-options(width = 90)
-f.gg.summary <- ghtml(c("
", capture.output(stmp), "
"),
-                        cont = f.gn, label = "Summary")
-options(width = oldwidth)
-
-# Plot options {{{4
-f.gg.plotopts <- ggroup(cont = f.gn, label = "Plot options", horizontal = FALSE)
-f.gg.po.update <- gbutton("Update plot", 
-                          handler = function(h, ...) show_plot("Optimised"), 
-                          cont = f.gg.plotopts)
-f.gg.po.obssel <- gcheckboxgroup(names(m[[m.cur]]$spec), cont = f.gg.plotopts, 
-                                 checked = TRUE)
-svalue(f.gn) <- 1
-
-# Update the plotting and fitting area {{{3
-update_plotting_and_fitting <- function() {
-  svalue(pf) <- paste0("Fit ", f.cur, ": Dataset ", ftmp$ds.index, 
-                       ", Model ", ftmp$mkinmod$name)
-  # Parameters
-  f.gg.parms[,] <- get_Parameters(stmp, TRUE)
-
-  # Fit options
-  delete(f.gg.buttons, get.initials.gc)
-  get.initials.gc <<- gcombobox(paste("Fit", f.df$Fit), cont = f.gg.buttons)
-
-  svalue(f.gg.opts.st) <- ftmp$solution_type
-  svalue(f.gg.opts.weight) <- ftmp$weight.ini
-  svalue(f.gg.opts.reweight.method) <- ifelse(is.null(ftmp$reweight.method),
-                                                      "none", 
-                                                      ftmp$reweight.method)
-  svalue(f.gg.opts.reweight.tol) <- ftmp$reweight.tol
-  svalue(f.gg.opts.reweight.max.iter) <- ftmp$reweight.max.iter
-
-  # Summary
-  oldwidth <<- options()$width
-  options(width = 90)
-  svalue(f.gg.summary) <- c("
", capture.output(stmp), "
")
-  options(width = oldwidth)
-
-  # Plot options
-  delete(f.gg.plotopts, f.gg.po.obssel)
-  f.gg.po.obssel <<- gcheckboxgroup(names(ftmp$mkinmod$spec), cont = f.gg.plotopts, 
-                                   checked = TRUE)
-  # Plot
-  show_plot("Optimised")  
- 
-}
-# vim: set foldmethod=marker ts=2 sw=2 expandtab: {{{1
diff --git a/man/FOCUS_2006_Z_gmkin.Rd b/man/FOCUS_2006_Z_gmkin.Rd
deleted file mode 100644
index 4f6a5e4d..00000000
--- a/man/FOCUS_2006_Z_gmkin.Rd
+++ /dev/null
@@ -1,27 +0,0 @@
-\name{FOCUS_2006_Z_gmkin}
-\Rdversion{1.1}
-\alias{FOCUS_2006_Z_gmkin}
-\docType{data}
-\title{
-  Example gmkin workspace for Dataset Z from the FOCUS Kinetics report
-}
-\description{
-  Data taken from FOCUS (2006), Appendix 7, p. 350.
-}
-\usage{FOCUS_2006_Z_gmkin}
-\format{
-  A list named \code{FOCUS_2006_Z_gmkin} containing the components
-  needed to populate the \code{\link{gmkin}} user interface.
-}
-\examples{
-  save(FOCUS_2006_Z_gmkin, file = "FOCUS_2006_gmkin_Z.RData")
-  # Now you can load the file "FOCUS_2006_gmkin_Z.RData" from gmkin
-}
-\source{
-  FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and
-  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
-  Registration} Report of the FOCUS Work Group on Degradation Kinetics,
-  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-  \url{http://focus.jrc.ec.europa.eu/dk} 
-}
-\keyword{datasets}
diff --git a/man/FOCUS_2006_gmkin.Rd b/man/FOCUS_2006_gmkin.Rd
deleted file mode 100644
index 371ddc70..00000000
--- a/man/FOCUS_2006_gmkin.Rd
+++ /dev/null
@@ -1,28 +0,0 @@
-\name{FOCUS_2006_gmkin}
-\Rdversion{1.1}
-\alias{FOCUS_2006_gmkin}
-\docType{data}
-\title{
-  Example gmkin workspace for Datasets C and D from the FOCUS Kinetics report
-}
-\description{
-  Data taken from FOCUS (2006), Appendix 3. This is the the workspace that is
-  loaded into \code{\link{gmkin}} by default.
-}
-\usage{FOCUS_2006_gmkin}
-\format{
-  A list named \code{FOCUS_2006_gmkin} containing the components
-  needed to populate the gmkin user interface.
-}
-\examples{
-  save(FOCUS_2006_gmkin, file = "FOCUS_2006_gmkin.RData")
-  # Now you can load the file "FOCUS_2006_gmkin.RData" from gmkin
-}
-\source{
-  FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and
-  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
-  Registration} Report of the FOCUS Work Group on Degradation Kinetics,
-  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-  \url{http://focus.jrc.ec.europa.eu/dk} 
-}
-\keyword{datasets}
diff --git a/man/gmkin.Rd b/man/gmkin.Rd
deleted file mode 100644
index 8a7d1320..00000000
--- a/man/gmkin.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-\name{gmkin}
-\alias{gmkin}
-\title{
-  Start a graphical user interface (GUI) based on the \code{gWidgetsWWW2} toolkit.
-}
-\description{
-  This function starts a browser based GUI. Please visit the 
-  \href{http://github.com/jverzani/gWidgetsWWW2}{github page of gWidgetsWWW2} 
-  for an explanation how this toolkit works.
-}
-\note{
-  This GUI is experimental and not recommended for real work.
-}
-\usage{
-  gmkin()
-}
-\value{
-  The function is called for its side effect, namely starting the GUI in a browser.
-}
-\author{
-  Johannes Ranke
-}
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