A new layout for the GUI and an update of the staticdocs, as I just

uploaded 0.9-22 for publication on CRAN



git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@125 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

1 files changed, 445 insertions, 0 deletions

diff --git a/inst/GUI/mkinGUI.R b/inst/GUI/mkinGUI.R
new file mode 100644
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+# $Id: mkinGUI.R 122 2013-10-21 20:19:57Z jranke $ {{{1

+

+# gWidgetsWWW2 GUI for mkin

+

+# Copyright (C) 2013 Johannes Ranke

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

+

+# 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 <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)

+pg     <- gpanedgroup(cont = w, default.size = 400)

+center <- gnotebook(cont = pg)

+left   <- gvbox(cont = pg)

+# 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)

+}

+# Set default values for project data {{{1

+# Initial project file name {{{2

+project_file <- "mkin_FOCUS_2006.RData"

+# Initial studies {{{2

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

+                         Author = "FOCUS kinetics workgroup",

+                         Year = "2006", 

+                         Title = "FOCUS Kinetics",

+                         stringsAsFactors = FALSE)

+# Initial datasets {{{2

+ds <- list()

+observed.all <- vector()

+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(

+    study_nr = 1,

+    title = paste("FOCUS example dataset", ds.letter),

+    sampling_times = unique(get(ds.name)$time),

+    time_unit = "",

+    observed = as.character(unique(get(ds.name)$name)),

+    unit = "% AR",

+    replicates = 1,

+    data = get(ds.name)

+  )

+  ds[[ds.index]]$data$name <- as.character(ds[[ds.index]]$data$name)

+  ds[[ds.index]]$data$override = as.numeric(NA)

+  ds[[ds.index]]$data$err = 1

+}

+# 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)

+  }

+}

+ds.df <- data.frame()

+update_ds.df()

+ds.cur = "1"

+# Initial models {{{2

+m <- list()

+m[["1"]] <- mkinmod(parent = list(type = "SFO"))

+m[["1"]]$name = "SFO"

+m[["2"]] <- mkinmod(parent = list(type = "FOMC"))

+m[["2"]]$name = "FOMC"

+m[["3"]] <- mkinmod(parent = list(type = "DFOP"))

+m[["3"]]$name = "DFOP"

+m[["4"]] <- mkinmod(parent = list(type = "SFO", to = "m1"),

+                          m1 = list(type = "SFO"),

+                          use_of_ff = "max")

+m[["4"]]$name = "SFO_SFO"

+# 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

+  }

+}

+m.df <- data.frame()

+update_m.df()

+m.cur = "1"

+# Widgets and handlers for project data {{{1

+prg <- gexpandgroup("Project file management", cont = left, horizontal = FALSE)

+visible(prg) <- FALSE

+# Project data management handler functions {{{2

+upload_file_handler <- function(h, ...)

+{

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

+  try(load(tmpfile))

+  project_file <<- pr.gf$filename

+  svalue(pr.ge) <- project_file

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

+  ds.cur <<- "1"

+  ds <<- ds

+  update_ds.df()

+  ds.gtable[,] <- ds.df

+  update_ds_editor()

+  m.cur <<- "1"

+  m <<- m

+  update_m.df()

+  m.gtable[,] <- m.df

+  update_m_editor()

+}

+save_to_file_handler <- function(h, ...)

+{

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

+   save(studies.df, ds, m, file = project_file)

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

+}

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

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

+}

+# 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)

+# The save button is always visible {{{1

+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 = 390, height = 200, cont = stg)

+studies.gdf$set_column_width(1, 35)

+studies.gdf$set_column_width(2, 150)

+studies.gdf$set_column_width(3, 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, width = 390, multiple = TRUE, cont = dsm)

+addHandlerDoubleClick(ds.gtable, ds.switcher)

+size(ds.gtable) <- list(columnWidths = c(40, 300, 40))

+

+# 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, width = 390, multiple = TRUE, cont = dsm)

+addHandlerDoubleClick(m.gtable, m.switcher)

+size(m.gtable) <- list(columnWidths = c(40, 340))

+

+# 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) <<- names(plots) <<- names(prows) <<- 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 = "NA",

+                        observed = "parent",

+                        unit = "NA",

+                        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()

+}

+

+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 = rep(sampling_times, each = replicates, times = length(obs)),

+    value = NA,

+    override = NA,

+    err = 1

+  )

+  ds.e.gdf[,] <- new.data

+}

+

+save_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()

+  update_plot()

+}

+ 

+# 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)

+gbutton("Copy dataset", cont = ds.e.2, handler = copy_dataset_handler)

+gbutton("Delete dataset", cont = ds.e.2, handler = delete_dataset_handler)

+gbutton("New dataset", cont = ds.e.2, handler = new_dataset_handler)

+

+# Line 3 with forms {{{4

+ds.e.forms <- ggroup(cont= ds.editor, 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)

+gbutton("Generate empty grid for kinetic data", cont = ds.e.3b, 

+        handler = empty_grid_handler)

+

+# Save button {{{4

+gbutton("Save changes", cont = ds.editor, handler = save_ds_changes_handler)

+

+# 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

+

+  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()

+}

+

+save_m_changes_handler <- function(h, ...) {

+  spec <- list()

+  for (obs.i in 1:length(m.e.rows)) {

+    spec[[obs.i]] <- list(type = svalue(m.e.type[[obs.i]]),

+                          to = svalue(m.e.to[[obs.i]]),

+                          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("Save changes", cont = m.e.b, handler = save_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.observed)) {

+    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]]) <<- 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), "",

+                 m[[m.cur]]$spec[[obs.i]]$to)

+    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}}}

+# 1}}}

+

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