Add GUI start function, keep GUI here in mkin

1 files changed, 0 insertions, 826 deletions

diff --git a/inst/GUI/mkinGUI.R b/inst/GUI/mkinGUI.R
deleted file mode 100644
index 07f892e..0000000
--- a/inst/GUI/mkinGUI.R
+++ /dev/null
@@ -1,826 +0,0 @@
-# $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 = 300)

-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), 

-                         Citation = "FOCUS (2006) Guidance on degradation 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"

-# Initial fit lists {{{2

-# The fits and summaries are collected in lists of lists

-f <- s <- list()

-# Dataframe with fits for selection {{{2

-update_f.df <- function() {

-  f.df <<- data.frame(Fit = character(),

-                      Dataset = character(),

-                      Model = character(), 

-                      stringsAsFactors = FALSE)

-  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)

-  }

-}

-f.df.empty <- f.df <- data.frame(Fit = "0", 

-                               Dataset = "", 

-                               Model = "",

-                               stringsAsFactors = FALSE)

-# 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 = "/")

-  try(load(tmpfile))

-  project_file <<- pr.gf$filename

-  svalue(pr.ge) <- project_file

-

-  # Studies

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

-

-  # Datasets

-  ds.cur <<- ds.cur

-  ds <<- ds

-  update_ds.df()

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

-  update_ds_editor()

-

-  # Models

-  m.cur <<- ds.cur

-  m <<- 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.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)

-}

-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 = 290, height = 200, cont = stg)

-studies.gdf$set_column_width(1, 40)

-studies.gdf$set_column_width(2, 240)

-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 = 290, cont = dsm)

-addHandlerDoubleClick(ds.gtable, ds.switcher)

-size(ds.gtable) <- list(columnWidths = c(40, 200, 40))

-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, width = 290, cont = dsm)

-addHandlerDoubleClick(m.gtable, m.switcher)

-size(m.gtable) <- list(columnWidths = c(40, 240))

-m.gtable$value <- 1

-

-# Button for setting up a fit for the selected dataset and model

-gbutton("Configure fit for selected model and dataset", cont = dsm, 

-        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)

-          show_plot("Initial", default = TRUE)

-          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.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)

-          svalue(f.gg.summary) <- capture.output(stmp)

-          svalue(center) <- 3

-        })

-

-# Fits {{{1

-f.gf <- gframe("Fits", cont = left, horizontal = FALSE)

-# Fit table with handler {{{2

-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, width = 290, cont = f.gf)

-addHandlerDoubleClick(f.gtable, f.switcher)

-size(f.gtable) <- list(columnWidths = c(40, 60, 180))

-

-# 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()

-}

-

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

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

-  tmpd <- try(read.table(tmpfile, sep = "\t", header = TRUE, stringsAsFactors = FALSE))

-  tmpdw <- mkin_wide_to_long(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(tmpdw$name),

-                          unit = "",

-                          replicates = max(aggregate(tmpdw$time,

-                                                       list(tmpdw$time,

-                                                            tmpdw$name),

-                                                     length)$x),

-                          data = tmpdw)

-    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()

-}

- 

-# 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)

-

-upload_dataset.gf <- gfile(text = "Upload text file", cont = ds.e.2, 

-        handler = new_ds_from_csv_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)

-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"

-

-# Keep button {{{4

-gbutton("Keep changes", cont = ds.editor, handler = keep_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()

-}

-

-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),

-                                      state.ini = stateparms, 

-                                      parms.ini = deparms,

-                                      err = "err", 

-                                      control.modFit = list(maxiter = 0)))

-    ftmp$ds.index <<- ds.i

-    ftmp$ds <<- ds[[ds.i]]

-  } 

-

-  svg(tf, width = 7, height = 5)

-  plot(ftmp, main = ftmp$ds$title,

-       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)))

-  dev.off()

-  svalue(plot.gs) <<- tf

-}

-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)),

-                   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) <- capture.output(stmp)

-}

-ds.i <- m.i <- "1"

-f.cur <- "0"

-

-# GUI widgets {{{2

-pf <- gframe("Dataset 1, Model SFO", horizontal = FALSE, 

-             cont = center, label = "Plotting and fitting")

-

-# Mid group with plot and options {{{3

-f.gg.mid <- ggroup(cont = pf)

-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)

-tf <- get_tempfile(ext=".svg")

-svg(tf, width = 7, height = 5)

-plot(ftmp)

-dev.off()

-plot.gs <- gsvg(tf, container = f.gg.mid, width = 420, height = 300)

-f.gg.opts <- gformlayout(cont = f.gg.mid)

-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)

-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)

-

-# Dataframe with initial and optimised parameters {{{3

-f.gg.parms <- gdf(Parameters, width = 420, height = 300, cont = pf, 

-                   do_add_remove_buttons = FALSE)

-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)

-

-# Row with buttons {{{3

-f.gg.buttons <- ggroup(cont = pf)

-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"

-run.fit.gb <- gbutton("Run", 

-                      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", 

-                       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

-                          }, cont = f.gg.buttons)

-tooltip(keep.fit.gb) <- "Store the optimised model with all settings and the current dataset in the fit list"

-

-show.plots.gb <- gbutton("Show plots", 

-                      handler = function(h, ...) show_plot_window(), 

-                      cont = f.gg.buttons)

-tooltip(show.plots.gb) <- "Show a window with plots including residual plots"

-

-# Summary {{{3

-f.gg.summary <- gtext(capture.output(stmp), cont = pf,

-                      use.codemirror = TRUE)

-

-

-delete.fit.gb <- gbutton("Delete", 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"

-

-# 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)

-  show_plot("Optimised")  

-  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

-  f.gg.parms[,] <- get_Parameters(stmp, TRUE)

-  svalue(f.gg.summary) <- capture.output(stmp)

-}

-

-# Show plot window with residual plots {{{3

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

-  n.obs = length(ftmp$mkinmod$spec)

-  obs.vars = names(ftmp$mkinmod$spec)

-  parent = obs.vars[1]

-  if(n.obs == 1) {

-    n.rows = 1

-    ps = 7

-  } else {

-    n.rows = 1 + ceiling(n.obs / 2)

-    ps = 10

-  }

-  imgwidth = 800

-  imgheight = 360 * n.rows

-  pw <- gwindow("Plot window", parent = w,

-                width = imgwidth + 20, height = imgheight + 100)

-  pwg <- ggroup(cont = pw, horizontal = FALSE)

-  make_plots <- function() {

-    par(mfrow = c(n.rows, 2))

-    plot(ftmp, main = ftmp$ds$title,

-         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)))

-    if (n.obs > 1) {

-      plot(ftmp, legend = FALSE,

-           main = paste0("Zoomed in on metabolite", 

-                         ifelse(n.obs > 2, "s", "")),

-           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)),

-           ylim = c(0, max(subset(ftmp$data, 

-                        variable != parent)$observed)))

-      for (met in obs.vars[-1]) {

-        mkinresplot(ftmp, met, legend = FALSE,

-                    main = paste("Residual plot for", met))

-      }

-    } else {

-      mkinresplot(ftmp, parent, legend = FALSE,

-                  main = paste("Residual plot for", parent),

-           xlab = ifelse(ftmp$ds$time_unit == "", "Time", 

-                         paste("Time in", ftmp$ds$time_unit)),

-           ylab = ifelse(ds[[ds.i]]$unit == "", "Residuals", 

-                         paste("Residuals in", ftmp$ds$unit)))

-    }

-  }

-

-  tf2 <- get_tempfile(ext = ".png")

-  png(tf2,  width = imgwidth / 50 , height = imgheight / 50,

-    units = "cm", res = 300, pointsize = ps)

-  make_plots()

-  dev.off()

-

-  ghtml(paste0("<img width='", imgwidth, "' height='", imgheight,

-               "' src='", get_tempfile_url(tf2), "' />"), 

-        cont = pwg)

-}

-# vim: set foldmethod=marker ts=2 sw=2 expandtab: {{{1