# gWidgetsWWW2 GUI for mkin {{{1 # Copyright (C) 2013-2016,2018,2019 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 gmkin # gmkin 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 # Configuration {{{1 # Widgets {{{2 left_width = 250 right_width = 500 ds_height = 142 m_height = 142 f_height = 142 save_keybinding = "Shift-F12" gcb_observed_width = 100 gcb_type_width = 70 gcb_to_width = 160 gcb_sink_width = 70 # Plotting {{{2 plot_formats <- c("png", "pdf") if (requireNamespace("devEMF", quietly = TRUE)) { plot_formats = c("emf", plot_formats) } plot_format <- plot_formats[[1]] # Options {{{2 options(width = 75) # For summary # Set the GUI title and create the basic widget layout {{{1 # Three panel layout {{{2 window_title <- paste0("gmkin ", packageVersion("gmkin"), "- Browser based GUI for kinetic evaluations using mkin") w <- gwindow(window_title) sb <- gstatusbar(paste("Powered by gWidgetsWWW2 (ExtJS, Rook)", "and mkin (deSolve, numDeriv)", "--- Working directory is", getwd()), cont = w) bl <- gborderlayout(cont = w, panels = c("center", "west", "east"), collapsible = list(west = FALSE)) bl$set_panel_size("west", left_width) bl$set_panel_size("east", right_width) center <- gnotebook(cont = bl, where = "center") center$add_handler("tabchange", function(h, ...) { if (svalue(h$obj) == 1) { svalue(right) <<- 1 } }) left <- gvbox(cont = bl, use.scrollwindow = TRUE, where = "west", spacing = 0) right <- gnotebook(cont = bl, use.scrollwindow = TRUE, where = "east") right$add_handler("tabchange", function(h, ...) { if (svalue(h$obj) == 3 && ! model_gallery_created) { create_model_gallery() } }) # }) # Helper functions {{{1 # Override function for making it possible to override original data points using the GUI {{{2 override <- function(d) { if (!is.null(d$override)) { d_new <- data.frame(name = d$name, time = d$time, value = ifelse(is.na(d$override), d$value, d$override), err = d$err) return(d_new) } else { return(d) } } # Update dataframe with projects {{{2 update_p.df <- function() { wd_projects <- gsub(".gmkinws", "", dir(pattern = ".gmkinws$")) if (length(wd_projects) > 0) { p.df.wd <- data.frame(Name = wd_projects, Source = rep("working directory", length(wd_projects)), stringsAsFactors = FALSE) p.df <<- rbind(p.df.package, p.df.wd) } else { p.df <<- p.df.package } p.gtable[,] <- p.df p.line.import.p[,] <- c("", p.df$Name) } # Update dataframe with datasets {{{2 update_ds.df <- function() { if (is.na(ws$ds[1])) ds.df <<- ds.df.empty else ds.df <<- data.frame(Title = sapply(ws$ds, function(x) x$title), stringsAsFactors = FALSE) ds.gtable[,] <- ds.df ds.delete$call_Ext("disable") ds.copy$call_Ext("disable") } # Update dataframe with models {{{2 update_m.df <- function() { if (length(ws$m) == 0) { m.df <<- m.df.empty m.cur <<- m.empty } else m.df <<- data.frame(Name = sapply(ws$m, function(x) x$name), stringsAsFactors = FALSE) m.gtable[,] <- m.df update_m_editor() m.delete$call_Ext("disable") m.copy$call_Ext("disable") } # Update dataframe with fits {{{2 update_f.df <- function() { f.df <- data.frame(Name = ws$ftmp$Name, stringsAsFactors = FALSE) if (length(ws$f) > 0) { f.df.ws <- data.frame(Name = sapply(ws$f, function(x) x$name), stringsAsFactors = FALSE) f.df <- rbind(f.df, f.df.ws) } f.df <<- f.df f.gtable[,] <- f.df get.initials.gc[,] <- paste("Result", f.df$Name) f.delete$call_Ext("disable") } # Generate the initial workspace {{{1 # Project workspace {{{2 ws <- gmkinws$new() ws.import <- NA # Initialise meta data objects so assignments within functions using <<- will {{{2 # update them in the right environment. # Also create initial versions of meta data in order to be able to clear the workspace p.df <- p.df.package <- data.frame(Name = c("FOCUS_2006", "FOCUS_2006_Z"), Source = rep("gmkin package", 2), stringsAsFactors = FALSE) # Datasets {{{2 ds.empty <- mkinds$new( title = "New dataset", time_unit = "", unit = "", data = data.frame( name = rep(c("parent", "m1"), each = 5), time = rep(c(0, 1, 4, 7, 14), 2), value = c(100, rep(NA, 9)), override = as.numeric(NA), err = 1, stringsAsFactors = FALSE)) ds.cur <- ds.empty$clone() ds.df <- ds.df.empty <- data.frame(Title = "", stringsAsFactors = FALSE) # Models {{{2 m.empty <- mkinmod(parent = mkinsub("SFO")) m.empty$name <- "" m.empty$spec <- list() m.cur <- m.empty m.df <- m.df.empty <- data.frame(Name = "", stringsAsFactors = FALSE) # Fits {{{2 f.df <- data.frame(Name = "", stringsAsFactors = FALSE) ws$ftmp <- list(Name = "") # For storing the current configured fit ftmp <- stmp <- NA # For storing the currently active fit # left: Explorer tables {{{1 # Frames {{{2 p.gf <- gexpandgroup("Projects", cont = left, horizontal = FALSE, spacing = 0) ds.gf <- gframe("Datasets", cont = left, horizontal = FALSE, spacing = 0) m.gf <- gframe("Models", cont = left, horizontal = FALSE, spacing = 0) c.gf <- gframe("Configuration", cont = left, horizontal = FALSE, spacing = 0) f.gf <- gframe("Results", cont = left, horizontal = FALSE, spacing = 0) # Project explorer {{{2 # Initialize project list from the gmkin package and the current working directory # The former must be manually amended if additional workspaces should be available p.gtable <- gtable(p.df, cont = p.gf, width = left_width - 10, height = 120, ext.args = list(resizable = TRUE, resizeHandles = 's')) size(p.gtable) <- list(columnWidths = c(130, 100)) p.loaded <- NA # The index of the loaded project. We reset the selection to this when the user # does not confirm p.modified <- FALSE # Keep track of modifications after loading p.switcher <- function(h, ...) { p.cur <- h$row_index # h$row_index for clicked or doubleclick handlers, h$value for change project_switched <- FALSE switch_project <- function() { Name <- p.df[p.cur, "Name"] if (p.df[p.cur, "Source"] == "working directory") { load(paste0(Name, ".gmkinws")) ws <<- ws } else { ws <<- get(Name)$clone() } svalue(center) <- 1 svalue(c.ds) <- empty_conf_labels[1] svalue(c.m) <- empty_conf_labels[2] f.conf$call_Ext("disable") update_p_editor(p.cur) update_ds.df() update_m.df() update_f.df() show_fit_option_widgets(FALSE) f.run$call_Ext("disable") svalue(f.running.label) <- f.running_noconf p.loaded <<- p.cur project_switched <- TRUE p.modified <<- FALSE svalue(p.gtable) <<- p.cur } if (p.modified) { gconfirm("When you switch projects, you loose any unsaved changes. Proceed to switch?", handler = function(h, ...) { switch_project() }) } else { switch_project() svalue(right) <<- 1 } # We can reset the selection only if the project was not # switched. The following code gets executed during the confirmation dialogue, # i.e. before the potential switching if (!project_switched) { if (is.na(p.loaded)) { p.gtable$clear_selection() } else { p.gtable$set_index(p.loaded) } } } addHandlerClicked(p.gtable, p.switcher) # Dataset explorer {{{2 ds.switcher <- function(h, ...) { ds.i <- h$row_index svalue(c.ds) <- ds.df[ds.i, "Title"] ds.cur <<- ws$ds[[ds.i]] update_ds_editor() ds.delete$call_Ext("enable") ds.copy$call_Ext("enable") if (!is.null(svalue(m.gtable, index = TRUE))) { if (length(svalue(m.gtable)) > 0) { if (!is.na(svalue(m.gtable))) f.conf$call_Ext("enable") } } svalue(center) <- 2 svalue(right) <- 2 } ds.gtable <- gtable(ds.df, cont = ds.gf, width = left_width - 10, height = ds_height, ext.args = list(resizable = TRUE, resizeHandles = 's', hideHeaders = TRUE)) addHandlerClicked(ds.gtable, ds.switcher) # Model explorer {{{2 m.switcher <- function(h, ...) { m.i <- h$row_index svalue(c.m) <- m.df[m.i, "Name"] m.cur <<- ws$m[[m.i]] update_m_editor() m.delete$call_Ext("enable") m.copy$call_Ext("enable") if (!is.null(svalue(ds.gtable, index = TRUE))) { if (length(svalue(ds.gtable)) > 0) { if (!is.na(svalue(ds.gtable))) f.conf$call_Ext("enable") } } svalue(center) <- 3 } m.gtable <- gtable(m.df, cont = m.gf, width = left_width - 10, height = m_height, ext.args = list(resizable = TRUE, resizeHandles = 's', hideHeaders = TRUE)) addHandlerClicked(m.gtable, m.switcher) # Fit explorer {{{2 f.switcher <- function(h, ...) { if (h$row_index > 1) { f.i <- h$row_index - 1 ftmp <<- ws$f[[f.i]] if (is.null(ftmp$optimised)) ftmp$optimised <<- TRUE f.delete$call_Ext("enable") f.keep$call_Ext("disable") } else { ftmp <<- ws$ftmp } c.ds$call_Ext("setText", paste0("", ftmp$ds$title, ""), FALSE) c.m$call_Ext("setText", paste0("", ftmp$mkinmod$name, ""), FALSE) f.conf$call_Ext("disable") ds.gtable$set_index(NA) m.gtable$set_index(NA) show.initial.gb.o$call_Ext("enable") update_f_conf() show_plot("Optimised") update_f_results() } f.gtable <- gtable(f.df, cont = f.gf, width = left_width - 10, height = f_height, ext.args = list(resizable = TRUE, resizeHandles = 's', hideHeaders = TRUE)) addHandlerClicked(f.gtable, f.switcher) # Configuration {{{2 empty_conf_labels <- paste0("Current ", c("dataset", "model"), "") c.ds <- glabel(empty_conf_labels[1], cont = c.gf, ext.args = list(margin = "0 0 0 5")) c.m <- glabel(empty_conf_labels[2], cont = c.gf, ext.args = list(margin = "0 0 0 5")) update_f_conf <- function() { # {{{3 stmp <<- suppressWarnings(summary(ftmp)) svalue(f.gg.opts.st) <<- ftmp$solution_type svalue(f.gg.opts.atol) <<- ftmp$atol svalue(f.gg.opts.rtol) <<- ftmp$rtol svalue(f.gg.opts.transform_rates) <<- ftmp$transform_rates svalue(f.gg.opts.transform_fractions) <<- ftmp$transform_fractions if (!is.null(ftmp$error_model_algorithm)) { svalue(f.gg.opts.error_model_algorithm) <<- ftmp$error_model_algorithm if (ftmp$error_model_algorithm == "OLS") { svalue(f.gg.opts.error_model) <<- "const" } else { svalue(f.gg.opts.error_model) <<- ftmp$error_model } } svalue(f.gg.opts.reweight.tol) <<- ftmp$reweight.tol svalue(f.gg.opts.reweight.max.iter) <<- ftmp$reweight.max.iter if (!is.null(ftmp$maxit)) { svalue(f.gg.opts.maxit) <<- ftmp$maxit } show_fit_option_widgets(TRUE) update_plot_obssel() f.gg.parms[,] <- get_Parameters(stmp, ftmp$optimised) } update_f_results <- function() { # {{{3 svalue(r.name) <- ftmp$name r.parameters[] <- cbind(Parameter = rownames(stmp$bpar), stmp$bpar[, c(1, 4, 5, 6)]) err.min <- 100 * stmp$errmin$err.min r.frames.chi2.gt[] <- cbind(Variable = rownames(stmp$errmin), Error = signif(err.min, 3), n.opt = stmp$errmin$n.optim, df = stmp$errmin$df) if (is.null(stmp$ff)) r.frames.ff.gt[] <- ff.df.empty else r.frames.ff.gt[] <- cbind(Path = names(stmp$ff), ff = round(stmp$ff, 4)) distimes <- format(stmp$distimes, digits = 3) delete(r.frames.distimes, r.frames.distimes.gt) delete(r.frames, r.frames.distimes) r.frames.distimes <<- gframe("Disappearance times", cont = r.frames, use.scrollwindow = TRUE, horizontal = TRUE, spacing = 0) r.frames.distimes.gt <<- gtable(cbind(data.frame(Variable = rownames(stmp$distimes)), distimes), cont = r.frames.distimes, height = 150) size(r.frames.distimes.gt) <- list(columnWidths = c(60, rep(45, ncol(stmp$distimes)))) svalue(f.gg.summary.filename) <- paste(ftmp$ds$title, "_", ftmp$mkinmod$name, ".txt", sep = "") svalue(f.gg.summary.listing) <- c("
 ", capture.output(summary(ftmp)), "
") ds.e.gdf[,] <- ftmp$ds$data svalue(center) <- 5 } update_plot_obssel <- function() { delete(f.gg.plotopts, f.gg.po.obssel) f.gg.po.obssel <<- gcheckboxgroup(names(ftmp$mkinmod$spec), cont = f.gg.plotopts, checked = TRUE) } configure_fit_handler <- function(h, ...) { # Configure fit button {{{3 if (length(intersect(names(m.cur$spec), ds.cur$observed)) > 0) { if (is.null(m.cur$cf) && Sys.which("gcc") != "") { mtmp <- mkinmod(speclist = m.cur$spec, use_of_ff = m.cur$use_of_ff) mtmp$name <- m.cur$name m.cur <<- mtmp } ftmp <<- suppressWarnings(mkinfit(m.cur, override(ds.cur$data), quiet = TRUE, control = list(iter.max = 0))) ftmp$optimised <<- FALSE ftmp$ds <<- ds.cur ws$ftmp <<- ftmp ws$ftmp$Name <<- "Temporary (not fitted)" update_f.df() update_f_conf() f.run$call_Ext("enable") svalue(f.running.label) <- "Fit configured and ready to run" } else { svalue(f.running.label) <- paste("No fit configured:", "The model and the dataset you selected do", "not share names for observed variables!") f.run$call_Ext("disable") show_fit_option_widgets(FALSE) show.initial.gb.u$call_Ext("disable") show.initial.gb.o$call_Ext("disable") f.gg.parms[,] <- Parameters.empty } svalue(center) <- 4 } f.conf.line <- ggroup(cont = c.gf, ext.args = list(layout = list(type = "vbox", align = "center"))) f.conf <- gbutton("Configure fit", width = 100, cont = f.conf.line, handler = configure_fit_handler, ext.args = list(disabled = TRUE)) # center: Project editor {{{1 p.editor <- gframe("", horizontal = FALSE, cont = center, label = "Project") # Line with buttons {{{2 p.line.buttons <- ggroup(cont = p.editor, horizontal = TRUE) # New {{{3 p.new.handler <- function(h, ...) { project_name <- "New project" svalue(p.name) <- project_name svalue(p.filename) <- file.path(getwd(), paste0(project_name, ".gmkinws")) svalue(p.observed) <- "" p.delete$call_Ext("disable") ws <<- gmkinws$new() update_ds.df() update_m.df() update_f.df() } p.new <- gbutton("New project", cont = p.line.buttons, handler = p.new.handler) # Delete {{{3 p.delete.handler = function(h, ...) { filename <- file.path(getwd(), paste0(svalue(p.name), ".gmkinws")) gconfirm(paste0("Are you sure you want to delete ", filename, "?"), parent = w, handler = function(h, ...) { if (inherits(try(unlink(filename)), "try-error")) { gmessage("Deleting failed for an unknown reason", cont = w) } else { svalue(sb) <- paste("Deleted", filename) svalue(p.filename) <- "" svalue(p.observed) <- "" p.delete$call_Ext("disable") update_p.df() } }) } p.delete <- gbutton("Delete project", cont = p.line.buttons, handler = p.delete.handler, ext.args = list(disabled = TRUE)) # Save {{{3 p.save.action <- gaction("Save project to project file", parent = w, handler = function(h, ...) { filename <- paste0(svalue(p.name), ".gmkinws") if (filename == ".gmkinws") { gmessage("Please enter a project name", parent = w) } else { try_to_save <- function (filename) { ws$clear_compiled() if (!inherits(try(save(ws, file = filename)), "try-error")) { svalue(sb) <- paste("Saved project to file", filename, "in working directory", getwd()) update_p.df() p.modified <<- FALSE p.cur <- nrow(p.df) svalue(p.filename) <<- file.path(getwd(), filename) p.delete$call_Ext("enable") svalue(p.observed) <- paste(ws$observed, collapse = ", ") # gWidgetsWWW2 problem: #svalue(p.gtable) <<- p.cur # does not set the selection } else { gmessage("Saving failed for an unknown reason", parent = w) } } if (file.exists(filename)) { gconfirm(paste("File", filename, "exists. Overwrite?"), parent = w, handler = function(h, ...) { try_to_save(filename) }) } else { try_to_save(filename) } } }) p.save.action$add_keybinding(save_keybinding) p.save <- gbutton(action = p.save.action, cont = p.line.buttons) tooltip(p.save) <- paste("Press", save_keybinding, "to save") # Project name {{{2 p.line.name <- ggroup(cont = p.editor, horizontal = TRUE) p.name <- gedit(label = "Project name", initial.msg = "Enter project name", width = 50, cont = p.line.name) update_p_editor <- function(p.cur) { project_name <- as.character(p.df[p.cur, "Name"]) svalue(p.name) <- project_name if (p.df[p.cur, "Source"] == "gmkin package") { svalue(p.filename) <- "" p.delete$call_Ext("disable") } else { svalue(p.filename) <- file.path(getwd(), paste0(project_name, ".gmkinws")) p.delete$call_Ext("enable") } svalue(p.observed) <- paste(ws$observed, collapse = ", ") } # Working directory {{{2 p.line.wd <- ggroup(cont = p.editor, horizontal = TRUE) wd_handler <- function(h, ...) { target_wd <- svalue(p.wde) if (!dir.exists(target_wd)) { gmessage(paste("Directory", target_wd, "does not exist"), parent = w) } else { wd <- try(setwd(target_wd)) if (inherits(wd, "try-error")) { gmessage(paste("Could not set working directory to", target_wd), parent = w) } else { svalue(sb) <- paste("Changed working directory to", wd) update_p.df() } } } p.wde <- gedit(getwd(), cont = p.line.wd, label = "Working directory", width = 50) p.wde$add_handler_enter(wd_handler) p.wdb <- gbutton("Change", cont = p.line.wd, handler = wd_handler) tooltip(p.wdb) <- "Edit the box on the left and press enter to change" # File name {{{2 p.line.file <- ggroup(cont = p.editor, horizontal = TRUE) p.filename.gg <- ggroup(width = 135, cont = p.line.file) # for spacing p.filename.label <- glabel("Project file:", cont = p.filename.gg) p.filename <- glabel("", cont = p.line.file) # Observed variables {{{2 p.line.observed <- ggroup(cont = p.editor, horizontal = TRUE) p.observed.gg <- ggroup(width = 135, cont = p.line.observed) # for spacing p.observed.label <- glabel("Observed variables:", cont = p.observed.gg) p.observed <- glabel("", cont = p.line.observed) # Import {{{2 p.line.import <- ggroup(cont = p.editor, horizontal = TRUE) p.line.import.p <- gcombobox(c("", p.df$Name), label = "Import from", cont = p.line.import, handler = function(h, ...) { p.import <- svalue(h$obj, index = TRUE) - 1 Name <- p.df[p.import, "Name"] if (p.df[p.import, "Source"] == "working directory") { load(paste0(Name, ".gmkinws")) ws.import <<- ws } else { ws.import <<- get(Name) } p.line.import.dst[,] <- data.frame(Title = sapply(ws.import$ds, function(x) x$title), stringsAsFactors = FALSE) p.line.import.mt[,] <- data.frame(Name = sapply(ws.import$m, function(x) x$name), stringsAsFactors = FALSE) }) p.line.import.frames <- ggroup(cont = p.editor, horizontal = TRUE) p.line.import.dsf <- gframe("Datasets for import", cont = p.line.import.frames, horizontal = FALSE, spacing = 0) p.line.import.dst <- gtable(ds.df.empty, cont = p.line.import.dsf, multiple = TRUE, width = left_width - 10, height = 160, handler = function(h, ...) p.line.import.dsb$call_Ext("enable")) p.line.import.dsb <- gbutton("Import selected", cont = p.line.import.dsf, ext.args = list(disabled = TRUE), handler = function(h, ...) { i <- svalue(p.line.import.dst, index = TRUE) ws$add_ds(ws.import$ds[i]) update_ds.df() svalue(p.observed) <- paste(ws$observed, collapse = ", ") p.modified <<- TRUE } ) p.line.import.mf <- gframe("Models for import", cont = p.line.import.frames, horizontal = FALSE, spacing = 0) p.line.import.mt <- gtable(m.df.empty, cont = p.line.import.mf, multiple = TRUE, width = left_width - 10, height = 160, handler = function(h, ...) p.line.import.mb$call_Ext("enable")) p.line.import.mb <- gbutton("Import selected", cont = p.line.import.mf, ext.args = list(disabled = TRUE), handler = function(h, ...) { i <- svalue(p.line.import.mt, index = TRUE) ws$add_m(ws.import$m[i]) update_m.df() m.gtable[,] <- m.df svalue(p.observed) <- paste(ws$observed, collapse = ", ") p.modified <<- TRUE } ) # center: Dataset editor {{{1 ds.editor <- gframe("", horizontal = FALSE, cont = center, width = 540, label = "Dataset") # Handler functions {{{2 # For top row buttons {{{3 stage_dataset <- function(ds.new) { ds.cur <<- ds.new update_ds_editor() ds.copy$call_Ext("disable") ds.delete$call_Ext("disable") } new_dataset_handler <- function(h, ...) { ds.new <- ds.empty$clone() ds.new$title <- "New dataset" stage_dataset(ds.new) } copy_dataset_handler <- function(h, ...) { ds.new <- ds.cur$clone() ds.new$title <- paste("Copy of ", ds.cur$title) stage_dataset(ds.new) } delete_dataset_handler <- function(h, ...) { ds.i <- svalue(ds.gtable, index = TRUE) ws$delete_ds(ds.i) update_ds.df() p.modified <<- TRUE } keep_ds_changes_handler <- function(h, ...) { ds.i <- svalue(ds.gtable, index = TRUE) editor_title <- svalue(ds.title.ge) editor_ds <- mkinds$new( title = editor_title, data = ds.e.gdf[,], time_unit = svalue(ds.e.stu), unit = svalue(ds.e.obu)) if (!is.null(ds.i) && !is.na(ds.i) && ws$ds[[ds.i]]$title == editor_title) { gconfirm(paste("Do you want to overwrite dataset", editor_title, "?"), parent = w, handler = function(h, ...) { ws$ds[[ds.i]] <<- editor_ds ds.cur <<- editor_ds update_ds.df() svalue(p.observed) <- paste(ws$observed, collapse = ", ") p.modified <<- TRUE update_ds_editor() }) } else { ws$add_ds(list(editor_ds)) ds.cur <<- editor_ds update_ds.df() svalue(p.observed) <- paste(ws$observed, collapse = ", ") ds.gtable$set_index(length(ws$ds)) update_ds_editor() } } # For populating the dataset editor {{{3 empty_grid_handler <- function(h, ...) { obs <- strsplit(svalue(ds.e.obs), ", ")[[1]] sampling_times_to_parse <- paste0("c(", svalue(ds.e.st), ")") sampling_times <- eval(parse(text = sampling_times_to_parse)) replicates <- as.numeric(svalue(ds.e.rep)) new.data = data.frame( name = rep(obs, each = replicates * length(sampling_times)), time = as.numeric(rep(sampling_times, each = replicates, times = length(obs))), value = as.numeric(NA), override = as.numeric(NA), err = 1, stringsAsFactors = FALSE ) ds.e.gdf[,] <- new.data svalue(right) <- 2 } # For uploading {{{3 tmptextheader <- character(0) load_text_file_with_data <- function(h, ...) { tmptextfile <<- normalizePath(svalue(h$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("
", c(tmptext[1:5], "\n...\n"), "
") visible(ds.e.import) <- TRUE } 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))) tmpdl$name <- as.character(tmpdl$name) tmpdl$override <- NA tmpdl$err <- 1 } else { tmpdl <- data.frame( name = tmpd[[svalue(ds.e.up.long.name)]], time = tmpd[[svalue(ds.e.up.long.time)]], value = tmpd[[svalue(ds.e.up.long.value)]]) tmpderr <- tmpd[[svalue(ds.e.up.long.err)]] if (!is.null(tmpderr)) tmpdl$err <- tmpderr } if (class(tmpd) != "try-error") { ds.cur <<- mkinds$new( title = "New import", time_unit = "", unit = "", data = tmpdl) if (is.null(ds.cur$data$err)) ds.cur$data$err <<- 1 update_ds.df() update_ds_editor() svalue(right) <- 2 } else { galert("Uploading failed", parent = "w") } } # Update the dataset editor {{{3 update_ds_editor <- function() { svalue(ds.title.ge) <- ds.cur$title svalue(ds.e.st) <- paste(ds.cur$sampling_times, collapse = ", ") svalue(ds.e.stu) <- ds.cur$time_unit svalue(ds.e.obs) <- paste(ds.cur$observed, collapse = ", ") svalue(ds.e.obu) <- ds.cur$unit svalue(ds.e.rep) <- ds.cur$replicates ds.e.gdf[,] <- ds.cur$data ds.keep$call_Ext("enable") visible(ds.e.import) <- FALSE svalue(ds.e.up.text) <- "
"
}
# Widget setup {{{2
# Line 1 with buttons {{{3
ds.e.buttons <- ggroup(cont = ds.editor, horizontal = TRUE)
ds.e.new <- gbutton("New dataset", cont = ds.e.buttons, handler = new_dataset_handler)
ds.copy <- gbutton("Copy dataset", cont = ds.e.buttons,
  handler = copy_dataset_handler, ext.args = list(disabled = TRUE))
ds.delete <- gbutton("Delete dataset", cont = ds.e.buttons,
  handler = delete_dataset_handler, ext.args = list(disabled = TRUE))
ds.keep <- gbutton("Keep changes", cont = ds.e.buttons, handler = keep_ds_changes_handler)
ds.keep$call_Ext("disable")

# Formlayout for meta data {{{3
ds.e.gfl <- gformlayout(cont = ds.editor)
ds.title.ge <- gedit(label = "Dataset title", width = 60, cont = ds.e.gfl)
addHandlerChanged(ds.title.ge, handler = function(h, ...) ds.keep$call_Ext("enable"))
ds.e.st     <- gedit(width = 60, label = "Sampling times", cont = ds.e.gfl)
ds.e.stu    <- gedit(width = 20, label = "Unit", cont = ds.e.gfl)
ds.e.rep    <- gedit(width = 20, label = "Replicates", cont = ds.e.gfl)
ds.e.obs    <- gedit(width = 60, label = "Observed", cont = ds.e.gfl)
ds.e.obu    <- gedit(width = 20, label = "Unit", cont = ds.e.gfl)
generate_grid.gb.line <- ggroup(cont = ds.editor)
generate_grid.gb <- gbutton("Generate grid for entering kinetic data", cont = generate_grid.gb.line,
  width = 250, handler = empty_grid_handler)
tooltip(generate_grid.gb) <- "Overwrites the kinetic data shown to the right"

# Data upload area {{{3
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.editor,
        handler = load_text_file_with_data)


# Import options {{{3
ds.e.import <- ggroup(cont = ds.editor, horizontal = FALSE)
visible(ds.e.import) <- FALSE
ds.e.preview <- ggroup(cont = ds.e.import,
                      # width = 540,  height = 150,
                       ext.args = list(layout = list(type="vbox", align = "center")))
ds.e.up.text <- ghtml("
", cont = ds.e.preview, width = 530, height = 150)

ds.e.up.import.line <- ggroup(cont = ds.e.import)
ds.e.up.import <- gbutton("Import using options specified below", cont = ds.e.up.import.line,
                          width = 250, handler = new_ds_from_csv_handler)
ds.e.up.options <- ggroup(cont = ds.e.import, width = 200, horizontal = FALSE)
ds.e.up.skip <- gedit(tmptextskip, label = "Comment lines", width = 20, 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, width = 50,
                         selected = 1, label = "Separator")
ds.e.up.dec <- gcombobox(c(".", ","), cont = ds.e.up.options, width = 50,
                         selected = 1, label = "Decimal")
ds.e.up.widelong <- gradio(c("wide", "long"), horizontal = TRUE, width = 100,
                           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.import)
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

# center: Model editor {{{1
m.editor  <- gframe("", horizontal = FALSE, cont = center, width = 600,
                    label = "Model")
# Handler functions {{{2
# For top row buttons {{{3
stage_model <- function(m.new) {
  m.cur <<- m.new
  update_m_editor()
  m.copy$call_Ext("disable")
  m.delete$call_Ext("disable")
}

new_model_handler <- function(h, ...) {
  m.new <- m.empty
  m.new$name <- "New model"
  stage_model(m.new)
}

copy_model_handler <- function(h, ...) {
  m.new <- m.cur
  m.new$name <- paste("Copy of ", m.cur$name)
  stage_model(m.new)
}

delete_model_handler <- function(h, ...) {
  m.i <- svalue(m.gtable, index = TRUE)
  ws$delete_m(m.i)
  update_m.df()
  p.modified <<- TRUE
}

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

  spec <- list()
  for (obs.i in 1:length(m.e.rows)) {
    to_string <- svalue(m.e.to[[obs.i]])
    if (length(to_string) == 0) to_vector = NULL
    else to_vector = strsplit(svalue(m.e.to[[obs.i]]), ", ")[[1]]
    spec[[obs.i]] <- mkinsub(svalue(m.e.type[[obs.i]]),
                          to = to_vector,
                          sink = svalue(m.e.sink[[obs.i]]))
    names(spec)[[obs.i]] <- svalue(m.e.obs[[obs.i]])
  }

  m.cur <<- mkinmod(use_of_ff = svalue(m.ff.gc),
                    speclist = spec)
  m.cur$name <<- svalue(m.name.ge)

  m.i <- svalue(m.gtable, index = TRUE)
  if (!is.null(m.i) && !is.na(m.i) && ws$m[[m.i]]$name == m.cur$name) {
    gconfirm(paste("Do you want to overwrite model", m.cur$name, "?"), parent = w,
      handler = function(h, ...) {
        ws$m[[m.i]] <- m.cur
        update_m.df()
        p.modified <<- TRUE
        svalue(p.observed) <- paste(ws$observed, collapse = ", ")
      })
  } else {
    ws$add_m(list(m.cur))
    update_m.df()
    p.modified <<- TRUE
    svalue(p.observed) <- paste(ws$observed, collapse = ", ")
  }
}
# Add and remove observed variables {{{3
add_observed <- function(obs.i) {
  if (obs.i == length(ws$observed)) {
    m.add_observed$call_Ext("disable")
  }
  m.e.rows[[obs.i]] <<- ggroup(cont = m.editor, horizontal = TRUE)
  m.e.obs[[obs.i]] <<- gcombobox(ws$observed,
                                 selected = obs.i,
                                 width = gcb_observed_width,
                                 cont = m.e.rows[[obs.i]])
  obs.types <- if (obs.i == 1) c("SFO", "FOMC", "DFOP", "HS", "SFORB")
    else c("SFO", "SFORB")
  m.e.type[[obs.i]] <<- gcombobox(obs.types, width = gcb_type_width,
                                  selected = 1L, cont = m.e.rows[[obs.i]])
  glabel("to", cont = m.e.rows[[obs.i]])
  m.e.to[[obs.i]] <<- gcombobox(ws$observed, selected = 0L,
                                width = gcb_to_width,
                                editable = TRUE,
                                ext.args = list(multiSelect = TRUE),
                                cont = m.e.rows[[obs.i]])
  m.e.sink[[obs.i]] <<- gcheckbox("Sink", width = gcb_sink_width,
                                  checked = TRUE, cont = m.e.rows[[obs.i]])
  if (obs.i > 1) {
    gbutton("Remove observed variable", handler = remove_observed_handler,
            action = obs.i, cont = m.e.rows[[obs.i]])
  }
}

add_observed_handler <- function(h, ...) {
  obs.i <- length(m.e.rows) + 1
  add_observed(obs.i)
}

remove_observed_handler <- function(h, ...) {
  m.cur$spec[[h$action]] <<- NULL
  update_m_editor()
}
# Update the model editor {{{3
update_m_editor <- function() {
  svalue(m.name.ge) <- m.cur$name
  svalue(m.ff.gc) <- m.cur$use_of_ff
  for (oldrow.i in seq_along(m.e.rows)) {
    delete(m.editor, m.e.rows[[oldrow.i]])
  }
  m.keep$call_Ext("enable")
  m.e.rows <<- m.e.obs <<- m.e.type <<- m.e.to <<- m.e.sink <<- list()
  if (length(m.cur$spec) == length(ws$observed)) {
    m.add_observed$call_Ext("disable")
  } else {
    m.add_observed$call_Ext("enable")
  }
  show_m_spec()
}
# Widget setup {{{2
# Line 1 with buttons {{{3
m.e.buttons <- ggroup(cont = m.editor, horizontal = TRUE)
m.e.new <- gbutton("New model", cont = m.e.buttons, handler = new_model_handler)
m.copy <- gbutton("Copy model", cont = m.e.buttons,
  handler = copy_model_handler, ext.args = list(disabled = TRUE))
m.delete <- gbutton("Delete model", cont = m.e.buttons,
  handler = delete_model_handler, ext.args = list(disabled = TRUE))
m.keep <- gbutton("Keep changes", cont = m.e.buttons, handler = keep_m_changes_handler)
m.keep$call_Ext("disable")

# Formlayout for meta data {{{3
m.e.gfl <- gformlayout(cont = m.editor)
m.name.ge <- gedit(label = "Model name", width = 60, cont = m.e.gfl)
m.ff.gc <- gcombobox(c("min", "max"), label = "Use of formation fractions",
                     cont = m.e.gfl)
svalue(m.ff.gc) <- m.cur$use_of_ff
m.add_observed.line <- ggroup(cont = m.editor)
m.add_observed <- gbutton("Add observed variable",
  width = 150,
  cont = m.add_observed.line,
  handler = add_observed_handler)
m.add_observed$call_Ext("disable")


# Model specification {{{3
m.e.rows <- m.e.obs <- m.e.type <- m.e.to <- m.e.sink <- list()

# Show the model specification {{{4
show_m_spec <- function() {
  for (obs.i in seq_along(m.cur$spec)) {
    obs.name <- names(m.cur$spec)[[obs.i]]

    add_observed(obs.i)

    svalue(m.e.obs[[obs.i]]) <<- obs.name
    svalue(m.e.type[[obs.i]]) <<- m.cur$spec[[obs.i]]$type
    obs.to = m.cur$spec[[obs.i]]$to
    obs.to_string_R = paste(obs.to, collapse = ", ")
    obs.to_string_JS = paste0("['", paste(obs.to, collapse = "', '"), "']")
    # Set R and Ext values separately, as multiple selections are not supported
    svalue(m.e.to[[obs.i]]) <<- obs.to_string_R
    m.e.to[[obs.i]]$call_Ext("select", String(obs.to_string_JS))
    svalue(m.e.sink[[obs.i]]) <<- m.cur$spec[[obs.i]]$sink
  }
}
show_m_spec()


# center: Fit configuration {{{1
f.config  <- gframe("", horizontal = FALSE, cont = center,
                    label = "Configuration")
# Handler functions {{{2
run_confirm_message <- paste("The progress of the fit is shown in the R console. ",
                             if (interactive()) { paste("You can cancel",
                               "the optimisation by switching to the window running R",
                               "and pressing Ctrl-C (in terminals) or Escape (in",
                               "the Windows R GUI). " ) } else "",
                             "Proceed to start the fit?", sep = "")
run_fit_handler <- function(h, ...) { #{{{3
  gconfirm(run_confirm_message, handler = function(h, ...)
    {
      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])
      if (svalue(f.gg.opts.plot)) {
        if (.Platform$OS.type == "windows") {
          # When on windows, check for an active windows device. If not present,
          # open one
          if (attr(dev.cur(), "names") != "windows") windows()
        }
      }
      ftmp <<- mkinfit(m.cur, override(ds.cur$data),
                       state.ini = iniparms,
                       fixed_initials = inifixed,
                       parms.ini = deparms,
                       fixed_parms = defixed,
                       plot = svalue(f.gg.opts.plot),
                       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),
                       reweight.tol = as.numeric(svalue(f.gg.opts.reweight.tol)),
                       reweight.max.iter = as.numeric(svalue(f.gg.opts.reweight.max.iter)),
                       error_model = svalue(f.gg.opts.error_model),
                       error_model_algorithm = svalue(f.gg.opts.error_model_algorithm)
                       )
      ftmp$optimised <<- TRUE
      ftmp$ds <<- ds.cur
      ws$ftmp <<- ftmp
      ws$ftmp$Name <<- "Temporary (fitted)"
      ftmp$name <<- paste(m.cur$name, "-", ds.cur$title)
      update_f.df()
      stmp <<- summary(ftmp)
      f.gg.parms[,] <- get_Parameters(stmp, TRUE)

      show_plot("Optimised")

      f.keep$call_Ext("enable")
      show.initial.gb.o$call_Ext("enable")
      svalue(f.gg.opts.st) <- ftmp$solution_type

      svalue(f.running.label) <- "Terminated"
      update_f_results()
    })
  svalue(f.running.label) <- "Running..."
}
delete_fit_handler <- function(h, ...) { # {{{3
  f.i <- svalue(f.gtable, index = TRUE)
  if (f.i == 1) {
    gmessage("Will not delete temporary fit")
  } else {
    ws$delete_f(f.i - 1)
    update_f.df()
    p.modified <<- TRUE
  }
}
keep_fit_handler <- function(h, ...) { # {{{3
  ftmp$name <<- svalue(r.name)
  ws$add_f(list(ftmp))
  ws$ftmp <<- list(Name = "")
  update_f.df()
  update_plot_obssel()
  p.modified <<- TRUE
}
export_csv_handler <- function(h, ...) { # {{{3
  csv_file <- paste(ftmp$ds$title, "_", ftmp$mkinmod$name, ".csv", sep = "")

  solution_type = ftmp$solution_type
  parms.all <- c(ftmp$bparms.optim, ftmp$bparms.fixed)

  ininames <- c(
    rownames(subset(ftmp$start, type == "state")),
    rownames(subset(ftmp$fixed, type == "state")))
  odeini <- parms.all[ininames]

  # Order initial state variables
  names(odeini) <- sub("_0", "", names(odeini))
  odeini <- odeini[names(ftmp$mkinmod$diffs)]

  xlim = range(ftmp$data$time)
  outtimes <- seq(xlim[1], xlim[2], length.out=200)

  odenames <- c(
    rownames(subset(ftmp$start, type == "deparm")),
    rownames(subset(ftmp$fixed, type == "deparm")))
  odeparms <- parms.all[odenames]

  out <- mkinpredict(ftmp$mkinmod, odeparms, odeini, outtimes,
          solution_type = solution_type, atol = ftmp$atol, rtol = ftmp$rtol)

  write.csv(out, csv_file)
  svalue(sb) <- paste("Wrote model predictions to", file.path(getwd(), csv_file))
}
get_Parameters <- function(stmp, optimised) # {{{3
{
  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"),
                      subset(Parameters, Type == "error"))
  rownames(Parameters) <- Parameters$Name
  if (optimised) {
    Parameters[rownames(stmp$bpar), "Optimised"] <- stmp$bpar[, "Estimate"]
  }
  return(Parameters)
}
show_plot <- function(type) {
  Parameters <- f.gg.parms[,]
  Parameters.de <- subset(Parameters, Type == "deparm", type)
  stateparms <- subset(Parameters, Type == "state")[[type]]
  deparms <- as.numeric(Parameters.de[[type]])
  names(deparms) <- rownames(Parameters.de)
  if (type == "Initial") {
    ftmp <<- suppressWarnings(mkinfit(m.cur,
                                      override(ds.cur$data),
                                      parms.ini = deparms,
                                      state.ini = stateparms,
                                      fixed_parms = names(deparms),
                                      fixed_initials = names(stateparms),
                                      transform_fraction = FALSE, # to be able to fix ff
                                      quiet = TRUE,
                                      control = list(iter.max = 0)))
    ftmp$ds <<- ds.cur
  }
  svalue(plot.ftmp.gi) <<- plot_ftmp_png()
  svalue(plot.ftmp.savefile) <- paste0(ftmp$mkinmod$name, " - ", ftmp$ds$title, ".", plot_format)
  svalue(plot.confint.gi) <<- if (type == "Initial") NA
    else  plot_confint_png()
  svalue(right) <- 4
}
# Widget setup {{{2
# Line 1 with buttons {{{3
f.run.line <- ggroup(cont = f.config)
f.run <- gbutton("Run fit",
                 width = 100,
                 cont = f.run.line,
                 handler = run_fit_handler,
                 ext.args = list(disabled = TRUE))

f.running.line <- ggroup(cont = f.config)
f.running_noconf <- paste("No fit configured. Please select a dataset and a model and",
                          "press the button 'Configure fit' on the left.")
f.running.label <- glabel(f.running_noconf, cont = f.running.line)

# Fit options forms {{{3
f.gg.opts.g <- ggroup(cont = f.config)

# First group {{{4
f.gg.opts.1 <- gformlayout(cont = f.gg.opts.g)
solution_types <- c("auto", "analytical", "eigen", "deSolve")
f.gg.opts.plot <- gcheckbox("Plot during the fit",
                            cont = f.gg.opts.1, checked = FALSE)
f.gg.opts.st <- gcombobox(solution_types, selected = 1,
                          label = "solution_type", width = 160,
                          cont = f.gg.opts.1)
f.gg.opts.atol <- gedit(1e-8, label = "atol", width = 20,
                         cont = f.gg.opts.1)
f.gg.opts.rtol <- gedit(1e-10, label = "rtol", width = 20,
                         cont = f.gg.opts.1)
error_models <- c("const", "obs", "tc")
f.gg.opts.error_model <- gcombobox(error_models, selected = 1,
                                   label = "error_model",
                                   width = 160,
                                   cont = f.gg.opts.1)
error_model_algorithms <- c("d_3", "direct", "threestep", "IRLS", "OLS")
f.gg.opts.error_model_algorithm <- gcombobox(error_model_algorithms, selected = 5,
                                   label = "error_model_algorithm",
                                   width = 160,
                                   cont = f.gg.opts.1)
f.gg.opts.maxit <- gedit(200, label = "maxit",
                         width = 20, cont = f.gg.opts.1)

# Second group {{{4
f.gg.opts.2 <- gformlayout(cont = f.gg.opts.g)
f.gg.opts.transform_rates <- gcheckbox("transform_rates",
                         cont = f.gg.opts.2, checked = TRUE)
f.gg.opts.transform_fractions <- gcheckbox("transform_fractions",
                         cont = f.gg.opts.2, checked = TRUE)
weights <- c("manual", "none", "std", "mean")
f.gg.opts.reweight.tol <- gedit(1e-8, label = "reweight.tol",
                                 width = 20, cont = f.gg.opts.2)
f.gg.opts.reweight.max.iter <- gedit(10, label = "reweight.max.iter",
                                 width = 20, cont = f.gg.opts.2)

f.gg.plotopts <- ggroup(cont = f.gg.opts.g, horizontal = FALSE, width = 80)

f.gg.po.format <- gcombobox(plot_formats, selected = 1,
                  cont = f.gg.plotopts, width = 50,
                  handler = function(h, ...) {
                    plot_format <<- svalue(h$obj)
                    svalue(plot.ftmp.savefile) <<- gsub("...$", plot_format,
                                                       svalue(plot.ftmp.savefile))
                  })
plot_format <- svalue(f.gg.po.format)
f.gg.po.legend <- gcheckbox("legend", cont = f.gg.plotopts, checked = TRUE)
f.gg.po.obssel <- gcheckboxgroup("", cont = f.gg.plotopts,
                                 checked = TRUE)
visible(f.gg.po.obssel) <- FALSE
# Parameter table {{{3
f.parameters.line <- ggroup(cont = f.config, horizontal = TRUE)
get_initials_handler <- function(h, ...)
{
  f.i <- svalue(get.initials.gc, index = TRUE)
  fit <- if (f.i == 1) ftmp
    else ws$f[[f.i - 1]]
  got_initials <- c(fit$bparms.fixed, fit$bparms.optim)
  parnames <- f.gg.parms[,"Name"]
  newparnames <- names(got_initials)
  commonparnames <- intersect(parnames, newparnames)
  f.gg.parms[commonparnames, "Initial"] <- got_initials[commonparnames]
}
get.initials.gb <- gbutton("Get starting parameters from", cont = f.parameters.line,
                           handler = get_initials_handler)
get.initials.gc <- gcombobox(paste("Result", f.df$Name), width = 200, cont = f.parameters.line)
show.initial.gb.u <- gbutton("Plot unoptimised",
                             handler = function(h, ...) show_plot("Initial"),
                             cont = f.parameters.line)
tooltip(show.initial.gb.u) <- "Show model with inital parameters shown below"
show.initial.gb.o <- gbutton("Plot optimised", ext.args = list(disabled = TRUE),
                             handler = function(h, ...) show_plot("Optimised"),
                             cont = f.parameters.line)
tooltip(show.initial.gb.o) <- "Show model with optimised parameters shown below"

# Empty parameter table
Parameters <- Parameters.empty <- data.frame(
  Name = "",
  Type = factor("state", levels = c("state", "deparm")),
  Initial = numeric(1),
  Fixed = logical(1),
  Optimised = numeric(1))
# Dataframe with initial and optimised parameters {{{4
f.gg.parms <- gdf(Parameters, cont = f.config, height = 500,
                  name = "Starting parameters",
                  do_add_remove_buttons = FALSE)
size(f.gg.parms) <- list(columnWidths = c(220, 50, 65, 50, 65))

# Do not show fit option widgets when no fit is configured
show_fit_option_widgets <- function(show)
{
  visible(f.gg.opts.g) <- show
  visible(f.parameters.line) <- show
  visible(f.gg.parms) <- show
}
show_fit_option_widgets(FALSE)

# center: Results viewer {{{1
r.viewer  <- gframe("", horizontal = FALSE, cont = center,
                    label = "Result")
# Row with buttons {{{2
r.buttons <- ggroup(cont = r.viewer, horizontal = TRUE)
f.delete <- gbutton("Delete fit", cont = r.buttons,
  handler = delete_fit_handler, ext.args = list(disabled = TRUE))
f.keep <- gbutton("Keep fit", cont = r.buttons, handler = keep_fit_handler)
tooltip(f.keep) <- "Store the optimised model with all settings and the current dataset in the fit list"
f.keep$call_Ext("disable")
f.csv <- gbutton("Export csv", cont = r.buttons, handler = export_csv_handler)
tooltip(f.csv) <- "Save model predictions in a text file as comma separated values for plotting"
# Result name {{{2
r.line.name <- ggroup(cont = r.viewer, horizontal = TRUE)
r.name  <- gedit("", label = "Result name",
                 width = 50, cont = r.line.name)

# Optimised parameter table {{{2
par.df.empty <- data.frame(
  Parameter = character(1),
  Estimate = numeric(1), "Pr(>t)" = numeric(1),
  Lower = numeric(1), Upper = numeric(1), check.names = FALSE)
r.par.gf <- gframe("Optimised parameters", cont = r.viewer,
                   horizontal = FALSE, spacing = 0)
r.parameters <- gtable(par.df.empty, cont = r.par.gf, height = 200,
                       ext.args = list(resizable = TRUE, resizeHandles = 's'))

# Tables with chi2, ff, DT50 {{{2
r.frames <- ggroup(cont = r.viewer, horizontal = TRUE, spacing = 0)

r.frames.chi2 <- gframe("Chi2 errors [%]", cont = r.frames,
                        horizontal = TRUE, spacing = 0)
chi2.df.empty = data.frame(Variable = character(1), Error = character(1),
                           n.opt = character(1), df = character(1),
                           stringsAsFactors = FALSE)
r.frames.chi2.gt <- gtable(chi2.df.empty, cont = r.frames.chi2,
                            width = 180, height = 150)
size(r.frames.chi2.gt) <- list(columnWidths = c(60, 35, 35, 15))

r.frames.ff <- gframe("Formation fractions", cont = r.frames,
                      horizontal = TRUE, spacing = 0)
ff.df.empty = data.frame(Path = character(1), ff = character(1),
                         stringsAsFactors = FALSE)
r.frames.ff.gt <- gtable(ff.df.empty, cont = r.frames.ff,
                         width = 150, height = 150)
size(r.frames.ff.gt) <- list(columnWidths = c(80, 15))

r.frames.distimes <- gframe("Disappearance times", cont = r.frames,
                            horizontal = TRUE, spacing = 0)
distimes.df.empty = data.frame(Variable = character(1), DT50 = character(1),
                               stringsAsFactors = FALSE)
r.frames.distimes.gt <- gtable(distimes.df.empty, cont = r.frames.distimes,
                               width = 150, height = 150)

# Summary {{{2
f.gg.summary <- gframe("Summary", height = 400, use.scrollwindow = TRUE,
                       cont = r.viewer, horizontal = FALSE)
f.gg.summary.topline <- ggroup(cont = f.gg.summary, horizontal = TRUE)
f.gg.summary.filename <- gedit("", width = 40, cont = f.gg.summary.topline)
f.gg.summary.savebutton <-  gbutton("Save summary", cont = f.gg.summary.topline,
                                    handler = function(h, ...) {
                                      filename <- svalue(f.gg.summary.filename)
                                      if (file.exists(filename))
                                      {
                                        gconfirm(paste("File", filename, "exists. Overwrite?"),
                                                 parent = w,
                                                 handler = function(h, ...) {
                                                   capture.output(stmp,  file = filename)
                                                 })
                                      } else {
                                        capture.output(summary(ftmp),  file = filename)
                                      }
                                    })
f.gg.summary.listing <- ghtml("", cont = f.gg.summary)

svalue(center) <- 1
# right: Viewing area {{{1
# Workflow {{{2
workflow.gg <- ggroup(cont = right, label = "Workflow", width = 480,  height = 570,
                      ext.args = list(layout = list(type="vbox", align = "center")))

workflow_url <- "/custom/gmkin_png/workflow/gmkin_workflow_434x569.png"
workflow.gi <- gimage(workflow_url, size = c(434, 569), label = "Workflow", cont = workflow.gg)

# Data editor {{{2
ds.e.gdf <- gdf(ds.cur$data, label = "Data", name = "Kinetic data",
                do_add_remove_buttons = FALSE,
                width = 488, height = 577, cont = right)

# Model Gallery {{{2
m.g.gg <- ggroup(cont = right, label = "Model gallery",
                 ext.args = list(layout = list(type="vbox", align = "center")))

m.g.rows <- list()
m.g.buttonrows <- list()
m.g.fields <- list()
m.g.buttons <- list()
add_gallery_model_handler <- function(h, ...) {
  i_j <- h$action
  ws$add_m(UBA_model_gallery[[i_j[1]]][i_j[2]])
  update_m.df()
  m.i <- nrow(m.df)
  svalue(c.m) <- m.df[m.i, "Name"]
  m.cur <<- ws$m[[m.i]]
  update_m_editor()
  m.delete$call_Ext("enable")
  m.copy$call_Ext("enable")
  if (!is.null(svalue(ds.gtable, index = TRUE))) {
    if (length(svalue(ds.gtable)) > 0) {
      if (!is.na(svalue(ds.gtable))) f.conf$call_Ext("enable")
    }
  }
  svalue(center) <- 3
}
model_gallery_created <- FALSE
m.g.loading <- glabel("Loading the model gallery, please wait...
If nothing happens, please try switching to the Data tab and back here.", cont = m.g.gg) create_model_gallery <- function() { delete(m.g.gg, m.g.loading) for (i in 1:9) { m.g.rows[[i]] <<- ggroup(cont = m.g.gg, horizontal = TRUE) m.g.buttonrows[[i]] <<- ggroup(cont = m.g.gg, horizontal = TRUE) m.g.fields[[i]] <<- list() m.g.buttons[[i]] <<- list() for (j in 1:4) { model <- UBA_model_gallery[[i]][[j]] m.url = paste0("/custom/gmkin_png/", gsub(" ", "_", model$name), ".png") m.g.fields[[i]][[j]] <<- gimage(m.url, width = 110, height = if (i == 1) 80 else if (i == 2) 160 else 220, cont = m.g.rows[[i]]) m.g.buttons[[i]][[j]] <<- gbutton(model$name, width = 110, cont = m.g.buttonrows[[i]], handler = add_gallery_model_handler, action = c(i, j)) tooltip(m.g.buttons[[i]][[j]]) <<- model$name } } model_gallery_created <<- TRUE } # Plots {{{2 plot.gg <- ggroup(cont = right, label = "Plot", width = 460, ext.args = list(layout = list(type="vbox", align = "center"))) plot_ftmp <- function() { if (length(svalue(f.gg.po.obssel)) == 0) { gmessage("Please select more than one variable for plotting.") } else { if(svalue(f.gg.po.obssel)[1] != "") { obs_vars_plot = svalue(f.gg.po.obssel) } else { obs_vars_plot = names(ftmp$mkinmod$spec) } if(exists("f.gg.po.legend")) { plot_legend = svalue(f.gg.po.legend) } else { plot_legend = TRUE } plot(ftmp, main = paste(ftmp$mkinmod$name, "-", ftmp$ds$title), obs_vars = obs_vars_plot, xlab = ifelse(ftmp$ds$time_unit == "", "Time", paste("Time in", ftmp$ds$time_unit)), ylab = ifelse(ftmp$ds$unit == "", "Observed", paste("Observed in", ftmp$ds$unit)), legend = plot_legend, show_residuals = TRUE) } } plot_ftmp_png <- function() { tf <- get_tempfile(ext=".png") png(tf, width = 400, height = 400) plot_ftmp() dev.off() return(tf) } plot_ftmp_save <- function(filename) { switch(plot_format, png = png(filename, width = 400, height = 400), pdf = pdf(filename), emf = devEMF::emf(filename)) plot_ftmp() dev.off() svalue(sb) <- paste("Saved plot to", filename, "in working directory", getwd()) } 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(NA, container = plot.gg, width = 400, height = 400) plot.ftmp.saveline <- ggroup(cont = plot.gg, horizontal = TRUE) plot.ftmp.savefile <- gedit("", width = 40, cont = plot.ftmp.saveline) plot.ftmp.savebutton <- gbutton("Save plot", cont = plot.ftmp.saveline, handler = function(h, ...) { filename <- svalue(plot.ftmp.savefile) if (file.exists(filename)) { gconfirm(paste("File", filename, "exists. Overwrite?"), parent = w, handler = function(h, ...) { plot_ftmp_save(filename) } ) } else { plot_ftmp_save(filename) } }) plot.space <- ggroup(cont = plot.gg, horizontal = FALSE, height = 8) plot.confint.label <- glabel("Parameter confidence intervals", cont = plot.gg) plot.confint.gi <- gimage(NA, container = plot.gg, width = 400, height = 400) # Manual {{{2 manual_html <- readLines(system.file("GUI/manual.html", package = "gmkin")) manual.gh <- ghtml(label = "Manuals", paste0("
", paste(manual_html, collapse = '\n'), "
"), width = 460, cont = right) # Changes {{{2 gmkin_news <- markdown::markdownToHTML(system.file("NEWS.md", package = "gmkin"), fragment.only = TRUE) changes.gh <- ghtml(label = "Changes", paste0("
", gmkin_news, "
"), width = 460, cont = right) # Things to do in the end {{{1 # Update meta objects and their depending widgets svalue(right) <- 1 update_p.df() # vim: set foldmethod=marker ts=2 sw=2 expandtab: {{{1