Rearrange initialisation of workspace and metadata

1 files changed, 34 insertions, 63 deletions

diff --git a/inst/GUI/gmkin.R b/inst/GUI/gmkin.R
index 5376588..8b1fd89 100644
--- a/inst/GUI/gmkin.R
+++ b/inst/GUI/gmkin.R
@@ -27,6 +27,30 @@ sb     <- gstatusbar(paste("Powered by gWidgetsWWW2, ExtJS, Rook, FME, deSolve",
 pg     <- gpanedgroup(cont = w, default.size = 260)

 center <- gnotebook(cont = pg)

 left   <- gvbox(cont = pg, use.scrollwindow = TRUE)

+# Set initial values {{{1

+# Initial project workspace contents {{{2

+project_name <- "FOCUS_2006_gmkin"

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

+workspace <- get(project_name)     # From dataset distributed with mkin

+studies.df <- workspace$studies.df # dataframe containing study titles

+ds <- workspace$ds                 # list of datasets

+ds.cur <- workspace$ds.cur         # current dataset index

+m <- workspace$m                   # list with mkinmod models, amended with mkinmod$name

+m.cur <- workspace$m.cur           # m.cur current model index

+f <- workspace$f                   # f list of fitted mkinfit objects

+f.cur <- workspace$f.cur           # current fit index

+s <- workspace$s                   # list of summaries of the fitted mkinfit objects

+# Initialise meta data objects so assignments within functions using <<- will {{{2

+# update them in the right environment

+observed.all <- vector()           # vector of names of observed variables in datasets

+ds.df <- data.frame()

+m.df <- data.frame()

+f.df <- data.frame()

+# Empty versions of meta data {{{2

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

+                         Dataset = "", 

+                         Model = "",

+                         stringsAsFactors = FALSE)

 # Helper functions {{{1

 # Override function for making it possible to override original data in the GUI {{{2

 override <- function(d) {

@@ -34,36 +58,7 @@ override <- function(d) {
              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_name <- "mkin_FOCUS_2006"

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

-# Initial studies {{{2

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

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

-                         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 dataframe with datasets for selection {{{2

 update_ds.df <- function() {

   ds.n <- length(ds)

   ds.df <<- data.frame(Index = 1:ds.n, 

@@ -79,22 +74,7 @@ update_ds.df <- function() {
     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 dataframe with models for selection {{{2

 update_m.df <- function() {

   m.n <- length(m)

   m.df <<- data.frame(Index = 1:m.n, 

@@ -105,31 +85,20 @@ update_m.df <- function() {
     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 dataframe with fits for selection {{{2

 update_f.df <- function() {

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

-                      Dataset = character(),

-                      Model = character(), 

-                      stringsAsFactors = FALSE)

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

   f.count <- 0

   for (fit.index in names(f)) {

     f.count <- f.count + 1

     ftmp <- f[[fit.index]]

     f.df[f.count, ] <<- c(as.character(f.count), ftmp$ds.index, ftmp$mkinmod$name)

   }

-  delete(f.gg.buttons, get.initials.gc)

-  get.initials.gc <<- gcombobox(paste("Fit", f.df$Fit), cont = f.gg.buttons)

 }

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

-                               Dataset = "", 

-                               Model = "",

-                               stringsAsFactors = FALSE)

+# Initialise meta data objects {{{1

+update_ds.df()

+update_m.df()

+update_f.df()

 # Widgets and handlers for project data {{{1

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

 # Project data management handler functions {{{2

@@ -915,6 +884,8 @@ svalue(f.gn) <- 1
 

 # Update the plotting and fitting area {{{3

 update_plotting_and_fitting <- function() {

+  delete(f.gg.buttons, get.initials.gc)

+  get.initials.gc <<- gcombobox(paste("Fit", f.df$Fit), cont = f.gg.buttons)

   svalue(pf) <- paste0("Fit ", f.cur, ": Dataset ", ftmp$ds.index, 

                        ", Model ", ftmp$mkinmod$name)

   show_plot("Optimised")