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-rw-r--r--inst/GUI/gmkin.R93
-rw-r--r--inst/GUI/png/FOMC,_two_sequential,_one_parallel_met.pngbin2912 -> 2989 bytes
-rw-r--r--inst/GUI/png/SFO,_no_mets.pngbin1871 -> 1871 bytes
-rw-r--r--inst/GUI/png/Water_sediment,_met_in_both.pngbin2694 -> 2575 bytes
-rw-r--r--inst/GUI/png/Water_sediment,_met_in_sediment.pngbin2094 -> 2066 bytes
-rw-r--r--inst/GUI/png/Water_sediment,_met_in_water.pngbin2247 -> 2226 bytes
-rw-r--r--inst/GUI/png/Water_sediment_P-II.pngbin1837 -> 1716 bytes
7 files changed, 54 insertions, 39 deletions
diff --git a/inst/GUI/gmkin.R b/inst/GUI/gmkin.R
index 3459179..7a91aef 100644
--- a/inst/GUI/gmkin.R
+++ b/inst/GUI/gmkin.R
@@ -23,6 +23,9 @@
# Widgets {{{2
left_width = 250
right_width = 500
+ds_height = 142
+m_height = 142
+f_height = 142
save_keybinding = "Ctrl-X"
gcb_observed_width = 100
gcb_type_width = 70
@@ -55,10 +58,8 @@ bl$set_panel_size("west", left_width)
bl$set_panel_size("east", right_width)
center <- gnotebook(cont = bl, where = "center")
-left <- gvbox(cont = bl, use.scrollwindow = TRUE, where = "west")
+left <- gvbox(cont = bl, use.scrollwindow = TRUE, where = "west", spacing = 0)
right <- gnotebook(cont = bl, use.scrollwindow = TRUE, where = "east")
-# right$add_handler("tabchange", handler = function(h, ...) {
-# if (svalue(h$obj) == 3) bl$set_panel_size("east", 1000)
# })
# Helper functions {{{1
@@ -151,11 +152,11 @@ ws$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)
-ds.gf <- gframe("Datasets", cont = left)
-m.gf <- gframe("Models", cont = left)
-c.gf <- gframe("Configuration", cont = left, horizontal = FALSE)
-f.gf <- gframe("Results", cont = left)
+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
@@ -188,6 +189,7 @@ p.switcher <- function(h, ...) {
project_switched <- TRUE
p.gtable$set_index(p.cur)
p.modified <<- FALSE
+ visible(p.gf) <- FALSE
}
if (p.modified) {
gconfirm("When you switch projects, you loose any unsaved changes. Proceed to switch?",
@@ -218,13 +220,15 @@ ds.switcher <- function(h, ...) {
ds.delete$call_Ext("enable")
ds.copy$call_Ext("enable")
if (!is.null(svalue(m.gtable, index = TRUE))) {
- if (!is.na(svalue(m.gtable))) f.conf$call_Ext("enable")
+ if (length(svalue(m.gtable)) > 0) {
+ if (!is.na(svalue(m.gtable))) f.conf$call_Ext("enable")
+ }
}
svalue(center) <- 2
svalue(right) <- 2
}
-ds.gtable <- gtable(ds.df, cont = ds.gf, width = left_width - 10, height = 160,
- ext.args = list(resizable = TRUE, resizeHandles = 's'))
+ds.gtable <- gtable(ds.df, cont = ds.gf, width = left_width - 10, height = ds_height,
+ ext.args = list(resizable = TRUE, resizeHandles = 's', hideHeaders = TRUE))
addHandlerClicked(ds.gtable, ds.switcher)
# Model explorer {{{2
m.switcher <- function(h, ...) {
@@ -235,13 +239,14 @@ m.switcher <- function(h, ...) {
m.delete$call_Ext("enable")
m.copy$call_Ext("enable")
if (!is.null(svalue(ds.gtable, index = TRUE))) {
- if (!is.na(svalue(ds.gtable))) f.conf$call_Ext("enable")
+ if (length(svalue(ds.gtable)) > 0) {
+ if (!is.na(svalue(ds.gtable))) f.conf$call_Ext("enable")
+ }
}
svalue(center) <- 3
- svalue(right) <- 3
}
-m.gtable <- gtable(m.df, cont = m.gf, width = left_width - 10, height = 160,
- ext.args = list(resizable = TRUE, resizeHandles = 's'))
+m.gtable <- gtable(m.df, cont = m.gf, width = left_width - 10, height = m_height,
+ ext.args = list(resizable = TRUE, resizeHandles = 's', hideHeaders = TRUE))
addHandlerClicked(m.gtable, m.switcher)
# Fit explorer {{{2
f.switcher <- function(h, ...) {
@@ -266,13 +271,13 @@ f.switcher <- function(h, ...) {
show_plot("Optimised")
update_f_results()
}
-f.gtable <- gtable(f.df, cont = f.gf, width = left_width - 10, height = 160,
- ext.args = list(resizable = TRUE, resizeHandles = 's'))
+f.gtable <- gtable(f.df, cont = f.gf, width = left_width - 10, height = f_height,
+ ext.args = list(resizable = TRUE, resizeHandles = 's', hideHeaders = TRUE))
addHandlerClicked(f.gtable, f.switcher)
# Configuration {{{2
empty_conf_labels <- paste0("<font color='gray'>Current ", c("dataset", "model"), "</font>")
-c.ds <- glabel(empty_conf_labels[1], cont = c.gf)
-c.m <- glabel(empty_conf_labels[2], cont = c.gf)
+c.ds <- glabel(empty_conf_labels[1], cont = c.gf, ext.args = list(margin = "0 0 0 5"))
+c.m <- glabel(empty_conf_labels[2], cont = c.gf, ext.args = list(margin = "0 0 0 5"))
update_f_conf <- function() { # {{{3
stmp <<- summary(ftmp)
@@ -304,13 +309,14 @@ update_f_results <- function() { # {{{3
delete(r.frames.distimes, r.frames.distimes.gt)
delete(r.frames, r.frames.distimes)
r.frames.distimes <<- gframe("Disappearance times", cont = r.frames, use.scrollwindow = TRUE,
- horizontal = TRUE)
+ horizontal = TRUE, spacing = 0)
r.frames.distimes.gt <<- gtable(cbind(data.frame(Variable = rownames(stmp$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$name, ".txt", sep = "")
svalue(f.gg.summary.listing) <- c("<pre>", capture.output(summary(ftmp)), "</pre>")
+ ds.e.gdf[,] <- ftmp$ds$data
svalue(center) <- 5
}
update_plot_obssel <- function() {
@@ -469,7 +475,8 @@ p.line.import.p <- gcombobox(c("", p.df$Name), label = "Import from", cont = p.l
})
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)
+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$call_Ext("enable"))
@@ -484,7 +491,8 @@ p.line.import.dsb <- gbutton("Import selected", cont = p.line.import.dsf,
}
)
-p.line.import.mf <- gframe("Models for import", cont = p.line.import.frames, horizontal = FALSE)
+p.line.import.mf <- gframe("Models for import", cont = p.line.import.frames,
+ horizontal = FALSE, spacing = 0)
p.line.import.mt <- gtable(m.df.empty, cont = p.line.import.mf, multiple = TRUE,
width = left_width - 10, height = 160,
handler = function(h, ...) p.line.import.mb$call_Ext("enable"))
@@ -849,7 +857,7 @@ show_m_spec <- function() {
show_m_spec()
-# center: Fit manager {{{1
+# center: Fit configuration {{{1
f.config <- gframe("", horizontal = FALSE, cont = center,
label = "Configuration")
# Handler functions {{{2
@@ -989,12 +997,14 @@ f.running.label <- glabel("No fit configured", 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 = 200,
+ 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)
@@ -1003,10 +1013,12 @@ f.gg.opts.rtol <- gedit(1e-10, label = "rtol", width = 20,
optimisation_methods <- c("Port", "Marq", "SANN")
f.gg.opts.method.modFit <- gcombobox(optimisation_methods, selected = 1,
label = "method.modFit",
- width = 200,
+ width = 160,
cont = f.gg.opts.1)
f.gg.opts.maxit.modFit <- gedit("auto", label = "maxit.modFit",
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)
@@ -1014,20 +1026,19 @@ f.gg.opts.transform_fractions <- gcheckbox("transform_fractions",
cont = f.gg.opts.2, checked = TRUE)
weights <- c("manual", "none", "std", "mean")
f.gg.opts.weight <- gcombobox(weights, selected = 1, label = "weight",
- width = 200, cont = f.gg.opts.2)
+ width = 180, cont = f.gg.opts.2)
f.gg.opts.reweight.method <- gcombobox(c("none", "obs"), selected = 1,
label = "IRLS",
- width = 200,
+ width = 180,
cont = f.gg.opts.2)
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)
+f.gg.plotopts <- ggroup(cont = f.gg.opts.g, horizontal = FALSE, width = 80)
f.gg.po.format <- gcombobox(plot_formats, selected = 1,
- #label = "File format",
cont = f.gg.plotopts, width = 50,
handler = function(h, ...) {
plot_format <<- svalue(h$obj)
@@ -1054,7 +1065,7 @@ get_initials_handler <- function(h, ...)
}
get.initials.gb <- gbutton("Get starting parameters from", cont = f.parameters.line,
handler = get_initials_handler)
-get.initials.gc <- gcombobox(paste("Result", f.df$Name), width = 250, cont = f.parameters.line)
+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)
@@ -1098,14 +1109,16 @@ 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)
+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)
+r.frames <- ggroup(cont = r.viewer, horizontal = TRUE, spacing = 0)
-r.frames.chi2 <- gframe("Chi2 errors [%]", cont = r.frames, horizontal = TRUE)
+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)
@@ -1113,14 +1126,16 @@ 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)
+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)
+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,
@@ -1158,10 +1173,10 @@ workflow.gi <- gimage(workflow_url, size = c(434, 569), label = "Workflow", cont
# Data editor {{{2
ds.e.gdf <- gdf(ds.cur$data, label = "Data", name = "Kinetic data",
- width = 488, height = 600, cont = right)
+ width = 488, height = 577, cont = right)
# Model Gallery {{{2
-m.g.gg <- ggroup(cont = right, label = "Model gallery",
+m.g.gg <- ggroup(cont = right, label = "Model gallery",
ext.args = list(layout = list(type="vbox", align = "center")))
m.g.rows <- list()
@@ -1202,7 +1217,7 @@ for (i in 1:9) {
}
}
# Plots {{{2
-plot.gg <- ggroup(cont = right, label = "Plot", width = 480, height = 900,
+plot.gg <- ggroup(cont = right, label = "Plot", width = 460,
ext.args = list(layout = list(type="vbox", align = "center")))
plot_ftmp <- function() {
@@ -1276,7 +1291,7 @@ plot.ftmp.savebutton <- gbutton("Save plot", cont = plot.ftmp.saveline,
plot_ftmp_save(filename)
}
})
-plot.space <- ggroup(cont = plot.gg, horizontal = TRUE, height = 18)
+plot.space <- ggroup(cont = plot.gg, horizontal = FALSE, height = 18)
plot.confint.gi <- gimage(NA, container = plot.gg, width = 400, height = 400)
# Manual {{{2
gmkin_manual <- readLines(system.file("GUI/gmkin_manual.html", package = "gmkin"))
diff --git a/inst/GUI/png/FOMC,_two_sequential,_one_parallel_met.png b/inst/GUI/png/FOMC,_two_sequential,_one_parallel_met.png
index 9096acd..74a23db 100644
--- a/inst/GUI/png/FOMC,_two_sequential,_one_parallel_met.png
+++ b/inst/GUI/png/FOMC,_two_sequential,_one_parallel_met.png
Binary files differ
diff --git a/inst/GUI/png/SFO,_no_mets.png b/inst/GUI/png/SFO,_no_mets.png
index 5704bcc..c36ce14 100644
--- a/inst/GUI/png/SFO,_no_mets.png
+++ b/inst/GUI/png/SFO,_no_mets.png
Binary files differ
diff --git a/inst/GUI/png/Water_sediment,_met_in_both.png b/inst/GUI/png/Water_sediment,_met_in_both.png
index 74ea0e7..fcc38d9 100644
--- a/inst/GUI/png/Water_sediment,_met_in_both.png
+++ b/inst/GUI/png/Water_sediment,_met_in_both.png
Binary files differ
diff --git a/inst/GUI/png/Water_sediment,_met_in_sediment.png b/inst/GUI/png/Water_sediment,_met_in_sediment.png
index 81caa93..72811b5 100644
--- a/inst/GUI/png/Water_sediment,_met_in_sediment.png
+++ b/inst/GUI/png/Water_sediment,_met_in_sediment.png
Binary files differ
diff --git a/inst/GUI/png/Water_sediment,_met_in_water.png b/inst/GUI/png/Water_sediment,_met_in_water.png
index c668c0c..b2dd975 100644
--- a/inst/GUI/png/Water_sediment,_met_in_water.png
+++ b/inst/GUI/png/Water_sediment,_met_in_water.png
Binary files differ
diff --git a/inst/GUI/png/Water_sediment_P-II.png b/inst/GUI/png/Water_sediment_P-II.png
index 08e2c72..9eef311 100644
--- a/inst/GUI/png/Water_sediment_P-II.png
+++ b/inst/GUI/png/Water_sediment_P-II.png
Binary files differ

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