diff options
| -rw-r--r-- | DESCRIPTION | 7 | ||||
| -rw-r--r-- | NEWS.md | 6 | ||||
| -rw-r--r-- | README.md | 6 | ||||
| -rw-r--r-- | inst/GUI/gmkin.R | 45 | ||||
| -rw-r--r-- | test.R | 21 |
5 files changed, 51 insertions, 34 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index f8765e0..9316135 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: gmkin Type: Package Title: Graphical User Interface for Fitting Kinetic Models to Chemical Degradation Data Version: 0.6.10 -Date: 2019-07-05 +Date: 2019-07-08 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de"), person("Stefan", "Meinecke", role = "ctb"), @@ -10,7 +10,7 @@ Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), Description: Browser based graphical user interface for R package mkin, based on the gWidgetsWWW2 package. Both gmkin and gWidgetsWWW2 are developed on GitHub, but are also available from the R-Forge repository. -Depends: mkin (>= 0.9.47.3), gWidgetsWWW2 (>= 0.4-7) +Depends: mkin (>= 0.9.49.6), gWidgetsWWW2 (>= 0.4-7) Imports: R6, markdown, plyr, devEMF Suggests: knitr, rmarkdown License: GPL @@ -19,6 +19,5 @@ LazyData: yes Encoding: UTF-8 VignetteBuilder: knitr BugReports: http://github.com/jranke/gmkin/issues -URL: http://kinfit.r-forge.r-project.org/gmkin_static, - http://pkgdown.jrwb.de/gmkin +URL: http://pkgdown.jrwb.de/gmkin RoxygenNote: 6.1.1 @@ -1,11 +1,13 @@ # NEWS for package 'gmkin' -## gmkin 0.6-10 (2019-07-06) +## gmkin 0.6-10 (2019-07-08) -- Adapt to mkin 0.9.49.1 +- Adapt to mkin 0.9.49.6 - Use devEMF for better vector graphics export for Windows +- Manual weighting is not possible as this functionality is currently not present in mkin versions > 0.9.48.1 + ## gmkin 0.6-9 (2018-09-13) - Enable fits with the two-component error model during iterative reweighting (IRLS) @@ -15,8 +15,7 @@ For running gmkin you need a system running a recent version of R (version (Firefox/Iceweasel and Chrome work for me) with JavaScript enabled. It should be possible to run gmkin on most laptop or desktop computers running -Linux, Mac OS X, Windows XP or Windows 7. It is frequently checked under Linux and -Windows 7. +Linux, Mac OS X, Windows 7 or Windows 10. To view the complete set of widgets in the browser window without resizing anything, it needs a screen space of 1366x740 pixels. @@ -168,3 +167,6 @@ Agency ([Umweltbundesamt](http://www.umweltbundesamt.de)) in two projects in gratefully acknowledged. In particular, Stefan Meinecke contributed with a lot of user feedback and suggestions for improvement in that time. +The adaptation to mkin versions > 0.9.49.6 that can do fits using a two-component +error model was supported by another project by the Umweltbundesamt in 2018/2019. + diff --git a/inst/GUI/gmkin.R b/inst/GUI/gmkin.R index b7ddc13..1320da0 100644 --- a/inst/GUI/gmkin.R +++ b/inst/GUI/gmkin.R @@ -299,17 +299,25 @@ c.ds <- glabel(empty_conf_labels[1], cont = c.gf, ext.args = list(margin = "0 0 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)
+ 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$transform_fractions
- svalue(f.gg.opts.error_model) <<- ftmp$error_model
- svalue(f.gg.opts.error_model_algorithm) <<- ftmp$error_model_algorithm
+ if (!is.null(ftmp$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$reweight.max.iter
- svalue(f.gg.opts.maxit) <<- ftmp$maxit
+ 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$optimised)
@@ -369,7 +377,6 @@ configure_fit_handler <- function(h, ...) { # Configure fit button {{{3 update_f_conf()
f.run$call_Ext("enable")
- print("test")
svalue(f.running.label) <- "Fit configured and ready to run"
} else {
svalue(f.running.label) <- paste("No fit configured:",
@@ -977,13 +984,6 @@ run_fit_handler <- function(h, ...) { #{{{3 iniparms <- Parameters.ini$Initial
names(iniparms) <- sub("_0", "", Parameters.ini$Name)
inifixed <- names(iniparms[Parameters.ini$Fixed])
- weight <- svalue(f.gg.opts.weight)
- if (weight == "manual") {
- err = "err"
- } else {
- err = NULL
- }
- reweight.method <- svalue(f.gg.opts.reweight.method)
if (svalue(f.gg.opts.plot)) {
if (.Platform$OS.type == "windows") {
# When on windows, check for an active windows device. If not present,
@@ -991,7 +991,6 @@ run_fit_handler <- function(h, ...) { #{{{3 if (attr(dev.cur(), "names") != "windows") windows()
}
}
- if (reweight.method == "none") reweight.method = NULL
ftmp <<- mkinfit(m.cur, override(ds.cur$data),
state.ini = iniparms,
fixed_initials = inifixed,
@@ -1022,7 +1021,6 @@ run_fit_handler <- function(h, ...) { #{{{3 f.keep$call_Ext("enable")
show.initial.gb.o$call_Ext("enable")
svalue(f.gg.opts.st) <- ftmp$solution_type
- svalue(f.gg.opts.weight) <- ftmp$weight.ini
svalue(f.running.label) <- "Terminated"
update_f_results()
@@ -1089,7 +1087,8 @@ get_Parameters <- function(stmp, optimised) # {{{3 Fixed = pars$fixed,
Optimised = as.numeric(NA))
Parameters <- rbind(subset(Parameters, Type == "state"),
- subset(Parameters, Type == "deparm"))
+ subset(Parameters, Type == "deparm"),
+ subset(Parameters, Type == "error"))
rownames(Parameters) <- Parameters$Name
if (optimised) {
Parameters[rownames(stmp$bpar), "Optimised"] <- stmp$bpar[, "Estimate"]
@@ -1154,13 +1153,13 @@ f.gg.opts.error_model <- gcombobox(error_models, selected = 1, label = "error_model",
width = 160,
cont = f.gg.opts.1)
-error_model_algorithms <- c("d_3", "direct", "threestep", "IRLS")
-f.gg.opts.error_model_algorithm <- gcombobox(error_model_algorithms, selected = 1,
+error_model_algorithms <- c("d_3", "direct", "threestep", "IRLS", "OLS")
+f.gg.opts.error_model_algorithm <- gcombobox(error_model_algorithms, selected = 5,
label = "error_model_algorithm",
width = 160,
cont = f.gg.opts.1)
-f.gg.opts.maxit <- gedit("auto", label = "maxit",
- width = 20, cont = f.gg.opts.1)
+f.gg.opts.maxit <- gedit(200, label = "maxit",
+ width = 20, cont = f.gg.opts.1)
# Second group {{{4
f.gg.opts.2 <- gformlayout(cont = f.gg.opts.g)
@@ -1169,12 +1168,6 @@ f.gg.opts.transform_rates <- gcheckbox("transform_rates", f.gg.opts.transform_fractions <- gcheckbox("transform_fractions",
cont = f.gg.opts.2, checked = TRUE)
weights <- c("manual", "none", "std", "mean")
-f.gg.opts.weight <- gcombobox(weights, selected = 1, label = "weight",
- width = 180, cont = f.gg.opts.2)
-f.gg.opts.reweight.method <- gcombobox(c("none", "obs", "tc"), selected = 1,
- label = "IRLS",
- width = 180,
- cont = f.gg.opts.2)
f.gg.opts.reweight.tol <- gedit(1e-8, label = "reweight.tol",
width = 20, cont = f.gg.opts.2)
f.gg.opts.reweight.max.iter <- gedit(10, label = "reweight.max.iter",
@@ -1421,7 +1414,7 @@ plot_ftmp_save <- function(filename) { switch(plot_format,
png = png(filename, width = 400, height = 400),
pdf = pdf(filename),
- wmf = win.metafile(filename))
+ emf = devEMF::emf(filename))
plot_ftmp()
dev.off()
svalue(sb) <- paste("Saved plot to", filename, "in working directory", getwd())
@@ -0,0 +1,21 @@ +library(gmkin) + +app <- gmkin(script = "~/git/gmkin/inst/GUI/gmkin.R") +s <- gmkin:::get_current_session(app) + +s$show_fit_option_widgets(TRUE) +s$f.run$call_Ext("enable") + +names(s) +s$ftmp$reweight.max.iter +s$ftmp$maxit +names(s$ftmp) + +s$ws$ftmp$maxit +s$f.run$call_Ext("enable") +s$f.gg.parms[,] +s$show_fit_option_widgets +svalue(s$f.gg.opts.reweight.tol) <- +svalue(s$f.gg.opts.error_model) +svalue(s$f.gg.opts.error_model_algorithm) +visible(s$f.gg.opts.g) <- TRUE |