diff options
| -rw-r--r-- | ChangeLog | 13 | ||||
| -rw-r--r-- | R/plot.mkinfit.R | 2 | ||||
| -rw-r--r-- | inst/GUI/TODO | 5 | ||||
| -rw-r--r-- | inst/GUI/simple.R | 130 | ||||
| -rw-r--r-- | man/mkinfit.Rd | 2 |
5 files changed, 120 insertions, 32 deletions
@@ -1,3 +1,9 @@ +2013-10-17 Johannes Ranke <jranke@stiller> for mkin (0.9-22)
+
+ * Fix plot.mkinfit as it passed graphical arguments like main to the solver
+ * Do not use plot=TRUE in mkinfit example
+ * The first successful fits in the not so simple GUI
+
2013-10-16 Johannes Ranke<jranke@uni-bremen.de> for mkin (0.9-22)
* Unify naming of initial values of state variables
@@ -12,10 +18,9 @@ 2013-10-09 Johannes Ranke <jranke@uni-bremen.de> for mkin (0.9-22)
- * Do not use 0 values at time zero for chi2 error level calculations.
- This is the way it is done in KinGUII and it makes sense
-
+ * Do not use 0 values at time zero for chi2 error level calculations.
+ This is the way it is done in KinGUII and it makes sense
Changes performed in earlier versions are documented in the subversion log
files on R-Forge http://www.r-forge.r-project.org/scm/?group_id=615
-vim: set expandtab ts=2 sw=2:
+vim: set noexpandtab ts=2 sw=2:
diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R index 5e2db39..a07ddea 100644 --- a/R/plot.mkinfit.R +++ b/R/plot.mkinfit.R @@ -48,7 +48,7 @@ plot.mkinfit <- function(x, fit = x, odeparms <- parms.all[odenames] out <- mkinpredict(fit$mkinmod, odeparms, odeini, outtimes, - solution_type = solution_type, atol = fit$atol, rtol = fit$rtol, ...) + solution_type = solution_type, atol = fit$atol, rtol = fit$rtol) # Set up the plot if not to be added to an existing plot if (add == FALSE) { diff --git a/inst/GUI/TODO b/inst/GUI/TODO index ea875ce..e9089ed 100644 --- a/inst/GUI/TODO +++ b/inst/GUI/TODO @@ -1 +1,4 @@ -- Write the model editor +- Import of csv files +- Create widgets for model configuration only once per dataset, it takes too much time +- Make summary text file accessible +- Make plot of fit and residuals accessible diff --git a/inst/GUI/simple.R b/inst/GUI/simple.R index f5eafb6..f53b064 100644 --- a/inst/GUI/simple.R +++ b/inst/GUI/simple.R @@ -38,8 +38,8 @@ studies.df <- data.frame(Index = as.integer(1), # Initial datasets {{{2
ds <- list()
observed.all <- vector()
-for (i in 1:5) {
- ds.letter = LETTERS[i]
+for (i in 1:2) {
+ ds.letter = LETTERS[i + 2]
ds.index <- as.character(i)
ds.name = paste0("FOCUS_2006_", ds.letter)
ds[[ds.index]] <- list(
@@ -74,15 +74,13 @@ override <- function(d) { value = ifelse(is.na(d$override), d$value, d$override),
err = d$err)
}
-f <- s <- f.gg <- f.gg.rows <- list()
-f.gg.ini <- f.gg.fixed <- f.gg.optim <- list()
+f <- s <- f.gg <- list()
+f.gg.parms <- f.gg.opts <- list()
for (ds.i in 1:length(ds)) {
f[[as.character(ds.i)]] <- list()
f.gg[[as.character(ds.i)]] <- list()
- f.gg.rows[[as.character(ds.i)]] <- list()
- f.gg.ini[[as.character(ds.i)]] <- list()
- f.gg.fixed[[as.character(ds.i)]] <- list()
- f.gg.optim[[as.character(ds.i)]] <- list()
+ f.gg.parms[[as.character(ds.i)]] <- list()
+ f.gg.opts[[as.character(ds.i)]] <- list()
s[[as.character(ds.i)]] <- list()
}
# Data frames with datasets, models and fits to be continuosly updated {{{1
@@ -220,30 +218,112 @@ size(m.gtable) <- list(columnWidths = c(40, 200)) # Section for selecting datasets and model {{{2
dsmsel <- gvbox(cont = dsm)
+show_plot <- function(ds.i, m.i, type) {
+ ow <- options("warn")
+ options(warn = -1)
+ Parameters <- f.gg.parms[[ds.i]][[m.i]][,]
+ Parameters.de <- subset(Parameters, Type == "deparm", type)
+ stateparms <- subset(Parameters, Type == "state")[[type]]
+ deparms <- as.numeric(Parameters.de[[type]])
+ names(deparms) <- rownames(Parameters.de)
+ if (type == "Initial") {
+ f[[ds.i]][[m.i]] <<- mkinfit(m[[m.i]], override(ds[[ds.i]]$data),
+ state.ini = stateparms,
+ parms.ini = deparms,
+ err = "err", control.modFit = list(maxiter = 0))
+ }
+ options(ow)
+ ftmp <- f[[ds.i]][[m.i]]
+ f <- get_tempfile(ext=".svg")
+ svg(f, width = 7, height = 5)
+ plot(ftmp, main = ds[[ds.i]]$title,
+ xlab = ifelse(ds[[ds.i]]$time_unit == "", "Time",
+ paste("Time in", ds[[ds.i]]$time_unit)),
+ ylab = ifelse(ds[[ds.i]]$unit == "", "Observed",
+ paste("Observed in", ds[[ds.i]]$unit)))
+ dev.off()
+ svalue(plots[[ds.i]]) <<- f
+}
+get_Parameters <- function(stmp, optimised)
+{
+ pars <- rbind(stmp$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(ds.i, m.i) {
+ Parameters <- f.gg.parms[[ds.i]][[m.i]][,]
+ Parameters.de <- subset(Parameters, Type == "deparm")
+ deparms <- Parameters.de$Initial
+ names(deparms) <- rownames(Parameters.de)
+ f[[ds.i]][[m.i]] <<- mkinfit(m[[m.i]], override(ds[[ds.i]]$data),
+ state.ini = subset(Parameters,
+ Type == "state")$Initial,
+ parms.ini = deparms,
+ err = "err")
+ s[[ds.i]][[m.i]] <<- summary(f[[ds.i]][[m.i]])
+
+ f.gg.parms[[ds.i]][[m.i]][,] <- get_Parameters(s[[ds.i]][[m.i]], TRUE)
+
+ show_plot(ds.i, m.i, "Optimised")
+}
+show_fit_config <- function(ds.i, m.i) {
+ ftmp <- f[[ds.i]][[m.i]]
+ stmp <- summary(ftmp)
+ Parameters <- get_Parameters(stmp, FALSE)
+
+ f.gg.parms[[ds.i]][[m.i]] <<- gdf(Parameters,
+ width = 420, height = 300,
+ cont = f.gg[[ds.i]][[m.i]],
+ do_add_remove_buttons = FALSE)
+ f.gg.parms[[ds.i]][[m.i]]$set_column_width(1, 200)
+ f.gg.parms[[ds.i]][[m.i]]$set_column_width(2, 50)
+ f.gg.parms[[ds.i]][[m.i]]$set_column_width(3, 60)
+ f.gg.parms[[ds.i]][[m.i]]$set_column_width(4, 50)
+ f.gg.parms[[ds.i]][[m.i]]$set_column_width(5, 60)
+
+ f.gg.rest <- gvbox(cont = f.gg[[ds.i]][[m.i]])
+ f.gg.buttons <- ggroup(cont = f.gg.rest)
+ gbutton("Show initial", handler = function(h, ...) show_plot(ds.i, m.i, "Initial"),
+ cont = f.gg.buttons)
+ gbutton("Run", handler = function(h, ...) run_fit(ds.i, m.i),
+ cont = f.gg.buttons)
+ f.gg.opts[[ds.i]][[m.i]] <<- gformlayout(cont = f.gg.rest)
+ solution_types <- character()
+ if (length(ftmp$mkinmod$map) == 1) solution_types <- "analytical"
+ if (is.matrix(ftmp$mkinmod$coefmat)) solution_types <- c(solution_types, "eigen")
+ solution_types <- c(solution_types, "deSolve")
+
+ gcombobox(solution_types, selected = 1, label = "solution_type",
+ cont = f.gg.opts[[ds.i]][[m.i]])
+}
configure_fits_handler <- function(h, ...) {
ds.sel <- as.character(svalue(ds.gtable))
m.sel <- as.character(svalue(m.gtable))
+ ow <- options("warn")
+ options("warn" = -1)
for (ds.i in ds.sel) {
for (m.i in m.sel) {
f.gg[[ds.i]][[m.i]] <<- ggroup(cont = f.gn[[ds.i]], label = m[[m.i]]$name)
- f.gg.parms <- gvbox(cont = f.gg[[ds.i]][[m.i]])
- f.gg.rows[[ds.i]][[m.i]] <<- list()
- f.gg.ini[[ds.i]][[m.i]] <<- list()
- f[[ds.i]][[m.i]] <- ftmp <- mkinfit(m[[m.i]], override(ds[[ds.i]]$data),
+ f[[ds.i]][[m.i]] <<- mkinfit(m[[m.i]], override(ds[[ds.i]]$data),
err = "err", control.modFit = list(maxiter = 0))
- s[[ds.i]][[m.i]] <- stmp <- summary(ftmp)
- pars <- rbind(stmp$start[1:2], stmp$fixed)
- pars$fixed <- c(rep(FALSE, length(stmp$start$value)),
- rep(TRUE, length(stmp$fixed$value)))
-
- for (parm in c(paste0(names(ftmp$mkinmod$map), "_0"), names(ftmp$bparms.ode))) {
- f.gg.rows[[ds.i]][[m.i]][[parm]] <- ggroup(cont = f.gg.parms)
- glabel(parm, cont = f.gg.rows[[ds.i]][[m.i]][[parm]])
- f.gg.ini[[ds.i]][[m.i]][[parm]] <- gedit(pars[parm, "value"],
- cont = f.gg.rows[[ds.i]][[m.i]][[parm]])
- }
+ show_fit_config(ds.i, m.i)
}
}
+ options(ow)
}
dsconfig <- gbutton("Configure fits for selections", cont = dsmsel,
handler = configure_fits_handler)
@@ -262,7 +342,7 @@ copy_dataset_handler <- function(h, ...) { ds.gtable[,] <- ds.df
prows[[ds.cur]] <<- ggroup(cont = pfv)
plots[[ds.cur]] <<- gsvg(svg_plot(ds.cur),
- container=prows[[ds.cur]],
+ container = prows[[ds.cur]],
width = 490, height = 350)
}
@@ -560,7 +640,7 @@ for (ds.i in 1:length(ds)) { plots[[ds.plot]] <- gsvg(svg_plot(ds.plot),
container=prows[[ds.plot]],
width = 490, height = 350)
- f.gn[[ds.plot]] <- gnotebook(cont = prows[[ds.plot]], width = 600,
+ f.gn[[ds.plot]] <- gnotebook(cont = prows[[ds.plot]], width = 750,
handler = function(h, ...) galert("test", parent = w))
}
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index 750c346..c15c084 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -198,7 +198,7 @@ SFORB_SFO <- mkinmod( fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D) # Use starting parameters from parent only SFORB fit (not really needed in this case) fit.SFORB = mkinfit(SFORB, FOCUS_2006_D) -fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode, plot=TRUE) +fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode) # Weighted fits, including IRLS SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"), |