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-rw-r--r--R/add_err.R48
-rw-r--r--R/plot.mmkin.R15
2 files changed, 56 insertions, 7 deletions
diff --git a/R/add_err.R b/R/add_err.R
new file mode 100644
index 00000000..0995e634
--- /dev/null
+++ b/R/add_err.R
@@ -0,0 +1,48 @@
+# Copyright (C) 2015-2016 Johannes Ranke
+# Contact: jranke@uni-bremen.de
+
+# This file is part of the R package mkin
+
+# mkin 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 <http://www.gnu.org/licenses/>
+
+add_err = function(prediction, sdfunc,
+ n = 1000, LOD = 0.1, reps = 2,
+ digits = 1, seed = NA)
+{
+ if (!is.na(seed)) set.seed(seed)
+
+ # The output of mkinpredict is in wide format
+ d_long = mkin_wide_to_long(prediction, time = "time")
+
+ # Set up the list to be returned
+ d_return = list()
+
+ # Generate datasets one by one in a loop
+ for (i in 1:n) {
+ d_rep = data.frame(lapply(d_long, rep, each = 2))
+ d_rep$value = rnorm(length(d_rep$value), d_rep$value, sdfunc(d_rep$value))
+
+ d_rep[d_rep$time == 0 & d_rep$name %in% c("M1", "M2"), "value"] <- 0
+
+ # Set values below the LOD to NA
+ d_NA <- transform(d_rep, value = ifelse(value < LOD, NA, value))
+
+ # Round the values for convenience
+ d_NA$value <- round(d_NA$value, digits)
+
+ d_return[[i]] <- d_NA
+ }
+
+ return(d_return)
+}
diff --git a/R/plot.mmkin.R b/R/plot.mmkin.R
index 02bf4d6e..7b54be4b 100644
--- a/R/plot.mmkin.R
+++ b/R/plot.mmkin.R
@@ -20,12 +20,17 @@ plot.mmkin <- function(x, main = "auto", legends = 1, errmin_var = "All data", e
cex = 0.7, rel.height.middle = 0.9, ...) {
n.m <- nrow(x)
n.d <- ncol(x)
+
+ # We can handle either a row (different models, same dataset)
+ # or a column (same model, different datasets)
if (n.m > 1 & n.d > 1) stop("Please select fits either for one model or for one dataset")
if (n.m == 1 & n.d == 1) loop_over = "none"
if (n.m > 1) loop_over <- "models"
if (n.d > 1) loop_over <- "datasets"
n.fits <- length(x)
+ # Set the main plot titles from the names of the models or the datasets
+ # Will be integer indexes if no other names are present in the mmkin object
if (main == "auto") {
main = switch(loop_over,
none = paste(rownames(x), colnames(x)),
@@ -34,11 +39,13 @@ plot.mmkin <- function(x, main = "auto", legends = 1, errmin_var = "All data", e
}
oldpar <- par(no.readonly = TRUE)
+
+ # Set relative plot heights, so the first and the last plot are the norm
+ # and the middle plots (if n.fits >2) are smaller by rel.height.middle
rel.heights <- if (n.fits > 2) c(1, rep(rel.height.middle, n.fits - 2), 1)
else rep(1, n.fits)
layout(matrix(1:(2 * n.fits), n.fits, 2, byrow = TRUE), heights = rel.heights)
- #par(mfrow = c(n.fits, 2))
par(mar = c(3.0, 4.1, 4.1, 2.1)) # Reduce bottom margin by 2.1 - hides x axis legend
par(cex = cex)
@@ -48,12 +55,6 @@ plot.mmkin <- function(x, main = "auto", legends = 1, errmin_var = "All data", e
# reduced plot height, therefore we need rel.height.middle in the layout
par(mar = c(3.0, 4.1, 2.1, 2.1))
}
- if (i.fit == n.fits) {
- # Reduce top margin by 2 after the first plot as we have no main title,
- # plot height remains about constant
- par(mar = c(5.1, 4.1, 2.1, 2.1))
-
- }
fit <- x[[i.fit]]
plot(fit, legend = legends == i.fit, ...)

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