Convert main vignette to Rmd/html, add_err(), fixes

1 files changed, 48 insertions, 0 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)
+}