From 5219ba4b321b2aeb85af8683aaeea8f3108583ce Mon Sep 17 00:00:00 2001
From: hsonne <hauke.sonnenberg@gmx.de>
Date: Wed, 27 Nov 2019 07:40:51 +0100
Subject: [PATCH] Add argument "no.iff" -> switch off iff in gompred

The modified version of gompred accepts an additional
command line parameter "no-iff". If this parameter is
set to "1", the condition probabilities for inspected
pipes for are calculated differently. No pipe and
age-specific iff values are calculated and the transition matrixes that are used in the Markov Chain
are based on the marginal survival curves instead of
on the non-marginal survival curves.
---
 R/gompred.R                  | 7 +++++--
 R/run.R                      | 7 +++++--
 man/runGompitzPrediction.Rd  | 5 ++++-
 man/runGompredInDirectory.Rd | 6 +++++-
 4 files changed, 19 insertions(+), 6 deletions(-)

diff --git a/R/gompred.R b/R/gompred.R
index a2d2072..603a1fa 100644
--- a/R/gompred.R
+++ b/R/gompred.R
@@ -11,6 +11,8 @@
 #' @param strategy strategy identifier. Must be one of 0 (do nothing), 1
 #'   (length-driven strategy), 2 (budget-driven strategy), or 3 (optimised
 #'   strategy).")
+#' @param no.iff logical whether to let Gompitz use iff values 
+#'   (\code{no.iff = FALSE}, the default) or not (\code{no.iff = TRUE})
 #' @param \dots arguments passed to the corresponding
 #'   \code{.fileContentStrategy} functions, such as \code{range.years}
 #'   (two-element vector with first and last year of prediction),
@@ -39,8 +41,8 @@
 #' # For an example, see the Tutorial vignette "How to Use the Package"
 #' 
 runGompitzPrediction <- function(
-  input.data, subset = NULL, calibration, strategy = 0, ..., verbose = 1, 
-  do.stop = TRUE, clear.observations = TRUE, 
+  input.data, subset = NULL, calibration, strategy = 0, no.iff = FALSE, ..., 
+  verbose = 1, do.stop = TRUE, clear.observations = TRUE, 
   VERSION = getOperatingSystemType(), 
   use.data.table = getOption("kwbGompitz.use.data.table", FALSE)
 )
@@ -156,6 +158,7 @@ runGompitzPrediction <- function(
     input.file = paths$input.file,
     sep = sep,
     strategy = strategy,
+    no.iff = no.iff,
     verbose = verbose,
     VERSION = VERSION
   ))
diff --git a/R/run.R b/R/run.R
index ad5de5d..3db3c05 100644
--- a/R/run.R
+++ b/R/run.R
@@ -24,17 +24,19 @@ runGompcalInDirectory <- function(
 #' @param input.file path to input file
 #' @param sep column separator
 #' @param strategy integer number specifying the strategy to be applied
+#' @param no.iff logical whether to let Gompitz use iff values 
+#'   (\code{no.iff = FALSE}, the default) or not (\code{no.iff = TRUE})
 #' @param \dots arguments that are passed to .runModuleInDirectory, such as
 #'   \code{verbose} or \code{show.error}
 #' 
 runGompredInDirectory <- function(
   target.dir = tempdir(), input.file = exampleFile("obs.txt"), sep = ";",
-  strategy = 0, ...
+  strategy = 0, no.iff = FALSE, ...
 )
 {
   error_code <- .runModuleInDirectory(
     "gompred", target.dir, input.file, sep, ..., 
-    options = as.character(strategy)
+    options = c(as.character(strategy), if (no.iff) "1" else NULL)
   )
 
   # Check the output for an error message  
@@ -140,6 +142,7 @@ open_file_if_not_on_unix <- function(file)
   files <- file.path("log", sprintf("%s_%s.txt", module, c("out", "err")))
 
   .catLogMessageIf(verbose > 1, sprintf("command: '%s'\n", command))
+  
   kwb.utils::printIf(verbose > 1, args)
 
   error_code <- system2(command, args, stdout = files[1], stderr = files[2])
diff --git a/man/runGompitzPrediction.Rd b/man/runGompitzPrediction.Rd
index 322cdb3..5a6bc0d 100644
--- a/man/runGompitzPrediction.Rd
+++ b/man/runGompitzPrediction.Rd
@@ -5,7 +5,7 @@
 \title{Run Gompitz Predicion}
 \usage{
 runGompitzPrediction(input.data, subset = NULL, calibration,
-  strategy = 0, ..., verbose = 1, do.stop = TRUE,
+  strategy = 0, no.iff = FALSE, ..., verbose = 1, do.stop = TRUE,
   clear.observations = TRUE, VERSION = getOperatingSystemType(),
   use.data.table = getOption("kwbGompitz.use.data.table", FALSE))
 }
@@ -23,6 +23,9 @@ if \code{NULL}, all rows in \code{input.data} will be used.}
 (length-driven strategy), 2 (budget-driven strategy), or 3 (optimised
 strategy).")}
 
+\item{no.iff}{logical whether to let Gompitz use iff values 
+(\code{no.iff = FALSE}, the default) or not (\code{no.iff = TRUE})}
+
 \item{\dots}{arguments passed to the corresponding
 \code{.fileContentStrategy} functions, such as \code{range.years}
 (two-element vector with first and last year of prediction),
diff --git a/man/runGompredInDirectory.Rd b/man/runGompredInDirectory.Rd
index 6f9026a..309ce9f 100644
--- a/man/runGompredInDirectory.Rd
+++ b/man/runGompredInDirectory.Rd
@@ -5,7 +5,8 @@
 \title{Run gompred.exe in given Directory}
 \usage{
 runGompredInDirectory(target.dir = tempdir(),
-  input.file = exampleFile("obs.txt"), sep = ";", strategy = 0, ...)
+  input.file = exampleFile("obs.txt"), sep = ";", strategy = 0,
+  no.iff = FALSE, ...)
 }
 \arguments{
 \item{target.dir}{path to target directory}
@@ -16,6 +17,9 @@ runGompredInDirectory(target.dir = tempdir(),
 
 \item{strategy}{integer number specifying the strategy to be applied}
 
+\item{no.iff}{logical whether to let Gompitz use iff values 
+(\code{no.iff = FALSE}, the default) or not (\code{no.iff = TRUE})}
+
 \item{\dots}{arguments that are passed to .runModuleInDirectory, such as
 \code{verbose} or \code{show.error}}
 }