From 7e721e76ba97a7412b0becb663686cca5d914364 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Roland=20Holl=C3=B3s?= <hollorol@gmail.com>
Date: Fri, 3 Jan 2020 13:28:06 +0100
Subject: [PATCH] skipZero option in sensitivity

---
 RBBGCMuso/R/musoMonte.R              |  6 ++++++
 RBBGCMuso/R/musoSensi.R              |  4 +++-
 RBBGCMuso/man/getAnnualOutputList.Rd | 14 ++++++++++++++
 3 files changed, 23 insertions(+), 1 deletion(-)
 create mode 100644 RBBGCMuso/man/getAnnualOutputList.Rd

diff --git a/RBBGCMuso/R/musoMonte.R b/RBBGCMuso/R/musoMonte.R
index f72443c..9e4cd5c 100644
--- a/RBBGCMuso/R/musoMonte.R
+++ b/RBBGCMuso/R/musoMonte.R
@@ -31,6 +31,7 @@ musoMonte <- function(settings=NULL,
                      debugging = FALSE,
                      keepEpc = FALSE,
                      constrains = NULL,
+                     skipZero = TRUE,
                      ...){
 
 
@@ -150,6 +151,11 @@ musoMonte <- function(settings=NULL,
                 for(j in 1:numVars){
                     tmp2[j]<-funct[[j]](tmp[,j])
                 }
+                if(skipZero){
+                    if(tmp2[j]==0){
+                        tmp2[j] <- NA
+                    }
+                }
             } else {
                 for(j in 1:numVars){
                     tmp2[j]<-NA
diff --git a/RBBGCMuso/R/musoSensi.R b/RBBGCMuso/R/musoSensi.R
index 1c09542..49c9d74 100644
--- a/RBBGCMuso/R/musoSensi.R
+++ b/RBBGCMuso/R/musoSensi.R
@@ -30,6 +30,7 @@ musoSensi <- function(monteCarloFile = NULL,
                      plotName = "sensitivity.png",
                      plotTitle = "Sensitivity",
                      skipSpinup = TRUE,
+                     skipZero = TRUE,
                      dpi=300){
 
     if(is.null(parameters)){
@@ -91,7 +92,8 @@ musoSensi <- function(monteCarloFile = NULL,
                       outVars = outVars,
                       fun = fun,
                       varIndex = varIndex,
-                      skipSpinup = skipSpinup
+                      skipSpinup = skipSpinup,
+                      skipZero=skipZero
                       )
         M <- cbind(seq_along(M[,1]),M)
         yInd <-  grep("mod.", colnames(M))[varIndex]
diff --git a/RBBGCMuso/man/getAnnualOutputList.Rd b/RBBGCMuso/man/getAnnualOutputList.Rd
new file mode 100644
index 0000000..ac956c8
--- /dev/null
+++ b/RBBGCMuso/man/getAnnualOutputList.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/getOutPutList.R
+\name{getAnnualOutputList}
+\alias{getAnnualOutputList}
+\title{getAnnualOutputList}
+\usage{
+getAnnualOutputList(settings = NULL)
+}
+\arguments{
+\item{settings}{bla}
+}
+\description{
+bla bla
+}