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Merge the debugging from unstable branch

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hollorol 2018-05-14 10:15:09 +02:00
commit 15c174fa18
8 changed files with 165 additions and 15 deletions
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3
RBBGCMuso/DESCRIPTION
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@ -17,7 +17,8 @@ Imports:
Rcpp,
magrittr,
dplyr,
ggplot2
ggplot2,
rmarkdown
LinkingTo: Rcpp
Maintainer: Roland Hollo's <hollorol@gmail.com>
RoxygenNote: 6.0.1

14
RBBGCMuso/R/OtableMaker.R
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@ -25,13 +25,17 @@ OtableMaker <- function(parametersReal){
OTFzero <- OTF[OTF$GROUP==0,]
OT0 <- constMatrix [constMatrix$INDEX %in% zeroIndexes,] %>%
mutate(MIN=OTFzero$MIN,MAX=OTFzero$MAX)
sliced <- constMatrix %>%
if(nrow(OT0)!=nrow(OTF)){
sliced <- constMatrix %>%
dplyr::filter(GROUP %in% groupIDs)
slicedIndexes<- which(sliced[,"INDEX"] %in% intersect(sliced[,"INDEX"],otfIndexes))
sliced[slicedIndexes,c("MIN","MAX")] <- OTF[which(OTF["GROUP"] == groupIDs),c("MIN","MAX")]
slicedIndexes<- which(sliced[,"INDEX"] %in% intersect(sliced[,"INDEX"],otfIndexes))
sliced[slicedIndexes,c("MIN","MAX")] <- OTF[which(OTF["GROUP"] == groupIDs),c("MIN","MAX")]
OTbig <- rbind(OT0,sliced) %>% data.frame()
} else {
OTbig <- OT0 %>% data.frame()
}
OTbig <- rbind(OT0,sliced) %>% data.frame()
parnumbers <- nrow(OTbig)
for(i in 1:parnumbers){

2
RBBGCMuso/R/calibMuso.R
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@ -57,7 +57,7 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
if(silent!=TRUE){
if(length(grep("(dayout$)|(log$)",list.files(inputLoc)))>0){
cat(" \n \n WARMING: there is a log or dayout file nearby the ini files, that may cause problemes. \n \n If you want to avoid that possible problemes, please copy the log or dayout files into a save place, and after do a cleanupMuso(), or delete these manually, or run the rungetMuso(), with the agressive=TRUE parameter \n \n")
warning("there is a log or dayout file nearby the ini files, that may cause problemes. \n \n If you want to avoid that possible problemes, please copy the log or dayout files into a save place, and after do a cleanupMuso(), or delete these manually, or run the rungetMuso(), with the agressive=TRUE parameter \n \n")
}

10
RBBGCMuso/R/musoSensi.R
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@ -25,7 +25,7 @@ musoSensi <- function(monteCarloFile = NULL,
settings = NULL,
parametersFromFile=FALSE,
inputDir = "./",
outLoc = "./calib",
outLoc = "./calib",
iterations = 30,
preTag = "mont-",
outputType = "moreCsv",
@ -56,12 +56,14 @@ musoSensi <- function(monteCarloFile = NULL,
varNames<- colnames(M)[1:npar]
w <- lm(y~M)$coefficients[-1]
Sv <- apply(M,2,var)
overalVar <- sum(Sv^2*w^2)
overalVar <- sum(Sv*w^2)
S=numeric(npar)
for(i in 1:npar){
S[i] <- ((w[i]^2*Sv[i]^2)/overalVar)*100
S[i] <- ((w[i]^2*Sv[i])/(overalVar))*100
}
S <- round(S)
S <- round(S,digits=2)
names(S)<-varNames
write.csv(file = outputFile, x = S)

13
RBBGCMuso/R/parametersweep.R Normal file
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@ -0,0 +1,13 @@
## #' paramsweep
## #'
## #' This function update the the muso outputcode-variable matrix
## #' @author Roland Hollos
## #' @return The outputcode-variable matrix, and also change the global variable
## #' @import rmarkdown
## #' @export
## paramSweep <- function(inputDir="./",parameters=NULL,outputDir=NULL){
## read.csv(system.file("markdowns","parameters.csv",package="RBBGCMuso"))
## }

115
RBBGCMuso/inst/markdowns/parameterSweep.rmd Normal file
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@ -0,0 +1,115 @@
---
title: "ParameterSweep"
auth or: ""
date: "`r format(Sys.time(), '%d %B, %Y')`"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r,echo=FALSE}
library("RBBGCMuso")
quickAndDirty <- function(settings, parameters, inputDir= "./", outLoc, iterations=2, outVar=8,){
outLocPlain <- basename(outLoc)
currDir <- getwd()
inputDir <- normalizePath(inputDir)
tmp <- file.path(outLoc,"tmp/")
if(!dir.exists(outLoc)){
dir.create(outLoc)
warning(paste(outLoc," is not exists, so it was created"))
}
if(dir.exists(tmp)){
stop("There is a tmp directory inside the output location, please replace it. tmp is an important temporary directory for the function")
}
dir.create(tmp)
outLoc <- normalizePath(outLoc)
tmp <- normalizePath(tmp)
inputFiles <- file.path(inputDir,grep(basename(outLoc),list.files(inputDir),invert = TRUE,value = TRUE))
for(i in inputFiles){
file.copy(i,tmp)
}
setwd(tmp)
if(is.null(settings)){
settings <- setupMuso()
}
file.copy(settings$epcInput[2],"epc-save",overwrite = TRUE)
calibrationPar <- matrix[,"INDEX"]
npar <- nrow(matrix)
paramMatrices <- list()
parameters <- matrix(nrow = npar,ncol = iterations)
paramtest <- parameters
rownames(paramtest) <- matrix[,1]
for(i in 1:npar){
parameters[i,] <- seq(from=matrix[i,5],to=matrix[i,6],length=iterations)
#print(parameters[i,])
settings$calibrationPar <- calibrationPar[i]
for(j in 1:iterations){
p <- try(calibMuso(settings,parameters =parameters[i,j],silent=TRUE))
if(length(p)>1){
paramtest[i,j] <- max(p[,outVar])
# print(paramtest)
} else {
paramtest[i,j] <- NA
# print(paramtest)
}
}
file.copy("epc-save",settings$epcInput[2],overwrite = TRUE)
}
print("###################################################")
paramMatrices <- (function(){
for(i in 1:nrow(paramtest)){
matrx <- matrix(ncol = 2,nrow=iterations)
matrx[,1] <- parameters[i,]
matrx[,2] <- paramtest[i,]
paramMatrices[[i]] <- matrx
names(paramMatrices)[i] <- rownames(paramtest)[i]
}
return(paramMatrices)
})()
return(list(paramtest,paramMatrices))
}
```
```{r, echo=FALSE,cache=TRUE}
parconstrains <- read.csv("parconstrains_extended.csv")
settings <- setupMuso()
parSeq<-quickAndDirty(settings = settings,matrix = parconstrains,outVar = 8,iterations = 5)
```
```{r}
parSeq
```
```{r,echo=FALSE}
parlist<-parSeq[[2]]
lparlist<-length(parlist)
for(i in 1:lparlist){
title<-names(parlist)[i]
plot(x = parlist[[i]][,1], y= parlist[[i]][,2], ylim=c(0,15), main=title,ylab="LAI")
}
```

14
RBBGCMuso/inst/markdowns/parameters.csv Normal file
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@ -0,0 +1,14 @@
NAME,INDEX,MIN,MAX
BASETEMP,25,3,9
WPM,36,0,0.1
CN_lv,38,10,50
CN_li,39,32,70
CN_root,40,20,70
CN_fruit,41,10.50,70
CN_stem,42,0,70
CLEC,55,0.4,0.8
FLNR,61,0.05,0.8
STOMA,63,0.003,0.015
ROOTDEPTH,74,0.3,2.
SWCGERMIN,87,0.2,0.9
NH4MOBILEPROP,120,0.05,0.7
1 NAME INDEX MIN MAX
2 BASETEMP 25 3 9
3 WPM 36 0 0.1
4 CN_lv 38 10 50
5 CN_li 39 32 70
6 CN_root 40 20 70
7 CN_fruit 41 10.50 70
8 CN_stem 42 0 70
9 CLEC 55 0.4 0.8
10 FLNR 61 0.05 0.8
11 STOMA 63 0.003 0.015
12 ROOTDEPTH 74 0.3 2.
13 SWCGERMIN 87 0.2 0.9
14 NH4MOBILEPROP 120 0.05 0.7

9
RBBGCMuso/man/musoSensi.Rd
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@ -4,10 +4,11 @@
\alias{musoSensi}
\title{musoSensi}
\usage{
musoSensi(monteCarloFile = NULL, parameters, settings = NULL,
inputDir = "./", outLoc = "./calib", iterations = 30,
preTag = "mont-", outputType = "moreCsv", fun = mean, varIndex = 1,
outputFile = "sensitivity.csv", plotName = "sensitivity")
musoSensi(monteCarloFile = NULL, parameters = NULL, settings = NULL,
parametersFromFile = FALSE, inputDir = "./", outLoc = "./calib",
iterations = 30, preTag = "mont-", outputType = "moreCsv", fun = mean,
varIndex = 1, outputFile = "sensitivity.csv",
plotName = "sensitivity.png", plotTitle = "Sensitivity", dpi = 300)
}
\arguments{
\item{monteCarloFile}{If you run musoMonte function previously, you did not have to rerun the monteCarlo, just provide the preservedEpc.csv file with its path. If you do not set this parameter, musoSensi will fun the musoMonte function to get all of the information.}