Merge pull request #1 from JetteReeg/Initialize-Model

first running version of BiTZ

.gitignore

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+# This file is used to ignore files which are generated
+# ----------------------------------------------------------------------------
+
+*~
+*.autosave
+*.a
+*.core
+*.moc
+*.o
+*.obj
+*.orig
+*.rej
+*.so
+*.so.*
+*_pch.h.cpp
+*_resource.rc
+*.qm
+.#*
+*.*#
+core
+!core/
+tags
+.DS_Store
+.directory
+*.debug
+Makefile*
+*.prl
+*.app
+moc_*.cpp
+ui_*.h
+qrc_*.cpp
+Thumbs.db
+*.res
+*.rc
+/.qmake.cache
+/.qmake.stash
+
+# qtcreator generated files
+*.pro.user*
+
+# xemacs temporary files
+*.flc
+
+# Vim temporary files
+.*.swp
+
+# Visual Studio generated files
+*.ib_pdb_index
+*.idb
+*.ilk
+*.pdb
+*.sln
+*.suo
+*.vcproj
+*vcproj.*.*.user
+*.ncb
+*.sdf
+*.opensdf
+*.vcxproj
+*vcxproj.*
+
+# MinGW generated files
+*.Debug
+*.Release
+
+# Python byte code
+*.pyc
+
+# Binaries
+# --------
+*.dll
+*.exe
+

Analyse.R

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+require(ggplot2)
+require(ggthemes)
+require(data.table)
+data<-fread("GridOut_1.txt", header=T)
+data<-data[FT_ID!=0,]
+setkey(data, Year, FT_ID, LU_ID)
+data[LU_ID==0,LU:="bare"]
+data[LU_ID==1,LU:="arable"]
+data[LU_ID==2,LU:="forest"]
+data[LU_ID==3,LU:="grassland"]
+data[LU_ID==4,LU:="urban"]
+data[LU_ID==5,LU:="water"]
+data1<-data[,.(mean=mean(Popsize), sd=sd(Popsize)),by=.(Year, FT_ID, LU_ID, LU)]
+g1<-ggplot(data=data1, aes(y=mean, x=Year)) +
+  geom_line(aes( color=factor(FT_ID))) +
+  facet_wrap(~LU, scales="free")
+
+data<-fread("GridOut.txt", header=T)
+data<-data[FT_ID!=0,]
+data<-data[FT_ID!=107998672,]
+data<-data[FT_ID!=1225530629,]
+setkey(data, Year, FT_ID, LU_ID)
+data[LU_ID==0,LU:="bare"]
+data[LU_ID==1,LU:="arable"]
+data[LU_ID==2,LU:="forest"]
+data[LU_ID==3,LU:="grassland"]
+data[LU_ID==4,LU:="urban"]
+data[LU_ID==5,LU:="water"]
+data1<-data[,.(mean=mean(Popsize), sd=sd(Popsize)),by=.(Year, FT_ID, LU_ID, LU)]
+g2<-ggplot(data=data1, aes(y=mean, x=Year)) +
+  geom_line(aes( color=factor(FT_ID))) +
+  facet_wrap(~LU)

BiTZ.pro

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+QT -= gui
+
+CONFIG += c++11 console
+CONFIG -= app_bundle
+
+# The following define makes your compiler emit warnings if you use
+# any Qt feature that has been marked deprecated (the exact warnings
+# depend on your compiler). Please consult the documentation of the
+# deprecated API in order to know how to port your code away from it.
+DEFINES += QT_DEPRECATED_WARNINGS
+
+# You can also make your code fail to compile if it uses deprecated APIs.
+# In order to do so, uncomment the following line.
+# You can also select to disable deprecated APIs only up to a certain version of Qt.
+#DEFINES += QT_DISABLE_DEPRECATED_BEFORE=0x060000    # disables all the APIs deprecated before Qt 6.0.0
+
+SOURCES += \
+        cell.cpp \
+        ft_pop.cpp \
+        ft_traits.cpp \
+        gridenvironment.cpp \
+        lcg.cpp \
+        main.cpp \
+        runparameter.cpp \
+        runtimeenvironment.cpp
+
+# Default rules for deployment.
+qnx: target.path = /tmp/$${TARGET}/bin
+else: unix:!android: target.path = /opt/$${TARGET}/bin
+!isEmpty(target.path): INSTALLS += target
+
+HEADERS += \
+    cell.h \
+    ft_pop.h \
+    ft_traits.h \
+    gridenvironment.h \
+    lcg.h \
+    runparameter.h \
+    runtimeenvironment.h

First_Sim/Analyse.R

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+# required packages
+require(ggplot2)
+require(ggthemes)
+require(data.table)
+
+# read in simulation file
+scenarios<-fread("Simulations.txt", header=T)
+data_container<-data.table()
+
+# read in data
+for (z in min(scenarios$SimNb):max(scenarios$SimNb)){
+  data<-fread(paste("GridOut_", z, ".txt", sep=""), header=T)
+  data[,TZ_width:=scenarios[SimNb==z,TZ_width]]
+  data[,disturbances:=scenarios[SimNb==z,disturbances]]
+  repetitions <- c()
+  for (i in 1:scenarios[SimNb==z,Nrep]){
+    repetitions = c(repetitions, rep(i,nrow(data)/scenarios[SimNb==z,Nrep]))
+    }
+  data[,repetition:=repetitions]
+  l<-list(data_container,data)
+  data_container=rbindlist(l)
+}
+
+setkey(data_container, Year, FT_ID, LU_ID, repetition)
+data_container[LU_ID==0,LU:="bare"]
+data_container[LU_ID==1,LU:="arable"]
+data_container[LU_ID==2,LU:="forest"]
+data_container[LU_ID==3,LU:="grassland"]
+data_container[LU_ID==4,LU:="urban"]
+data_container[LU_ID==5,LU:="water"]
+data<-data_container[,.(mean=mean(Popsize), sd=sd(Popsize)),by=.(Year, FT_ID, LU_ID, LU, TZ_width, disturbances)]
+data2<-data_container[,.(mean=mean(Popsize), sd=sd(Popsize)),by=.(Year, LU_ID, LU, TZ_width, disturbances)]
+
+# calculate nb_FT/land use type
+tmp<-data_container[Popsize!=0,]
+tmp <- tmp[,.(nb_FT=length(Popsize), totalN=sum(Popsize)),by=.(Year, LU_ID, LU, TZ_width, disturbances, repetition)]
+setkey(data_container, Year, FT_ID, LU_ID, LU, repetition, TZ_width, disturbances) 
+setkey(tmp, Year, LU_ID, LU, repetition, TZ_width, disturbances) 
+test<-merge(tmp,data_container)
+test<-test[Popsize!=0,]
+test[,pi:=Popsize/totalN]
+test<-test[,.(div=-sum(pi*log(pi))),by=.(Year, LU_ID, LU, TZ_width, disturbances, repetition, nb_FT, totalN)]
+data.com<-test[,.(mean.div=mean(div), sd.div=sd(div), mean.nb_FT=mean(nb_FT), sd.nb_FT=sd(nb_FT), mean.totalN=mean(totalN), sd.totalN=sd(totalN)),by=.(Year, LU_ID, LU, TZ_width, disturbances)]
+
+
+
+# read landscape configuration
+landscape<-fread("Patch_ID_definitions.txt", header=T)
+landscape_proportions<-landscape[,.(cumArea=sum(AREA)), by=.(TYPE)]
+totalArea=sum(landscape_proportions[,cumArea])
+landscape_proportions[,relativeArea:=cumArea/totalArea]
+landscape_proportions[,LU:=TYPE]
+
+# merging
+setkey(data, Year, FT_ID, LU_ID, LU, TZ_width, disturbances)
+setkey(data.com, Year, LU_ID, LU, TZ_width, disturbances)
+setkey(landscape_proportions, TYPE, LU)
+data3<-merge(data, landscape_proportions)
+data3[,relPop:=mean/cumArea]
+
+data4<-merge(data.com, landscape_proportions)
+data4[,relPop:=mean/cumArea]
+
+relPop1<-ggplot(data=data3[LU!="water"&FT_ID<9]) +
+  theme_few() +
+  geom_line(aes(x=Year, y=relPop, colour=factor(TZ_width), linetype=factor(disturbances))) +
+  ylab("nb individuals/ha") +
+  facet_grid(LU~FT_ID, scales="free")
+ ggsave("relPop1.png", relPop1)
+relPop2<-ggplot(data=data3[LU!="water"&FT_ID>=9]) +
+  theme_few() +
+  geom_line(aes(x=Year, y=relPop, colour=factor(TZ_width), linetype=factor(disturbances))) +
+  ylab("nb individuals/ha") +
+  facet_grid(LU~FT_ID, scales="free")
+ggsave("relPop2.png", relPop2)
+
+div<-ggplot(data=data.com) +
+  theme_few() +
+  geom_line(aes(x=Year, y=mean.div, colour=factor(TZ_width), linetype=factor(disturbances))) +
+  geom_ribbon(aes(x=Year, ymin=mean.div-sd.div, ymax=mean.div+sd.div, group=factor(TZ_width+disturbances)), alpha=0.1) +
+  ylab("mean diversity") +
+  facet_wrap(~LU, scales="free")
+ggsave("Shannon.png", div)
+
+nb_FT<-ggplot(data=data.com) +
+  theme_few() +
+  geom_line(aes(x=Year, y=mean.nb_FT, colour=factor(TZ_width), linetype=factor(disturbances))) +
+  geom_ribbon(aes(x=Year, ymin=mean.nb_FT-sd.nb_FT, ymax=mean.nb_FT+sd.nb_FT, group=factor(TZ_width+disturbances)), alpha=0.1) +
+  ylab("mean number of FT") +
+  facet_wrap(~LU, scales="free")
+ggsave("NB_FT.png", nb_FT)
+
+totalN<-ggplot(data=data.com) +
+  theme_few() +
+  geom_line(aes(x=Year, y=mean.totalN, colour=factor(TZ_width), linetype=factor(disturbances))) +
+  geom_ribbon(aes(x=Year, ymin=mean.totalN-sd.totalN, ymax=mean.totalN+sd.totalN, group=factor(TZ_width+disturbances)), alpha=0.1) +
+  ylab("mean total N") +
+  facet_wrap(~LU, scales="free")
+ggsave("totalN.png", totalN)
+
+
+
+
+
+
+g<-ggplot(data=data[LU=="arable",]) +
+  geom_line(aes(x=Year, y=mean, colour=factor(TZ_width), linetype=factor(disturbances))) +
+  facet_wrap(~FT_ID, scales="free")
+
+g<-ggplot(data=data[LU=="grassland",]) +
+  geom_line(aes(x=Year, y=mean, colour=factor(TZ_width), linetype=factor(disturbances))) +
+  facet_wrap(~FT_ID, scales="free")