# Path to results
path.results<-"C:/Users/cpacioni/Documents/Wild dogs/NorthernArea/NorthernArea_Analysis_May2016/Dingo200IterAnalysis/Analysis_strategic_baiting"

library("HexSimR")


#  ***NOTE***
# I have been removing or pasting in the folders for the ST depending on whether
# I wanted to have these data in the outputs. 
# ***********


#### Genetics ####
# batch file to generate genepop files. Pass this to OutputTransformer.exe
w.genepop.batch (path.results, scenarios="all", time.steps=c(30), 
                 pop.name="Dingoes", traits="PopID")

system.time(
multi.clean.genepop(path.results, scenarios="all", pop.name="Dingoes")
)

# Calculate genetic distance
system.time(
multi.gen.dist(path.results, scenarios="all", pop.name="Dingoes")
)

# calculate mean genetic distance
system.time(
m.gen.dist(path.results, scenarios = "all", pop.name="Dingoes", traits="PopID")
)


# Genetic distance plot
p<-gen.plot(path.results = path.results, pop.name = "Dingoes", time.step = 30,
         traits = "PopID")

load(paste(path.results, "plot_gen_distance.rda", sep="/"))
library(ggplot2)
s<-c("DingoBase_Bait_Shoot05_Ag_hi", 
     "DingoBase_Bait_Shoot05_Ag_low", 
     "DingoBase",
     "DingoBase_Bait_Shoot10", 
     "DingoBase_Bait_Shoot05", 
     "DingoBase_Shoot10",
     "DingoBase_Shoot05", 
     "DingoBaseSBF_Bait_Shoot05_Ag_hi", 
     "DingoBaseSBF_Bait_Shoot05_Ag_low",
     "DingoBaseSBF_Strat_Bait_shoot5", # Strat baiting
     "DingoBaseSBF", 
     "DingoBaseSBF_Bait_Shoot10", 
     "DingoBaseSBF_Bait_Shoot05",
     "DingoBaseSBF_Shoot10", 
     "DingoBaseSBF_Shoot05", 
     "DingoBaseSBF_Strat_Bait_shoot10", # Strat baiting
     "DingoBaseSBF02_Bait_Shoot05_Ag_hi",
     "DingoBaseSBF02_Bait_Shoot05_Ag_low", 
     "DingoBaseSBF02", 
     "DingoBaseSBF02_Bait_Shoot10",
     "DingoBaseSBF02_Bait_Shoot05", 
     "DingoBaseSBF02_Shoot10", 
     "DingoBaseSBF02_Shoot05",
     "DingoBaseSBF05_Bait_Shoot05_Ag_hi", 
     "DingoBaseSBF05_Bait_Shoot05_Ag_low",
     "DingoBaseSBF05",
     "DingoBaseSBF05_Bait_Shoot10",
     "DingoBaseSBF05_Bait_Shoot05",
     "DingoBaseSBF05_Shoot10",
     "DingoBaseSBF05_Shoot05") 
p[[1]]$Scenario<-s

new_ord<-c("DingoBase", 
           "DingoBaseSBF05", 
           "DingoBaseSBF02", 
           "DingoBaseSBF", 
           
           "DingoBase_Shoot05", 
           "DingoBaseSBF05_Shoot05", 
           "DingoBaseSBF02_Shoot05", 
           "DingoBaseSBF_Shoot05", 
           
           "DingoBase_Shoot10",
           "DingoBaseSBF05_Shoot10",
           "DingoBaseSBF02_Shoot10",
           "DingoBaseSBF_Shoot10",
           
           "DingoBase_Bait_Shoot05",
           "DingoBaseSBF05_Bait_Shoot05",
           "DingoBaseSBF02_Bait_Shoot05",
           "DingoBaseSBF_Bait_Shoot05",
           
           "DingoBase_Bait_Shoot10",
           "DingoBaseSBF05_Bait_Shoot10",
           "DingoBaseSBF02_Bait_Shoot10",
           "DingoBaseSBF_Bait_Shoot10",
           
           "DingoBase_Bait_Shoot05_Ag_low",
           "DingoBaseSBF05_Bait_Shoot05_Ag_low",
           "DingoBaseSBF02_Bait_Shoot05_Ag_low",
           "DingoBaseSBF_Bait_Shoot05_Ag_low",
           
           "DingoBase_Bait_Shoot05_Ag_hi", 
           "DingoBaseSBF05_Bait_Shoot05_Ag_hi", 
           "DingoBaseSBF02_Bait_Shoot05_Ag_hi", 
           "DingoBaseSBF_Bait_Shoot05_Ag_hi",
           "DingoBaseSBF_Strat_Bait_shoot5", # strat baiting
           "DingoBaseSBF_Strat_Bait_shoot10")

p[[1]]$Scenario<-factor(p[[1]]$Scenario, levels=new_ord)
p
g<-p + theme_classic() + 
  ylab("Mean genetic distance") + 
  theme(legend.position="none", 
        axis.text.x=element_text(angle=-90, hjust=0, vjust=0.3)) +
  theme(axis.line.x = element_line(color="black", size = 0.5),
        axis.line.y = element_line(color="black", size = 0.5))
# The last line is needed because of a bug in ggplot2.1
g

dir_out<-"C:/Users/cpacioni/Documents/Wild dogs/NorthernArea/NorthernArea_Analysis_May2016/Dingo200IterAnalysis/Plots_strategic_baiting"
dir.create(dir_out)
ggsave(paste0(dir_out, "/", "plot_gen_dist_sorted.pdf"), plot=g, 
       heigh=297, width=210, unit="mm")

ggsave(paste0(dir_out, "/", "plot_gen_dist_sorted.jpeg"), plot=g, 
       heigh=297, width=210, unit="mm")

#### Reports ####
# batch file to generate combined log files. Pass this to HexSimCommandLine.exe
w.combine.log.batch(path.results, scenarios="all", dir.out=path.results)

# Generate batch file for move and ranges reports. Pass this to OutputTransformer.exe
system.time(
report.batch(path.results, scenarios="all", ranges=TRUE, move=TRUE)
)

# After reports are generated...
multi.reports(path.results, scenarios="all", pop.name="Dingoes", 
                      type="move", all=TRUE, hx=NULL, events=NULL, 
                      start="min", end="max") 

multi.reports(path.results, scenarios="all", pop.name="Dingoes", 
                     type="ranges", all=TRUE, hx=1122.4, 
                     events=c("Lonersexplore", "Adjustterritories2"), 
                     start="min", end="max") 
system.time(
SSMD.ranges(path.results, scenarios="all", base="DingoBase_SelDist", 
                       sum.ranges="summary_ranges.xlsx")
)

# I had run SSMD.move but I then discarded these because they were all not-sign

#### Invasion front ####
invasion.front(path.results, ncensus=3, value = 1, patch.width=3.6*4,
               scenarios = "all")
p <- invasion.plot(fname = paste(path.results, "Invasion.front.xlsx", sep="/"))

load(paste(path.results, "plot_invasion.rda",sep="/"))
library(ggplot2)
s<-c("DingoBase" ,                  "DingoBase_Bait_Shoot10" ,    
 "DingoBase_Bait_Shoot05" ,      "DingoBase_Shoot10"  ,        
 "DingoBase_Shoot05"   ,         "DingoBaseSBF"    ,           
 "DingoBaseSBF_Bait_Shoot10",   "DingoBaseSBF_Bait_Shoot05"  , 
 "DingoBaseSBF_Shoot10",        "DingoBaseSBF_Shoot05"     ,   
 "DingoBaseSBF02" ,             "DingoBaseSBF02_Bait_Shoot10",
 "DingoBaseSBF02_Bait_Shoot05" , "DingoBaseSBF02_Shoot10" ,    
 "DingoBaseSBF02_Shoot05",       "DingoBase_PreEmpt50" ,      
 "DingoBase_STSurvival",        "DingoBase_Bait_Shoot05_Ag_hi"  ,  
 "DingoBase_Bait_Shoot05_Ag_low",      "DingoBaseSBF_Bait_Shoot05_Ag_hi" ,
 "DingoBaseSBF_Bait_Shoot05_Ag_low",   "DingoBaseSBF02_Bait_Shoot05_Ag_hi" ,
 "DingoBaseSBF02_Bait_Shoot05_Ag_low", "DingoBaseSBF05_Bait_Shoot05_Ag_hi" ,
 "DingoBaseSBF05_Bait_Shoot05_Ag_low", "DingoBaseSBF05"  ,           
 "DingoBaseSBF05_Bait_Shoot10", "DingoBaseSBF05_Bait_Shoot05" ,
 "DingoBaseSBF05_Shoot10",      "DingoBaseSBF05_Shoot05",
 "DingoBaseSBF_Strat_Bait_shoot5", "DingoBaseSBF_Strat_Bait_shoot10") 
p[[1]]$Scenario<-s

new_ord<-c("DingoBase_STSurvival", 
           "DingoBase_PreEmpt50",
           # end of ST
           
           "DingoBase", 
           "DingoBaseSBF05", 
           "DingoBaseSBF02", 
           "DingoBaseSBF", 
           
           "DingoBase_Shoot05", 
           "DingoBaseSBF05_Shoot05", 
           "DingoBaseSBF02_Shoot05", 
           "DingoBaseSBF_Shoot05", 
           
           "DingoBase_Shoot10",
           "DingoBaseSBF05_Shoot10",
           "DingoBaseSBF02_Shoot10",
           "DingoBaseSBF_Shoot10",
           
           "DingoBase_Bait_Shoot05",
           "DingoBaseSBF05_Bait_Shoot05",
           "DingoBaseSBF02_Bait_Shoot05",
           "DingoBaseSBF_Bait_Shoot05",
           
           "DingoBase_Bait_Shoot10",
           "DingoBaseSBF05_Bait_Shoot10",
           "DingoBaseSBF02_Bait_Shoot10",
           "DingoBaseSBF_Bait_Shoot10",
           
           "DingoBase_Bait_Shoot05_Ag_low",
           "DingoBaseSBF05_Bait_Shoot05_Ag_low",
           "DingoBaseSBF02_Bait_Shoot05_Ag_low",
           "DingoBaseSBF_Bait_Shoot05_Ag_low",
           
           "DingoBase_Bait_Shoot05_Ag_hi", 
           "DingoBaseSBF05_Bait_Shoot05_Ag_hi", 
           "DingoBaseSBF02_Bait_Shoot05_Ag_hi", 
           "DingoBaseSBF_Bait_Shoot05_Ag_hi",
           "DingoBaseSBF_Strat_Bait_shoot5",
           "DingoBaseSBF_Strat_Bait_shoot10")

p[[1]]$Scenario<-factor(p[[1]]$Scenario, levels=new_ord)
p
g<-p + theme_classic() + 
  ylab("Mean km/year") + 
  theme(legend.position="none", 
        axis.text.x=element_text(angle=-90, hjust=0, vjust=0.3)) +
  theme(axis.line.x = element_line(color="black", size = 0.5),
        axis.line.y = element_line(color="black", size = 0.5))
# The last line is needed because of a bug in ggplot2.1
g

ggsave(paste0(dir_out, "/", "plot_invasion_sorted.pdf"), plot=g, 
       heigh=297, width=210, unit="mm")

ggsave(paste0(dir_out, "/", "plot_invasion_sorted.jpg"), plot=g, dpi=300,
       heigh=297, width=210, unit="mm")


#### census file calculations ####
#### total pop size inside and outside #### 
temp <- census.calc(path.results, ncensus=2, 
                     headers=c("Trait Index  2", "Trait Index  3"), 
                     var.name = "Inside", bin.f = "+", scenarios = "all")
temp<-census.calc(path.results, ncensus=2, headers=c("Trait Index  4", "Trait Index  5"), 
            var.name = "Outside", bin.f = "+", scenarios = "all")

# Proportion of floaters
temp<-census.calc(path.results, ncensus=2, headers=c("Trait Index  2", "Inside"), 
            var.name = "PropFloat_In", bin.f = "/", scenarios = "all")
temp<-census.calc(path.results, ncensus=2, headers=c("Trait Index  4", "Outside"), 
            var.name = "PropFloat_Out", bin.f = "/", scenarios = "all")


#### By gender#### 
#### Pre_breeding #### 
# Sum by gender
temp<-census.calc(path.results, ncensus=0, 
            headers=c("Trait Index  6", "Trait Index  7", 
                      "Trait Index 18", "Trait Index 19", 
                      "Trait Index 30", "Trait Index 31"), 
            var.name = "Males_In", bin.f = "+", scenarios = "all")

temp<-census.calc(path.results, ncensus=0, 
            headers=c("Trait Index 10", "Trait Index 11", 
                      "Trait Index 22", "Trait Index 23", 
                      "Trait Index 34", "Trait Index 35"), 
            var.name = "Males_Out", bin.f = "+", scenarios = "all")

temp<-census.calc(path.results, ncensus=0, 
            headers=c("Trait Index  4", "Trait Index  5", 
                      "Trait Index 16", "Trait Index 17", 
                      "Trait Index 28", "Trait Index 29"), 
            var.name = "Females_In", bin.f = "+", scenarios = "all")

temp<-census.calc(path.results, ncensus=0, 
            headers=c("Trait Index  8", "Trait Index  9", 
                      "Trait Index 20", "Trait Index 21", 
                      "Trait Index 32", "Trait Index 33"), 
            var.name = "Females_Out", bin.f = "+", scenarios = "all")

# Floaters
temp<-census.calc(path.results, ncensus=0, 
            headers=c("Trait Index  6",  
                      "Trait Index 18",  
                      "Trait Index 30"), 
            var.name = "MalesFlo_In", bin.f = "+", scenarios = "all")

temp<-census.calc(path.results, ncensus=0, 
            headers=c("Trait Index 10",  
                      "Trait Index 22",  
                      "Trait Index 34"),
            var.name = "MalesFlo_Out", bin.f = "+", scenarios = "all")

temp<-census.calc(path.results, ncensus=0, 
            headers=c("Trait Index  4",  
                      "Trait Index 16",  
                      "Trait Index 28"), 
            var.name = "FemalesFlo_In", bin.f = "+", scenarios = "all")

temp<-census.calc(path.results, ncensus=0, 
            headers=c("Trait Index  8",  
                      "Trait Index 20",  
                      "Trait Index 32"), 
            var.name = "FemalesFlo_Out", bin.f = "+", scenarios = "all")

temp<-census.calc(path.results, ncensus=0, 
            headers=c("MalesFlo_In",  "Males_In"), 
            var.name = "PropMalesFlo_In", bin.f = "/", scenarios = "all")

temp<-census.calc(path.results, ncensus=0, 
            headers=c("MalesFlo_Out",  "Males_Out"),
            var.name = "PropMalesFlo_Out", bin.f = "/", scenarios = "all")

temp<-census.calc(path.results, ncensus=0, 
            headers=c("FemalesFlo_In",  "Females_In"), 
            var.name = "PropFemalesFlo_In", bin.f = "/", scenarios = "all")

temp<-census.calc(path.results, ncensus=0, 
            headers=c("FemalesFlo_Out",  "Females_Out"), 
            var.name = "PropFemalesFlo_Out", bin.f = "/", scenarios = "all")

temp<-census.calc(path.results, ncensus=0, 
            headers=c("Trait Index 30",  "Males_In"), 
            var.name = "PropAdMalesFlo_In", bin.f = "/", scenarios = "all")

temp<-census.calc(path.results, ncensus=0, 
            headers=c("Trait Index 34",  "Males_Out"),
            var.name = "PropAdMalesFlo_Out", bin.f = "/", scenarios = "all")

temp<-census.calc(path.results, ncensus=0, 
            headers=c("Trait Index 28",  "Females_In"), 
            var.name = "PropAdFemalesFlo_In", bin.f = "/", scenarios = "all")

temp<-census.calc(path.results, ncensus=0, 
            headers=c("Trait Index 32",  "Females_Out"), 
            var.name = "PropAdFemalesFlo_Out", bin.f = "/", scenarios = "all")


# Sex-ratios
temp<-census.calc(path.results, ncensus=0, 
            headers=c("Males_In", "Females_In"), 
            var.name = "SexRatio_In", bin.f = "/", scenarios = "all")

temp<-census.calc(path.results, ncensus=0, 
            headers=c("Males_Out", "Females_Out"), 
            var.name = "SexRatio_Out", bin.f = "/", scenarios = "all")



#### By gender  #### 
#### Post_breeding #### 
# Sum by gender
temp<-census.calc(path.results, ncensus=1, 
            headers=c("Trait Index  6", "Trait Index  7", 
                      "Trait Index 18", "Trait Index 19", 
                      "Trait Index 30", "Trait Index 31"), 
            var.name = "Males_In", bin.f = "+", scenarios = "all")

temp<-census.calc(path.results, ncensus=1, 
            headers=c("Trait Index 10", "Trait Index 11", 
                      "Trait Index 22", "Trait Index 23", 
                      "Trait Index 34", "Trait Index 35"), 
            var.name = "Males_Out", bin.f = "+", scenarios = "all")

temp<-census.calc(path.results, ncensus=1, 
            headers=c("Trait Index  4", "Trait Index  5", 
                      "Trait Index 16", "Trait Index 17", 
                      "Trait Index 28", "Trait Index 29"), 
            var.name = "Females_In", bin.f = "+", scenarios = "all")

temp<-census.calc(path.results, ncensus=1, 
            headers=c("Trait Index  8", "Trait Index  9", 
                      "Trait Index 20", "Trait Index 21", 
                      "Trait Index 32", "Trait Index 33"), 
            var.name = "Females_Out", bin.f = "+", scenarios = "all")

# Floaters
temp<-census.calc(path.results, ncensus=1, 
            headers=c("Trait Index  6",  
                      "Trait Index 18",  
                      "Trait Index 30"), 
            var.name = "MalesFlo_In", bin.f = "+", scenarios = "all")

temp<-census.calc(path.results, ncensus=1, 
            headers=c("Trait Index 10",  
                      "Trait Index 22",  
                      "Trait Index 34"),
            var.name = "MalesFlo_Out", bin.f = "+", scenarios = "all")

temp<-census.calc(path.results, ncensus=1, 
            headers=c("Trait Index  4",  
                      "Trait Index 16",  
                      "Trait Index 28"), 
            var.name = "FemalesFlo_In", bin.f = "+", scenarios = "all")

temp<-census.calc(path.results, ncensus=1, 
            headers=c("Trait Index  8",  
                      "Trait Index 20",  
                      "Trait Index 32"), 
            var.name = "FemalesFlo_Out", bin.f = "+", scenarios = "all")

temp<-census.calc(path.results, ncensus=1, 
            headers=c("MalesFlo_In",  "Males_In"), 
            var.name = "PropMalesFlo_In", bin.f = "/", scenarios = "all")

temp<-census.calc(path.results, ncensus=1, 
            headers=c("MalesFlo_Out",  "Males_Out"),
            var.name = "PropMalesFlo_Out", bin.f = "/", scenarios = "all")

temp<-census.calc(path.results, ncensus=1, 
            headers=c("FemalesFlo_In",  "Females_In"), 
            var.name = "PropFemalesFlo_In", bin.f = "/", scenarios = "all")

temp<-census.calc(path.results, ncensus=1, 
            headers=c("FemalesFlo_Out",  "Females_Out"), 
            var.name = "PropFemalesFlo_Out", bin.f = "/", scenarios = "all")

temp<-census.calc(path.results, ncensus=1, 
            headers=c("Trait Index 30",  "Males_In"), 
            var.name = "PropAdMalesFlo_In", bin.f = "/", scenarios = "all")

temp<-census.calc(path.results, ncensus=1, 
            headers=c("Trait Index 34",  "Males_Out"),
            var.name = "PropAdMalesFlo_Out", bin.f = "/", scenarios = "all")

temp<-census.calc(path.results, ncensus=1, 
            headers=c("Trait Index 28",  "Females_In"), 
            var.name = "PropAdFemalesFlo_In", bin.f = "/", scenarios = "all")

temp<-census.calc(path.results, ncensus=1, 
            headers=c("Trait Index 32",  "Females_Out"), 
            var.name = "PropAdFemalesFlo_Out", bin.f = "/", scenarios = "all")


# Sex-ratios
temp<-census.calc(path.results, ncensus=1, 
            headers=c("Males_In", "Females_In"), 
            var.name = "SexRatio_In", bin.f = "/", scenarios = "all")

temp<-census.calc(path.results, ncensus=1, 
            headers=c("Males_Out", "Females_Out"), 
            var.name = "SexRatio_Out", bin.f = "/", scenarios = "all")

#### Collate and plot census ####
system.time(
collate.census(path.results, scenarios="all")
)

# Plot census
# ST
ST<-c("DingoBase_SelDist", "DingoBase_SelDist_STSurvival", 
      "DingoBase_SelDist_PreEmpty50")
census.plot(path.results, scenarios=ST, traits=c("Inside", "Outside"), 
            ncensus=2, ngroups=1)
census.plot(path.results, scenarios=ST, traits=c("PropFloat_In", "PropFloat_Out"), 
            ncensus=2, ngroups=1)

load("C:/Users/30373314/Documents/DAFWA/Wild dogs/PVA/Analysis/Dingo200IterAnalysis/Plots_ST/plots_census.2.group.1.rda")
library(ggplot2)
unique(p[[1]]$Scenario)
p[[1]]$Scenario[p[[1]]$Scenario=="DingoBase_SelDist"]<-"DingoBase"
p[[1]]$Scenario[p[[1]]$Scenario=="DingoBase_SelDist_STSurvival"]<-"DingoBase_STSurvival"
p[[1]]$Scenario[p[[1]]$Scenario=="DingoBase_SelDist_PreEmpty50"]<-"DingoBase_PreEmpt50"
new_ord<-c("DingoBase_STSurvival", 
           "DingoBase_PreEmpt50",
           "DingoBase")

p[[1]]$Scenario<-factor(p[[1]]$Scenario, levels=new_ord)
p
g<-p + theme_classic() + 
  ylab("Mean population size") + 
  theme(legend.position="none") 
g
dir_out<-"C:/Users/30373314/Documents/DAFWA/Wild dogs/PVA/Analysis/Dingo200IterAnalysis/Plots_ST"
ggsave(paste0(dir_out, "/", "plots_census.ST_sorted.pdf"), plot=g, 
       heigh=80, width=150, unit="mm")
ggsave(paste0(dir_out, "/", "plots_census.ST_sorted.jpeg"), plot=g, dpi=300, 
       heigh=80, width=150, unit="mm")

# note: I have removed the two ST folders to generate the plots without them 
p<-census.plot(path.results, scenarios="all", traits=c("Inside", "Outside"), 
                ncensus=2, ngroups=4)
p<-census.plot(path.results, scenarios="all", traits=c("PropFloat_In", "PropFloat_Out"), 
                ncensus=2, ngroups=4)

load("C:/Users/30373314/Documents/DAFWA/Wild dogs/PVA/Analysis/Dingo200IterAnalysis/Plots/Plots.census/plots_census.2.group.2.rda")
library(ggplot2)
unique(p[[1]]$Scenario)
p[[1]]$Scenario[p[[1]]$Scenario=="DingoBaseSBF_SD_Bait_shoot5_aghi"]<-"DingoBaseSBF_Bait_Shoot05_Ag_hi"
p[[1]]$Scenario[p[[1]]$Scenario=="DingoBaseSBF_SD_Bait_shoot5_aglow"]<-"DingoBaseSBF_Bait_Shoot05_Ag_low"
p[[1]]$Scenario[p[[1]]$Scenario=="DingoBaseSBF_SelDist"]<-"DingoBaseSBF"
p[[1]]$Scenario[p[[1]]$Scenario=="DingoBaseSBF_SelDist_Bait_shoot10"]<-"DingoBaseSBF_Bait_Shoot10"
p[[1]]$Scenario[p[[1]]$Scenario=="DingoBaseSBF_SelDist_Bait_shoot5"]<-"DingoBaseSBF_Bait_Shoot05" 
p[[1]]$Scenario[p[[1]]$Scenario=="DingoBaseSBF_SelDist_shoot10"]<-"DingoBaseSBF_Shoot10"
p[[1]]$Scenario[p[[1]]$Scenario=="DingoBaseSBF_SelDist_shoot5"]<-"DingoBaseSBF_Shoot05"      
new_ord<-c("DingoBaseSBF_Bait_Shoot05_Ag_hi", 
           "DingoBaseSBF_Bait_Shoot05_Ag_low",
           "DingoBaseSBF_Bait_Shoot05",
           "DingoBaseSBF_Bait_Shoot10",
           "DingoBaseSBF_Shoot05",
           "DingoBaseSBF_Shoot10",
           "DingoBaseSBF")

p[[1]]$Scenario<-factor(p[[1]]$Scenario, levels=new_ord)
p
g<-p + theme_classic() + 
  ylab("Mean population size") + 
  theme(legend.position="none") 
g
dir_out<-"C:/Users/30373314/Documents/DAFWA/Wild dogs/PVA/Analysis/Dingo200IterAnalysis/Plots/Plots.census"
ggsave(paste0(dir_out, "/", "plots_census.SBF.pdf"), plot=g, 
       heigh=297, width=210, unit="mm")
pres<-p + ylab("Mean population size") 
pres
ggsave(paste0(dir_out, "/", "plots_census.SBF.pres.jpeg"), plot=pres, dpi=300,
       heigh=297, width=210, unit="mm")

# Prop Flot
load("C:/Users/30373314/Documents/DAFWA/Wild dogs/PVA/Analysis/Dingo200IterAnalysis/Plots/Plots_PropFlot/plots_census.2.group.2.rda")
p[[1]]$Scenario[p[[1]]$Scenario=="DingoBaseSBF_SD_Bait_shoot5_aghi"]<-"DingoBaseSBF_Bait_Shoot05_Ag_hi"
p[[1]]$Scenario[p[[1]]$Scenario=="DingoBaseSBF_SD_Bait_shoot5_aglow"]<-"DingoBaseSBF_Bait_Shoot05_Ag_low"
p[[1]]$Scenario[p[[1]]$Scenario=="DingoBaseSBF_SelDist"]<-"DingoBaseSBF"
p[[1]]$Scenario[p[[1]]$Scenario=="DingoBaseSBF_SelDist_Bait_shoot10"]<-"DingoBaseSBF_Bait_Shoot10"
p[[1]]$Scenario[p[[1]]$Scenario=="DingoBaseSBF_SelDist_Bait_shoot5"]<-"DingoBaseSBF_Bait_Shoot05" 
p[[1]]$Scenario[p[[1]]$Scenario=="DingoBaseSBF_SelDist_shoot10"]<-"DingoBaseSBF_Shoot10"
p[[1]]$Scenario[p[[1]]$Scenario=="DingoBaseSBF_SelDist_shoot5"]<-"DingoBaseSBF_Shoot05"  
p[[1]]$Scenario<-factor(p[[1]]$Scenario, levels=new_ord)
p
g<-p + theme_classic() + 
  ylab("Proportion of loners ") + 
  theme(legend.position="none") +
  theme(axis.line.x = element_line(color="black", size = 0.5),
        axis.line.y = element_line(color="black", size = 0.5))
# The last line is needed because of a bug in ggplot2.1

g 
dir_out<-"C:/Users/30373314/Documents/DAFWA/Wild dogs/PVA/Analysis/Dingo200IterAnalysis/Plots/Plots_PropFlot"
ggsave(paste0(dir_out, "/", "plots_PropFlot.SBF.pdf"), plot=g, 
       heigh=297, width=210, unit="mm")

ggsave(paste0(dir_out, "/", "plots_PropFlot.SBF.tiff"), plot=g, 
       heigh=297, width=210, unit="mm")

library(ggplot2)
p<-p[[1]]
unique(p[[1]]$Scenario)
p[[1]]$Scenario[p[[1]]$Scenario=="DingoBaseSBF_AD_Bait_shoot5_aghi"]<-"DingoBaseSBF_Bait_Shoot05_Ag_hi"
p[[1]]$Scenario[p[[1]]$Scenario=="DingoBaseSBF05_NoAgD_Bait_shoot5_aghi"]<-"DingoBaseSBF05_NoAg_Bait_Shoot05_Ag_hi"
new_ord<-c("DingoBaseSBF_Bait_Shoot05_Ag_hi", 
           "DingoBaseSBF05_NoAg_Bait_Shoot05_Ag_hi")

p[[1]]$Scenario<-factor(p[[1]]$Scenario, levels=new_ord)
p
g<-p + theme_classic() + 
  ylab("Mean population size") + 
  theme(legend.position="none") +
  theme(axis.line.x = element_line(color="black", size = 0.5),
        axis.line.y = element_line(color="black", size = 0.5))
g
dir_out<-path.results
ggsave(paste0(dir_out, "/", "plots_census.AD.pdf"), plot=g, 
       heigh=297, width=210, unit="mm")
ggsave(paste0(dir_out, "/", "plots_census.AD.jpeg"), plot=g, 
       heigh=110, width=161, unit="mm")
pres<-p + ylab("Mean population size") 
pres
ggsave(paste0(dir_out, "/", "plots_census.AD.pres.jpeg"), plot=g, dpi=300,
       heigh=297, width=210, unit="mm")

#### SSMD census #### 
# I first create some helper functions to process all ssdm at once for each group
# of comparisons
#######################Helper FUNs##########################
f.move<-function(f.name, wspace, dir.out) {
  file.copy(from=f.name, to=paste(wspace, dir.out, sep="/") )
}

apply.ssmd<-function(scen, path.results, ncs, suf, base) {
  lapply(ncs, SSMD.census, path.results=path.results, scenarios=scen, base=base)
  dir.out<-paste("SSMD.census", suf, sep=".")
  wspace <- sub(pattern = "Results", replacement = "", path.results)
  dir.create(paste(wspace, dir.out, sep="/"))
  file.list<-list.files(path = path.results, pattern = "^SSMD_census",
                        full.names = T)
  lapply(file.list, f.move, wspace, dir.out=dir.out)
  lapply(file.list, file.remove)  
}
#######################End Helper FUNs#########################
# ST
ncs <- 0:2
ST<-c("DingoBase_SelDist", "DingoBase_SelDist_STSurvival", 
      "DingoBase_SelDist_PreEmpty50")

system.time(       
  apply.ssmd(scen=ST, path.results, ncs, suf="ST", base=ST[1])
)

# Grouped by fence permeability
ncs <- 0:2
NoSBF<-c("DingoBase_SelDist" , "DingoBase_SelDist_Bait_shoot10", 
         "DingoBase_SelDist_Bait_shoot5", "DingoBase_SD_Bait_shoot5_aglow",
         "DingoBase_SD_Bait_shoot5_aghi", "DingoBase_SelDist_shoot10", 
         "DingoBase_SelDist_shoot5")
SBF<-c("DingoBaseSBF_SelDist", "DingoBaseSBF_SelDist_Bait_shoot10", 
       "DingoBaseSBF_SelDist_Bait_shoot5", "DingoBaseSBF_SD_Bait_shoot5_aglow",
       "DingoBaseSBF_SD_Bait_shoot5_aghi", "DingoBaseSBF_SelDist_shoot10",
       "DingoBaseSBF_SelDist_shoot5", "DingoBaseSBF_SD_Strat_Bait_shoot5", 
       "DingoBaseSBF_SelDist_Strat_Bait_shoot10")
SBF02<-c("DingoBaseSBF02_SelDist" , "DingoBaseSBF02_SelDist_Bait_shoot10", 
         "DingoBaseSBF02_SelDist_Bait_shoot5", "DingoBaseSBF02_SD_Bait_shoot5_aglow", 
         "DingoBaseSBF02_SD_Bait_shoot5_aghi", "DingoBaseSBF02_SelDist_shoot10", 
         "DingoBaseSBF02_SelDist_shoot5")
SBF05<-c("DingoBaseSBF05_SelDist", "DingoBaseSBF05_SelDist_Bait_shoot10", 
         "DingoBaseSBF05_SelDist_Bait_shoot5", "DingoBaseSBF05_SD_Bait_shoot5_aglow",
         "DingoBaseSBF05_SD_Bait_shoot5_aghi", "DingoBaseSBF05_SelDist_shoot10", 
         "DingoBaseSBF05_SelDist_shoot5")

system.time(       
apply.ssmd(scen="all", path.results, ncs, suf="all", base=SBF[1])
)
apply.ssmd(scen=NoSBF, path.results, ncs, suf="NoSBF", base=NoSBF[1])
apply.ssmd(scen=SBF, path.results, ncs, suf="SBF", base=SBF[1])
apply.ssmd(scen=SBF02, path.results, ncs, suf="SBF02", base=SBF02[1])
apply.ssmd(scen=SBF05, path.results, ncs, suf="SBF05", base=SBF05[1])

# Grouped by management option
ncs <- 0:2
NoControl<-c("DingoBase_SelDist", "DingoBaseSBF_SelDist", "DingoBaseSBF02_SelDist",
             "DingoBaseSBF05_SelDist")
             
Bait_shoot10<-c("DingoBase_SelDist_Bait_shoot10", "DingoBaseSBF_SelDist_Bait_shoot10",
                "DingoBaseSBF02_SelDist_Bait_shoot10", "DingoBaseSBF05_SelDist_Bait_shoot10")
                
Bait_shoot05<-c("DingoBase_SelDist_Bait_shoot5", "DingoBaseSBF_SelDist_Bait_shoot5",
                "DingoBaseSBF02_SelDist_Bait_shoot5", "DingoBaseSBF05_SelDist_Bait_shoot5")

Shoot10<-c("DingoBase_SelDist_shoot10", "DingoBaseSBF_SelDist_shoot10",
           "DingoBaseSBF02_SelDist_shoot10", "DingoBaseSBF05_SelDist_shoot10")
           
Shoot05<-c("DingoBase_SelDist_shoot5", "DingoBaseSBF_SelDist_shoot5",
           "DingoBaseSBF02_SelDist_shoot5", "DingoBaseSBF05_SelDist_shoot5")
Bait_shoot05_ag_low<-c("DingoBase_SD_Bait_shoot5_aglow", 
                       "DingoBaseSBF_SD_Bait_shoot5_aglow",
                       "DingoBaseSBF02_SD_Bait_shoot5_aglow", 
                       "DingoBaseSBF05_SD_Bait_shoot5_aglow")
Bait_shoot05_ag_hi<-c("DingoBase_SD_Bait_shoot5_aghi", 
                       "DingoBaseSBF_SD_Bait_shoot5_aghi",
                       "DingoBaseSBF02_SD_Bait_shoot5_aghi", 
                       "DingoBaseSBF05_SD_Bait_shoot5_aghi")

apply.ssmd(scen=NoControl, path.results, ncs, suf="NoControl", base=NoControl[1])
apply.ssmd(scen=Bait_shoot10, path.results, ncs, suf="Bait_shoot10", base=Bait_shoot10[1])
apply.ssmd(scen=Bait_shoot05, path.results, ncs, suf="Bait_shoot05", base=Bait_shoot05[1])
apply.ssmd(scen=Shoot10, path.results, ncs, suf="Shoot10", base=Shoot10[1])
apply.ssmd(scen=Shoot05, path.results, ncs, suf="Shoot05", base=Shoot05[1])
apply.ssmd(scen=Bait_shoot05_ag_low, path.results, ncs, suf="Bait_shoot05_ag_low", 
           base=Bait_shoot05_ag_low[1])
apply.ssmd(scen=Bait_shoot05_ag_hi, path.results, ncs, suf="Bait_shoot05_ag_hi", 
           base=Bait_shoot05_ag_hi[1])


#### Copy results #### 
# copy all SSMD_census in a saparate folder outside path.results
# These results don't have normal HexSimR layout because I have created them with
# a function (above) that removed the results as they were created into a folder
# because otherwise these would have been overwritten. I'll use this sub-folder 
# structure below to contruct the tables.
SSMD_census_fold<-"C:/Users/cpacioni/Documents/Wild dogs/NorthernArea/NorthernArea_Analysis_May2016/Dingo200IterAnalysis/SSMD.census_strategic_baiting"
dir.create(SSMD_census_fold)
setwd(path.results)
fold_lilst<-list.dirs()
fold_lilst<-fold_lilst[grep("SSMD.census*.", x = fold_lilst)]
file.copy(fold_lilst, to=SSMD_census_fold, recursive = T)
unlink(fold_lilst, recursive=T)

# Path to back up destination
dir.out<-"\\\\10.0.0.1\\Public\\Carlo\\DingoPVA\\Dingo200IterAnalysis\\Analysis"
copy.results(path.results, out = dir.out, copy.invasion = TRUE,
             comp.census = F, comp.move = F,
             comp.ranges = F,
             plots = T, scen.results = TRUE,
             scenarios = "all")


#### Make table ####
# Table descriptive results
table <- make.table(path.results, 
                    scenarios="all", 
                    fnames=paste0( 2:1, ".all.xlsx"), 
                    SSMD=FALSE, 
                    colh=list(c("Inside", "Outside", "PropFloat_In", "PropFloat_Out"),
                              c("SexRatio_In", "SexRatio_Out")),
                    vround=1, sdround=2, time.steps=c(5, 30), table.name="Tables.xlsx", 
                    tab.name="Dem_descrip", save2disk=TRUE, 
                    dir.out=NULL)


# The following four lines remove the base scenario
NoSBF<-NoSBF[-1]
SBF<-SBF[-1]
SBF02<-SBF02[-1]
SBF05<-SBF05[-1]

# This group the scenarios for each comparison in a list
g<-list(NoSBF, SBF, SBF02, SBF05)

# Creates a vector with the path where the SSMD_census subfolders are
path.SSMD.subfolders<-paste(SSMD_census_fold, fold_lilst[6:9], sep="/")

# The following creates a function that passes to make.table one element at the time 
# from g and path.SSMD.subfolders created above base on an index i
# NOTE that fence permeability is in the same order in g and path.SSMD.subfolders
# Also, note that file names and colh are hard coded, but these can be changed 
# wither in the function before sourcing it or programmatically
# (i.e. as function's arguments) 
pass.make.table <- function(i, path.SSMD.subfolders, g) {
                            make.table(path.results=path.SSMD.subfolders[i], 
                            scenarios=g[[i]], 
                            fnames=c("SSMD_census2.xlsx", "SSMD_census1.xlsx"), 
                            SSMD=TRUE, 
                            colh=list(c("Inside", "Outside", 
                                        "PropFloat_In", "PropFloat_Out"), 
                                      c("SexRatio_In", "SexRatio_Out")),
                            vround=3, sdround=3, time.steps=c(5,30), 
                            table.name="Tables.xlsx", 
                            tab.name="SSMD_dem", save2disk=TRUE, 
                            dir.out=NULL)
}

l<-lapply(1:4, pass.make.table, path.SSMD.subfolders, g)
# load data.table if not already
library(data.table)
data<-rbindlist(l, use.names = T)

library(XLConnect)
wb <- loadWorkbook("Tables.xlsx", create=TRUE)
createSheet(wb, name="SSMD_dem_pval")
writeWorksheet(wb, data, sheet="SSMD_dem_pval")
saveWorkbook(wb)


# Ranges
path.results<-"C:/Users/cpacioni/Documents/Wild dogs/NorthernArea/NorthernArea_Analysis_May2016/Dingo10IterAnalysis/Results"

# remove strategic baiting scenarios because these where not included in the 
# SSMD ranges analysis
SBF<-SBF[1:6]

# create a vector with the names of the scenairos
scens<-c(NoSBF, SBF, SBF02, SBF05)

# Create the table. NOTE that time.steps=NULL (default) because these are already
# subsetted when the SSMD comparison is done
table <- make.table(path.results, 
                    scenarios=scens, 
                    fnames="SSMD_ranges.xlsx", 
                    SSMD=TRUE, 
                    colh=list(c("GroupSize",	"Resources",	"nGroups", "sqkm")),
                    vround=3, sdround=2, time.steps=NULL, table.name="Tables.xlsx", 
                    tab.name="SSMD_pval_Ranges", save2disk=TRUE, 
                    dir.out=NULL)


# SSMD for Move statistics
table <- make.table(path.results, 
                    scenarios=scens, 
                    fnames="SSMD_move.xlsx", 
                    SSMD=TRUE, 
                    colh=list(c("X.Dispersal.male.floaters",	"X.Dispersal.female.floaters",	
                                "X.Dispersal.adult.and.juv.males.from.pack",	
                                "X.Dispersal.adult.and.juv.females.from.pack")),
                    vround=3, sdround=2, time.steps=NULL, table.name="Tables.xlsx", 
                    tab.name="SSMD_pval_move", save2disk=TRUE, 
                    dir.out=NULL)