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RNL_new trans model_with DEB_1.6.2.1_juvenile.R
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RNL_new trans model_with DEB_1.6.2.1_juvenile.R
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# RNL_new trans model_with DEB_1.6.2.1_juvenile
#19-6-18
# time stamp for updated file RNL_new trans model_with DEB_1.6.2.1_juvenile
#8-6-17
#updated microclimate conditions for adults and juveniles
# 5-6-17 RNL_new trans model_with DEB_1.6.2.1_juvenile
# added report of juv DEB params every hour
# added E_H_pres and fecundity to 'results' output
#29-5-17
# set new juv params to newborn: mass, L_b = debpars[25]^3, E_H_init = debpars[20]+5, and V_pres_init = debpars[25]^3. search @newborn
#1-5-17
# 'RNL_new trans model_with DEB_1.6.2.1_juvenile' uses 'Sleepy IBM_v.6.1.1_two strategies_shadedens.nlogo' which excludes restcount when turtle is searching for shade
# changed results and turtle file outputs from .R to .csv
#25-1-17
# simplified dense and sparse resource input to model env setup ("density")
# added juvenile pars for V_pres_init, E_pres_init, and E_H_init. juvenile pars = <DEB par> / (ultimate length / puberty length). search @juvenile.
# changed working directory inputs to general ones
# added results path for juvenile outputs
# 10-1-17 RNL_new trans model_with DEB_1.6.2.1_juvenile
# added juvenile input (microclimate inputs)
# shifted daystart and dayfin code location to clean up microclimate input section
# 5-1-17 RNL_new trans model_with DEB_1.6.2
# moved gutfull from 'auxiliary params' to 'update animal and env traits'
# added Random and Clumped shade density input (shadedens) for "Sleepy IBM_v.6.1.1_two strategies_shadedens.nlogo"
# updated 'Sleepy IBM_v.6.1.1_two strategies.nlogo' NL model so food patch input matches output (Food-patches / 10)
# updated movement strategy input
# 1-12-16 RNL_new trans model_with DEB_1.6.2
# updated zenith angle code
# 30-11-16 RNL_new trans model_with DEB_1.6.1_olve_movement cost
# added new DEB estimations (Mike)
# updated soil moisture input (Mike)
# updated mass input from DEB calcs
#24-10-16 RNL_new trans model_with DEB_1.6.1_olve_movement cost
# added movement cost (loco), spatial movement, spdf, and homerange plot outputs to export results loop
# set movement cost to miniscule amount when not searching to fix feeding behav on green food patches (NLCommand("set Movement-cost", 1e-09)
# added new direct movement cost (loco)
# changed V_pres to debout[2]
#20-10-16
# updated movement cost loop to reset to 0 in NL when not searching
# added NL_strategy variable to NL setup ... in progress
#28-7-16
# added direct movement cost (loco) estimated from ml 02 g-km (John-Adler 1986) and converted to J
#16-5-16
# added direct movement cost (NL_move) to DEB loop (if (actstate == "S") {NLCommand("set Movement-cost", NL_move)})
# added direct movement cost initial par values
# updated NL_move var
# uses DEB model that includes direct movement cost (cost of locomotion) ('DEB_movecost.R')
# changed all instances of Min-T_b and Max-T_b to T_opt_lower and T_opt_upper to relfect changes in Netlogo (v6.1.1_two strategies)
# changed VTMIN and VTMAX to activity range Tb limits
#29-1-16
# created sim count (sc) and function to replace results with most recent results of sim run. use to have access to all previous sim runs. Used for getting mean results from multiple sims.
# added results, spdf, homerange, and NL plots to write results loop
#14-1-15
# added days to turtle homerange spdf to plot movement paths by day
# added wetmass (V_pres, wetfood, wetgonad, wetstorage) NL plotting function in DEB loop
# updated DEB loop to run on 2-min time steps
# updated initial debout variables in loop to user friendly values
# added gutfull and gutthresh pars within DEB loop to update feeding behav (decision-making part in NL)
#6-1-15
# defined gutfull and X_food pars prior to sim loop (also fixes error of not recognising gutfull in sim loop)
# added V_pres, wetgonad, wetstorage, and wetfood from debout to results output
#30-12-15 / RNL_new trans model_with DEB_1.6.1_olve
# added plot function to compare gutfill 75% and 100%
# updated reserve level in loop with 'X_food' and 'actfeed' vars
# updated mass var in NL plot output file name
#24-12-15 modularised with NicheMapR functions
# 15-6-15
# Added hr<-4*emis*sigma*((Tc+Trad)/2+273)^3 # radiation resistance (Line 270)
#22-5-15
# updated with new DEB model parameters ... still needs Mike to check discrepancies against his params
#11-5-15 (v.1.6)
# Added ctminthresh parameter to keep turtle alive when under VTMIN (12 hours)
# Added plot export function from NL.
#30-4-15
# Updated movement path plot functions to accomodate for new NL spatial plot output in NL model.
# Movement path plots accept dynamic month input-- sep, nov, dec, etc.
#25-4-15
# Fixed NLGetAgentSet error and homerange plot error (changed 'die' in Soft foraging model (NL))
# 30-3-15
# Added home range polygon plotting function
# Added plotting code for new monthly simulations
#23-3-15
# Added lower and upper activity ranges (NL_T_opt_l, NL_T_opt_u)
# Added procedure for plotting per simulation month
#2-12-14
# new analytical transient model (one lump trans)
# TO DO
# Confirm if new VTMAX of 51 C works for month of November
# Feedcount in NL doesn't match 'NLfoodcount', ........ under progress
# Need to change q to something other than 0?
# 27-11-14
# WORKING VERSION
# X_food variable changed to X_food<-NLReport("[energy-gain] of turtle 0]")
# DEB loop now runs on one NL hour
# 3-10-14
# Uses simulation part from RNL_new trans model_with DEB.R, but with the following:
# - NLCommand("set T_b precision", Tb, "2") # Updating Tb
# - acthr<-NLGetAgentSet("in-food?","turtles", as.data.frame=T) ; acthr<-as.numeric(acthr) # Reports true if turtle is in food. For cum. feeding bouts: acthr<- NLReport("feedcount") (# hours of activity. This would change with input from IBM)
# - X_food<-NLCommand("ask turtle 0 [set energy-gain Low-food-gain]") # sets energy intake from feeding. (changes with input from IBM)
# - Reports reserve-level
# 1-10-14
# Now opens NL version 5.1.0
# Removed f==1 from 'Regulates X_food dynamics' loop (Line 1116)
# 16-9-14
# Tb updated after DEB simulation
# acthr reports when turtle in food patch
# Feeding dynamics updates with movement (: 1098)
#12-9-14
# NL reserve level updated in NL setup procedure (:634)
# X_food updates with NL "[handle-food]"" procedure (:695)
# install packages
install.packages(c("RNetLogo", "adehabitatHR","rgeos","sp", "maptools", "raster","rworldmap","rgdal","dplyr"))
library(RNetLogo); library(adehabitatHR); library(sp); library(rgeos); library(maptools); library(raster); library(rworldmap); library(rgdal);library(dplyr)
library(rJava) # run rJava
# ---------------------------------------------------------------------------
# ------------------- initial Mac OS and R config ---------------------------
# ---------------------------------------------------------------------------
#if using Mac OSX Mountain Lion + and not already in JQR, download and open JGR
# after downloading, load JGR
Sys.setenv(NOAWT=1)
library(JGR)
Sys.unsetenv("NOAWT")
JGR()
# JGR onwards
# if already loaded, uninstall RNetlogo and rJava
p<-c("rJava", "RNetlogo")
remove.packages(p)
# install Netlogo and rJava from source if haven't already
install.packages("/Users/malishev/Documents/Melbourne Uni/Programs/R code/RNetlogo/RNetLogo_1.0-2.tar.gz", repos = NULL, type="source")
install.packages("/Users/malishev/Documents/Melbourne Uni/Programs/R code/rJava/rJava_0.9-8.tar.gz", repos = NULL, type="source")
# ------------------- for PC and working Mac OSX ---------------------------
# ------------------- model setup ---------------------------
#working dir for data
wd<-"/Users/malishev/Documents/Melbourne Uni/Programs/"
# install.packages(NicheMapR)
# library(NicheMapR)
setwd("/Users/malishev/Documents/Melbourne Uni/Programs/Sleepy IBM")
source('DEB.R')
source('onelump_varenv.R')
# choose a day(s) to simulate
daystart<-paste('09/09/05',sep="") # yy/mm/dd
dayfin<-paste('10/12/31',sep="") # yy/mm/dd
days<-as.numeric(as.POSIXlt(dayfin)-as.POSIXlt(daystart))
tzone<-paste("Etc/GMT-",10,sep="")
# using juvenile? 1 for yes; 0 for no
juv<-1
report_juv<-0 # report juvenile DEB output every hour
#----------- read in microclimate data ---------------
if (juv == 1){
metout<-read.csv('metout_juv.csv')
soil<-read.csv('soil_juv.csv')
shadmet<-read.csv('shadmet_juv.csv')
shadsoil<-read.csv('shadsoil_juv.csv')
}else{
metout<-read.csv('metout_adult.csv')
soil<-read.csv('soil_adult.csv')
shadmet<-read.csv('shadmet_adult.csv')
shadsoil<-read.csv('shadsoil_adult.csv')
}
micro_sun_all<-cbind(metout[,2:5],metout[,9],soil[,6],metout[,14:16])
colnames(micro_sun_all)<-c('dates','JULDAY','TIME','TALOC','VLOC','TS','ZEN','SOLR','TSKYC')
micro_shd_all<-cbind(shadmet[,2:5],shadmet[,9],shadsoil[,6],shadmet[,14:16])
colnames(micro_shd_all)<-c('dates','JULDAY','TIME','TALOC','VLOC','TS','ZEN','SOLR','TSKYC')
micro_sun<-subset(micro_sun_all, format(as.POSIXlt(micro_sun_all$dates), "%y/%m/%d")>=daystart & format(as.POSIXlt(micro_sun_all$dates), "%y/%m/%d")<=dayfin)
micro_shd<-subset(micro_shd_all, format(as.POSIXlt(micro_shd_all$dates), "%y/%m/%d")>=daystart & format(as.POSIXlt(micro_shd_all$dates), "%y/%m/%d")<=dayfin)
# create time vectors
time<-seq(0,(days+1)*60*24,60) #60 minute intervals from microclimate output
time<-time[-1]
times2<-seq(0,(days+1)*60*24,2) #two minute intervals for prediction
time<-time*60 # minutes to seconds
times2<-times2*60 # minutes to seconds
# apply interpolation functions
velfun<- approxfun(time, micro_sun[,5], rule = 2)
Zenfun<- approxfun(time, micro_sun[,7], rule = 2)
Qsolfun_sun<- approxfun(time, micro_sun[,8], rule = 2)
Tradfun_sun<- approxfun(time, rowMeans(cbind(micro_sun[,6],micro_sun[,9])), rule = 2)
Tairfun_sun<- approxfun(time, micro_sun[,4], rule = 2)
Qsolfun_shd<- approxfun(time, micro_shd[,8]*.1, rule = 2)
Tradfun_shd<- approxfun(time, rowMeans(cbind(micro_shd[,6],micro_shd[,9])), rule = 2)
Tairfun_shd<- approxfun(time, micro_shd[,4], rule = 2)
VTMIN<- 26 # lower activity Tb
VTMAX<- 35 # upper activity Tb
# ****************************************** read in DEB parameters *******************************
debpars=as.data.frame(read.csv('DEB_pars_Tiliqua_rugosa.csv',header=FALSE))$V1 # read in DEB pars
# set core parameters
z=debpars[8] # zoom factor (cm)
F_m = 13290 # max spec searching rate (l/h.cm^2)
kap_X=debpars[11] # digestion efficiency of food to reserve (-)
v=debpars[13] # energy conductance (cm/h)
kap=debpars[14] # kappa, fraction of mobilised reserve to growth/maintenance (-)
kap_R=debpars[15] # reproduction efficiency (-)
p_M=debpars[16] # specific somatic maintenance (J/cm3)
k_J=debpars[18] # maturity maint rate coefficient (1/h)
E_G=debpars[19] # specific cost for growth (J/cm3)
E_Hb=debpars[20] # maturity at birth (J) @newborn
E_Hp=debpars[21] # maturity at puberty (J)
h_a=debpars[22]*10^-1 # Weibull aging acceleration (1/h^2)
s_G=debpars[23] # Gompertz stress coefficient (-)
L_b = debpars[25]^3 # structural length at birth (cm) @newborn
# set thermal respose curve paramters
T_REF = debpars[1]-273
TA = debpars[2] # Arrhenius temperature (K)
TAL = debpars[5] # low Arrhenius temperature (K)
TAH = debpars[6] # high Arrhenius temperature (K)
TL = debpars[3] # low temp boundary (K)
TH = debpars[4] # hight temp boundary (K)
# set auxiliary parameters
del_M=debpars[9] # shape coefficient (-)
E_0=debpars[24] # energy of an egg (J)
mh = 1 # survivorship of hatchling in first year
mu_E = 585000 # molar Gibbs energy (chemical potential) of reserve (J/mol)
E_sm=186.03*6
# set initial state # @juvenile @newborn
# initial reserve
E_pres_init <- (debpars[16]*debpars[8]/debpars[14])/(debpars[13])
E_m <- E_pres_init
#initial maturity
#ifelse(juv==1, E_H_init <- (debpars[21] + 5)/1.43, E_H_init <- (debpars[21] + 5)) # old juvenile
ifelse(juv==1, E_H_init <- (E_Hb + 5), E_H_init <- (E_Hp + 5))
#### change inital size here by multiplying by < 0.85 ####
# for @juvenile = adult size / (ultimate length / puberty length) = 0.85 / (1.43) = 0.594
# for newborn (new juvenile) = L_b
#ifelse(juv == 1,V_pres_init <- (debpars[26] ^ 3) * 0.594, V_pres_init <- (debpars[26] ^ 3) * 0.85)
ifelse(juv == 1,V_pres_init <- L_b, V_pres_init <- (debpars[26] ^ 3) * 0.85)
d_V<-0.3
mass <- V_pres_init + V_pres_init*E_pres_init/mu_E/d_V*23.9; writeLines(paste("Mass = ",mass))
# check juvenile outputs
if(juv==1){
writeLines(paste("\n Juvenile outputs \nE_pres_init = ", E_pres_init, "\nE_H_init = ", E_H_init, "\nV_pres_init = ", V_pres_init,"\nMass = ",mass, "\n"))
}
# test params for juvenile
#E_pres_init<- 3000
#E_H_init <- 20000
#V_pres_init <- 30
#mass <- 50
# ***************** end TRANSIENT MODEL SETUP ***************
# ***********************************************************
# initial setup complete, now run the model for a particular 2 min interval
# **************************************************************************************************************
# ***************************************** start NETLOGO SIMULATION ******************************************
# ****************************************** open NETLOGO *****************************************
nl.path<-paste0(wd,"NetLogo 5.3.1/")
#nl.path<-"/Users/malishev/Documents/Melbourne Uni/Programs/NetLogo 5.3.1/app" # for running in El Capitan
#NLStart(nl.path, gui=F, nl.obj=NULL, is3d=FALSE)
NLStart(nl.path)
model.path<-paste0(wd,"/Sleepy IBM/Sleepy IBM_v.6.1.1_two strategies_shadedens.nlogo")
NLLoadModel(model.path)
# ****************************************** setup NETLOGO MODEL **********************************
# 1. update animal and env traits
month<-"sep"
density<-"high" # resource density
NL_days<-1 # No. of days simulated
mass
if(density=="high"){
NL_shade<-100000L # Shade patches
NL_food<-100000L # Food patches
}else{
NL_shade<-1000L # Shade patches
NL_food<-1000L # Food patches
}
NL_gutthresh<-0.75
gutfull<-0.8
# 2. update initial conditions for DEB model
Es_pres_init<-(E_sm*gutfull)*V_pres_init
acthr<-1
Tb_init<-20
step = 1/24
debout<-DEB(step = step, z = z, del_M = del_M, F_m = F_m *
step, kap_X = kap_X, v = v * step, kap = kap, p_M = p_M *
step, E_G = E_G, kap_R = kap_R, k_J = k_J * step, E_Hb = E_Hb,
E_Hj = E_Hb, E_Hp = E_Hp, h_a = h_a/(step^2), s_G = s_G,
T_REF = T_REF, TA = TA, TAL = TAL, TAH = TAH, TL = TL,
TH = TH, E_0 = E_0, E_pres=E_pres_init, V_pres=V_pres_init, E_H_pres=E_H_init, acthr = acthr, breeding = 1, Es_pres = Es_pres_init, E_sm = E_sm)
# 3. calc direct movement cost
# ------- New loco cost 16-10-16 -------
#V_pres = 3.9752^3 #structure
V_pres<-debout[2]
step<-1/24 #hourly
#step<-2/1440 #2min
p_M2<-p_M*step #J/h
p_M2<-p_M2*V_pres # loco cost * structure
names(p_M2)<-NULL # remove V_pres name attribute from p_M
# movement cost for time period
VO2<-0.45 # O2/g/h JohnAdler etal 1986
# multiple p_M by structure = movement cost (diff between p_M with loco cost and structure for movement period)
# p_M with loco cost
loco<-VO2*mass*20.1 # convert ml O2 to J = J/h
loco<-loco+p_M2 # add to p_M = J/h
loco<-loco/30/V_pres ; loco #J/cm3/2min
Es_pres_init<-(E_sm*gutfull)*V_pres_init
X_food<-3000
V_pres<-debout[2]
wetgonad<-debout[19]
wetstorage<-debout[20]
wetfood<-debout[21]
ctminthresh<-120000
Tairfun<-Tairfun_shd
Tc_init<-Tairfun(1)+0.1 # Initial core temperature
# set NL pars
NL_T_b<-Tc_init # Initial T_b
NL_T_b_min<-VTMIN # Min foraging T_b
NL_T_b_max<-VTMAX # Max foraging T_b
NL_ctminthresh<-ctminthresh # No. of consecutive hours below CTmin that leads to death
NL_reserve<-E_m # Initial reserve density
NL_max_reserve<-E_m # Maximum reserve level
NL_maint<-round(p_M, 3) # Maintenance cost
NL_move<-round(loco, 3) # Movement cost
NL_zen<-Zenfun(1*60*60) # Zenith angle
strategy<-function(strategy){ # set movement strategy
if (strategy == "O"){
NLCommand("set strategy \"Optimising\" ")
}else{
NLCommand("set strategy \"Satisficing\" ")
}
}
strategy("O") # "O" or "S"
# if using shade clumping
#if (model.path==paste0(wd,"/Sleepy IBM/Sleepy IBM_v.6.1.1_two strategies_shadedens.nlogo")){
shadedens<-function(shadedens){ # set movement strategy
if (shadedens == "Random"){
NLCommand("set Shade-density \"Random\" ")
}else{
NLCommand("set Shade-density \"Clumped\" ")
}
}
shadedens("Clumped") # "Random" or "Clumped"
#}
# set results path
ifelse(juv==1, results.path<-"/Users/malishev/Documents/Melbourne Uni/Programs/Sleepy IBM/Results/juvenile/", results.path<-"/Users/malishev/Documents/Melbourne Uni/Programs/Sleepy IBM/Results/adult/")
### start sim ###
sc<-1 # sim count for automating writing of each sim results to file (set before NL loop)
for (i in 1:sc){ # start sc sim loop
NLCommand("set Shade-patches",NL_shade,"set Food-patches",NL_food,"set No.-of-days",NL_days,"set T_b precision",
NL_T_b, "2","set T_opt_lower precision", NL_T_b_min, "2","set T_opt_upper precision", NL_T_b_max, "2",
"set reserve-level", NL_reserve, "set Maximum-reserve", NL_max_reserve, "set Maintenance-cost", NL_maint,
"set Movement-cost precision", NL_move, "3", "set zenith", NL_zen, "set ctminthresh", NL_ctminthresh,
"set gutthresh", NL_gutthresh, 'set gutfull', gutfull, 'set V_pres precision', V_pres, "5", 'set wetstorage precision', wetstorage, "5",
'set wetfood precision', wetfood, "5", 'set wetgonad precision', wetgonad, "5","setup")
#NLCommand("inspect turtle 0") # zoom into turtle
NL_ticks<-NL_days / (2 / 60 / 24) # No. of NL ticks (measurement of days)
NL_T_opt_l<-NLReport("[T_opt_lower] of turtle 0")
NL_T_opt_u<-NLReport("[T_opt_upper] of turtle 0")
# data frame setup for homerange polygon
turtles<-data.frame() # make an empty data frame
NLReport("[X] of turtle 0"); NLReport("[Y] of turtle 0")
who<-NLReport("[who] of turtle 0")
# **********************************************************
# ******************** start NETLOGO SIMULATION ***********
debcall<-0 # check for first call to DEB
stepcount<-0 # DEB model step count
for (i in 1:NL_ticks){
stepcount<-stepcount+1
NLDoCommand(1, "go")
######### Reporting presence of shade
#if (NLReport("any? turtles")){
shade<-NLGetAgentSet("in-shade?","turtles", as.data.frame=T); shade<-as.numeric(shade) # returns an agentset of whether turtle is currently in shade patch
#food<-NLGetAgentSet("in-food?","turtles", as.data.frame=T) ; food<-as.numeric(food)
#}
# choose sun or shade
tick<-i
times3<-c(times2[tick],times2[tick+1])
if(shade==0){
Qsolfun<-Qsolfun_sun
Tradfun<-Tradfun_sun
Tairfun<-Tairfun_sun
}else{
Qsolfun<-Qsolfun_shd
Tradfun<-Tradfun_shd
Tairfun<-Tairfun_shd
}
if(i==1){
Tc_init<-Tairfun(1)+0.1 #initial core temperature
#Zenf<-Zenf(1*60*60) # initial zenith angle at 1 a.m (?)
}
# ----------------------------------- 2-12-14 new one_lump_trans params
Qsol<-Qsolfun(mean(times3)); Qsol
vel<-velfun(mean(times3)) ;vel
Tair<-Tairfun(mean(times3));Tair
Trad<-Tradfun(mean(times3)); Trad
Zen<-Zenfun(mean(times3)); Zen
# calc Tb params at 2 mins interval
Tbs<-onelump_varenv(t=120,time=times3[2],Tc_init=Tc_init,thresh = 30, AMASS = mass, lometry = 3, Tairf=Tairfun,Tradf=Tradfun,velf=velfun,Qsolf=Qsolfun,Zenf=Zenfun)
Tb<-Tbs$Tc
rate<-Tbs$dTc
Tc_init<-Tb
NLCommand("set T_b precision", Tb, "2") # Updating Tb
#NLCommand("set zenith", Zenfun(i*60*60)) # Updating zenith
NLCommand("set zenith", Zenfun(times3[2])) # Updating zenith
# time spent below VTMIN
ctminhours<-NLReport("[ctmincount] of turtle 0") * 2/60 # ticks to hours
if (ctminhours == NL_ctminthresh) {NLCommand("ask turtle 0 [stop]")}
# ******************** start DEB SIMULATION ***************
if(stepcount==1) { # run DEB loop every time step (2 mins)
stepcount<-0
# report juv DEB params every hour
if (report_juv==1){
for(j in seq(0, (NL_ticks),by=720/24)){ # for every hour
if(i == j){
writeLines(paste("\n Juvenile outputs \n Hour = ",j / 30,
"\n E_pres = ", debout[1],
"\nE_H = ", debout[3],
"\nV_pres = ", debout[2],
"\nMass = ",mass,
"\n"))
}
}
}
# report activity state
actstate<-NLReport("[activity-state] of turtle 0")
# Reports true if turtle is in food
actfeed<-NLGetAgentSet("in-food?","turtles", as.data.frame=T); actfeed<-as.numeric(actfeed)
n<-1 # time steps
step<-2/1440 # step size (2 mins) for debout. For hourly: 1/24
# update direct movement cost
if(actstate == "S"){
NLCommand("set Movement-cost", NL_move)
}else{
NLCommand("set Movement-cost", 1e-09)
}
# if within activity range, it's daytime, and gut below threshold
if(Tbs$Tc>=VTMIN & Tbs$Tc<=VTMAX & Zen!=90 & gutfull<=NL_gutthresh){
acthr=1 # activity state = 1
if(actfeed==1){ # if in food patch
X_food<-NLReport("[energy-gain] of turtle 0") # report joules intake
}
}else{
X_food = 0
acthr=0
}
# calculate DEB output
if(debcall==0){
# initialise DEB
debout<-matrix(data = 0, nrow = n, ncol = 26)
deb.names<-c("E_pres","V_pres","E_H_pres","q_pres","hs_pres","surviv_pres","Es_pres","cumrepro","cumbatch","p_B_past","O2FLUX","CO2FLUX","MLO2","GH2OMET","DEBQMET","DRYFOOD","FAECES","NWASTE","wetgonad","wetstorage","wetfood","wetmass","gutfreemass","gutfull","fecundity","clutches")
colnames(debout)<-deb.names
# initial conditions
debout<-DEB(E_pres=E_pres_init, V_pres=V_pres_init, E_H_pres=E_H_init, acthr = acthr, Tb = Tb_init, breeding = 1, Es_pres = Es_pres_init, E_sm = E_sm, step = step, z, del_M = del_M, F_m = F_m *
step, kap_X = kap_X, v = v * step, kap = kap, p_M = p_M *
step, E_G = E_G, kap_R = kap_R, k_J = k_J * step, E_Hb = E_Hb,
E_Hj = E_Hb, E_Hp = E_Hp, h_a = h_a/(step^2), s_G = s_G,
T_REF = T_REF, TA = TA, TAL = TAL, TAH = TAH, TL = TL,
TH = TH, E_0 = E_0)
debcall<-1
}else{
debout<-DEB(step = step, z = z, del_M = del_M, F_m = F_m *
step, kap_X = kap_X, v = v * step, kap = kap, p_M = p_M *
step, E_G = E_G, kap_R = kap_R, k_J = k_J * step, E_Hb = E_Hb,
E_Hj = E_Hb, E_Hp = E_Hp, h_a = h_a/(step^2), s_G = s_G,
T_REF = T_REF, TA = TA, TAL = TAL, TAH = TAH, TL = TL,
TH = TH, E_0 = E_0,
X=X_food,acthr = acthr, Tb = Tbs$Tc, breeding = 1, E_sm = E_sm, E_pres=debout[1],V_pres=debout[2],E_H_pres=debout[3],q_pres=debout[4],hs_pres=debout[5],surviv_pres=debout[6],Es_pres=debout[7],cumrepro=debout[8],cumbatch=debout[9],p_B_past=debout[10])
}
mass<-debout[22] # mass
gutfull<-debout[24] # gut level
NL_reserve<-debout[1] #E_pres reserve
V_pres<-debout[2] #structure
wetgonad<-debout[19] # reproductive mass
wetstorage<-debout[20] # wet mass volume
wetfood<-debout[21] # converted food mass
E_H_pres<-debout[3]
fecundity<-debout[25]
#update NL wetmass properties
NLCommand("set V_pres precision", V_pres, "5")
NLDoCommand("plot xcor ycor")
NLCommand("set wetgonad precision", wetgonad, "5")
NLDoCommand("plot xcor ycor")
NLCommand("set wetstorage precision", wetstorage, "5")
NLDoCommand("plot xcor ycor")
NLCommand("set wetfood precision", wetfood, "5")
NLDoCommand("plot xcor ycor")
} ###--- end DEB loop
NLCommand("set reserve-level", NL_reserve) # update reserve
NLCommand("set gutfull", debout[24])# update gut level
# ******************** end DEB SIMULATION ******************
# generate results, with V_pres, wetgonad, wetstorage, and wetfood from debout
if(i==1){
results<-cbind(tick,Tb,rate,shade,V_pres,wetgonad,wetstorage,wetfood,NL_reserve,E_H_pres,fecundity)
}else{
results<-rbind(results,c(tick,Tb,rate,shade,V_pres,wetgonad,wetstorage,wetfood,NL_reserve,E_H_pres,fecundity))
}
results<-as.data.frame(results)
# generate data frames for homerange polygon
if (tick == NL_ticks - 1){
X<-NLReport("[X] of turtle 0"); head(X)
Y<-NLReport("[Y] of turtle 0"); head(Y)
turtles<-data.frame(X,Y)
who1<-rep(who,NL_ticks); who # who1<-rep(who,NL_ticks - 1); who
turtledays<-rep(1:NL_days,length.out=NL_ticks,each=720)
turtle<-data.frame(ID = who1,days=turtledays)
turtles<-cbind(turtles,turtle)
}
} # *************** end NL loop **************************
# get hr data
spdf<-SpatialPointsDataFrame(turtles[1:2], turtles[3]) # creates a spatial points data frame (adehabitatHR package)
homerange<-mcp(spdf,percent=95)
# writing new results
if (exists("results")){ #if results exist
sc<-sc-1
nam <- paste("results", sc, sep = "") # generate new name with added sc count
rass<-assign(nam,results) #assign new name to results. call 'results1, results2 ... resultsN'
namh <- paste("turtles", sc, sep = "") #generate new name with added sc count
rassh<-assign(namh,turtles) #assign new name to results. call 'results1, results2 ... resultsN'
nams <- paste("spdf", sc, sep = "")
rasss<-assign(nams,spdf)
namhr <- paste("homerange", sc, sep = "")
rasshr<-assign(namhr,homerange)
# write each result for each sim to file dir getwd()
#CAMEL comp dir
#"C:/NicheMapR_Working/projects/sleepy_ibm_transient/"
#using NL file handle variable to export files (fh = "/Users/malishev/Documents/Melbourne Uni/Programs/Sleepy IBM/Results/")
#no error, but no file in dir
#NLCommand(paste("export-plot \"Movement costs\" \"fh",lfh,".csv\"",sep=""))
# no error and exports to dir when NL 'fh' variable has "name.csv"
# NLCommand('export-plot \"Movement costs\"','fh')
# working R version of 'fh'
# paste("export-plot \"Body temperature (T_b)\"",fh,tfh,".csv",sep="")
fh<-results.path; fh
for (i in rass){
# export all results
write.table(results,file=paste(fh,nam,".csv",sep=""))
}
for (i in rassh){
# export turtle location data
write.table(turtles,file=paste(fh,namh,".csv",sep=""))
}
# for (i in rasss){
# export spdf data
# write.table(spdf,file=paste(fh,nams,".R",sep=""))
# }
# for (i in rasshr){
# export hr data
# write.table(homerange,file=paste(fh,namhr,".R",sep=""))
# }
#export NL plots
#spatial plot
sfh<-paste(month,NL_days,round(mass,0),NL_shade,as.integer(NL_food),"_",sc,"_move","",sep="");sfh
NLCommand(paste("export-plot \"Spatial coordinates of transition between activity states\" \"",results.path,sfh,".csv\"",sep=""))
#temp plot
tfh<-paste(month,NL_days,round(mass,0),NL_shade,as.integer(NL_food),"_",sc,"_temp",sep="")
NLCommand(paste("export-plot \"Body temperature (T_b)\" \"",results.path,tfh,".csv\"",sep=""))
#activity budget
afh<-paste(month,NL_days,round(mass,0),NL_shade,as.integer(NL_food),"_",sc,"_act","",sep="");afh
NLCommand(paste("export-plot \"Global time budget\" \"",results.path,afh,".csv\"",sep=""))
#text output
xfh<-paste(month,NL_days,round(mass,0),NL_shade,as.integer(NL_food),"_",sc,"_txt",sep="");xfh
NLCommand(paste("export-output \"",results.path,xfh,".csv\"",sep=""))
#gut level
gfh<-paste(month,NL_days,round(mass,0),NL_shade,as.integer(NL_food),"_",sc,"_gut","",sep="");gfh
NLCommand(paste("export-plot \"Gutfull\" \"",results.path,gfh,".csv\"",sep=""))
#wet mass
mfh<-paste(month,NL_days,round(mass,0),NL_shade,as.integer(NL_food),"_",sc,"_wetmass","",sep="");mfh
NLCommand(paste("export-plot \"Total wetmass plot\" \"",results.path,mfh,".csv\"",sep=""))
#movement cost (loco)
lfh<-paste(month,NL_days,round(mass,0),NL_shade,as.integer(NL_food),"_",sc,"_loco","",sep="");lfh
NLCommand(paste("export-plot \"Movement costs\" \"",results.path,lfh,".csv\"",sep=""))
}
} # ********************** end sc sim loop **********************
ifelse(juv==1,print("Juvenile"),print("Adult")); NLReport("strategy"); density
#*********************** end NETLOGO SIMULATION ****************************
#***************************************************************************
results<-as.data.frame(results);results7<-as.data.frame(results7)
# plotting debout results
plot(results$V_pres,type='h',ylim=c(0,max(results$V_pres)))
with(results,points(wetstorage,type='h',col='light blue'))
with(results,points(wetfood,type='h',col='red'))
with(results,points(wetgonad,type='h',col='green'))
with(results,points(NL_reserve,type='h',col='orange'))
plot(results$NL_reserve,type='h',col='orange')
plot(results7$V_pres,type='l',ylim=c(0,max(results7$V_pres)))
with(results7,points(wetstorage,type='l',col='light blue'))
with(results7,points(wetfood,type='l',col='red'))
with(results7,points(wetgonad,type='h',col='green'))
with(results7,points(NL_reserve,type='h',col='red'))
plot(results7$NL_reserve,type='l',col='orange')
# compare Tb for 75% and 100% gutfull
plot(results$Tb,col='black',las=1,type='l',
xaxt='n',
xlab="Days",
ylab='Tb',
main = paste('Tb with 75% (red) and 100% (black) gutfull par from ',daystart,' for ',NL_days,' days',sep=''),
)
with(results7,points(Tb,col='red', type='l'))
axis(1,at=c(0,(length(results$Tb)/2),length(results$Tb)),labels=c(0,NL_days/2,NL_days))
# ---------------------- home range plots
spdf<-SpatialPointsDataFrame(turtles[1:2], turtles[3]) # creates a spatial points data frame (adehabitatHR package)
homerange<-mcp(spdf,percent=100)
# change this with each sim
hr7<-homerange
hrpath7<-spdf
# original code. NB: using min/maxpcors doesn't work for exporting plot to pdf or jpeg
minpxcor<-NLReport("min-pxcor");maxpxcor<-NLReport("max-pxcor")
minpycor<-NLReport("min-pycor");maxpycor<-NLReport("max-pycor")
# plot 75% and 100% gutfull HRs
colvec = adjustcolor(c("black"), alpha = 0.5)
plot(hr7,lty=1,bty="o",pch=21,col=colvec, xlim=c(minpxcor,maxpxcor),ylim=c(minpycor,maxpycor),axes=F)
plot(hrpath7,pch=3,col=turtles$days,add=T)
colvec = adjustcolor(c("red"), alpha = 0.5)
plot(hr7,lty=1,bty="o",col=colvec,add=T)
plot(hrpath7,pch=3,col=turtles$days,add=T)
# use if axes = F
realaxis<-c(minpxcor*2,minpxcor,0,maxpxcor,maxpxcor*2)
axis(1,at=c(minpxcor,minpxcor/2,0,maxpxcor/2,maxpxcor),labels=realaxis)
axis(2,at=c(minpycor,minpycor/2,0,maxpycor/2,maxpycor),labels=realaxis)
text(maxpxcor/2,minpycor/2,paste("100% area = \n",hr$area,sep=""))# hr
text(minpxcor/2,minpycor,paste("75% area = \n",hr7$area,sep=""))# hr7
par(new=T); plot(0, type="n",xlab="X",ylab="Y",
main=paste('Homerange for 75% gut threshold for ',NL_days,' days from ',daystart,sep=''),
main=paste('Red=75% gutfull , black=100% gutfull for ',NL_days,' days from ',daystart,sep=''),
axes=F)
box(which="plot")
# summary stats for homerange sizes
summary(turtles)
max(turtles$X) - min(turtles$X) # width of HR
max(turtles$Y) - min(turtles$Y) # height of HR
# diff in HR
diffhr<-hr-hr7; diffhr
plot(diffhr,lty=1,bty='o',col=colvec_h)
# ------------------------ export plots from NL --------------------------
month<-"sep"
#dir = /Applications/Programs/NetLogo 5.0.5/Soft foraging model/Simulations
#spatial plot
sfh<-paste(month,NL_days,round(mass,0),NL_shade,NL_food,"_move","",sep="");sfh
#NLCommand("export-plot \"Spatial coordinates of transition between activity states\" \"Simulations/spatialplot.csv\"")
NLCommand(paste("export-plot \"Spatial coordinates of transition between activity states\" \"Simulations/",sfh,".csv\"",sep=""))
# home range
hfh<-paste(month,NL_days,round(mass,0),NL_shade,NL_food,"_homerange","",sep="");hfh
# reserve plot
rfh<-paste(month,NL_days,round(mass,0),NL_shade,NL_food,"_reserve","",sep="");rfh
#NLCommand("export-plot \"Reserve level and starvation reserve over time\" \"Simulations/reserveplot.csv\"")
NLCommand(paste("export-plot \"Reserve level and starvation reserve over time\" \"Simulations/",rfh,".csv\"",sep=""))
#temp plot
tfh<-paste(month,NL_days,round(mass,0),NL_shade,NL_food,"_temp",sep="");tfh
#NLCommand("export-plot \"Body temperature (T_b)\" \"Simulations/tempplot.csv\"")
NLCommand(paste("export-plot \"Body temperature (T_b)\" \"Simulations/",tfh,".csv\"",sep=""))
# activity budget
afh<-paste(month,NL_days,round(mass,0),NL_shade,NL_food,"_act","",sep="");afh
#NLCommand("export-plot \"Global time budget\" \"Simulations/activitybudget.csv\"")
NLCommand(paste("export-plot \"Global time budget\" \"Simulations/",afh,".csv\"",sep=""))
# world view
NLCommand("export-view \"Simulations/worldview.png\"")
# text output
xfh<-paste(month,NL_days,round(mass,0),NL_shade,NL_food,"_txt",sep="");xfh
NLCommand(paste("export-output \"Simulations/",xfh,".csv\"",sep=""))
# gut level
gfh<-paste(month,NL_days,round(mass,0),NL_shade,NL_food,"_gut","",sep="");gfh
#NLCommand("export-plot \"Global time budget\" \"Simulations/activitybudget.csv\"")
NLCommand(paste("export-plot \"Gutfull\" \"Simulations/",gfh,".csv\"",sep=""))
#-----------------------------------------------------------
#------------------------ plot NETLOGO RESULTS -------------
#-----------------------------------------------------------
###
### add export function that saves plot as e.g. "sep15"
###
#fh<-paste(daystart,NL_days,mass,NL_shade,NL_food,sep="")
ttl<-paste("From ",daystart," + ",NL_days,"days ;","Weight =",mass,"g ; Shade =", NL_shade,"; Food =", NL_food,"; VTMIN", NL_T_b_min,"C")
pdf(paste("/Applications/Programs/NetLogo 5.0.5/NL_transient_outputs/",fh,".pdf",sep=""),width=15,height=15,paper="a4r",title=ttl)
par(mfrow=c(1,1)) # new plot window with x rows and y columns, fills by rows
par(mar=c(5,6,5,5))
#------------------ regular results plot ------------------------
#NL_shade<-NLReport("Shade-patches"); NL_food<-NLReport("Food-patches")
results<-as.data.frame(results)
ticktime<-results$tick * 2 / 60 / 24 # convert to real days
# Plot with title
# with(results,plot(Tb~ticktime,type='l',las=1,xlab="Days",ylab = expression(paste("Body temperature (" * degree,"C)")),main=paste("From ",daystart," + ",NL_days,"days ;","Weight =",mass,"g ; Shade =", NL_shade,"; Food =", NL_food,"; VTMIN", NL_T_b_min,"C")))
with(results,plot(Tb~ticktime,type='l',las=1,xlab="Days",ylab = expression(paste("Body temperature (" * degree,"C)"))))
shade.results<-results[results$shade %in% 1,] ; head(shade.results)
sticktime<-shade.results$tick * 2 / 60 / 24 # convert to real days
shade.results_Tb<-results[results$shade %in% 1,'Tb'] ; head(shade.results_Tb)
#with(results,points(shade.results$Tb~shade.results$tick, type='p', col="blue"))
with(results,points(shade.results$Tb~sticktime, type='p', col="blue"))
#with(results,points(shade*20~tick,type='p',col="red"))
abline(h = c(NL_T_opt_l,NL_T_opt_u), col = "red", lty = 3)
text(0,28, "Activity range", col = "red", adj = c(.3, 1))
# dev.off() # use only with jpeg function above
hist(shade.results$Tb, main="Proportion of Tb when in shade", xlab="Tb (C) when in shade")
plot(shade.results$tick,shade.results$Tb, col="blue")
# ------------------ Tb plot per month ------------------------
if (exists("results")){
newones<-results
}
# change this to reflect new data period and save as dataframe
dec15<-newones
ticktime<-newones$tick * 2 / 60 / 24 # convert to real days
# define shade data frame
shade.newones<-newones[newones$shade %in% 1,]
shade.newones_Tb<-newones[newones$shade %in% 1,'Tb'] ; head(shade.newones_Tb)
sticktime<-shade.newones$tick * 2 / 60 / 24 # convert to real days
#sep15: lty=3
#nov1: lty=2
#dec15: lty=1
month<-"dec15"
par(pty="m")
fh<-paste(month,NL_days,mass,NL_shade,NL_food,"_2",sep="")
ttl<-paste("From ",daystart," + ",NL_days,"days ;","Weight =",mass,"g ; Shade =", NL_shade,"; Food =", NL_food,"; VTMIN", NL_T_b_min,"C")
pdf(paste("/Users/matthewmalishev/Documents/Manuscripts/Malishev and Kearney/Figures/Simulations/Tb plot/",fh,".pdf",sep=""),width=15,height=15,paper="a4r",title=ttl)
#plot.new()
#par(new=T)
# make data points transparent
colvec = adjustcolor(c("red"), alpha = 0.5)
col=colvec[sep15$Tb]
# Plot with title
# with(results,plot(Tb~ticktime,type='l',las=1,xlab="Days",ylab = expression(paste("Body temperature (" * degree,"C)")),main=paste("From ",daystart," + ",NL_days,"days ;","Weight =",mass,"g ; Shade =", NL_shade,"; Food =", NL_food,"; VTMIN", NL_T_b_min,"C")))
with(newones,plot(Tb~ticktime,type='l',las=1,lwd=1,lty=1,col=colvec,xlim=c(0,NL_days),ylim=c(0,45),xlab="Days",ylab = expression(paste("Body temperature (" * degree,"C)"))))
#with(results,points(shade.results$Tb~shade.results$tick, type='p', col="blue"))
with(newones,points(shade.newones$Tb~sticktime, type='p', col=colvec))
#with(results,points(shade*20~tick,type='p',col="red"))
abline(h = c(NL_T_opt_l,NL_T_opt_u), col = "red", lty = 3)
text(0,28, "Activity range", col = "red", adj = c(.3, 1))
dev.off()
# ------------------ simultaneous simulation plots --------------------
par(mfrow=c(1,1),mar=c(5,6,5,5),pty="m")
month<-"all"
fh<-paste(month,NL_days,mass,NL_shade,NL_food,"",sep="");fh
ttl<-paste("From ",daystart," + ",NL_days,"days ;","Weight =",mass,"g ; Shade =", NL_shade,"; Food =", NL_food,"; VTMIN", NL_T_b_min,"C")
pdf(paste("/Users/matthewmalishev/Documents/Manuscripts/Malishev and Kearney/Figures/Simulations/Tb plot/",fh,".pdf",sep=""),width=15,height=15,paper="a4r",title=ttl)
#plot.new()
# sep15
# make data points transparent
colvec = adjustcolor(c("black"), alpha = 0.3)
#col=colvec[sep15$Tb]
ticktime<-sep15$tick * (2 / 60 / 24) # convert to real days
sticktime<-shade.sep15$tick * 2 / 60 / 24 # convert to real days
with(sep15,plot(Tb~ticktime,type='l',las=1,lwd=2,lty=1,,col=colvec,xlim=c(0,max(ticktime)),ylim=c(0,45),xlab="",ylab="",axes=F))
shade.sep15<-sep15[sep15$shade %in% 1,] ; head(shade.sep15)
shade.sep15_Tb<-sep15[sep15$shade %in% 1,'Tb'] ; head(shade.sep15_Tb)
#with(results,points(shade.results$Tb~shade.results$tick, type='p', col="blue"))
with(sep15,points(shade.sep15$Tb~sticktime, type='p', col=colvec))
#nov1
colvec = adjustcolor(c("blue"), alpha = 0.3)
ticktime<-nov1$tick * (2 / 60 / 24) # convert to real days
sticktime<-shade.nov1$tick * 2 / 60 / 24 # convert to real days
par(new=T)
with(nov1,plot(Tb~ticktime,type='l',las=1,lwd=2,lty=1,col=colvec,xlim=c(0,max(ticktime)),ylim=c(0,45),xlab="",ylab="",axes=F))
shade.nov1<-nov1[nov1$shade %in% 1,] ; head(shade.nov1)
shade.nov1_Tb<-nov1[nov1$shade %in% 1,'Tb'] ; head(shade.nov1_Tb)
#with(results,points(shade.results$Tb~shade.results$tick, type='p', col="blue"))
with(nov1,points(shade.nov1$Tb~sticktime, type='p', col=colvec))
#dec15
colvec = adjustcolor(c("red"), alpha = 0.3)
ticktime<-dec15$tick * (2 / 60 / 24) # convert to real days
sticktime<-shade.dec15$tick * 2 / 60 / 24 # convert to real days
par(new=T)
with(dec15,plot(Tb~ticktime,type='l',las=1,lwd=2,lty=1,col=colvec,xlim=c(0,max(ticktime)),ylim=c(0,45),xlab="Days",ylab = expression(paste("Body temperature (" * degree,"C)"))))
shade.dec15<-dec15[dec15$shade %in% 1,] ; head(shade.dec15)
shade.dec15_Tb<-nov1[dec15$shade %in% 1,'Tb'] ; head(shade.dec15_Tb)
#with(results,points(shade.results$Tb~shade.results$tick, type='p', col="blue"))
with(dec15,points(shade.dec15$Tb~sticktime, type='p', col=colvec))
abline(h = c(NL_T_opt_l,NL_T_opt_u), col = "red", lty = 3)
text(0,30, "Activity range", col = "red", adj = c(.3, 1))
dev.off() # use only with jpeg function above
hist(shade.results$Tb, main="Proportion of Tb when in shade", xlab="Tb (C) when in shade")
plot(shade.results$tick,shade.results$Tb, col="blue")
# ----------- home range plot ------------------
# get homerange ------------------
#X<-NLReport("[X] of turtle 0"); head(X)
#Y<-NLReport("[Y] of turtle 0"); head(Y)
# turtles<-data.frame(X,Y)
# who1<-rep(who,NL_ticks); who #
#who1<-rep(who,NL_ticks); who
# turtle<-data.frame(ID = who1)
# turtles<-cbind(turtles,turtle)
#
#
# need to make new variable for new spdf (movement paths) ........ under progress
spdf<-SpatialPointsDataFrame(turtles[1:2], turtles[3]) # creates a spatial points data frame (adehabitatHR package)
homerange<-mcp(spdf,percent=100)
# draw-homerange ------------------
#calculate homerange points
temp <- slot(homerange,'polygons')[[which(slot(homerange,'data')$id == who)]]@Polygons[[1]]@coords
tempX<-temp[,1]
tempY<- temp[,2]
#tempXY<-cbind(tempX,tempY); tempXY<-as.list(tempXY)
tempXY<-NLCommand("set tempXY (map [list ?1 ?2]",tempX,tempY, ")" )
# Setting as.list makes no difference
#as.list(tempXY)
# The below command doesn't work yet, so the model calls the NL 'draw-homerange' procedure instead
#NLCommand("set tempX", tempX, "set tempY", tempY, "set tempXY", tempXY)
NLCommand("draw-homerange")
# hatch a turtle to draw the homerange boundary points
NLCommand("ask turtle 0 [hatch-homeranges 1", "hide-turtle","set color red]")
# draw the homerange
NLCommand("foreach tempXY [ask homeranges", "[move-to patch (item 0 ?) (item 1 ?)", "pd]]")
# close the homerange polygon
NLCommand("ask homeranges [let lastpoint first tempXY","move-to patch (item 0 lastpoint) (item 1 lastpoint)","]")
# to save-homerange ---------------
# change this with each sim
sep15_homerange<-homerange
month<-"all"
par(new=T)
par(pty="s")
#save the homerange polygon into a pdf
fh<-paste(month,NL_days,mass,NL_shade,NL_food,"_homerange","",sep="");fh
ttl<-paste("From ",daystart," + ",NL_days,"days ;","Weight =",mass,"g ; Shade =", NL_shade,"; Food =", NL_food,"; VTMIN", NL_T_b_min,"C")
#pdf(paste("/Users/matthewmalishev/Documents/Manuscripts/Malishev and Kearney/Figures/Simulations/Home range polygon/",fh,".pdf",sep=""),width=15,height=15,paper="a4r",title=ttl)
pdf(paste("/Users/matthewmalishev/Documents/Manuscripts/Malishev and Kearney/Figures/Simulations/Home range polygon/",fh,".pdf",sep=""))
jpeg(paste("/Users/matthewmalishev/Documents/Manuscripts/Malishev and Kearney/Figures/Simulations/Home range polygon/",fh,".jpeg",sep=""))
# plot polygon
colvec_h = adjustcolor(c("black"), alpha = 0.5)
plot(sep15_homerange,lty=1,bty="o",col=colvec_h,lwd=2,xlim=c(-25,25),ylim=c(-25,25),axes=F)
# plot animal tracks in polygon. NB: col = white. ........ under progress
plot(spdf,col=as.data.frame(spdf)[,1],pch=4,add=T)
# adding 2nd homerange polygon
colvec_h = adjustcolor(c("blue"), alpha = 0.2)
plot(nov1_homerange,lty=1,bty="o",col=colvec_h,lwd=2,xlim=c(-25,25),ylim=c(-25,25),axes=F,add=T)
# plot animal tracks in polygon. NB: col = white......... under progress
plot(spdf,col=as.data.frame(spdf)[,1],pch=4,add=T)
# adding 3rd homerange polygon
colvec_h = adjustcolor(c("red"), alpha = 0.2)
plot(dec15_homerange,lty=1,bty="o",col=colvec_h,lwd=2,xlim=c(-25,25),ylim=c(-25,25),axes=F,add=T)
# plot animal tracks in polygon. NB: col = white......... under progress
plot(spdf,col=as.data.frame(spdf)[,1],pch=4,add=T)
text(-16,5,labels="A",cex=1.5);text(0,5,labels="B",cex=1.5); text(14,5,labels="C",cex=1.5)