--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BMSB.R	Thu Dec 15 11:04:41 2016 -0500
@@ -0,0 +1,578 @@
+#!/usr/bin/env Rscript
+
+suppressPackageStartupMessages(library("optparse"))
+
+options_list <- list(
+    make_option(c("-adult_mort", "--adult_mort"), action="store", help="Adjustment rate for adult mortality"),
+    make_option(c("-adult_nymph_accum", "--adult_nymph_accum"), action="store", help="Adjustment of DD accumulation (old nymph->adult)"),
+    make_option(c("-egg_mort", "--egg_mort"), action="store", help="Adjustment rate for egg mortality"),
+    make_option(c("-latitude", "--latitude"), action="store", help="Latitude of selected location"),
+    make_option(c("-location", "--location"), action="store", help="Selected location"),
+    make_option(c("-min_clutch_size", "--min_clutch_size"), action="store", help="Adjustment of minimum clutch size"),
+    make_option(c("-max_clutch_size", "--max_clutch_size"), action="store", help="Adjustment of maximum clutch size"),
+    make_option(c("-nymph_mort", "--nymph_mort"), action="store", help="Adjustment rate for nymph mortality"),
+    make_option(c("-old_nymph_accum", "--old_nymph_accum"), action="store", help="Adjustment of DD accumulation (young nymph->old nymph)"),
+    make_option(c("-output", "--output"), action="store", help="Output dataset"),
+    make_option(c("-oviposition", "--oviposition"), action="store", help="Adjustment for oviposition rate"),
+    make_option(c("-photoperiod", "--photoperiod"), action="store", help="Critical photoperiod for diapause induction/termination"),
+    make_option(c("-replications", "--replications"), action="store", help="Number of replications"),
+    make_option(c("-se_plot", "--se_plot"), action="store", help="Plot SE"),
+    make_option(c("-start_year", "--start_year"), action="store", help="Starting year"),
+    make_option(c("-sim_year", "--sim_year"), action="store", help="Simulation year"),
+    make_option(c("-temperature_datasets", "--temperature_datasets"), action="store", help="Temperature data for selected location"),
+    make_option(c("-young_nymph_accum", "--young_nymph_accum"), action="store", help="Adjustment of DD accumulation (egg->young nymph)"),
+)
+
+parser <- OptionParser(usage="%prog [options] file", options_list)
+arguements <- parse_args(parser, positional_arguments=TRUE)
+opt <- args$options
+args <- arguments$args
+
+temperature_datasets <- strsplit(opt$temperature_datasets, ",")
+
+# read in the input temperature datafile
+data.input(opt$location, opt$start_year, temperature_datasets)
+
+input.name<-paste(opt$location, opt$sim_year, ".Rdat" ,sep="")
+output.name<-paste(opt$location, opt$sim_year, "sim.Rdat", sep="")
+load(input.name)
+
+# initialize matrix for results from all replications
+S0.rep<-S1.rep<-S2.rep<-S3.rep<-S4.rep<-S5.rep<-matrix(rep(0,365*n.rep),ncol=n.rep)
+newborn.rep<-death.rep<-adult.rep<-pop.rep<-g0.rep<-g1.rep<-g2.rep<-g0a.rep<-g1a.rep<-g2a.rep<-matrix(rep(0,365*n.rep),ncol=n.rep)
+
+# loop through replications
+for (N.rep in 1:n.rep)
+{
+    # during each replication
+    n<-1000 # start with 1000 individuals -- user definable as well?
+    # Generation, Stage, DD, T, Diapause
+    vec.ini<-c(0,3,0,0,0)
+    # overwintering, previttelogenic,DD=0, T=0, no-diapause
+    vec.mat<-rep(vec.ini,n)
+    vec.mat<-t(matrix(vec.mat,nrow=5)) # complete matrix for the population
+    ph.p<-daylength(L) # complete photoperiod profile in a year, requires daylength function
+
+    tot.pop<-NULL # time series of population size
+    gen0.pop<-rep(0,365) # gen.0 pop size
+    gen1.pop<-rep(0,365)
+    gen2.pop<-rep(0,365)
+    S0<-S1<-S2<-S3<-S4<-S5<-rep(0,365)
+    g0.adult<-g1.adult<-g2.adult<-rep(0,365)
+    N.newborn<-N.death<-N.adult<-rep(0,365)
+    dd.day<-rep(0,365)
+
+    ptm <- proc.time() # start tick
+
+    # all the days
+    for (day in 1:365)
+    {
+        photoperiod<-ph.p[day] # photoperiod in the day
+        temp.profile<-hourtemp(L,day)
+        mean.temp<-temp.profile[1]
+        dd.temp<-temp.profile[2]
+        dd.day[day]<-dd.temp
+        death.vec<-NULL # trash bin for death
+        birth.vec<-NULL # new born
+        #n<-length(vec.mat[,1]) # population size at previous day
+
+        # all individuals
+        for (i in 1:n)
+        {
+            vec.ind<-vec.mat[i,] # find individual record
+            # first of all, still alive?  
+            # adjustment for late season mortality rate
+            if (L<40)
+            {
+                post.mort<-1
+                day.kill<-300
+            }
+            else
+            {
+                post.mort<-2
+                day.kill<-250
+            }
+            # egg
+            if(vec.ind[2]==0)
+            {
+                death.prob=ar.em*mortality.egg(mean.temp)
+            }
+            else if (vec.ind[2]==1 | vec.ind[2]==2)
+            {
+                death.prob=ar.nm*mortality.nymph(mean.temp)
+            }
+            # for adult
+            else if (vec.ind[2]==3 | vec.ind[2]==4 | vec.ind[2]==5)
+            {
+                if (day<day.kill)
+                {
+                    death.prob=ar.am*mortality.adult(mean.temp)
+                }
+                else
+                {
+                    death.prob=ar.am*post.mort*mortality.adult(mean.temp)} # increase adult mortality after fall equinox
+                }
+                #(or dependent on temperature and life stage?)
+                u.d<-runif(1)
+                if (u.d<death.prob)
+                {
+                    death.vec<-c(death.vec,i)
+                } 
+                else
+                {
+                    # aggregrate index of dead bug
+                    # event 1 end of diapause
+                    if (vec.ind[1]==0 && vec.ind[2]==3)
+                    {
+                        # overwintering adult (previttelogenic)
+                        if (photoperiod>ph.cr && vec.ind[3]>68 && day<180)
+                        {
+                            # add 68C to become fully reproductively matured
+                            vec.ind<-c(0,4,0,0,0) # transfer to vittelogenic
+                            vec.mat[i,]<-vec.ind
+                        }
+                        else
+                        {
+                            vec.ind[3]<-vec.ind[3]+dd.temp # add to DD
+                            vec.ind[4]<-vec.ind[4]+1 # add 1 day in current stage
+                            vec.mat[i,]<-vec.ind
+                        }
+                    }
+                    if (vec.ind[1]!=0 && vec.ind[2]==3)
+                    {
+                        # NOT overwintering adult (previttelogenic)
+                        current.gen<-vec.ind[1]
+                        if (vec.ind[3]>68)
+                        {
+                            # add 68C to become fully reproductively matured
+                            vec.ind<-c(current.gen,4,0,0,0) # transfer to vittelogenic
+                            vec.mat[i,]<-vec.ind
+                        }
+                        else
+                        {
+                            vec.ind[3]<-vec.ind[3]+dd.temp # add to DD
+                            vec.ind[4]<-vec.ind[4]+1 # add 1 day in current stage
+                            vec.mat[i,]<-vec.ind
+                        }
+                    }
+
+                    # event 2 oviposition -- where population dynamics comes from
+                    if (vec.ind[2]==4 && vec.ind[1]==0 && mean.temp>10)
+                    {
+                        # vittelogenic stage, overwintering generation
+                        if (vec.ind[4]==0)
+                        {
+                            # just turned in vittelogenic stage
+                            n.birth=round(runif(1,2+min.ovi.adj,8+max.ovi.adj))
+                        }
+                        else
+                        {
+                            p.birth=ar.ovi*0.01 # daily probability of birth
+                            u1<-runif(1)
+                            if (u1<p.birth)
+                            {
+                                n.birth=round(runif(1,2,8))
+                            }
+                        }
+                        vec.ind[3]<-vec.ind[3]+dd.temp # add to DD
+                        vec.ind[4]<-vec.ind[4]+1 # add 1 day in current stage
+                        vec.mat[i,]<-vec.ind
+                        if (n.birth>0)
+                        {
+                            # add new birth -- might be in different generations
+                            new.gen<-vec.ind[1]+1 # generation +1
+                            new.ind<-c(new.gen,0,0,0,0) # egg profile
+                            new.vec<-rep(new.ind,n.birth)
+                            new.vec<-t(matrix(new.vec,nrow=5)) # update batch of egg profile
+                            birth.vec<-rbind(birth.vec,new.vec) # group with total eggs laid in that day
+                        }
+                    }
+
+                    # event 2 oviposition -- for gen 1.
+                    if (vec.ind[2]==4 && vec.ind[1]==1 && mean.temp>12.5 && day<222)
+                    {
+                        # vittelogenic stage, 1st generation
+                        if (vec.ind[4]==0)
+                        {
+                            # just turned in vittelogenic stage
+                            n.birth=round(runif(1,2+min.ovi.adj,8+max.ovi.adj))
+                        }
+                        else
+                        {
+                            p.birth=ar.ovi*0.01 # daily probability of birth
+                            u1<-runif(1)
+                            if (u1<p.birth)
+                            {
+                                n.birth=round(runif(1,2,8))
+                            }
+                        }
+                        vec.ind[3]<-vec.ind[3]+dd.temp # add to DD
+                        vec.ind[4]<-vec.ind[4]+1 # add 1 day in current stage
+                        vec.mat[i,]<-vec.ind
+                        if (n.birth>0)
+                        {
+                            # add new birth -- might be in different generations
+                            new.gen<-vec.ind[1]+1 # generation +1
+                            new.ind<-c(new.gen,0,0,0,0) # egg profile
+                            new.vec<-rep(new.ind,n.birth)
+                            new.vec<-t(matrix(new.vec,nrow=5)) # update batch of egg profile
+                            birth.vec<-rbind(birth.vec,new.vec) # group with total eggs laid in that day
+                        }
+                    }
+
+                    # event 3 development (with diapause determination)
+                    # event 3.1 egg development to young nymph (vec.ind[2]=0 -> egg)
+                    if (vec.ind[2]==0)
+                    {
+                        # egg stage
+                        vec.ind[3]<-vec.ind[3]+dd.temp # add to DD
+                        if (vec.ind[3]>=(68+dd.adj1))
+                        {
+                            # from egg to young nymph, DD requirement met
+                            current.gen<-vec.ind[1]
+                            vec.ind<-c(current.gen,1,0,0,0) # transfer to young nym stage
+                        }
+                        else
+                        {
+                            vec.ind[4]<-vec.ind[4]+1 # add 1 day in current stage
+                        }
+                        vec.mat[i,]<-vec.ind
+                    }
+
+                    # event 3.2 young nymph to old nymph (vec.ind[2]=1 -> young nymph: determines diapause)
+                    if (vec.ind[2]==1)
+                    {
+                        # young nymph stage
+                        vec.ind[3]<-vec.ind[3]+dd.temp # add to DD
+                        if (vec.ind[3]>=(250+dd.adj2))
+                        {
+                            # from young to old nymph, DD requirement met
+                            current.gen<-vec.ind[1]
+                            vec.ind<-c(current.gen,2,0,0,0) # transfer to old nym stage
+                            if (photoperiod<ph.cr && day > 180)
+                            {
+                                vec.ind[5]<-1
+                            } # prepare for diapausing
+                        }
+                        else
+                        {
+                            vec.ind[4]<-vec.ind[4]+1 # add 1 day in current stage
+                        }
+                        vec.mat[i,]<-vec.ind
+                    }  
+
+                    # event 3.3 old nymph to adult: previttelogenic or diapausing?
+                    if (vec.ind[2]==2)
+                    {
+                        # old nymph stage
+                        vec.ind[3]<-vec.ind[3]+dd.temp # add to DD
+                        if (vec.ind[3]>=(200+dd.adj3))
+                        {
+                            # from old to adult, DD requirement met
+                            current.gen<-vec.ind[1]
+                            if (vec.ind[5]==0)
+                            {
+                                # non-diapausing adult -- previttelogenic
+                                vec.ind<-c(current.gen,3,0,0,0)
+                            }
+                            else
+                            {
+                                # diapausing 
+                                vec.ind<-c(current.gen,5,0,0,1)
+                            }
+                        }
+                        else
+                        {
+                            vec.ind[4]<-vec.ind[4]+1 # add 1 day in current stage
+                        }
+                        vec.mat[i,]<-vec.ind
+                    }
+
+                    # event 4 growing of diapausing adult (unimportant, but still necessary)## 
+                    if (vec.ind[2]==5)
+                    {
+                        vec.ind[3]<-vec.ind[3]+dd.temp
+                        vec.ind[4]<-vec.ind[4]+1
+                        vec.mat[i,]<-vec.ind
+                    }
+                } # else if it is still alive
+            } # end of the individual bug loop
+
+            # find how many died
+            n.death<-length(death.vec)
+            if (n.death>0)
+            {
+                vec.mat<-vec.mat[-death.vec, ]}
+                # remove record of dead
+                # find how many new born  
+                n.newborn<-length(birth.vec[,1])
+                vec.mat<-rbind(vec.mat,birth.vec)
+                # update population size for the next day
+                n<-n-n.death+n.newborn 
+
+                # aggregate results by day
+                tot.pop<-c(tot.pop,n) 
+                s0<-sum(vec.mat[,2]==0) #egg
+                s1<-sum(vec.mat[,2]==1) # young nymph
+                s2<-sum(vec.mat[,2]==2) # old nymph
+                s3<-sum(vec.mat[,2]==3) # previtellogenic
+                s4<-sum(vec.mat[,2]==4) # vitellogenic
+                s5<-sum(vec.mat[,2]==5) # diapausing
+                gen0<-sum(vec.mat[,1]==0) # overwintering adult
+                gen1<-sum(vec.mat[,1]==1) # first generation
+                gen2<-sum(vec.mat[,1]==2) # second generation
+                n.adult<-sum(vec.mat[,2]==3)+sum(vec.mat[,2]==4)+sum(vec.mat[,2]==5) # sum of all adults
+                gen0.pop[day]<-gen0 # gen.0 pop size
+                gen1.pop[day]<-gen1
+                gen2.pop[day]<-gen2
+                S0[day]<-s0
+                S1[day]<-s1
+                S2[day]<-s2
+                S3[day]<-s3
+                S4[day]<-s4
+                S5[day]<-s5
+                g0.adult[day]<-sum(vec.mat[,1]==0)
+                g1.adult[day]<-sum((vec.mat[,1]==1 & vec.mat[,2]==3) | (vec.mat[,1]==1 & vec.mat[,2]==4) | (vec.mat[,1]==1 & vec.mat[,2]==5))
+                g2.adult[day]<-sum((vec.mat[,1]==2 & vec.mat[,2]==3) | (vec.mat[,1]==2 & vec.mat[,2]==4) | (vec.mat[,1]==2 & vec.mat[,2]==5))
+
+                N.newborn[day]<-n.newborn
+                N.death[day]<-n.death
+                N.adult[day]<-n.adult
+                print(c(N.rep,day,n,n.adult))
+            }   # end of 365 days
+
+            #proc.time() - ptm
+            dd.cum<-cumsum(dd.day)
+            # save(dd.day,dd.cum,S0,S1,S2,S3,S4,S5,N.newborn,N.death,N.adult,tot.pop,gen0.pop,gen1.pop,gen2.pop,g0.adult,g1.adult,g2.adult,file="wenatchee2013sim.Rdat")
+            #newborn.rep<-death.rep<-adult.rep<-pop.rep<-g0.rep<-g1.rep<-g2.rep<-g0a.rep<-g1a.rep<-g2a.rep<-matrix(rep(0,365*n.rep),ncol=n.rep)
+            # collect all the outputs
+            S0.rep[,N.rep]<-S0
+            S1.rep[,N.rep]<-S1
+            S2.rep[,N.rep]<-S2
+            S3.rep[,N.rep]<-S3
+            S4.rep[,N.rep]<-S4
+            S5.rep[,N.rep]<-S5
+            newborn.rep[,N.rep]<-N.newborn
+            death.rep[,N.rep]<-N.death
+            adult.rep[,N.rep]<-N.adult
+            pop.rep[,N.rep]<-tot.pop
+            g0.rep[,N.rep]<-gen0.pop
+            g1.rep[,N.rep]<-gen1.pop
+            g2.rep[,N.rep]<-gen2.pop
+            g0a.rep[,N.rep]<-g0.adult
+            g1a.rep[,N.rep]<-g1.adult
+            g2a.rep[,N.rep]<-g2.adult
+        }
+
+save(dd.day,dd.cum,S0.rep,S1.rep,S2.rep,S3.rep,S4.rep,S5.rep,newborn.rep,death.rep,adult.rep,pop.rep,g0.rep,g1.rep,g2.rep,g0a.rep,g1a.rep,g2a.rep,file=opt$output)
+# maybe do not need to export this bit, but for now just leave it as-is
+# do we need to export this Rdat file? 
+
+
+#########################################
+# input starting year and how many years
+# n.yr and start.yr needs to be integer
+# loc.name needs to be CHARACTER and matches exactly the name in the csv file!!!
+data.input=function(loc, start.yr, temperature.datasets)
+{
+    n.yr <- length(temperature_datasets)
+    for (i in 1:n.yr)
+    {
+        expdata<-matrix(rep(0,365*3),nrow=365)
+        yr<-start.yr+i # replace 2004 with start. yr
+        name.input<-paste(temperature.datasets[i], ".csv", sep="")
+        namedat<-paste(loc, yr,".Rdat",sep="")
+        temp.data<-read.csv(file=name.input, header=T)
+
+        expdata[,1]<-c(1:365)
+        expdata[,2]<-temp.data[c(1:365),3] #minimum
+        expdata[,3]<-temp.data[c(1:365),2] #maximum
+        save(expdata,file=namedat)
+    }
+}
+#########################################
+
+#########################################
+daylength=function(L)
+{
+    # from Forsythe 1995
+    p=0.8333
+    dl<-NULL
+    for (i in 1:365)
+    {
+        theta<-0.2163108+2*atan(0.9671396*tan(0.00860*(i-186)))
+        phi<-asin(0.39795*cos(theta))
+        dl[i]<-24-24/pi*acos((sin(p*pi/180)+sin(L*pi/180)*sin(phi))/(cos(L*pi/180)*cos(phi)))
+    }
+    dl   # return a vector of daylength in 365 days
+}
+#########################################
+
+#########################################
+hourtemp=function(L,date)
+{
+    threshold<-14.17  # base development threshold for BMSB
+    dnp<-expdata[date,2]  # daily minimum
+    dxp<-expdata[date,3]  # daily maximum
+    dmean<-0.5*(dnp+dxp)
+    dd<-0  # initialize degree day accumulation
+
+    if (dxp<threshold)
+    {
+        dd<-0
+    }
+    else
+    {
+        dlprofile<-daylength(L)  # extract daylength data for entire year
+        T<-NULL  # initialize hourly temperature
+        dh<-NULL #initialize degree hour vector
+        # date<-200
+        y<-dlprofile[date]  # calculate daylength in given date
+        z<-24-y     # night length
+        a<-1.86     # lag coefficient
+        b<-2.20     # night coefficient
+        #tempdata<-read.csv("tempdata.csv") #import raw data set
+        # Should be outside function otherwise its redundant
+        risetime<-12-y/2      # sunrise time
+        settime<-12+y/2       # sunset time
+        ts<-(dxp-dnp)*sin(pi*(settime-5)/(y+2*a))+dnp
+        for (i in 1:24)
+        {
+            if (i>risetime && i<settime)
+            {
+                m<-i-5  # number of hours after Tmin until sunset
+                T[i]=(dxp-dnp)*sin(pi*m/(y+2*a))+dnp
+                if (T[i]<8.4)
+                {
+                    dh[i]<-0
+                }
+                else
+                {
+                    dh[i]<-T[i]-8.4
+                }
+            }
+            else if (i>settime)
+            { 
+                n<-i-settime
+                T[i]=dnp+(ts-dnp)*exp(-b*n/z)
+                if (T[i]<8.4)
+                {
+                    dh[i]<-0
+                }
+                else
+                {
+                    dh[i]<-T[i]-8.4
+                }
+            }
+            else
+            {
+                n<-i+24-settime
+                T[i]=dnp+(ts-dnp)*exp(-b*n/z)
+                if (T[i]<8.4)
+                {
+                    dh[i]<-0
+                }
+                else
+                {
+                    dh[i]<-T[i]-8.4
+                }
+            }
+        }
+        dd<-sum(dh)/24
+    }
+    return=c(dmean,dd)
+    return
+}
+#########################################
+
+#########################################
+dev.egg=function(temperature)
+{
+    dev.rate=-0.9843*temperature+33.438
+    return=dev.rate
+    return
+}
+#########################################
+
+#########################################
+dev.young=function(temperature)
+{
+    n12<--0.3728*temperature+14.68
+    n23<--0.6119*temperature+25.249
+    dev.rate=mean(n12+n23)
+    return=dev.rate
+    return
+}
+#########################################
+
+#########################################
+dev.old=function(temperature)
+{
+    n34<--0.6119*temperature+17.602
+    n45<--0.4408*temperature+19.036
+    dev.rate=mean(n34+n45)
+    return=dev.rate
+    return
+}
+#########################################
+
+#########################################
+dev.emerg=function(temperature)
+{
+    emerg.rate<--0.5332*temperature+24.147
+    return=emerg.rate
+    return
+}
+#########################################
+
+#########################################
+mortality.egg=function(temperature)
+{
+    if (temperature<12.7)
+    {
+        mort.prob=0.8
+    }
+    else 
+    {
+        mort.prob=0.8-temperature/40
+        if (mort.prob<0)
+        {
+            mort.prob=0.01
+        }
+    }
+    return=mort.prob
+    return
+}
+#########################################
+
+#########################################
+mortality.nymph=function(temperature)
+{
+    if (temperature<12.7)
+    {
+        mort.prob=0.03
+    }
+    else 
+    {
+        mort.prob=temperature*0.0008+0.03
+    }
+    return=mort.prob
+    return
+}
+#########################################
+
+#########################################
+mortality.adult=function(temperature)
+{
+    if (temperature<12.7)
+    {
+        mort.prob=0.002
+    }
+    else 
+    {
+        mort.prob=temperature*0.0005+0.02
+    }
+    return=mort.prob
+    return
+}
+#########################################
\ No newline at end of file