--- a/bmsb.R	Fri Aug 19 14:38:43 2016 -0400
+++ b/bmsb.R	Fri Aug 19 14:38:51 2016 -0400
@@ -1,9 +1,9 @@
 #!/usr/bin/env Rscript
 
-options_list <- list(
-    make_option(c("-i", "--input_temperatures"), action="store", help="Input temperatures csv file"),
-    make_option(c("-s", "--save_log"), action="store_true", default=FALSE, help="Save R logs"),
-    make_option(c("-m", "--output_r_log"), action="store", help="Output dataset for R logs"),
+suppressPackageStartupMessages(library("optparse"))
+
+option_list <- list(
+    make_option(c("-i", "--input"), action="store", help="Input dataset")
     make_option(c("-o", "--output"), action="store", help="Output dataset")
 )
 
@@ -11,14 +11,341 @@
 args <- parse_args(parser, positional_arguments=TRUE)
 opt <- args$options
 
+#########################################
+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
+}
+#########################################
 
-if (opt$save_log) {
-    rlogf <- file(opt$output_r_log, open="wt")
-} else {
-    # Direct R messaging to a temporary file.
-    rlogf <- file("tmpRLog", open="wt")
+#########################################
+# source("daylength.R")
+hourtemp=function(L,date){
+# L=37.5 specify this in main program
+threshold<-12.7  # base development threshold for BMSB
+# threshold2<-threshold/24 degree hour accumulation
+#expdata<-tempdata[1:365,11:13] # Use daily max, min, mean
+dnp<-expdata[date,2]  # daily minimum
+dxp<-expdata[date,3]  # daily maximum
+dmean<-0.5*(dnp+dxp)
+#if (dmean>0) {
+#dnp<-dnp-k1*dmean  
+#dxp<-dxp+k2*dmean 
+#} else {
+#dnp<-dnp+k1*dmean  
+#dxp<-dxp-k2*dmean
+#}
+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
+}
+#########################################
+
+
+#########################################
+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
+}
+#########################################
+
+# model initialization
+# setwd(“/home/lunarmouse/Dropbox/Nelson's project/") 
+# PLEASE CHANGE TO YOUR OWN DIRECTORY!!!
+# PLEASE LOAD BSMB FUNCTIONS FIRST!!!
+
+n<-1000 # start with 1000 individuals
+# 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
+L<-35.58 # latitude for Asheville NC
+ph.p<-daylength(L) # complete photoperiod profile in a year, requires daylength function
+
+#load("asheville2014.Rdat") # load temperature data@location/year
+load(opt$input) # load temperature data@location/year
+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
+
+for (day in 1:365) { # all the day
+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
+
+  for (i in 1:n) { # all individual
+  vec.ind<-vec.mat[i,] # find individual record
+  
+# first of all, still alive?  
+if(vec.ind[2]==0){ # egg
+death.prob=mortality.egg(mean.temp)
+ } else if (vec.ind[2]==1 | vec.ind[2]==2) {
+death.prob=mortality.nymph(mean.temp)
+}  else if (vec.ind[2]==3 | vec.ind[2]==4 | vec.ind[2]==5) { # for adult
+ if (day<120 && day>270) {death.prob=0.33*mortality.adult(mean.temp)
+  } else { 
+death.prob=mortality.adult(mean.temp)} # reduce adult mortality after fall equinox
 }
-sink(file=rlogf, type=c("output", "message"), append=FALSE, split=FALSE)
+
+
+#(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>13.5 && vec.ind[3]>77 && day<180) { # add 77C 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]>77) { # add 77C 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(1,2,8))} else{
+   p.birth=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(1,2,8))} else{
+   p.birth=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
+	 }
+}
+
+
 
-tempdata <- read.csv(opt$input_temperatures)
-save(tempdata, file=opt$output)
+# 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) { # 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) { # 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<13.5 && 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) { # 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(day,n,n.adult))
+}   
+
+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="opt$output")
+
+