Mercurial > repos > greg > bmsb

changeset 29:be7c61620bb1 draft

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Uploaded
author greg
date Sun, 21 Aug 2016 10:18:33 -0400
parents 22043dadfd2c
children 53d2ac56c953
files bmsb.R
diffstat 1 files changed, 35 insertions(+), 37 deletions(-) [+]
line wrap: on
line diff
--- a/bmsb.R	Fri Aug 19 14:52:06 2016 -0400
+++ b/bmsb.R	Sun Aug 21 10:18:33 2016 -0400
@@ -3,7 +3,7 @@
 suppressPackageStartupMessages(library("optparse"))
 
 options_list <- list(
-    make_option(c("-n", "--input"), action="store", help="Input dataset")
+    make_option(c("-i", "--input"), action="store", help="Input dataset"),
     make_option(c("-o", "--output"), action="store", help="Output dataset")
 )
 
@@ -181,12 +181,12 @@
 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
-	
+    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
+    vec.mat[i,]<-vec.ind
  }
 }
 
@@ -194,11 +194,11 @@
     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
+    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
+    vec.mat[i,]<-vec.ind
  }
 }
 
@@ -214,14 +214,14 @@
    }
     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
+    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
-	 }
+      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.
@@ -234,14 +234,14 @@
    }
     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
+    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
-	 }
+      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
+     }
 }
 
 
@@ -251,24 +251,24 @@
 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
+        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
-	}
+        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
 }  
   
@@ -282,7 +282,7 @@
           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
    }
@@ -341,11 +341,9 @@
 N.newborn[day]<-n.newborn
 N.death[day]<-n.death
 N.adult[day]<-n.adult
-print(c(day,n,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$output")
-
-
+save(dd.day,dd.cum,S0,S1,S2,S3,S4,S5,N.newborn,N.death,N.adult,tot.pop,gen0.pop,gen1.pop,gen2.pop,g0.adult,g1.adult,g2.adult,file=opt$output)