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Copy pathDisease_transmission_script.R
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237 lines (167 loc) · 22.4 KB
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##############################################################################################
# --- CODE OF THE MODEL TO ASSESS THE ROLE OF DENS IN THE SPREAD, INVASION AND PERSISTENCE---#
# --- OF SARCOPTIC MANGE IN THE SAN JOAQUIN FOX POPULATION LOCATED IN BAKERSFIELD, CA -------#
# --- SPECIFICALLY THIS SCRIPT MODELS SARCOPTIC MANGE TRANSMISSION FOX-FOX, INFESTATION -----#
# --- OF DENS AND DEN TO FOX TRANSMISSION (INDIRECT TRANSMISSION) ---------------------------#
##############################################################################################
# Author:Diego Montecino-Latorre
# dmontecino@ucdavis.edu
# Details of the model are published in the journal "Epidemics" January 2019
# For the parameters of the processes associated with disease transmission, they are
# located in the set_up_script.R and run_the_model_script.R
if(track.disease==T){ # If we want to track the disease process
#### INTRODUCE AN EXPOSED FOX IN THE POPULATION ####
if(epidemic==TRUE){ # if it is a epidemic scenario
if(d==45 & years.run==0){ # introduced an exposed infividual on the first year simulated during the 45th week
fams.north.bako=which(gIntersects(box, home_ranges, byid = T)) # which families are in the top north of the city
home_range_of_introduction_opcion=unique(fox[fox$Fam_id%in%paste('Fam_',fams.north.bako, sep='') & fox$Alive==1 & fox$E==0 & fox$S==1 & fox$Social==3,]$Fam_id) # the id's of the families int the north top of the city
if(length(home_range_of_introduction_opcion)>0){ # if there are families in this top corner (yes is it always tru for all simulations)
home_range_of_introduction=sample(home_range_of_introduction_opcion,1) # select the family of introduction
first_exposed_fox=sample(fox[fox$Fam_id==home_range_of_introduction & fox$Alive==1 & fox$E==0 & fox$S==1 & fox$Social==3,]$Fox_id,1) # select the first exposed fox in this family
fox[which(fox$Fox_id==first_exposed_fox), ]$E=0.1 # as exposed. By the end of the week the E moves to 1
fox[which(fox$Fox_id==first_exposed_fox), ]$S=0}} # correct susceptible. This exposed fox is not susceptible anymore.
} # if epidemic
# ---------------------------------------------- #
###### INFESTATION OF DENS WITH SARCOPTES SCABIEI #####
# infestation of the den that is used by a fox type I or II
# if an infected fox is using a den is infested again as it started from day 0.
if(nrow(den.data.set[den.data.set$Den_id%in%unique(c(fox[fox$I.1>0 & fox$Alive==1,]$Den_id, fox[fox$I.2>0 & fox$Alive==1,]$Den_id)),])>0){ # if there are occupied dens with infested foxes
new.dens.infected=unique(c(fox[fox$I.1>0 & fox$Alive==1,]$Den_id, fox[fox$I.2>0 & fox$Alive==1,]$Den_id)) # identfied these dens
den.data.set[den.data.set$Den_id%in%new.dens.infected,]$I=0.1} #make them infested
# ---------------------------------------------- #
###### SARCOPTIC MANGE TRANSMISSION DUE TO SOCIAL CONTACT, DEN SHARING AND INFESTED DEN #####
# a susceptible fox sharing den with an infectious fox can become infected due to social contact, because they share den or because the infectius foxes infest the den they are using.
if(sum(nrow(fox[fox$I.1>=0.1 & fox$Alive==1,]),nrow(fox[fox$I.2>=0.1 & fox$Alive==1,]))>0){# if there are infectious foxes at all.
temp.I=lapply(c(1:n_fam), function(x){c(as.character(fox[fox$Fam_id==paste('Fam_',x, sep='') & fox$Alive==1 & fox$S==0 & fox$E==0 & fox$I.1>=0.1 & fox$I.2==0 & fox$Disp%in%c(0,1),]$Fox_id), # id of infectius foxes per family type I
as.character(fox[fox$Fam_id==paste('Fam_',x, sep='') & fox$Alive==1 & fox$S==0 & fox$E==0 & fox$I.1==0 & fox$I.2>=0.1 & fox$Disp%in%c(0,1),]$Fox_id))}) # id of infectius foxes per family type II
if(nrow(fox[fox$S==1 & fox$Alive==1,])>0){ # if there are susceptible individuals in the system
temp.S=lapply(c(1:n_fam), function(x){c(as.character(fox[fox$Fam_id==paste('Fam_',x, sep='') & fox$Alive==1 & fox$S==1 & fox$E==0 & fox$I.1==0 & fox$I.2==0 & fox$Disp%in%c(0,1),]$Fox_id))}) # id of susceptibles individuals per family
# Fox-to-fox direct transmission due to social contact among members of the same family
temp.trans.matrix.1=lapply(c(1:59), function(x){if(length(temp.S[[x]])==0){rep(0, length(temp.S[[x]]))}
else{replicate(length(temp.S[[x]]), rbinom(length(temp.I[[x]]), 1, prob.trans.foxes.contact.fam[j]))}})
temp.trans.matrix.1=lapply(temp.trans.matrix.1, function(x){if(class(x)=='matrix'){colSums(x)}else{x}}) # summation of all transmission events per susceptible individual (if exposed to more than infectious fox)
temp.trans.matrix.1=lapply(temp.trans.matrix.1, function(x){if(class(x)=='list'){rep(0,length(x))}else{x}}) # summation of all transmission events per susceptible individual
# Fox-to-fox direct transmission due to den sharing
if(any(sapply(mapply(function(x,y){fox[fox$Fox_id%in%x,]$Den_id%in%fox[fox$Fox_id%in%y,]$Den_id}, temp.S, temp.I), function(z){any(z)==T}))){ # if any susceptible fox is sharing den with an infectious fox
dens.used.by.susc.fox=lapply(temp.S, function(x){sapply(x,function(y){fox[which(fox$Fox_id==y),]$Den_id})}) # id of dens used by susceptible foxes.
num.inf.foxes.each.susc.fox.share.den.with=lapply(dens.used.by.susc.fox, function(x){sapply(x, function(y){ #number of infectious individuals sharing den with susceptible fox
sum(nrow(fox[fox$Den_id%in%y & fox$S==0 & fox$I.1>=0.1 & fox$Alive==1,]),
nrow(fox[fox$Den_id%in%y & fox$S==0 & fox$I.2>=0.1 & fox$Alive==1,]))})})
temp.trans.matrix.2=lapply(num.inf.foxes.each.susc.fox.share.den.with, function(x){sapply(x, function(y){
rbinom(y, 1, prob.trans.foxes.share.den[j])})}) # transmission from infecitous foxes to susceptible foxes because of den sharing
temp.trans.matrix.2=lapply(temp.trans.matrix.2, function(x){if(class(x)=='list'){
sapply(x, function(y){if(length(y)==0){0}else{sum(y)}})}else{x}})} # sum the transmission event (if the susceptible fox is sharing den with more than one infectious fox)
else{ # if there are not susceptible foxes sharing den with infectious foxes then everything is zero
temp.trans.matrix.2=lapply(temp.S, function(x){rep(0,length(x))})}
# Transmission of sarcoptic mange from an infested den to a susceptible fox using that den. This adds to the previous trnasmission pathways if that is appropriate.
if(any(fox[fox$S==1,]$Den_id%in%unique(den.data.set[den.data.set$I>=0.1,]$Den_id))){ # if there are susceptible foxes using infested dens
dens.used.by.susc.fox=lapply(temp.S, function(x){sapply(x,function(y){fox[which(fox$Fox_id==y),]$Den_id})}) # id of dens used by susceptible foxes.
infested.dens=as.character(den.data.set[den.data.set$I>=0.1,]$Den_id) # id of infested dens
temp.trans.matrix.3=lapply(dens.used.by.susc.fox, function(x){x%in%infested.dens}) #dens used by teh foxes during the current week that are infested
temp.trans.matrix.3=lapply(temp.trans.matrix.3, function(x){sapply(x, function(y){if(y==T){
rbinom(1, 1, prob.trans.den.to.foxes[j])}else{0}})})}
else{ # if there arent susceptible foxes using the infested dens then there is no transmission
temp.trans.matrix.3=lapply(temp.S, function(x){rep(0,length(x))})}
# Finally here each susceptible individual become exposed by taking into account all the 3 previous transmission pathways and
# the exposure to all the infecctios individuals and or dens it was exposed to during the current week.
trans=mapply(rbind, temp.trans.matrix.1, temp.trans.matrix.2, temp.trans.matrix.3) # tranmisssion to the susceptible fox based on the previous 3 mechanisms
trans=lapply(trans, function(x){if(length(x)>0){colSums(x)}else{vector('integer', length=0)}}) # sum the tramissions
trans=lapply(trans, function(y){if(length(y)>0){ifelse(y>=1,1,0)}else{y}}) # tranmisssion =1 , no trasnmission =0
# based on the results of the trans matrix: actual transmission of disease. New exposed foxes
new.exposed.foxes=unlist(temp.S)[unname(unlist(trans))!=0]
if(length(new.exposed.foxes)>0){
fox[fox$Fox_id%in%new.exposed.foxes,]$E=0.1 # veery first week to be exposed. This will be converted to 1 one the current week is over
fox[fox$Fox_id%in%new.exposed.foxes,]$S=0} # correcting the susceptible status of the new exposed foxes.
# ---------------------------------------------- #
####### SARCOPTIC MANGE TRANSMISSION DUE TO NURSING #####
if(nrow(fox[fox$Social==1 & fox$Alive==1 & fox$S==1,])>0){ # if there are susceptible pups
if(nrow(fox[fox$Social==3 & fox$Alive==1 & fox$Gender==0 & fox$I.1>=0.1 | fox$Social==3 & fox$Alive==1 & fox$Gender==0 & fox$I.2>=0.1,])>0){ # if there are infectious females
fams.adult.fem.inf.and.pups.susc=as.character(fox[fox$Social==3 & fox$Alive==1 & fox$Gender==0 & fox$I.1>=0.1 | fox$Social==3 & fox$Alive==1 & fox$Gender==0 & fox$I.2>=0.1,]$Fam_id)[as.character(fox[fox$Social==3 & fox$Alive==1 & fox$Gender==0 & fox$I.1>=0.1 | fox$Social==3 & fox$Alive==1 & fox$Gender==0 & fox$I.2>=0.1,]$Fam_id)%in%as.character(fox[fox$Social==1 & fox$Alive==1 & fox$S==1,]$Fam_id)] # id those females that are infectious and have susceptiebl offspring
if(length(fams.adult.fem.inf.and.pups.susc)>0){ # if there are
new.pups.infected=unlist(lapply(fams.adult.fem.inf.and.pups.susc, function(x){
if(nrow(fox[fox$Fam_id%in%x & fox$Alive==1 & fox$Social==1 & fox$S==1,])==0){ # if there are not susceptible pups nursing frmo an infectious female then
vector('numeric', length(0))} # nothing happens
else{ #but if there are
rbinom(nrow(fox[fox$Fam_id%in%x & fox$Alive==1 & fox$Social==1 & fox$S==1,]), 1, prob.trans.pups.nursing.inf.female[j])}})) # new pups exposed based on probability
if(any(new.pups.infected==1)){# modify the disease status of new exposed pups if there are
fox[fox$Fam_id%in%fams.adult.fem.inf.and.pups.susc & fox$Alive==1 & fox$Social==1 & fox$S==1,]$E[new.pups.infected==1]=0.1 #new exposed
fox[fox$Fam_id%in%fams.adult.fem.inf.and.pups.susc & fox$Alive==1 & fox$Social==1 & fox$S==1 &fox$E==0.1,]$S=0} #not susceptible any more
}
}#if there are infectious females
}#if there are susceptible pups
} # if there are susceptible individuals
} # if there are infetious foxes
# ---------------------------------------------- #
###### SARCOPTIC MANGE TRANSMISSION DUE TO MATING #####
# Disease transmission through mating with the adult dominant of the opposite sex within the matin pair
if(d%in%cheat.t){ #if we are in cheating season
index.fams.current.week.fem.heat=which(adult.fem.mating.week==d) # families whose dominant pair is mating the current week
index.fams.current.week.fem.alive=as.numeric(sapply(strsplit(as.character(fox[fox$Gender==0 & fox$Social==3 & fox$Alive==1 & fox$I.2==0,]$Fam_id), "_"), function(x){x[[2]]})) # where the dominant female is alive and not type 2
index.fams.current.week.fem.heat.alive=index.fams.current.week.fem.heat[index.fams.current.week.fem.heat%in%index.fams.current.week.fem.alive] # where the dominant female is alive and in estrous
index.fams.with.alive.male=as.numeric(sapply(strsplit(as.character(fox[fox$Alive==1 & fox$Social==3 & fox$Gender==1 & fox$I.2==0,]$Fam_id), split = '_'), function(x){x[2]})) # where the dominant female is alive and not type 2
index.fams.with.alive.male.not.mating=index.fams.with.alive.male[!(index.fams.with.alive.male%in%which(adult.fem.mating.week%in%d))] #index of families where males are not mating during the current week, they are alive, they are not type 2 and, therefore, they could cheat
index.fams.current.week.fem.alive.male.alive=index.fams.current.week.fem.heat.alive[index.fams.current.week.fem.heat.alive%in%index.fams.with.alive.male] # families with couples that actually mate because the dominant pair is alive, the female is in estrous and non of them is type 2
if(length(index.fams.current.week.fem.alive.male.alive)>0){ # if there are such families during the current week
# transmission of mange from the infectious dominant male to the susceptible dominant female
for(fam in index.fams.current.week.fem.alive.male.alive){
if(nrow(fox[fox$Fam_id==paste('Fam_', fam, sep='') & fox$Alive==1 & fox$Social==3 & fox$Gender==1 & fox$I.1>0,])==1 &
nrow(fox[fox$Fam_id==paste('Fam_', fam, sep='') & fox$Alive==1 & fox$Social==3 & fox$Gender==0 & fox$S==1,])==1){ # if the dominant male is infectious and the dominant female is susceptible
fox[fox$Fam_id==paste('Fam_', fam, sep='') & fox$Alive==1 & fox$Social==3 & fox$Gender==0 & fox$S==1,]$E=rbinom(1,1, prob.trans.foxes.mating[j]) # probabilistic tranmission of mange from the dominant male is infectious to the dominant female
if(nrow(fox[fox$Fam_id==paste('Fam_', fam, sep='') & fox$Alive==1 & fox$Social==3 & fox$Gender==0 & fox$S==1 & fox$E==1,])>0){ # if transmission occurred, then move them to exposed and correct their susceptible status
fox[fox$Fam_id==paste('Fam_', fam, sep='') & fox$Alive==1 & fox$Social==3 & fox$Gender==0 & fox$S==1 & fox$E==1,]$E=0.1
fox[fox$Fam_id==paste('Fam_', fam, sep='') & fox$Alive==1 & fox$Social==3 & fox$Gender==0 & fox$S==1 & fox$E==0.1,]$S=0}}
# transmission of mange from the infectious dominant female to the susceptible dominant male
if(nrow(fox[fox$Fam_id==paste('Fam_', fam, sep='') & fox$Alive==1 & fox$Social==3 & fox$Gender==0 & fox$I.1>0,])==1 &
nrow(fox[fox$Fam_id==paste('Fam_', fam, sep='') & fox$Alive==1 & fox$Social==3 & fox$Gender==1 & fox$S==1,])==1){
fox[fox$Fam_id==paste('Fam_', fam, sep='') & fox$Alive==1 & fox$Social==3 & fox$Gender==1 & fox$S==1,]$E=rbinom(1,1,prob.trans.foxes.mating[j])
if(nrow(fox[fox$Fam_id==paste('Fam_', fam, sep='') & fox$Alive==1 & fox$Social==3 & fox$Gender==1 & fox$S==1 & fox$E==1,])>0){
fox[fox$Fam_id==paste('Fam_', fam, sep='') & fox$Alive==1 & fox$Social==3 & fox$Gender==1 & fox$S==1 & fox$E==1,]$E=0.1
fox[fox$Fam_id==paste('Fam_', fam, sep='') & fox$Alive==1 & fox$Social==3 & fox$Gender==1 & fox$S==1 & fox$E==0.1,]$S=0}}
fems.mate=unique(c(fems.mate, as.character(fox[fox$Fam_id==paste('Fam_', fam, sep='') & fox$Social==3 & fox$Gender==0,]$Fox_id))) # index of dominant females that mated during the current week
}}
# Disease transmission through extra mating pair copulations: cheating
for(i in sample(index.fams.current.week.fem.heat.alive)){ # for each dominant females alive and in estrous
index.fams.males.cheat.less.twice=as.numeric(sapply(strsplit(as.character(fox[!(fox$Fox_id%in%names(which(table(males.that.have.cheated)>=2))) & fox$Social==3 & fox$Gender==1,]$Fam_id), '_'), function(x){x[[2]]})) # identif dominant males that can cheat (those tha have had less than 2 extra mating pair mates)
index.fams.male.can.cheat.week.w=unique(index.fams.males.cheat.less.twice[index.fams.males.cheat.less.twice%in%index.fams.with.alive.male.not.mating]) # males alive and that can cheat because they have done it less than twice until the current female of week d and they are not currently mating with their apair
if(length(Fams.dom.male.could.cheat.in[[i]][Fams.dom.male.could.cheat.in[[i]]%in%index.fams.male.can.cheat.week.w])>0){ # if the female in heat has chances of males to come and cheat with her
# identify their relatives so they are not invovled in cheating (parents and siblings)
father.current.dom.males.could.cheat=as.character(fox[fox$Fam_id%in%paste('Fam_',index.fams.male.can.cheat.week.w, sep='') & fox$Social==3 & fox$Gender==1 & fox$Alive==1,]$Father_id)
father.current.dom.males.could.cheat[which(is.na(father.current.dom.males.could.cheat))]=rep(1, length(which(is.na(father.current.dom.males.could.cheat))))
mother.current.dom.males.could.cheat=as.character(fox[fox$Fam_id%in%paste('Fam_',index.fams.male.can.cheat.week.w, sep='') & fox$Social==3 & fox$Gender==1 & fox$Alive==1,]$Mother_id)
mother.current.dom.males.could.cheat[which(is.na(mother.current.dom.males.could.cheat))]=rep(1, length(which(is.na(mother.current.dom.males.could.cheat))))
current.fem.cheat.father.mother.id=fox[fox$Fam_id==paste('Fam_',i,sep='') & fox$Gender==0 & fox$Social==3, c('Fox_id', 'Mother_id', 'Father_id')]
current.fem.cheat.father.mother.id[,which(is.na(current.fem.cheat.father.mother.id))]=rep(2, length(which(is.na(current.fem.cheat.father.mother.id))))
#evaluating if the female in heat and potential males going to cheat with her are relatives
current.female.males.same.father=which(father.current.dom.males.could.cheat%in%as.character(current.fem.cheat.father.mother.id$Father_id))#which potenetial males cheating with are siblings with the actual female
current.female.males.same.mother=which(mother.current.dom.males.could.cheat%in%as.character(current.fem.cheat.father.mother.id$Mother_id))#which potenetial males cheating with are siblings with the actual female
current.female.mother.of.males= which(mother.current.dom.males.could.cheat==as.character(current.fem.cheat.father.mother.id$Fox_id))#which potenetial males cheating with are siblings with the actual female#which potential males to cheat is offspring of the female
current.males.father.of.female= which(father.current.dom.males.could.cheat%in%as.character(current.fem.cheat.father.mother.id$Father_id))#which potenetial males cheating with are siblings with the actual female#which potential males to cheat is offspring of the female
temp.males.relative.of.females=unique(c(current.female.males.same.father, current.female.males.same.mother, current.female.mother.of.males,current.males.father.of.female))
temp.males.relative.of.females=ifelse(length(temp.males.relative.of.females)!=0,temp.males.relative.of.females,60)
index.fams.with.alive.male.not.mating.not.relatives=index.fams.with.alive.male.not.mating[-temp.males.relative.of.females] # Dominat Males that can go and cheat with the dominant female becuase htey are not realtives
if(length(Fams.dom.male.could.cheat.in[[i]][Fams.dom.male.could.cheat.in[[i]]%in%index.fams.with.alive.male.not.mating.not.relatives])>0){ # if there are such dominant males
if(length(Fams.dom.male.could.cheat.in[[i]][Fams.dom.male.could.cheat.in[[i]]%in%index.fams.with.alive.male.not.mating.not.relatives])==1){ #if it is just one, take it
index.fams.male.come.to.cheat.with.i.fem=Fams.dom.male.could.cheat.in[[i]][Fams.dom.male.could.cheat.in[[i]]%in%index.fams.with.alive.male.not.mating.not.relatives]} # dominat female may cheat with none, one or 2 males when in heat
if(length(Fams.dom.male.could.cheat.in[[i]][Fams.dom.male.could.cheat.in[[i]]%in%index.fams.with.alive.male.not.mating.not.relatives])>=2){ # if there are more than 1 then randomly select 1
index.fams.male.come.to.cheat.with.i.fem=sample(Fams.dom.male.could.cheat.in[[i]][Fams.dom.male.could.cheat.in[[i]]%in%index.fams.with.alive.male.not.mating.not.relatives],sample(c(1,2),1))} # dominant female may cheat with none, one or 2 males when in heat
adult.male.cheating.with.the.i.fem.week.d=as.character(fox[fox$Fam_id%in%paste('Fam_', index.fams.male.come.to.cheat.with.i.fem, sep='') & fox$Social==3 & fox$Gender==1,]$Fox_id) # id the dominat male that will cheat with the current dominant female
males.that.have.cheated=c(males.that.have.cheated, adult.male.cheating.with.the.i.fem.week.d) #put this dominant male in the set of males that have cheated
## Actual transmission between the extra mating pair couples
if(nrow(fox[fox$Fox_id%in%adult.male.cheating.with.the.i.fem.week.d & fox$I.1>0,])>0 & # if the dominant male is infectious
nrow(fox[fox$Fam_id==paste('Fam_', i, sep='') & fox$Gender==0 & fox$Social==3 & fox$Alive==1 & fox$S==1,])>0){ # and if the dominant female is susceptible
fox[fox$Fam_id==paste('Fam_', i, sep='') & fox$Alive==1 & fox$Social==3 & fox$Gender==0 & fox$S==1,]$E=rbinom(1,1,prob.trans.foxes.mating[j]) # then the probabilistic realization of sarcoptic mange transmission from the male to the female
if(nrow(fox[fox$Fam_id==paste('Fam_', i, sep='') & fox$Alive==1 & fox$Social==3 & fox$Gender==0 & fox$S==1 & fox$E==1,])>0){ # if transission occurred, then correct S and E status of the dominant female
fox[fox$Fam_id==paste('Fam_', i, sep='') & fox$Alive==1 & fox$Social==3 & fox$Gender==0 & fox$S==1 & fox$E==1,]$E=0.1
fox[fox$Fam_id==paste('Fam_', i, sep='') & fox$Alive==1 & fox$Social==3 & fox$Gender==0 & fox$S==1 & fox$E==0.1,]$S=0}}
#the same idea but backwards (if the male is susceptible and the female is infectious)
if(nrow(fox[fox$Fox_id%in%adult.male.cheating.with.the.i.fem.week.d & fox$S==1,])>0 &
nrow(fox[fox$Fam_id==paste('Fam_', i, sep='') & fox$Gender==0 & fox$Social==3 & fox$Alive==1 & fox$I.1>0,])>0){
fox[fox$Fox_id%in%adult.male.cheating.with.the.i.fem.week.d & fox$S==1,]$E=rbinom(nrow(fox[fox$Fox_id%in%adult.male.cheating.with.the.i.fem.week.d & fox$S==1,]),1,prob.trans.foxes.mating[j])#rbeta(length(adult.male.cheating.with.the.i.fem.week.d),beta.dist.prob.trans.foxes.mating$shape1, beta.dist.prob.trans.foxes.mating$shape2)) # TRANSMISSION FROM THE MALE TO THE FEMALE
if(nrow(fox[fox$Fox_id%in%adult.male.cheating.with.the.i.fem.week.d & fox$S==1 & fox$E==1,])>0){ # if transission occurred, then correct S and E status of the dominant male
fox[fox$Fox_id%in%adult.male.cheating.with.the.i.fem.week.d & fox$S==1 & fox$E==1,]$E=0.1
fox[fox$Fox_id%in%adult.male.cheating.with.the.i.fem.week.d & fox$S==1 & fox$S==1 & fox$E==0.1,]$S=0}}
# add the female to the sets of females that already mate
fems.mate=unique(c(fems.mate, as.character(fox[fox$Fam_id==paste('Fam_', i, sep='') & fox$Gender==0 & fox$Social==3,]$Fox_id)))
}}}
}
} # end the loop of disease transmission