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analyze.R
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'analyze' <- function(LS,options="",verbose=FALSE) {
if (missing(LS))
return(list(input=NULL,p0=NULL,p1=NULL,p2=NULL,p3=NULL,p4=NULL,p5=NULL
,p6=NULL,p7=NULL,p8=NULL,p9=NULL,p10=NULL))
isNone <- length(grep("none",options,ignore.case=TRUE))>0
isAll <- length(options)==0 | nchar(options)==0 |
length(grep("all",options,ignore.case=TRUE))>0
isLitter <- isAll | length(grep("litter",options,ignore.case=TRUE))>0 ## p7 p8 p10
isSurvival <- isAll | length(grep("(surv|mort)",options,ignore.case=TRUE))>0 ## p9
isStructure <- isAll | length(grep("(struct|peer)",options,ignore.case=TRUE))>0 ## p6 p11
isGrowthRate <- isAll | length(grep("(growth|popsize)",options,ignore.case=TRUE))>0 ## p5
isInterbirth <- isAll | length(grep("interbirth",options,ignore.case=TRUE))>0 ## p1
isDenning <- isAll | length(grep("denning",options,ignore.case=TRUE))>0 ## p2 p3 p4
if (verbose)
print(c(All=isAll,None=isNone,Litter=isLitter,Survival=isSurvival
,Structure=isStructure,GrowthRate=isGrowthRate
,Interbirth=isInterbirth,Denning=isDenning))
isShiny <- (("shiny" %in% loadedNamespaces())&&(length(shiny::shinyOptions())>0))
if (isShiny)
showModal(modalDialog(title = "Analysis in progress","Please wait"
,size="s",easyClose = TRUE,footer = NULL))
input <- LS$input
lifestory <- LS$output
epoch <- sort(unique(lifestory$epoch))
season <- sort(unique(lifestory$season))
ns <- length(season)
max.age <- max(lifestory$age)
subad.ini <- 3
cs <- colorScheme()
p11 <- p10 <- p9 <- p8 <- p7 <- p6 <- p5 <- p4 <- p3 <- p2 <- p1 <- p0 <- NULL
if ("ggplot2" %in% loadedNamespaces())
p0 <- theme_grey()+
theme(panel.background=element_rect(fill=cs$bg))+
theme(strip.background=element_rect(fill=cs$strip))+#,colour="red"))
theme(legend.margin=margin(t=-1,b=0,unit='char'))
# theme(legend.key.size=size(1,unit="char"))
# pdf("res1.pdf",width=8,height=4)
res <- NULL
natalityRate <- NA
if (isLitter) {
if (isShiny)
showNotification(closeButton=TRUE,"Litter size...",id="litter"
,duration=99)
pop <- lifestory[lifestory$epoch>c(0,max.age)[2] &
lifestory$epoch<=max(epoch)-0*4 &
lifestory$season==0,]
res <- NULL
res3 <- NULL
if (nrow(pop)) {
age <- c('0Yr'=0,'1Yr'=1,'2Yr'=2)
pop3 <- pop[pop$age>3 & pop$sex=="F",]
epoch3 <- sort(unique(pop3$epoch))
nFemale <- aggregate(pop3$id,list(epoch=pop3$epoch),length)$x
# brokenFamily <- c(0.001,input$iC1,0.999) ## == input$indep.fraction
for (i in seq_along(age)) {
pop1 <- pop[pop$age==age[i] & !is.na(pop$parent),]
res2 <- aggregate(pop1$parent,list(epoch=pop1$epoch),function(x) {
lf <- unname(table(table(x)))
while (length(lf)<3) lf <- c(lf,0)
lf
})
ind <- match(epoch3,res2$epoch)
nCOY <- rep(0,length(epoch3))
nCOY[!is.na(ind)] <- aggregate(pop1$parent,list(epoch=pop1$epoch),length)$x
nFamily <- rep(0,length(epoch3))
nFamily[!is.na(ind)] <- apply(res2$x,1,sum)
L <- nCOY/nFamily ## litter size
L[is.nan(L)] <- 0
LP <- nFamily/nFemale ## litter production
CP <- L*LP ## cub production == natality rate
if (names(age)[i]=="0Yr")
natalityRate <- CP
LP2 <- LP*(1-input$indep.fraction[i])
# N <- nCOY/nFemale ## N = LS*LP ## natality rate
da3 <- data.frame(mean=c(mean(L),mean(LP),mean(LP2),mean(CP))
,sd=c(sd(L),sd(LP),sd(LP2),sd(CP))
,row.names=c("Litter Size","Litter Production"
,"Litter Production by mating"
,"Natality Rate"))
if (i==1)
print(da3[c(1,2,4),],digits=2)
else if (i==2)
print(da3[c(2,3),],digits=2)
else
print(da3[2,],digits=2)
lab <- sprintf("%s\n%.2f\u00B1%.2f",names(age[i]),mean(LP),sd(LP))
lab3 <- sprintf("%s\n%.3f\u00B1%.3f",names(age[i]),mean(LP),sd(LP))
if (!(names(age[i]) %in% "2Yr"))
res3 <- rbind(res3,data.frame(age=lab,age3=lab3,epoch=epoch3,value=LP))
if (names(age[i]) %in% c("1Yr","2Yr")[1]) {
lab <- sprintf("%s-\n%.2f\u00B1%.2f",names(age[i]),mean(LP2),sd(LP2))
lab3 <- sprintf("%s-\n%.3f\u00B1%.3f",names(age[i]),mean(LP2),sd(LP2))
res3 <- rbind(res3,data.frame(age=lab,age3=lab3,epoch=epoch3,value=LP2))
}
L <- apply(res2$x,1,function(lf) {
x <- lf/sum(lf)
sum(x*seq_along(x))
})
res2$x <- t(apply(res2$x,1,function(lf) lf/sum(lf)))
lab <- sprintf("%s\n%.2f\u00B1%.2f",names(age[i]),mean(L),sd(L))
res2 <- cbind(data.frame(age=lab,epoch=res2$epoch),res2$x)
res <- rbind(res,tidyr::gather(res2,cubs,value,-epoch,-age))
}
res3$age <- factor(res3$age,levels=unique(res3$age),ordered=TRUE)
res3$age3 <- factor(res3$age3,levels=unique(res3$age3),ordered=TRUE)
if ("ggplot2" %in% loadedNamespaces())
p7 <- ggplot(res,aes(epoch,value,colour=cubs))+geom_line()
if (T & "plotly" %in% loadedNamespaces()) {
res$age <- paste0("",gsub("\\n"," (",res$age),")")
# ind <- which(res$cubs=="1")
# res$cubs[ind] <- paste(res$cubs[ind],"cub")
# res$cubs[-ind] <- paste(res$cubs[-ind],"cubs")
res$cubs <- paste0(res$cubs,"C")
if (T & "highcharter" %in% loadedNamespaces()) {
p8 <- hcboxplot(x=res$value,var=res$age,var2=res$cubs) %>%
hc_chart(type = "column") %>%
hc_tooltip(pointFormat = 'mean = {point.obs}') %>%
hc_plotOptions(
boxplot=list(animation=list(duration=1000))
)
}
else {
ncub <- sort(unique(res$cubs))
p8 <- plot_ly(type="violin")
for (cubs in ncub)
p8 <- add_trace(p8,y=res$value[res$cubs==cubs],x=res$age[res$cubs==cubs]
,name=cubs)
p8 <- layout(p8,xaxis=cs$axis,yaxis=cs$axis,legend=cs$legend,title=cs$title)
p8 <- layout(p8
# ,yaxis=list(title="Proportion")
# ,xaxis=list(title=p$labels$x)
,title=list(text="Age specific litter size")
,violinmode='group'
)
prm <- cs$config
prm[[1]] <- p8
p8 <- do.call("config",prm)
}
}
else
p8 <- ggplot(res,aes(cubs,value))+
geom_violin(fill=cs$hist,colour=cs$base)+
xlab("Age-specific litter size")+ylab("Proportion")+
facet_grid(.~age)+p0
p8 <- list(plot=p8,data=res)
if (T & "plotly" %in% loadedNamespaces()) {
res3$label <- res3$stat <- res3$age
lab <- strsplit(levels(res3$age),split="\\n")
stat <- sapply(lab,function(x) x[2])
if (length(unique(stat))!=length(stat)) {
res3$age <- res3$age3
lab <- strsplit(levels(res3$age),split="\\n")
stat <- sapply(lab,function(x) x[2])
}
res3$age3 <- NULL
res3$hover <- gsub("\\n","<br>",res3$age)
levels(res3$label) <- sapply(lab,function(x) x[1])
levels(res3$stat) <- stat
ann <- levels(res3$label)
p10 <- plot_ly()
p10 <- add_trace(p10,data=res3,type="violin",showlegend=!FALSE
,split=~stat
,text=~stat
,name=~label
,hoverinfo="name"
,x=~stat
,y=~value
# ,hovertemplate="%{name}"
# ,orientation='v'
,meanline=list(visible=T)
)
if (FALSE)
p10 <- add_annotations(p10
,x=seq_along(ann)-1,y=-0.06
,xref="x",yref="paper"
,text=ann,showarrow=FALSE
,font=cs$font
)
p10 <- layout(p10,xaxis=cs$axis,yaxis=cs$axis,legend=cs$legend,title=cs$title)
#p10 <- layout(p10,legend=list(orientation="v",x=0.8,y=1))
p10 <- layout(p10,yaxis=list(title=""),xaxis=list(title="")
,title=list(text="Litter Production")
,legend=list(orientation="v")
)
#p10 <- layout(p10,xaxis=list(type="category"))
prm <- cs$config
prm[[1]] <- p10
p10 <- do.call("config",prm)
}
else
p10 <- ggplot(res3,aes(age,value))+
geom_violin(fill=cs$hist,colour=cs$base)+
xlab("Age")+ylab("Litter Production")+
scale_x_discrete(breaks=NULL)+
facet_grid(.~age,scales="free")+
p0
p10 <- list(plot=p10,data=res3)
}
if (isShiny)
removeNotification(id="litter")
# stop()
}
if (isSurvival) {
if (isShiny)
showNotification(closeButton=TRUE,"Actual survival",id="survival"
,duration=99)
# print(tail(lifestory[lifestory$season==9,],100))
# str(lifestory[lifestory$season==9 & lifestory$epoch==max(lifestory$epoch),])
# str(lifestory[lifestory$season==0 & lifestory$epoch==max(lifestory$epoch),])
# str(lifestory[lifestory$season==1 & lifestory$epoch==max(lifestory$epoch),])
# age <- list('0Yr'=1,'1Yr'=2,'2Yr'=3,'Sub-Ad'=4:5,'Adult'=6:99)
age <- list('0Yr'=1,'1Yr'=2,'2Yr'=3,'3Yr'=4,'4Yr'=5,'Adult'=6:99)
res <- NULL
ep <- max(lifestory$age)-4
label <- rep("",length(age))
toSkip <- FALSE
opW <- options(warn=10)
for (i in seq_along(age)) {
pop0 <- lifestory[lifestory$age %in% (age[[i]]-1) & lifestory$epoch>=ep,]
pop1 <- lifestory[lifestory$age %in% age[[i]] & lifestory$epoch>=ep,]
if ((!nrow(pop0))||(!nrow(pop1))) {
toSkip <- TRUE
break
}
spop0 <- pop0[pop0$season==0,]
spop1 <- pop1[pop1$season==1,]
spop9 <- pop1[pop1$season==9,]
if ((!nrow(spop0))||(!nrow(spop1))||(!nrow(spop9))) {
toSkip <- TRUE
break
}
s0 <- aggregate(id~epoch,data=spop0,length)
s1 <- aggregate(id~epoch,data=spop1,length)
s9 <- aggregate(id~epoch,data=spop9,length)
s0 <- s0[match(s1$epoch,s0$epoch),]
surv <- s1$id/s0$id
surv[surv>=1] <- 1-1e-3
res2 <- data.frame(Epoch=s0$epoch,Survival=surv#,Age=names(age)[i]
,Label="")
label[i] <- sprintf("%s\n%.2f\u00B1%.2f",names(age)[i]
,mean(res2$Survival),sd(res2$Survival))
res2$Label <- label[i]
res <- rbind(res,res2)
}
options(opW)
if (!toSkip) {
res$Label <- factor(res$Label,levels=label,ordered=TRUE)
if (T & "plotly" %in% loadedNamespaces()) {
res$name <- ""
res$stat <- res$hover <- res$lab <- res$age <- res$Label
levels(res$age) <- paste0("",gsub("\\n"," (",levels(res$Label)),")")
levels(res$hover) <- gsub("(.+)\\n(.+)","\\1",levels(res$Label)) ## 0yr
levels(res$lab) <- gsub("(.+)\\n(.+)","\\1",substr(levels(res$Label),1,1)) ## 012SA
levels(res$stat) <- gsub("(.+)\\n(.+)","\\2",levels(res$Label)) ## 0.75±0.05
p9 <- plot_ly()
p9 <- add_trace(p9,data=res,type="violin"
,split=~age
,x=~age
,y=~Survival
,name=~lab
,text=~hover
,hoverinfo="text+name"
,meanline=list(visible=T)
)
p9 <- layout(p9,xaxis=cs$axis,yaxis=cs$axis,legend=cs$legend,title=cs$title)
p9 <- layout(p9
,xaxis=list(title="Age Structure")
,title=list(text="Actual Survival")
)
prm <- cs$config
prm[[1]] <- p9
p9 <- do.call("config",prm)
}
else if ("ggplot2" %in% loadedNamespaces())
p9 <- ggplot(res,aes(Label,Survival))+
geom_violin(fill=cs$hist,colour=cs$base)+
xlab("Age Structure")+ylab("Actual Survival")+
scale_x_discrete(breaks=NULL)+
facet_grid(.~Label,scales="free")+
p0
p9 <- list(plot=p9,data=res)
}
# print(p9+p0);q()
if (isShiny)
removeNotification(id="survival")
}
if (isStructure) {
if (isShiny)
showNotification(closeButton=TRUE,"Population structure",id="structure"
,duration=99)
epoch <- epoch[(epoch*ns) %% ns == 0 & epoch>=max(lifestory$age)-4]
pop <- lifestory[lifestory$epoch %in% epoch & lifestory$season==0,]
if (nrow(pop)) {
a1 <- aggregate(id~age+epoch,data=pop,length)
colnames(a1)[ncol(a1)] <- "size"
if ("plotly" %in% loadedNamespaces()) {
p6 <- plot_ly()
p6 <- add_trace(p6,data=a1,x=~age,y=~size,type="box")
p6 <- layout(p6,xaxis=cs$axis,yaxis=cs$axis,legend=cs$legend,title=cs$title)
prm <- cs$config
prm[[1]] <- p6
p6 <- do.call("config",prm)
}
else
p6 <- ggplot(a1,aes(age,size))+
# geom_violin(aes(group=cut_width(age,1)))+
geom_boxplot(aes(group=cut_width(age,1)),outlier.alpha=0.5
,colour=cs$base,width=1)+
p0
p6 <- list(plot=p6,data=a1)
a2 <- a1
group <- list(0,1,2,3,4:5,6:8,9:16,16:max(a2$age))
grname <- sapply(group,function(x) paste0(paste(unique(range(x)),collapse="-"),"Yr"))
a2$group <- ""
for (i in seq_along(group))
a2$group[a2$age %in% group[[i]]] <- grname[i]
a2$group <- ordered(a2$group,levels=grname)
a2 <- aggregate(a2$size,by=list(group=a2$group),sum)
a2$prop <- a2$x/sum(a2$x)
a2$cum <- cumsum(a2$prop)
a2$x <- NULL
if ("plotly" %in% loadedNamespaces()) {
p11 <- plot_ly()
p11 <- add_trace(p11,data=a2,labels=~group,values=~prop,type="pie"
# ,showlegend=FALSE
,textposition = 'inside'
,textinfo = 'label+percent'
,sort = FALSE
# ,insidetextfont = list(color = '#FFFFFF')
# ,hoverinfo = 'text'
# ,text = ~paste('$', X1960, ' billions')
)
p11 <- layout(p11
,legend=c(list(orientation="v"),cs$legend)
,title=c(list(text="Age groups",side="bottom"),cs$title)
)
prm <- cs$config
prm[[1]] <- p11
p11 <- do.call("config",prm)
}
p11 <- list(plot=p11,data=a2)
}
if (isShiny)
removeNotification(id="structure")
}
if (isGrowthRate) {
if (isShiny)
showNotification(closeButton=TRUE,"Growth rate",id="growth"
,duration=99)
res <- NULL
growth <- NA
print(c('actual max.age'=max.age,'given max.age'=input$max.age))
for (s in c(0,1)) {
season <- ifelse(s==0,"After COY","Before COY")
pop <- lifestory[which(lifestory$season==s),] ## 0 - with C0, 1 - without C0
epoch <- sort(unique(pop$epoch))
res2 <- data.frame(epoch=epoch,size=NA,era="",season=season)
for (i in seq(nrow(res2))) {
ind <- which(pop$epoch==res2$epoch[i])
res2$size[i] <- nrow(pop[ind,])
era <- unique(pop[ind,"era"])
stopifnot(length(era)==1)
res2$era[i] <- era
}
if (s==0) {
pop1 <- unique(pop[pop$age==0,c("epoch","parent")])
parent <- aggregate(parent~epoch,data=pop1,length)
res3 <- with(parent,data.frame(epoch=epoch,size=parent*10
,era="",season="Dens (x10)"
))
}
if (!FALSE) {
for (j in c("I","R","C")) {
ind2 <- which(res2$era==j)
ind2 <- sort(c(ind2,which(res2$epoch==min(res2[ind2,"epoch"])-1L)))
res2[ind2,"era"] <- j
res <- rbind(res,res2[ind2,])
if (s==0) {
res3$era[ind2] <- j
res <- rbind(res,res3[ind2,])
}
if ((s==0)&&(j=="C")) {
size <- res2$size[ind2]
growth <- diff(size)/head(size,-1)
# print(size)
}
}
}
else {
for (j in c(1,2)) {
era <- ifelse(j==1,"Initialization","Implementation")
if (j==1)
ind <- which(res2$epoch<=max.age-0*subad.ini)
else
ind <- which(res2$epoch>=max.age-0*subad.ini)
res2$era[ind] <- era
res <- rbind(res,res2[ind,])
if (s==0) {
res3$era[ind] <- era
res <- rbind(res,res3[ind,])
}
if ((s==0)&&(j==2)) {
size <- res2$size[ind]
growth <- diff(size)/head(size,-1)
}
}
}
}
era <- res$era
res$epoch <- res$epoch-max(res$epoch[res$era %in% "I"])
res$era[era=="I"] <- "Initialization"
res$era[era=="R"] <- "Implementation"
res$era[era=="C"] <- "Control"
# res$era <- factor(res$era)
# res$season <- factor(res$season)
# str(res)
res$lab <- sprintf("CA Growth rate = %.3f\u00B1%.3f (%d)",mean(growth),sd(growth),length(growth))
if ("plotly" %in% loadedNamespaces()) {
da5 <- res
da5$name <- ""
da5init <- da5[da5$era %in% c("I","Initialization"),]
da5real <- da5[da5$era %in% c("R","Implementation"),]
da5ctrl <- da5[da5$era %in% c("C","Control"),]
if (nrow(da5init))
da5init$name <- "I"
if (nrow(da5real))
da5real$name <- "R"
if (nrow(da5ctrl))
da5ctrl$name <- "C"
if (nrow(da5real)) {
indIB <- grep("before",da5init$season,ignore.case=TRUE)
indIA <- grep("after",da5init$season,ignore.case=TRUE)
indID <- grep("den",da5init$season,ignore.case=TRUE)
da5init$name[indIB] <- paste0(da5init$name[indIB],"B")
da5init$name[indIA] <- paste0(da5init$name[indIA],"A")
da5init$name[indID] <- paste0(da5init$name[indID],"D")
}
if (nrow(da5real)) {
indRB <- grep("before",da5real$season,ignore.case=TRUE)
indRA <- grep("after",da5real$season,ignore.case=TRUE)
indRD <- grep("den",da5real$season,ignore.case=TRUE)
da5real$name[indRB] <- paste0(da5real$name[indRB],"B")
da5real$name[indRA] <- paste0(da5real$name[indRA],"A")
da5real$name[indRD] <- paste0(da5real$name[indRD],"D")
}
if (nrow(da5ctrl)) {
indCB <- grep("before",da5ctrl$season,ignore.case=TRUE)
indCA <- grep("after",da5ctrl$season,ignore.case=TRUE)
indCD <- grep("den",da5ctrl$season,ignore.case=TRUE)
da5ctrl$name[indCB] <- paste0(da5ctrl$name[indCB],"B")
da5ctrl$name[indCA] <- paste0(da5ctrl$name[indCA],"A")
da5ctrl$name[indCD] <- paste0(da5ctrl$name[indCD],"D")
}
d <- highlight_key(da5,~size)
# str(da5init)
p5 <- plot_ly() # type="scatter",mode="lines"
p5 <- add_lines(p5,data=da5init,y=~size,x=~epoch,split=~era
,color=~season,opacity=0.3,name=~name,showlegend=T
,text=~paste0("<b>",name,"</b>",": ",era," era, ",season,"")
,hovertemplate=paste("%{text}<br>epoch: %{x}<br>size: %{y} <extra></extra>")
)
p5 <- add_lines(p5,data=da5real,y=~size,x=~epoch,split=~era
,color=~season,opacity=0.6,name=~name,showlegend=T
,text=~paste0("<b>",name,"</b>",": ",era," era, ",season,"")
,hovertemplate=paste("%{text}<br>epoch: %{x}<br>size: %{y} <extra></extra>")
)
p5 <- add_lines(p5,data=da5ctrl,y=~size,x=~epoch,split=~era
,color=~season,opacity=1.0,name=~name,showlegend=T
,text=~paste0("<b>",name,"</b>",": ",era," era, ",season,"")
,hovertemplate=paste("%{text}<br>epoch: %{x}<br>size: %{y} <extra></extra>")
)
#p5 <- layout(p5,xaxis=list(rangemode="tozero",y=-1))
p5 <- layout(p5
,xaxis=c(list(title="Epoch",rangemode="nonnegative"),cs$axis)
,yaxis=c(list(title="Population Size"
,range=c(0,1.04*max(init$init.den*10,da5real$size,da5ctrl$size)))
,cs$axis)
,legend=c(list(orientation="v",x=NULL,y=0),cs$legend)
,title=c(list(text=res$lab),cs$title)
)
if (FALSE)
p5 <- hide_legend(p5)
prm <- cs$config
prm[[1]] <- p5
p5 <- do.call("config",prm)
}
else {
# p5 <- ggplot(res,aes(epoch,size,colour=era))+facet_grid(season~.)+
# geom_line()
p5 <- ggplot(res,aes(epoch,size))+
geom_line(aes(colour=era,linetype=season))+
xlab("Epoch")+ylab("Population Size")+
# scale_y_contionuos()
ylim(0,max(res$size))+
# geom_line(size=2)+
facet_grid(.~lab)+
p0+
theme(legend.position="bottom")+
theme(legend.title=element_blank())+
guides(colour=guide_legend(nrow=2))+
guides(linetype=guide_legend(nrow=2))+
NULL
}
p5 <- list(plot=p5,data=res)
if (isShiny)
removeNotification(id="growth")
}
if (isInterbirth | isDenning) {
# done <- lifestory$id[lifestory$season==9]
# print(lifestory[ind,])
# print(lifestory[lifestory$id=="dphefunx",])
# ind <- which(epoch>=c(0,max.age)[2] & round(epoch*ns) %% ns == 0)
# pop <- do.call("rbind",lifestory[ind])
pop <- lifestory[lifestory$epoch>c(0,max.age)[2] &
# lifestory$epoch<=max(epoch)-0*4 &
lifestory$season == 0 &
# lifestory$id %in% done &
1,]
rownames(pop) <- NULL
if (nrow(pop)) {
ind <- which(!is.na(pop$parent) & pop$age==0)
parent <- unique(pop$id[pop$id %in% pop$parent[ind]])
parent <- sample(parent)
}
else {
parent <- character()
if (isInterbirth)
isInterbirth <- FALSE
if (isDenning)
isDenning <- FALSE
}
}
if (isInterbirth) {
if (isShiny)
showNotification(closeButton=TRUE,"Interbirth interval",id="interbirth"
,duration=99)
ind <- which(!is.na(pop$parent) & pop$age==0)
parent <- unique(pop$id[pop$id %in% pop$parent[ind]])
parent <- sample(parent)
# ursa:::.elapsedTime("A1")
reprod.cycle <- unlist(lapply(parent,function(id) {
ind2 <- which(pop$parent==id & pop$age==0)
ta <- as.integer(names(table(pop$epoch[ind2])))
if (length(ta)<2)
return(NULL)
diff(ta)
}))
# ursa:::.elapsedTime("A2")
print(table(reprod.cycle))
print(summary(reprod.cycle))
lab <- sprintf("%.2f\u00B1%.2f",mean(reprod.cycle),sd(reprod.cycle))
res <- data.frame(v=reprod.cycle,lab=lab)
if (T & "plotly" %in% loadedNamespaces()) {
ta <- table(res$v)
maxy <- 1.04*max(ta/sum(ta))
p1 <- plot_ly()
p1 <- add_trace(p1,data=res,x=~v,split=~density
,type="histogram",histnorm="probability",name="")
p1 <- add_segments(p1,x=~mean(v),xend=~mean(v),y=0,yend=maxy,name="mean"
,hovertemplate="%{x:.2f}",showlegend=FALSE)
p1 <- add_segments(p1,x=~median(v),xend=~median(v),y=0,yend=maxy,name="median"
,hovertemplate="%{x:.2f}",showlegend=FALSE)
p1 <- layout(p1,xaxis=cs$axis,yaxis=cs$axis,legend=cs$legend,title=cs$title)
p1 <- layout(p1,title=list(text=unique(res$lab))
,xaxis=list(title="Interbirth interval, years")
)
prm <- cs$config
prm[[1]] <- p1
p1 <- do.call("config",prm)
}
else
p1 <- ggplot(res,aes(v,stat(density)))+
geom_histogram(binwidth=1,fill=cs$hist)+
geom_vline(xintercept=mean(reprod.cycle),col=cs$line)+
geom_vline(xintercept=median(reprod.cycle),col=cs$line
,linetype=2)+
scale_x_continuous(breaks=0:100,minor_breaks=NULL)+
xlab("Interbirth interval, years")+ylab("")+
facet_grid(.~lab)+
p0
p1 <- list(plot=p1,data=res)
if (isShiny)
removeNotification(id="interbirth")
}
if (isDenning) {
if (isShiny)
showNotification(closeButton=TRUE,"Lifespan denning",id="denning"
,duration=99)
# ursa:::.elapsedTime("B1")
res <- lapply(parent,function(id) {
if (length(parent)<3)
print(pop[pop$id==id,])
ind2 <- which(pop$parent==id & pop$age==0 &
pop$epoch<=max(epoch)-4*1)
ta <- table(pop$epoch[ind2])
if (length(parent)<3)
print(pop[ind2,])
child <- pop$id[ind2]
if (length(parent)<3)
print(child)
pop2 <- pop[pop$id %in% child & pop$age>subad.ini,,drop=FALSE]
if (!nrow(pop2))
adults <- 0
else {
if (length(parent)<3)
print(pop2)
ad <- aggregate(pop2$age,list(id=pop2$id),max)
if (length(parent)<3)
print(ad)
adults <- nrow(ad)
}
# print(ta)
list(dens=length(ta),cubs=sum(ta),adults=adults)
})
if (isShiny)
removeNotification(id="denning")
if (isShiny)
showNotification(closeButton=TRUE,"Lifespan fertililty",id="fertility"
,duration=99)
# ursa:::.elapsedTime("B2")
if (length(parent)<3)
str(res)
res <- do.call("rbind",lapply(res,as.data.frame))
rownames(res) <- parent
if (nrow(res)>2) {
if (FALSE) {
dens <- res$dens
cubs <- res$cubs
adults <- res$adults
print(table(dens))
print(table(cubs))
print(table(adults))
}
print(summary(res))
dens <- rep("",length(res$dens))
dens[res$dens==1] <- "single"
dens[res$dens==0] <- "none"
dens[res$dens>1] <- "multiple"
tden <- table(dens)
tden <- round(100*tden/sum(tden),1)
print(tden)
adults <- res$adults
tadult <- table(adults)
tadult <- round(100*tadult/sum(tadult),1)
print(tadult)
res$dens.lab <- sprintf("%.2f\u00B1%.2f Never=%.2f Once=%.2f"
,mean(res$dens),sd(res$dens)
,tden[2]/100,tden[3]/100)
res$cubs.lab <- sprintf("%.2f\u00B1%.2f Cub Production = %.2f\u00B1%.2f"
,mean(res$cubs),sd(res$cubs)
,mean(natalityRate),sd(natalityRate))
res$adults.lab <- sprintf("%.2f\u00B1%.2f",mean(res$adults),sd(res$adults))
if (T & "plotly" %in% loadedNamespaces()) {
ta <- table(res$dens)
maxy <- 1.04*max(ta/sum(ta))
p2 <- plot_ly()
p2 <- add_trace(p2,data=res,x=~dens,split=~density
,type="histogram",histnorm="probability",name="")
p2 <- add_segments(p2,x=~mean(dens),xend=~mean(dens),y=0,yend=maxy,name="mean"
,hovertemplate="%{x:.2f}",showlegend=FALSE)
p2 <- add_segments(p2,x=~median(dens),xend=~median(dens),y=0,yend=maxy,name="median"
,hovertemplate="%{x:.2f}",showlegend=FALSE)
p2 <- layout(p2,xaxis=cs$axis,yaxis=cs$axis,legend=cs$legend,title=cs$title)
p2 <- layout(p2,title=list(text=unique(res$dens.lab))
,xaxis=list(title="Dens diring lifespan")
)
prm <- cs$config
prm[[1]] <- p2
p2 <- do.call("config",prm)
}
else
p2 <- ggplot(res,aes(dens,stat(density)))+
geom_histogram(binwidth=1,fill=cs$hist)+
geom_vline(xintercept=mean(res$dens),col=cs$line)+
geom_vline(xintercept=median(res$dens),col=cs$line
,linetype=2)+
scale_x_continuous(breaks=0:100,minor_breaks=NULL)+
xlab("Dens during lifespan")+ylab("")+
facet_grid(.~dens.lab)+
p0
p2 <- list(plot=p2,data=res)
if (T & "plotly" %in% loadedNamespaces()) {
ta <- table(res$cubs)
maxy <- 1.04*max(ta/sum(ta))
p3 <- plot_ly()
p3 <- add_trace(p3,data=res,x=~cubs,split=~density
,type="histogram",histnorm="probability",name="")
p3 <- add_segments(p3,x=~mean(cubs),xend=~mean(cubs),y=0,yend=maxy,name="mean"
,hovertemplate="%{x:.2f}",showlegend=FALSE)
p3 <- add_segments(p3,x=~median(cubs),xend=~median(cubs),y=0,yend=maxy,name="median"
,hovertemplate="%{x:.2f}",showlegend=FALSE)
p3 <- layout(p3,xaxis=cs$axis,yaxis=cs$axis,legend=cs$legend,title=cs$title)
p3 <- layout(p3,title=list(text=unique(res$cubs.lab))
,xaxis=list(title="Cubs diring lifespan")
)
prm <- cs$config
prm[[1]] <- p3
p3 <- do.call("config",prm)
}
else
p3 <- ggplot(res,aes(cubs,stat(density)))+
geom_histogram(binwidth=1,fill=cs$hist)+
geom_vline(xintercept=mean(res$cubs),col=cs$line)+
geom_vline(xintercept=median(res$cubs),col=cs$line
,linetype=2)+
scale_x_continuous(breaks=0:100,minor_breaks=NULL)+
xlab("Cubs during lifespan")+ylab("")+
facet_grid(.~cubs.lab)+
p0
p3 <- list(plot=p3,data=res)
if (T & "plotly" %in% loadedNamespaces()) {
ta <- table(res$adults)
maxy <- 1.04*max(ta/sum(ta))
p4 <- plot_ly()
p4 <- add_trace(p4,data=res,x=~adults,split=~density
,type="histogram",histnorm="probability",name="")
p4 <- add_segments(p4,x=~mean(adults),xend=~mean(adults),y=0,yend=maxy,name="mean"
,hovertemplate="%{x:.2f}",showlegend=FALSE)
p4 <- add_segments(p4,x=~median(adults),xend=~median(adults),y=0,yend=maxy,name="median"
,hovertemplate="%{x:.2f}",showlegend=FALSE)
p4 <- layout(p4,xaxis=cs$axis,yaxis=cs$axis,legend=cs$legend,title=cs$title)
p4 <- layout(p4,title=list(text=unique(res$adults.lab))
,xaxis=list(title="Survived adults diring lifespan")
)
prm <- cs$config
prm[[1]] <- p4
p4 <- do.call("config",prm)
}
else
p4 <- ggplot(res,aes(adults,stat(density)))+
geom_histogram(binwidth=1,fill=cs$hist)+
geom_vline(xintercept=mean(res$adults),col=cs$line)+
geom_vline(xintercept=median(res$adults),col=cs$line
,linetype=2)+
scale_x_continuous(breaks=0:100,minor_breaks=NULL)+
xlab("Survived cubs during lifespan")+ylab("")+
facet_grid(.~adults.lab)+
p0
p4 <- list(plot=p4,data=res)
}
if (isShiny)
removeNotification(id="fertility")
}
if (isShiny)
removeModal()
input$subad.age <- subad.ini
list(input=input,p0=p0,p1=p1,p2=p2,p3=p3,p4=p4,p5=p5,p6=p6,p7=p7,p8=p8,p9=p9
,p10=p10,p11=p11)
}