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perturb.R
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'perturb' <- function(lifestory,set=c("primary","advanced","all"),pattern="") {
isShiny <- (("shiny" %in% loadedNamespaces())&&(length(shiny::shinyOptions())>0))
if (isShiny) {
showModal(modalDialog(title = "Perturbation in progress","Please wait"
,size="s",easyClose = TRUE,footer = NULL))
on.exit(removeModal())
}
# str(lifestory$input)
# prmDev[[1]] <- data.frame(name="mortality.adult",min=0.08,max=0.12,step=0.005)
# prmDev[[2]] <- data.frame(name="mortality.adult",min=0.08,max=0.12,step=0.005)
prmList <- c('1'="mortality.adult"
,'2'="mortality.cub"
,'3'="max.age"
,'4'="litter"
,'5'="broken.C1"
,'6'="pregnant"
,'7'="k1i"
,'8'="k1d"
,'9'="fertility"
,'10'="removal.rate"
)
canceled <- c("broken.C2")
if (nchar(pattern)) {
prmList <- grep(pattern,prmList,ignore.case=TRUE,value=TRUE)
}
else {
set <- match.arg(set)
if (set=="primary")
prmList <- prmList[1:9]
else if (set=="advanced")
prmList <- prmList[-c(1:9)]
}
standardized <- c("broken.C1","broken.C2","pregnant"
,"fertility","k1i","k1d")
ret <- vector("list",length(prmList))
names(ret) <- prmList
cs <- colorScheme()
if (isShiny)
showNotification(closeButton=TRUE,"check reference"
,id="ref",duration=99)
cat("---- basic -----\n")
# growthRate(lifestory) ## just for test with next line
g0 <- growthRate(lifestory,nochanged_dummy=TRUE)
cat("---- ===== -----\n")
if (isShiny)
removeNotification(id="ref")
if (!length(g0))
return(ret)
# return(ret)
gr0 <- mean(g0)
agr0 <- abs(gr0)
sgr0 <- sign(gr0)
k <- 0L
nk <- length(prmList)
initRange <- rangePrm()
# str(lifestory$input)
for (p in .sample(prmList)) {
rng <- initRange[[p]]
if (F & !length(grep("indep.fraction",p)))
next
lab <- switch(p
,'mortality.adult'="Adult mortality"
,'mortality.cub'="COY mortality"
,'max.age'="Maximal age"
,'litter'="COY litter size"
,'pregnant'="Birth success"
,'broken.C1'="Weaning C1 probability"
,'broken.C2'="Weaning C2 probability"
,'fertility'="Age specific fertility"
,'k1i'="Mort. slope of ind. youngs"
,'k1d'="Mort. slope of dep. youngs"
,'removal.rate'="Human-caused removal rate"
,paste("unspecified description for",dQuote(p)))
if (p=="broken.C1") {
pname <- "indep.fraction"
pind <- 2L
prm0 <- lifestory$input[[pname]][2]
}
else if (p=="broken.C2") {
pname <- "indep.fraction"
pind <- 3L
prm0 <- lifestory$input[[pname]][3]
}
else {
pname <- p
pind <- 1L
}
prm00 <- lifestory$input[[pname]]
prm0 <- prm00[pind]
message(paste0(lab,": ",prm0))
sc <- rng$forcing
# print(sc)
# if (agr0>0.005) {
# sc <- sc*round(100*agr0)^0.75
# }
if (gr0>(+0.005))
si <- seq(-5,3)*sign(sc)#*(-sgr0)
else if (gr0<(-0.005))
si <- seq(-3,5)*sign(sc)#*(-sgr0)
else
si <- seq(-4,4)
# print(gr0)
# print(si)
prm <- with(rng,seq(from,to,len=ifelse(agr0<0.002,11,ifelse(agr0<0.005,9,7))))
if (TRUE) {
d <- mean(diff(prm))
d <- round(d,-floor(log(d)/log(10)))
prm <- prm0+d*c(seq(-15,-1),0,seq(1,15))
prm <- prm[prm>=rng$from-1e-6 & prm<=rng$to+1e-6]
# print(prm)
}
indC <- which.min(abs(prm-prm0))
if (length(indC)>1)
indC <- .sample(indC)
ind <- si+indC
ind <- sort(ind[ind>0 & ind<=length(prm)])
# print(ind)
# prm <- prm[ind]
# print(prm)
repeat({
if (length(ind)<=5)
break
ind2 <- abs(range(ind)-indC)
ind3 <- which(ind2==max(ind2))
if (length(ind3)==2)
ind <- head(tail(ind,-1),-1)
else if (ind3==1)
ind <- tail(ind,-1)
else if (ind3==2)
ind <- head(ind,-1)
})
# print(ind)
prm[indC] <- prm0
prm <- c(na.omit(prm[ind]))
# print(prm)
indC <- which(prm==prm0)
k <- k+1L
if (isShiny)
showNotification(closeButton=TRUE,paste0(lab," (",k," of ",nk,") ...")
,id=p,duration=99)
prmlab <- round(prm,3)
res2 <- NULL
# print(sprintf("%+.3f\u00B1%.3f",mean(g0),sd(g0)))
arglist <- list(lifestory,NA)
names(arglist) <- c("",p)
desc <- rep("",length(prm))
res <- data.frame(prm=prmlab,desc="",mean=NA,sd=NA)
for (i in seq(nrow(res))) {
prm00[pind] <- prm[i]
arglist[[pname]] <- prm00 ## ++
# str(arglist[-1])
g1 <- if (i==indC) g0 else do.call("growthRate",arglist)
if (!length(g1))
break
# g1 <- growthRate(lifestory,mortality.adult=res$x[i])
# res$mean[i] <- mean(g1)
# res$sd[i] <- sd(g1)
# desc <- paste0(res$x[i],"\n",sprintf("%.3f\u00B1%.3f",res$mean[i],res$sd[i]))
desc[i] <- sprintf("%+.3f\u00B1%.3f",mean(g1),sd(g1))
res$mean[i] <- mean(g1)
res$sd[i] <- sd(g1)
res2 <- rbind(res2,data.frame(prm=prmlab[i],value=g1
,desc=desc[i]))
}
# if (p %in% c("pregnant","indep.fraction1"))
# print(res)
if (isShiny)
removeNotification(id=p)
if (is.null(res2))
next
if (length(desc)==length(unique(desc))) {
res$desc <- factor(desc,levels=desc[order(prm)],ordered=TRUE)
}
else {
desc2 <- paste0(prmlab,"\n",desc)
res$desc <- factor(desc2,levels=desc2[order(prm)],ordered=TRUE)
}
res$xlab <- factor(paste0(prmlab,"\n",desc))
if (length(desc)==length(unique(desc))) {
res2$desc <- factor(res2$desc,levels=desc[order(prm)]
,ordered=TRUE)
}
else {
res2$desc <- factor(paste0(res2$prm,"\n",res2$desc)
,levels=paste0(prmlab,"\n",desc)
,ordered=TRUE)
}
names(desc) <- prmlab
if ("plotly" %in% loadedNamespaces()) {
if (T) {
da <- res2
# da <- da[sample(nrow(da)),]
prm <- da$prm
prmS <- sort(unique(prm))
da$prm <- as.character(prm)
prm0 <- as.character(prm0)
ind <- which(da$prm %in% prm0)
da$prm[ind] <- paste0("<b>",prm[ind],"</b>")
indS <- which(prmS %in% prm0)
prmS[indS] <- paste0("<b>",prmS[indS],"</b>")
da$prm <- factor(da$prm,level=prmS,ordered=TRUE)
# print(levels(da$prm))
# print(levels(da$desc))
# da$desc <- as.character(da$desc)
res2 <- da
}
lab <- c(x="Growth Rate",y=lab)
res2$label <- gsub("((.+)(\\n))*(.+)","\\4",res2$desc)
s1 <- plot_ly()
s1 <- add_trace(s1,data=res2,type="violin",split=~prm
,text=~desc
,name=~label
,hoverinfo="name"
,y=~prm,x=~value,orientation='h'
# ,x=~prm,y=~value,orientation='v',showlegend=FALSE
,meanline=list(visible=T)
)
if (FALSE)
s1 <- layout(s1
,xaxis=c(list(title=lab["x"]),cs$axis)
,yaxis=c(list(title=lab["y"],type="category"),cs$axis)
,legend=cs$legend
)
else {
s1 <- layout(s1,xaxis=cs$axis,yaxis=cs$axis,legend=cs$legend)
s1 <- layout(s1
,xaxis=list(title=lab["x"])
,yaxis=list(title=lab["y"]
# ,categoryorder="array"
# ,categoryarray=prm2
)
,legend=list(orientation='v')
# ,legend=list(orientation='h',x=0.5,y=1.2)
)
prm <- cs$config
prm[[1]] <- s1
s1 <- do.call("config",prm)
}
}
else if (!FALSE)
s1 <- ggplot(res2,aes(prm,value))+
geom_violin(fill=cs$hist,colour=cs$base)+
geom_point(data=res,aes(prm,mean))+
xlab(lab)+ylab("Growth Rate")+
facet_grid(prm~.,scales="free",labeller=labeller(prm=desc))+
scale_x_continuous(breaks=prmlab)+
coord_flip()+
cs$p0+
NULL
else if (FALSE)
s1 <- ggplot(res2,aes(prm,value))+
geom_violin(fill=cs$hist,colour=cs$base)+
geom_point(data=res,aes(prm,mean))+
xlab(lab)+ylab("Growth Rate")+
facet_grid(.~desc,scales="free")+
scale_x_continuous(breaks=prmlab)+
cs$p0+
NULL
else {
res2$xlab <- factor(with(res2,paste0(prm,"\n",desc)))
s1 <- ggplot(res2,aes(xlab,value))+
geom_violin(fill=cs$hist,colour=cs$base)+
xlab(lab)+ylab("Growth Rate")+
geom_point(data=res,aes(xlab,mean))+
# geom_line(data=res,aes(xlab,mean))+
# facet_grid(.~desc,scales="free")+
# scale_x_discrete(breaks=desc)+
cs$p0+
NULL
}
ret[[p]] <- list(plot=s1,data=res2)
# break
}
ret
}