Nothing
R/sim.secr.R
In secr: Spatially Explicit Capture-Recapture
Defines functions
getpmixall
print.secrlist
print.secrdata
############################################################################################
## package 'secr'
## sim.secr.R
## uses Dsurface.R, utility.R, secrloglik.R
## Copyright (C) 2019 Murray Efford
## 2019-10-05 converted to cpp
## 2019-10-06 yet to fix: groups?
## 2019-10-06 excludes: knownclass (hcov, h2)
## 2019-10-06 excludes: mixed detector types
## 2019-10-06 excludes: individual covariates
## 2019-10-06 excludes: telemetry
## 2020-11-08 bad rownames for sim.detect when renumber = FALSE
############################################################################################
disinteraction <- function (capthist, groups, sep='.') {
ngv <- length(groups)
grouplevels <- group.levels(capthist, groups, sep=sep)
if (ngv>1)
temp <- matrix(unlist(strsplit(as.character(grouplevels), sep, fixed=TRUE)),
byrow = T, ncol = ngv)
else temp <- grouplevels
temp <- data.frame(temp)
names(temp) <- groups
temp
}
############################################################################################
simulate.secr <- function (object, nsim = 1, seed = NULL, maxperpoly = 100, chat = 1,
...)
## if CL, condition on n? what about distribution of covariates over n?
## locate according to IHP with lambda(X) controlled by f(X|covar), assuming homog Poisson
## i.e. use f(X|covar)/max(f(X|covar)) to reject until meet quota n?
## or f(X, covar | detected)?
## TOO HARD - cf MARK
## 2012-10-25
## other possible exclusions:
## mashed?
{
## check input
if (any(c("bn", "bkn", "bkc", "Bkc") %in% tolower(object$vars)))
stop ("simulate works only with binary behavioural responses")
if (!inherits(object,'secr'))
stop ("requires 'secr' object")
if (object$CL)
stop ("not implemented for conditional likelihood")
## density array dim(mask points, groups, sessions)
Darray <- getDensityArray (predictDsurface(object))
## setup
ngrp <- dim(Darray)[2]
nsession <- dim(Darray)[3]
if (!is.null(object$groups)) {
## individual covariates for foundation of g
di <- disinteraction (object$capthist, object$groups)
}
sesscapt <- vector('list', nsim)
##################
## set random seed
## copied from simulate.lm
if (!exists(".Random.seed", envir = .GlobalEnv, inherits = FALSE))
runif(1)
if (is.null(seed))
RNGstate <- get(".Random.seed", envir = .GlobalEnv)
else {
R.seed <- get(".Random.seed", envir = .GlobalEnv)
set.seed(seed)
RNGstate <- structure(seed, kind = as.list(RNGkind()))
on.exit(assign(".Random.seed", R.seed, envir = .GlobalEnv))
}
##################
## loop over replicates
runone <- function(r) {
## argument r is unused dummy
sesspopn <- list()
for (sessnum in 1:nsession) {
if (nsession==1) mask <- object$mask
else mask <- object$mask[[sessnum]]
popn <- list()
for (g in 1:ngrp) {
if (inherits(mask, 'linearmask')) {
density <- Darray[,g,sessnum] ## vector
mod2D <- 'linear' ## linear Poisson or IHP
}
else {
if (object$model$D == ~1) {
density <- Darray[1,g,sessnum] ## scalar
mod2D <- 'poisson' ## homogeneous
}
else {
density <- Darray[,g,sessnum] ## vector
mod2D <- 'IHP' ## inhomogeneous
}
}
if (chat > 1)
density <- density / chat
ND <- switch (object$details$distribution,
binomial = 'fixed',
poisson = 'poisson',
'poisson')
##-------------------------------------------------------------------
## sim.popn arguments omitted:
## buffer redundant when mask specified
## buffertype ditto
## poly ditto
## covariates ignored for now...
## number.from = 1 fine
## nsession = 1 fine here within session loop as long
## as there is no turnover model
## details = NULL not relevant (turnover and special model2D only)
## seed = NULL default mechanism -- needs attention 2014-09-07
popn[[g]] <- sim.popn (D = density, core = mask, model2D = mod2D, Ndist = ND)
## ------------------------------------------------------------------
## Add any needed covariates, first generating a clean dataframe
if (is.null(object$groups) & is.null(object$hcov))
covariates(popn[[g]]) <- NULL
else
covariates(popn[[g]]) <- data.frame(row.names = row.names(popn[[g]]))
## ---groups---
if (!is.null(object$groups)) {
grpcov <- as.data.frame(di[rep(g, nrow(popn[[g]])),]) ## 2014-08-08
names(grpcov) <- object$groups
covariates(popn[[g]]) <- cbind(covariates(popn[[g]]),grpcov)
}
## ---hcov---
## sample with replacement from original hcov field 2014-08-08
if (!is.null(object$hcov)) {
if (ms(object))
oldhcov <- covariates(object$capthist[[sessnum]])[,object$hcov]
else
oldhcov <- covariates(object$capthist)[,object$hcov]
covariates(popn[[g]])[object$hcov] <-
sample(oldhcov, size = nrow(popn[[g]]), replace = TRUE)
}
## ------------------------------------------------------------------
}
sesspopn[[sessnum]] <- do.call(rbind, popn) ## combine groups in one popn object
}
sim.detect(object, sesspopn, maxperpoly)
}
sesscapt <- lapply(1:nsim, runone)
## experimental
if (chat>1) sesscapt <- lapply(sesscapt, replicate, chat)
attr(sesscapt,'seed') <- RNGstate ## save random seed
class(sesscapt) <- c('secrdata', 'list')
sesscapt
}
############################################################################################
sim.secr <- function (object, nsim = 1, extractfn = function(x)
c(deviance=deviance(x), df=df.residual(x)), seed = NULL,
maxperpoly = 100, data = NULL, tracelevel = 1, hessian =
c('none','auto','fdHess'), start = object$fit$par, ncores = NULL) {
## parametric bootstrap simulations based on a fitted secr object
## extractfn is a required function to extract values from an secr fit
## it should return a vector of named values that does not vary in length
## 'hessian' overrides value in object$details
## set hessian='auto' if extractfn requires variance-covariance matrix
hessian <- match.arg(hessian)
cl <- match.call(expand.dots = TRUE)
cl <- paste(names(cl)[-1],cl[-1], sep=' = ', collapse=', ' )
cl <- paste('sim.secr(', cl, ')')
if (is.null(extractfn)) extractfn <- trim
test <- extractfn(object)
if (is.numeric(test)) {
n.extract <- length(test)
if (n.extract<=0)
stop ("invalid 'extractfn'")
}
detectnames <- names(object$design0[[1]]) ## names of real detection parameters
details <- replace(object$details, 'hessian', hessian)
tracelevel <- as.integer(tracelevel)
details$trace <- tracelevel > 1
min.detections <- 1
.localstuff$iter2 <- 0
if (any(detector(traps(object$capthist)) == 'single')) {
memo ('multi-catch likelihood used for single-catch traps', tracelevel>0)
}
if (is.null(data)) {
memo ('sim.secr simulating detections...', tracelevel>0)
## use multiple cores only for model fitting 2015-12-02
data <- simulate(object, nsim = nsim, seed = seed, maxperpoly = maxperpoly)
}
else {
if (any(class(data) != c('secrdata', 'list')))
stop("invalid data")
}
fitmodel <- function (sc) {
## i <<- i+1
## use second counter so as not to interfere with secrloglik
.localstuff$iter2 <- .localstuff$iter2 + 1 ## 2016-01-09
if (tracelevel>0)
memo (paste('sim.secr fitting replicate', .localstuff$iter2, '...'), TRUE)
nc <- sum(counts(sc)$'M(t+1)'[,'Total'])
if (nc >= min.detections) {
tempfit <- suppressWarnings( secr.fit(sc, model = object$model, mask = object$mask,
CL = object$CL, detectfn = object$detectfn, binomN = details$binomN,
start = start, link = object$link, fixed = object$fixed,
timecov = object$timecov, sessioncov = object$sessioncov,
groups = object$groups, dframe = object$dframe, details = details,
method = object$fit$method, verify = FALSE, biasLimit = NA,
ncores = ncores) )
extractfn(tempfit)
}
else if (is.list(test)) list() else rep(NA, n.extract)
}
output <- lapply (data, fitmodel)
if (is.numeric(test)) {
output <- do.call(rbind, output)
output <- data.frame(output)
}
else {
class(output) <- c('secrlist', 'list')
}
attr(output,'seed') <- attr(data,'seed')
attr(output,'call') <- cl
attr(output,'extractfn') <- extractfn
output
}
############################################################################################
print.secrdata <- function(x,...) {
## suggestion of Rolf Turner 19 Jan 2009 for printing without attributes
attributes(x) <- NULL
print(x)
}
############################################################################################
print.secrlist <- function(x,...) {
## suggestion of Rolf Turner 19 Jan 2009 for printing without attributes
attributes(x) <- NULL
print(x)
}
############################################################################################
## mixture proportions for representative animal
## (i.e. assuming no individual or group variation)
## assume dim(PIA)[1] == 1
getpmixall <- function(PIA, realparval)
{
nc <- dim(PIA)[2]
k <- dim(PIA)[4]
nmix <- dim(PIA)[5]
pmix <- 1 ## default single class
if (nmix>1) {
# index of first non-missing occasion s and detector k
fsk <- firstsk(PIA[1,1,,,1, drop = FALSE])
kc <- as.vector((fsk-1) %/% k + 1)[1]
sc <- as.vector((fsk-1) %/% k + 1)[1]
pmix <- PIA[cbind(1,1,sc,kc,1:nmix)]
}
pmix
}
sim.detect <- function (object, popnlist, maxperpoly = 100, renumber = TRUE)
## popnlist is always a list of popn objects, one per session
{
## we use fake CH to extract parameter value dependent on prev capt
## BUT this is slow and clunky...
dummycapthist<- function (capthist, pop, fillvalue=1) {
if (ms(capthist)) {
output <- list()
for (i in 1:nsession)
output[[i]] <- dummycapthist (capthist[[i]],
pop = pop[i], fillvalue = fillvalue)
class(output) <- c('capthist', 'list')
session(output) <- session(capthist) ## 2010 03 10
output
}
else {
newdim <- dim(capthist)
newdim[1] <- nrow(pop[[1]])
output <- array(fillvalue, dim = newdim)
## CAPTURE ON LAST OCCASION
## trick to keep array valid without misleading
output[,,newdim[3]] <- 1
class(output) <- 'capthist'
traps(output) <- traps(capthist)
session(output) <- session(capthist)
covariates(output) <- covariates(pop[[1]])
output
}
}
## --------------------------------------------------------------------
## Exclusions
## see also below dettype %in% c(-1,0,1,2,5,6,7)
if (!is.null(object$groups) & (object$details$param>1))
stop("simulation does not extend to groups when param>1")
if ('telemetry' %in% unlist(detector(traps(object$capthist))))
stop("telemetry models are not supported in simulate.secr")
## --------------------------------------------------------------------
## process behavioural responses
Markov <- any(c('B','Bk','K') %in% object$vars)
btype <- which (c("b", "bk", "k") %in% tolower(object$vars))
if (length(btype) > 1)
stop ("all behavioural responses must be of same type in sim.detect")
if (length(btype) == 0)
btype <- 0
## --------------------------------------------------------------------
## setup
if (is.null(object$details$ignoreusage))
object$details$ignoreusage <- FALSE
if (is.null(object$details$miscparm))
object$details$miscparm <- numeric(4)
N <- sapply(popnlist, nrow)
nocc <- if(ms(object)) sapply(object$capthist, ncol) else ncol(object$capthist)
ndet <- if(ms(object)) sapply(traps(object$capthist), nrow) else nrow(traps(object$capthist))
sessionlevels <- session(object$capthist) ## was names(capthist) 2009 08 15
nsession <- length(sessionlevels)
sessmask <- object$mask
if (!ms(sessmask)) sessmask <- list(sessmask) ## always a list
grplevels <- group.levels(object$capthist, object$groups, sep=".")
beta <- object$fit$par
userd <- is.null(object$details$userdist)
ncores <- setNumThreads()
grain <- if (ncores==1) 0 else 1
##------------------------------------------
## detection parameters for each session, animal, occasion, detector
## realparval is lookup table of values,
## design$PIA is index to lookup
## real parameter values for naive animals
## using existing design to save time in secr.design.MS...
if (length(unique(object$design0$PIA)) == 1) {
design0 <- object$design0
dim0 <- dim(design0$PIA)
design0$PIA <- array (1, dim = c(dim0[1], max(N), dim0[3:5]))
dummyCH <- NULL
}
else {
dummyCH <- dummycapthist(object$capthist, popnlist, fillvalue = 1)
design0 <- secr.design.MS (dummyCH, object$model, object$timecov, object$sessioncov,
object$groups, object$hcov, object$dframe,
naive = TRUE, CL = object$CL,
ignoreusage = object$details$ignoreusage,
contrasts = object$details$contrasts)
}
## uniform over individuals
## C++ code uses individual-specific PIA even in full-likelihood case
for (i in 1:nsession) {
if (is.null(object$groups)) {
## all animals the same...
matchedgroup <- rep(1, N[i])
}
else {
## group identities for simulated animals
## can treat popn as capthist in group.factor if not ms(object)
newgroup <- group.factor (popnlist[[i]], object$groups)
## here we assume original PIA is for a full-likelihood model with
## one row per group
matchedgroup <- (1:nlevels(newgroup))[as.numeric(newgroup)]
}
design0$PIA[i,1:N[i],,,] <- object$design0$PIA[i,matchedgroup,,,]
}
realparval0 <- makerealparameters (design0, beta, object$parindx, object$link,
object$fixed)
## real parameter values for 'caughtbefore' animals or detectors
## -- this definition of design1 differs from that in secr.fit()
## where parameter values are approppriate to the particular
## (realised) detection histories
if (btype > 0) {
if (is.null(dummyCH))
dummyCH <- dummycapthist(object$capthist, popnlist, fillvalue = 1)
design1 <- secr.design.MS (dummyCH, object$model, object$timecov, object$sessioncov,
object$groups, object$hcov, object$dframe, ignoreusage = object$details$ignoreusage,
contrasts = object$details$contrasts, CL = object$CL)
realparval1 <- makerealparameters (design1, beta, object$parindx, object$link,
object$fixed) # caught before
}
else { ## faster to just copy if no behavioural response
design1 <- design0
realparval1 <- realparval0
}
##------------------------------------------
# see loglikhelperfn.R for getD
# Density
if (!object$CL ) {
D <- getD (object$designD, beta, sessmask,
object$parindx, object$link, object$fixed,
grplevels, sessionlevels,
parameter = 'D')
}
# Non-Euclidean distance parameter
NE <- getD (object$designNE, beta, sessmask,
object$parindx, object$link, object$fixed,
grplevels, sessionlevels,
parameter = 'noneuc')
#--------------------------------------------------------------------
output <- list()
for (sessnum in 1:nsession) {
## in multi-session case must get session-specific data from lists
if (ms(object)) {
s <- ncol(object$capthist[[sessnum]])
session.traps <- traps(object$capthist)[[sessnum]]
session.mask <- if (userd | (object$details$param %in% c(2,6)))
object$mask[[sessnum]] else NULL
Dtemp <- if (object$details$param %in% c(4:6))
predict(object)[[sessnum]]['D','estimate']
else NA
nmash <- attr(object$capthist[[sessnum]], 'n.mash')
}
else {
s <- ncol(object$capthist)
session.traps <- traps(object$capthist)
session.mask <- if (userd | (object$details$param %in% c(2,6)))
object$mask else NULL
Dtemp <- if (object$details$param %in% c(4:6)) predict(object)['D','estimate']
else NA
nmash <- attr(object$capthist, 'n.mash')
}
## function reparameterize is in secrloglik.R
Xrealparval0 <- reparameterize (realparval0, object$detectfn, object$details,
session.mask, session.traps, Dtemp, s)
Xrealparval1 <- reparameterize (realparval1, object$detectfn, object$details,
session.mask, session.traps, Dtemp, s)
##------------------------------------------
session.animals <- popnlist[[sessnum]]
## pre-compute distances from detectors to animals
## pass miscellaneous unmodelled parameter(s)
nmiscparm <- length(object$details$miscparm)
if (nmiscparm > 0) {
miscindx <- max(unlist(object$parindx)) + (1:nmiscparm)
attr(session.mask, 'miscparm') <- coef(object)[miscindx, 1]
}
##------------------------------------------
dettype <- detectorcode(session.traps, MLonly = FALSE, noccasions = nocc[sessnum])
if (! all(dettype %in% c(-1,0,1,2,3,4,5,6,7)))
stop ("detector type ",
paste(detector(session.traps)),
" not implemented")
binomN <- expandbinomN(object$details$binomN, dettype)
if (all(detector(session.traps) %in% .localstuff$polydetectors)) {
k <- c(table(polyID(session.traps)),0)
K <- length(k)-1
}
else {
k <- nrow(session.traps)
K <- k
}
#------------------------------------------
## simulate this session...
usge <- usage(session.traps)
if (is.null(usge) | object$details$ignoreusage)
usge <- matrix(1, nrow = K, ncol = s)
NR <- N[sessnum]
if (all(detector(session.traps) %in% .localstuff$exclusivedetectors)) {
maxdet <- NR * s
}
else {
# safety margin : average detections per animal per detector per occasion
maxdet <- NR * s * K * maxperpoly
}
if ((object$detectfn==12) || (object$detectfn==13)) {
## muN, sdN
object$details$miscparm[2:3] <- beta[max(unlist(object$parindx))+(1:2)]
}
## requires session.animals has covariate named 'hcov'
knownclass <- getknownclass(session.animals, object$details$nmix, object$hcov)
## get fixed pmix for each class
pmix <- getpmixall(design0$PIA, Xrealparval0)
## TO BE FIXED
if (length(unique(dettype))>1 | length(unique(binomN))>1)
stop("simulation not yet updated for varying detector type")
if (all(dettype %in% c(-1,0,1,2,5,8))) {
if (is.function(object$details$userdist)) {
## only use of NE in this fn
noneuc <- getmaskpar(!is.null(NE), NE, nrow(session.mask), sessnum, FALSE, NULL)
density <- getmaskpar(!object$CL, D, nrow(session.mask), sessnum,
object$details$unmash, nmash)
distmat2 <- getuserdist(session.traps, session.animals, object$details$userdist, sessnum,
noneuc[,1], density[,1], object$details$miscparm, object$detectfn==20)
}
else {
distmat2 <- getdistmat2 (
session.traps,
session.animals,
object$details$userdist,
object$detectfn == 20)
}
## precompute gk, hk for point detectors
gkhk0 <- makegkPointcpp (
as.integer(object$detectfn),
as.integer(grain),
as.integer(ncores),
as.matrix(Xrealparval0),
as.matrix(distmat2),
as.double(object$details$miscparm))
gkhk <- makegkPointcpp (
as.integer(object$detectfn),
as.integer(grain),
as.integer(ncores),
as.matrix(Xrealparval1),
as.matrix(distmat2),
as.double(object$details$miscparm))
if (any(dettype == 8)) {
stop("sim.secr not ready for capped detectors")
# gkhk <- cappedgkhkcpp (as.integer(nrow(Xrealparval1)), as.integer(nrow(session.traps)),
# as.double(getcellsize(session.mask)), as.double(density[,1]),
# as.double(gkhk$gk), as.double(gkhk$hk))
}
}
# debug
# message('sessnum ', sessnum, ' NR ', NR, ' sum gkhk0$gk ', sum(gkhk0$gk))
if (all(dettype %in% c(-1,0,1,2,8))) {
temp <- simdetectpointcpp (
as.integer (dettype[1]), ## detector -1 single, 0 multi, 1 proximity, 2 count,...
as.integer (NR),
as.integer (nrow(Xrealparval0)), ## cc0
as.integer (nrow(Xrealparval1)), ## cc
as.double (gkhk0$gk),
as.double (gkhk$gk),
as.double (gkhk0$hk),
as.double (gkhk$hk),
as.integer (design0$PIA[sessnum,1:NR,1:s,1:K,]), ## naive
as.integer (design1$PIA[sessnum,1:NR,1:s,1:K,]),
as.integer (object$details$nmix),
as.integer (knownclass),
as.double (pmix),
as.matrix (usge),
as.integer (btype), ## code for behavioural response 0 none etc.
as.integer (Markov), ## learned vs transient behavioural response 0 learned 1 Markov
as.integer (binomN) ## number of trials for 'count' detector modelled with binomial
)
}
else if (all(dettype %in% c(3,4,6,7))) {
temp <- simdetectpolycpp (
as.integer (dettype[1]), ## detector 3 exclusive polygon, 4 exclusive transect, 6 polygon, 7 transecr
as.integer (object$detectfn), ## code 0 = halfnormal, 1 = hazard, 2 = exponential, 3 = uniform
as.integer (object$details$nmix), ## number of classes
as.integer (btype), ## code for behavioural response 0 none etc.
as.integer (Markov), ## learned vs transient behavioural response 0 learned 1 Markov
as.integer (k), ## number of vertices per polygon (zero-terminated vector)
as.matrix (session.animals), ## x,y points of animal range centres (first x, then y)
as.matrix (session.traps), ## x,y locations of traps (first x, then y)
as.matrix (Xrealparval0), ## Parameter values (matrix nr= comb of g0,sigma,b nc=3) [naive animal]
as.matrix (Xrealparval1), ## Parameter values (matrix nr= comb of g0,sigma,b nc=3) [caught before]
as.integer (design0$PIA[sessnum,1:NR,1:s,1:K,]), ## lookup which g0/sigma/b combination to use for given g, S, K [naive animal]
as.integer (design1$PIA[sessnum,1:NR,1:s,1:K,]), ## lookup which g0/sigma/b combination to use for given n, S, K [caught before]
as.integer (knownclass), ## known membership of 'latent' classes
as.double (pmix), ## membership probabilities
as.matrix (usge), ## ss x kk array of 0/1 usage codes or effort
as.integer (binomN), ## number of trials for 'count' detector modelled with binomial
as.integer (maxperpoly) ##
)
if ((temp$resultcode == 2) & (any(dettype %in% c(6,7)))) {
stop (">100 detections per animal per polygon per occasion")
}
}
else
if (all(dettype %in% c(5))) {
if (is.null(object$details$cutval))
stop ("sim.detect for signal model requires object$details$cutval")
temp <- simdetectsignalcpp (
as.integer(dettype[1]),
as.integer(object$details$nmix),
as.integer(object$detectfn),
as.integer(object$details$cutval),
as.matrix(Xrealparval0),
as.integer(design0$PIA[sessnum,1:NR,1:s,1:K,]), # index of N,S,K,x to rows in Xrealparval0
as.integer(pmix),
as.integer(knownclass),
as.matrix(session.animals),
as.matrix(session.traps),
as.matrix(distmat2),
as.matrix(usge),
as.double(object$details$miscparm)
)
}
if (temp$resultcode != 0) {
stop ("simulated detection failed, code ", temp$resultcode)
}
w <- array(temp$value, dim=c(s, K, NR), dimnames = list(1:s,NULL,NULL))
w <- aperm(w, c(3,1,2))
w <- w[apply(w,1,sum)>0,,, drop = FALSE]
class(w) <- 'capthist' # NOT data.frame
traps(w) <- session.traps
session(w) <- sessionlevels[sessnum]
if (!is.null(covariates(popnlist))) {
covariates(w) <- subset(covariates(popnlist[[sessnum]]), subset =
as.logical(temp$caught))
}
##---------------------
## signal
if (any(dettype %in% c(5,12)) & (temp$n>0)) {
nd <- sum(abs(w))
signal(w) <- temp$signal[1:nd]
if ((object$detectfn==12) || (object$detectfn==13))
noise(w) <- temp$signal[(nd+1):(2*nd)]
attr(w, 'cutval') <- object$details$cutval
}
else {
attr(w, 'signalframe') <- NULL
attr(w, 'cutval') <- NULL
}
##---------------------
## polygon or transect
if (any(dettype %in% c(3,4,6,7))) {
nd <- sum(abs(w))
if (nd>0)
xymat <- temp$detectedXY[1:nd, 1:2, drop = FALSE]
else
xymat <- matrix(nrow=0, ncol=2)
detectedXY <- data.frame(xymat)
names(detectedXY) <- c('x','y')
attr(w, 'detectedXY') <- detectedXY
}
else
attr(w, 'detectedXY') <- NULL
if (renumber & (temp$n>0)) {
rownames(w) <- 1:temp$n
}
else {
## rownames(w) <- (1:N[sessnum])[as.logical(temp$caught)]
## changed 2020-11-08
rownames(w) <- rownames(session.animals)[as.logical(temp$caught)]
}
output[[sessnum]] <- w
} ## end of session loop
if (nsession == 1) output <- output[[1]]
else {
names(output) <- sessionlevels
class(output) <- c('capthist', 'list')
}
output
}
############################################################################################
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Defines functions getpmixall print.secrlist print.secrdata
############################################################################################
## package 'secr'
## sim.secr.R
## uses Dsurface.R, utility.R, secrloglik.R
## Copyright (C) 2019 Murray Efford
## 2019-10-05 converted to cpp
## 2019-10-06 yet to fix: groups?
## 2019-10-06 excludes: knownclass (hcov, h2)
## 2019-10-06 excludes: mixed detector types
## 2019-10-06 excludes: individual covariates
## 2019-10-06 excludes: telemetry
## 2020-11-08 bad rownames for sim.detect when renumber = FALSE
############################################################################################
disinteraction <- function (capthist, groups, sep='.') {
ngv <- length(groups)
grouplevels <- group.levels(capthist, groups, sep=sep)
if (ngv>1)
temp <- matrix(unlist(strsplit(as.character(grouplevels), sep, fixed=TRUE)),
byrow = T, ncol = ngv)
else temp <- grouplevels
temp <- data.frame(temp)
names(temp) <- groups
temp
}
############################################################################################
simulate.secr <- function (object, nsim = 1, seed = NULL, maxperpoly = 100, chat = 1,
...)
## if CL, condition on n? what about distribution of covariates over n?
## locate according to IHP with lambda(X) controlled by f(X|covar), assuming homog Poisson
## i.e. use f(X|covar)/max(f(X|covar)) to reject until meet quota n?
## or f(X, covar | detected)?
## TOO HARD - cf MARK
## 2012-10-25
## other possible exclusions:
## mashed?
{
## check input
if (any(c("bn", "bkn", "bkc", "Bkc") %in% tolower(object$vars)))
stop ("simulate works only with binary behavioural responses")
if (!inherits(object,'secr'))
stop ("requires 'secr' object")
if (object$CL)
stop ("not implemented for conditional likelihood")
## density array dim(mask points, groups, sessions)
Darray <- getDensityArray (predictDsurface(object))
## setup
ngrp <- dim(Darray)[2]
nsession <- dim(Darray)[3]
if (!is.null(object$groups)) {
## individual covariates for foundation of g
di <- disinteraction (object$capthist, object$groups)
}
sesscapt <- vector('list', nsim)
##################
## set random seed
## copied from simulate.lm
if (!exists(".Random.seed", envir = .GlobalEnv, inherits = FALSE))
runif(1)
if (is.null(seed))
RNGstate <- get(".Random.seed", envir = .GlobalEnv)
else {
R.seed <- get(".Random.seed", envir = .GlobalEnv)
set.seed(seed)
RNGstate <- structure(seed, kind = as.list(RNGkind()))
on.exit(assign(".Random.seed", R.seed, envir = .GlobalEnv))
}
##################
## loop over replicates
runone <- function(r) {
## argument r is unused dummy
sesspopn <- list()
for (sessnum in 1:nsession) {
if (nsession==1) mask <- object$mask
else mask <- object$mask[[sessnum]]
popn <- list()
for (g in 1:ngrp) {
if (inherits(mask, 'linearmask')) {
density <- Darray[,g,sessnum] ## vector
mod2D <- 'linear' ## linear Poisson or IHP
}
else {
if (object$model$D == ~1) {
density <- Darray[1,g,sessnum] ## scalar
mod2D <- 'poisson' ## homogeneous
}
else {
density <- Darray[,g,sessnum] ## vector
mod2D <- 'IHP' ## inhomogeneous
}
}
if (chat > 1)
density <- density / chat
ND <- switch (object$details$distribution,
binomial = 'fixed',
poisson = 'poisson',
'poisson')
##-------------------------------------------------------------------
## sim.popn arguments omitted:
## buffer redundant when mask specified
## buffertype ditto
## poly ditto
## covariates ignored for now...
## number.from = 1 fine
## nsession = 1 fine here within session loop as long
## as there is no turnover model
## details = NULL not relevant (turnover and special model2D only)
## seed = NULL default mechanism -- needs attention 2014-09-07
popn[[g]] <- sim.popn (D = density, core = mask, model2D = mod2D, Ndist = ND)
## ------------------------------------------------------------------
## Add any needed covariates, first generating a clean dataframe
if (is.null(object$groups) & is.null(object$hcov))
covariates(popn[[g]]) <- NULL
else
covariates(popn[[g]]) <- data.frame(row.names = row.names(popn[[g]]))
## ---groups---
if (!is.null(object$groups)) {
grpcov <- as.data.frame(di[rep(g, nrow(popn[[g]])),]) ## 2014-08-08
names(grpcov) <- object$groups
covariates(popn[[g]]) <- cbind(covariates(popn[[g]]),grpcov)
}
## ---hcov---
## sample with replacement from original hcov field 2014-08-08
if (!is.null(object$hcov)) {
if (ms(object))
oldhcov <- covariates(object$capthist[[sessnum]])[,object$hcov]
else
oldhcov <- covariates(object$capthist)[,object$hcov]
covariates(popn[[g]])[object$hcov] <-
sample(oldhcov, size = nrow(popn[[g]]), replace = TRUE)
}
## ------------------------------------------------------------------
}
sesspopn[[sessnum]] <- do.call(rbind, popn) ## combine groups in one popn object
}
sim.detect(object, sesspopn, maxperpoly)
}
sesscapt <- lapply(1:nsim, runone)
## experimental
if (chat>1) sesscapt <- lapply(sesscapt, replicate, chat)
attr(sesscapt,'seed') <- RNGstate ## save random seed
class(sesscapt) <- c('secrdata', 'list')
sesscapt
}
############################################################################################
sim.secr <- function (object, nsim = 1, extractfn = function(x)
c(deviance=deviance(x), df=df.residual(x)), seed = NULL,
maxperpoly = 100, data = NULL, tracelevel = 1, hessian =
c('none','auto','fdHess'), start = object$fit$par, ncores = NULL) {
## parametric bootstrap simulations based on a fitted secr object
## extractfn is a required function to extract values from an secr fit
## it should return a vector of named values that does not vary in length
## 'hessian' overrides value in object$details
## set hessian='auto' if extractfn requires variance-covariance matrix
hessian <- match.arg(hessian)
cl <- match.call(expand.dots = TRUE)
cl <- paste(names(cl)[-1],cl[-1], sep=' = ', collapse=', ' )
cl <- paste('sim.secr(', cl, ')')
if (is.null(extractfn)) extractfn <- trim
test <- extractfn(object)
if (is.numeric(test)) {
n.extract <- length(test)
if (n.extract<=0)
stop ("invalid 'extractfn'")
}
detectnames <- names(object$design0[[1]]) ## names of real detection parameters
details <- replace(object$details, 'hessian', hessian)
tracelevel <- as.integer(tracelevel)
details$trace <- tracelevel > 1
min.detections <- 1
.localstuff$iter2 <- 0
if (any(detector(traps(object$capthist)) == 'single')) {
memo ('multi-catch likelihood used for single-catch traps', tracelevel>0)
}
if (is.null(data)) {
memo ('sim.secr simulating detections...', tracelevel>0)
## use multiple cores only for model fitting 2015-12-02
data <- simulate(object, nsim = nsim, seed = seed, maxperpoly = maxperpoly)
}
else {
if (any(class(data) != c('secrdata', 'list')))
stop("invalid data")
}
fitmodel <- function (sc) {
## i <<- i+1
## use second counter so as not to interfere with secrloglik
.localstuff$iter2 <- .localstuff$iter2 + 1 ## 2016-01-09
if (tracelevel>0)
memo (paste('sim.secr fitting replicate', .localstuff$iter2, '...'), TRUE)
nc <- sum(counts(sc)$'M(t+1)'[,'Total'])
if (nc >= min.detections) {
tempfit <- suppressWarnings( secr.fit(sc, model = object$model, mask = object$mask,
CL = object$CL, detectfn = object$detectfn, binomN = details$binomN,
start = start, link = object$link, fixed = object$fixed,
timecov = object$timecov, sessioncov = object$sessioncov,
groups = object$groups, dframe = object$dframe, details = details,
method = object$fit$method, verify = FALSE, biasLimit = NA,
ncores = ncores) )
extractfn(tempfit)
}
else if (is.list(test)) list() else rep(NA, n.extract)
}
output <- lapply (data, fitmodel)
if (is.numeric(test)) {
output <- do.call(rbind, output)
output <- data.frame(output)
}
else {
class(output) <- c('secrlist', 'list')
}
attr(output,'seed') <- attr(data,'seed')
attr(output,'call') <- cl
attr(output,'extractfn') <- extractfn
output
}
############################################################################################
print.secrdata <- function(x,...) {
## suggestion of Rolf Turner 19 Jan 2009 for printing without attributes
attributes(x) <- NULL
print(x)
}
############################################################################################
print.secrlist <- function(x,...) {
## suggestion of Rolf Turner 19 Jan 2009 for printing without attributes
attributes(x) <- NULL
print(x)
}
############################################################################################
## mixture proportions for representative animal
## (i.e. assuming no individual or group variation)
## assume dim(PIA)[1] == 1
getpmixall <- function(PIA, realparval)
{
nc <- dim(PIA)[2]
k <- dim(PIA)[4]
nmix <- dim(PIA)[5]
pmix <- 1 ## default single class
if (nmix>1) {
# index of first non-missing occasion s and detector k
fsk <- firstsk(PIA[1,1,,,1, drop = FALSE])
kc <- as.vector((fsk-1) %/% k + 1)[1]
sc <- as.vector((fsk-1) %/% k + 1)[1]
pmix <- PIA[cbind(1,1,sc,kc,1:nmix)]
}
pmix
}
sim.detect <- function (object, popnlist, maxperpoly = 100, renumber = TRUE)
## popnlist is always a list of popn objects, one per session
{
## we use fake CH to extract parameter value dependent on prev capt
## BUT this is slow and clunky...
dummycapthist<- function (capthist, pop, fillvalue=1) {
if (ms(capthist)) {
output <- list()
for (i in 1:nsession)
output[[i]] <- dummycapthist (capthist[[i]],
pop = pop[i], fillvalue = fillvalue)
class(output) <- c('capthist', 'list')
session(output) <- session(capthist) ## 2010 03 10
output
}
else {
newdim <- dim(capthist)
newdim[1] <- nrow(pop[[1]])
output <- array(fillvalue, dim = newdim)
## CAPTURE ON LAST OCCASION
## trick to keep array valid without misleading
output[,,newdim[3]] <- 1
class(output) <- 'capthist'
traps(output) <- traps(capthist)
session(output) <- session(capthist)
covariates(output) <- covariates(pop[[1]])
output
}
}
## --------------------------------------------------------------------
## Exclusions
## see also below dettype %in% c(-1,0,1,2,5,6,7)
if (!is.null(object$groups) & (object$details$param>1))
stop("simulation does not extend to groups when param>1")
if ('telemetry' %in% unlist(detector(traps(object$capthist))))
stop("telemetry models are not supported in simulate.secr")
## --------------------------------------------------------------------
## process behavioural responses
Markov <- any(c('B','Bk','K') %in% object$vars)
btype <- which (c("b", "bk", "k") %in% tolower(object$vars))
if (length(btype) > 1)
stop ("all behavioural responses must be of same type in sim.detect")
if (length(btype) == 0)
btype <- 0
## --------------------------------------------------------------------
## setup
if (is.null(object$details$ignoreusage))
object$details$ignoreusage <- FALSE
if (is.null(object$details$miscparm))
object$details$miscparm <- numeric(4)
N <- sapply(popnlist, nrow)
nocc <- if(ms(object)) sapply(object$capthist, ncol) else ncol(object$capthist)
ndet <- if(ms(object)) sapply(traps(object$capthist), nrow) else nrow(traps(object$capthist))
sessionlevels <- session(object$capthist) ## was names(capthist) 2009 08 15
nsession <- length(sessionlevels)
sessmask <- object$mask
if (!ms(sessmask)) sessmask <- list(sessmask) ## always a list
grplevels <- group.levels(object$capthist, object$groups, sep=".")
beta <- object$fit$par
userd <- is.null(object$details$userdist)
ncores <- setNumThreads()
grain <- if (ncores==1) 0 else 1
##------------------------------------------
## detection parameters for each session, animal, occasion, detector
## realparval is lookup table of values,
## design$PIA is index to lookup
## real parameter values for naive animals
## using existing design to save time in secr.design.MS...
if (length(unique(object$design0$PIA)) == 1) {
design0 <- object$design0
dim0 <- dim(design0$PIA)
design0$PIA <- array (1, dim = c(dim0[1], max(N), dim0[3:5]))
dummyCH <- NULL
}
else {
dummyCH <- dummycapthist(object$capthist, popnlist, fillvalue = 1)
design0 <- secr.design.MS (dummyCH, object$model, object$timecov, object$sessioncov,
object$groups, object$hcov, object$dframe,
naive = TRUE, CL = object$CL,
ignoreusage = object$details$ignoreusage,
contrasts = object$details$contrasts)
}
## uniform over individuals
## C++ code uses individual-specific PIA even in full-likelihood case
for (i in 1:nsession) {
if (is.null(object$groups)) {
## all animals the same...
matchedgroup <- rep(1, N[i])
}
else {
## group identities for simulated animals
## can treat popn as capthist in group.factor if not ms(object)
newgroup <- group.factor (popnlist[[i]], object$groups)
## here we assume original PIA is for a full-likelihood model with
## one row per group
matchedgroup <- (1:nlevels(newgroup))[as.numeric(newgroup)]
}
design0$PIA[i,1:N[i],,,] <- object$design0$PIA[i,matchedgroup,,,]
}
realparval0 <- makerealparameters (design0, beta, object$parindx, object$link,
object$fixed)
## real parameter values for 'caughtbefore' animals or detectors
## -- this definition of design1 differs from that in secr.fit()
## where parameter values are approppriate to the particular
## (realised) detection histories
if (btype > 0) {
if (is.null(dummyCH))
dummyCH <- dummycapthist(object$capthist, popnlist, fillvalue = 1)
design1 <- secr.design.MS (dummyCH, object$model, object$timecov, object$sessioncov,
object$groups, object$hcov, object$dframe, ignoreusage = object$details$ignoreusage,
contrasts = object$details$contrasts, CL = object$CL)
realparval1 <- makerealparameters (design1, beta, object$parindx, object$link,
object$fixed) # caught before
}
else { ## faster to just copy if no behavioural response
design1 <- design0
realparval1 <- realparval0
}
##------------------------------------------
# see loglikhelperfn.R for getD
# Density
if (!object$CL ) {
D <- getD (object$designD, beta, sessmask,
object$parindx, object$link, object$fixed,
grplevels, sessionlevels,
parameter = 'D')
}
# Non-Euclidean distance parameter
NE <- getD (object$designNE, beta, sessmask,
object$parindx, object$link, object$fixed,
grplevels, sessionlevels,
parameter = 'noneuc')
#--------------------------------------------------------------------
output <- list()
for (sessnum in 1:nsession) {
## in multi-session case must get session-specific data from lists
if (ms(object)) {
s <- ncol(object$capthist[[sessnum]])
session.traps <- traps(object$capthist)[[sessnum]]
session.mask <- if (userd | (object$details$param %in% c(2,6)))
object$mask[[sessnum]] else NULL
Dtemp <- if (object$details$param %in% c(4:6))
predict(object)[[sessnum]]['D','estimate']
else NA
nmash <- attr(object$capthist[[sessnum]], 'n.mash')
}
else {
s <- ncol(object$capthist)
session.traps <- traps(object$capthist)
session.mask <- if (userd | (object$details$param %in% c(2,6)))
object$mask else NULL
Dtemp <- if (object$details$param %in% c(4:6)) predict(object)['D','estimate']
else NA
nmash <- attr(object$capthist, 'n.mash')
}
## function reparameterize is in secrloglik.R
Xrealparval0 <- reparameterize (realparval0, object$detectfn, object$details,
session.mask, session.traps, Dtemp, s)
Xrealparval1 <- reparameterize (realparval1, object$detectfn, object$details,
session.mask, session.traps, Dtemp, s)
##------------------------------------------
session.animals <- popnlist[[sessnum]]
## pre-compute distances from detectors to animals
## pass miscellaneous unmodelled parameter(s)
nmiscparm <- length(object$details$miscparm)
if (nmiscparm > 0) {
miscindx <- max(unlist(object$parindx)) + (1:nmiscparm)
attr(session.mask, 'miscparm') <- coef(object)[miscindx, 1]
}
##------------------------------------------
dettype <- detectorcode(session.traps, MLonly = FALSE, noccasions = nocc[sessnum])
if (! all(dettype %in% c(-1,0,1,2,3,4,5,6,7)))
stop ("detector type ",
paste(detector(session.traps)),
" not implemented")
binomN <- expandbinomN(object$details$binomN, dettype)
if (all(detector(session.traps) %in% .localstuff$polydetectors)) {
k <- c(table(polyID(session.traps)),0)
K <- length(k)-1
}
else {
k <- nrow(session.traps)
K <- k
}
#------------------------------------------
## simulate this session...
usge <- usage(session.traps)
if (is.null(usge) | object$details$ignoreusage)
usge <- matrix(1, nrow = K, ncol = s)
NR <- N[sessnum]
if (all(detector(session.traps) %in% .localstuff$exclusivedetectors)) {
maxdet <- NR * s
}
else {
# safety margin : average detections per animal per detector per occasion
maxdet <- NR * s * K * maxperpoly
}
if ((object$detectfn==12) || (object$detectfn==13)) {
## muN, sdN
object$details$miscparm[2:3] <- beta[max(unlist(object$parindx))+(1:2)]
}
## requires session.animals has covariate named 'hcov'
knownclass <- getknownclass(session.animals, object$details$nmix, object$hcov)
## get fixed pmix for each class
pmix <- getpmixall(design0$PIA, Xrealparval0)
## TO BE FIXED
if (length(unique(dettype))>1 | length(unique(binomN))>1)
stop("simulation not yet updated for varying detector type")
if (all(dettype %in% c(-1,0,1,2,5,8))) {
if (is.function(object$details$userdist)) {
## only use of NE in this fn
noneuc <- getmaskpar(!is.null(NE), NE, nrow(session.mask), sessnum, FALSE, NULL)
density <- getmaskpar(!object$CL, D, nrow(session.mask), sessnum,
object$details$unmash, nmash)
distmat2 <- getuserdist(session.traps, session.animals, object$details$userdist, sessnum,
noneuc[,1], density[,1], object$details$miscparm, object$detectfn==20)
}
else {
distmat2 <- getdistmat2 (
session.traps,
session.animals,
object$details$userdist,
object$detectfn == 20)
}
## precompute gk, hk for point detectors
gkhk0 <- makegkPointcpp (
as.integer(object$detectfn),
as.integer(grain),
as.integer(ncores),
as.matrix(Xrealparval0),
as.matrix(distmat2),
as.double(object$details$miscparm))
gkhk <- makegkPointcpp (
as.integer(object$detectfn),
as.integer(grain),
as.integer(ncores),
as.matrix(Xrealparval1),
as.matrix(distmat2),
as.double(object$details$miscparm))
if (any(dettype == 8)) {
stop("sim.secr not ready for capped detectors")
# gkhk <- cappedgkhkcpp (as.integer(nrow(Xrealparval1)), as.integer(nrow(session.traps)),
# as.double(getcellsize(session.mask)), as.double(density[,1]),
# as.double(gkhk$gk), as.double(gkhk$hk))
}
}
# debug
# message('sessnum ', sessnum, ' NR ', NR, ' sum gkhk0$gk ', sum(gkhk0$gk))
if (all(dettype %in% c(-1,0,1,2,8))) {
temp <- simdetectpointcpp (
as.integer (dettype[1]), ## detector -1 single, 0 multi, 1 proximity, 2 count,...
as.integer (NR),
as.integer (nrow(Xrealparval0)), ## cc0
as.integer (nrow(Xrealparval1)), ## cc
as.double (gkhk0$gk),
as.double (gkhk$gk),
as.double (gkhk0$hk),
as.double (gkhk$hk),
as.integer (design0$PIA[sessnum,1:NR,1:s,1:K,]), ## naive
as.integer (design1$PIA[sessnum,1:NR,1:s,1:K,]),
as.integer (object$details$nmix),
as.integer (knownclass),
as.double (pmix),
as.matrix (usge),
as.integer (btype), ## code for behavioural response 0 none etc.
as.integer (Markov), ## learned vs transient behavioural response 0 learned 1 Markov
as.integer (binomN) ## number of trials for 'count' detector modelled with binomial
)
}
else if (all(dettype %in% c(3,4,6,7))) {
temp <- simdetectpolycpp (
as.integer (dettype[1]), ## detector 3 exclusive polygon, 4 exclusive transect, 6 polygon, 7 transecr
as.integer (object$detectfn), ## code 0 = halfnormal, 1 = hazard, 2 = exponential, 3 = uniform
as.integer (object$details$nmix), ## number of classes
as.integer (btype), ## code for behavioural response 0 none etc.
as.integer (Markov), ## learned vs transient behavioural response 0 learned 1 Markov
as.integer (k), ## number of vertices per polygon (zero-terminated vector)
as.matrix (session.animals), ## x,y points of animal range centres (first x, then y)
as.matrix (session.traps), ## x,y locations of traps (first x, then y)
as.matrix (Xrealparval0), ## Parameter values (matrix nr= comb of g0,sigma,b nc=3) [naive animal]
as.matrix (Xrealparval1), ## Parameter values (matrix nr= comb of g0,sigma,b nc=3) [caught before]
as.integer (design0$PIA[sessnum,1:NR,1:s,1:K,]), ## lookup which g0/sigma/b combination to use for given g, S, K [naive animal]
as.integer (design1$PIA[sessnum,1:NR,1:s,1:K,]), ## lookup which g0/sigma/b combination to use for given n, S, K [caught before]
as.integer (knownclass), ## known membership of 'latent' classes
as.double (pmix), ## membership probabilities
as.matrix (usge), ## ss x kk array of 0/1 usage codes or effort
as.integer (binomN), ## number of trials for 'count' detector modelled with binomial
as.integer (maxperpoly) ##
)
if ((temp$resultcode == 2) & (any(dettype %in% c(6,7)))) {
stop (">100 detections per animal per polygon per occasion")
}
}
else
if (all(dettype %in% c(5))) {
if (is.null(object$details$cutval))
stop ("sim.detect for signal model requires object$details$cutval")
temp <- simdetectsignalcpp (
as.integer(dettype[1]),
as.integer(object$details$nmix),
as.integer(object$detectfn),
as.integer(object$details$cutval),
as.matrix(Xrealparval0),
as.integer(design0$PIA[sessnum,1:NR,1:s,1:K,]), # index of N,S,K,x to rows in Xrealparval0
as.integer(pmix),
as.integer(knownclass),
as.matrix(session.animals),
as.matrix(session.traps),
as.matrix(distmat2),
as.matrix(usge),
as.double(object$details$miscparm)
)
}
if (temp$resultcode != 0) {
stop ("simulated detection failed, code ", temp$resultcode)
}
w <- array(temp$value, dim=c(s, K, NR), dimnames = list(1:s,NULL,NULL))
w <- aperm(w, c(3,1,2))
w <- w[apply(w,1,sum)>0,,, drop = FALSE]
class(w) <- 'capthist' # NOT data.frame
traps(w) <- session.traps
session(w) <- sessionlevels[sessnum]
if (!is.null(covariates(popnlist))) {
covariates(w) <- subset(covariates(popnlist[[sessnum]]), subset =
as.logical(temp$caught))
}
##---------------------
## signal
if (any(dettype %in% c(5,12)) & (temp$n>0)) {
nd <- sum(abs(w))
signal(w) <- temp$signal[1:nd]
if ((object$detectfn==12) || (object$detectfn==13))
noise(w) <- temp$signal[(nd+1):(2*nd)]
attr(w, 'cutval') <- object$details$cutval
}
else {
attr(w, 'signalframe') <- NULL
attr(w, 'cutval') <- NULL
}
##---------------------
## polygon or transect
if (any(dettype %in% c(3,4,6,7))) {
nd <- sum(abs(w))
if (nd>0)
xymat <- temp$detectedXY[1:nd, 1:2, drop = FALSE]
else
xymat <- matrix(nrow=0, ncol=2)
detectedXY <- data.frame(xymat)
names(detectedXY) <- c('x','y')
attr(w, 'detectedXY') <- detectedXY
}
else
attr(w, 'detectedXY') <- NULL
if (renumber & (temp$n>0)) {
rownames(w) <- 1:temp$n
}
else {
## rownames(w) <- (1:N[sessnum])[as.logical(temp$caught)]
## changed 2020-11-08
rownames(w) <- rownames(session.animals)[as.logical(temp$caught)]
}
output[[sessnum]] <- w
} ## end of session loop
if (nsession == 1) output <- output[[1]]
else {
names(output) <- sessionlevels
class(output) <- c('capthist', 'list')
}
output
}
############################################################################################
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