Created
November 28, 2016 21:12
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This function will return some intermediate results. Be warned that the objects may become large with time so think hard how many intermediate results you really can afford to save.
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library(scrbook) | |
scrPID.um2 <- function (n, X, y, M, mmax, obsmod = c("pois", "bern"), niters, | |
npics, xlims, ylims, inits, delta) | |
{ | |
obsmod <- match.arg(obsmod) | |
J <- nrow(n) | |
K <- ncol(n) | |
S <- inits$S | |
D <- e2dist(S, X) | |
sigma <- inits$sigma | |
lam0 <- inits$lam0 | |
lam <- lam0 * exp(-(D * D)/(2 * sigma * sigma)) | |
nObs <- nrow(y) | |
Y <- array(0, c(M + mmax, J, K)) | |
Y[1:nObs, , ] <- y | |
marked <- rep(FALSE, M + mmax) | |
marked[1:mmax] <- TRUE | |
psi <- inits$psi | |
psim <- inits$psim | |
z <- rbinom(M + mmax, 1, psi) | |
z[1:nObs] <- 1 | |
for (j in 1:J) { | |
for (k in 1:K) { | |
if (n[j, k] == 0) { | |
Y[!marked, j, k] <- 0 | |
next | |
} | |
nUnknown <- n[j, k] | |
probs <- lam[!marked, j] * z[!marked] | |
probs <- probs/sum(probs) | |
if (identical(obsmod, "pois")) | |
Y[!marked, j, k] <- rmultinom(1, nUnknown, probs) | |
else if (identical(obsmod, "bern")) { | |
Y[!marked, j, k] <- 0 | |
guys <- sample((mmax + 1):(M + mmax), nUnknown, | |
prob = probs) | |
Y[guys, j, k] <- 1 | |
} | |
} | |
} | |
cr <- rep(1, M + mmax) | |
if (missing(npics)) { | |
crat <- 1 | |
} | |
else { | |
crat <- npics[1]/npics[2] | |
} | |
cr[marked] <- crat | |
out <- matrix(NA, nrow = niters, ncol = 7) | |
colnames(out) <- c("sigma", "lam0", "c", "psi", "psim", "m", | |
"N") | |
cat("\nstarting values =", c(sigma, lam0, crat, psi, psim, | |
sum(z[marked]), sum(z)), "\n\n") | |
# Generate empty lists into which to store data. This may get large | |
# so perhaps it wouldn't make sense to store data from _every_ | |
# iteration. | |
Slist <- vector("list", niters) | |
Zlist <- vector("list", niters) | |
Zmlist <- vector("list", niters) | |
for (iter in 1:niters) { | |
if (iter%%100 == 0) { | |
cat("iter", iter, format(Sys.time(), "%H:%M:%S"), | |
"\n") | |
cat(" current =", out[iter - 1, ], "\n") | |
} | |
if (identical(obsmod, "pois")) { | |
ll <- sum(dpois(Y, lam * cr * z, log = TRUE)) | |
} | |
else if (identical(obsmod, "bern")) { | |
ll <- sum(dbinom(Y, 1, lam * cr * z, log = TRUE)) | |
} | |
if (!missing(npics)) { | |
crat <- rbeta(1, 1 + npics[1], 1 + npics[2] - npics[1]) | |
cr[marked] <- crat | |
} | |
sigma.cand <- rnorm(1, sigma, delta[1]) | |
if (sigma.cand > 0) { | |
lam.cand <- lam0 * exp(-(D * D)/(2 * sigma.cand * | |
sigma.cand)) | |
if (identical(obsmod, "pois")) { | |
ll <- sum(dpois(Y, lam * cr * z, log = TRUE)) | |
llcand <- sum(dpois(Y, lam.cand * cr * z, log = TRUE)) | |
} | |
else if (identical(obsmod, "bern")) { | |
ll <- sum(dbinom(Y, 1, lam * cr * z, log = TRUE)) | |
llcand <- sum(dbinom(Y, 1, lam.cand * cr * z, | |
log = TRUE)) | |
} | |
if (runif(1) < exp(llcand - ll)) { | |
ll <- llcand | |
lam <- lam.cand | |
sigma <- sigma.cand | |
} | |
} | |
lam0.cand <- rnorm(1, lam0, delta[2]) | |
test2 <- TRUE | |
if (identical(obsmod, "bern")) | |
test2 <- lam0.cand <= 1 | |
if (lam0.cand >= 0 & test2) { | |
lam.cand <- lam0.cand * exp(-(D * D)/(2 * sigma * | |
sigma)) | |
if (identical(obsmod, "pois")) | |
llcand <- sum(dpois(Y, lam.cand * cr * z, log = TRUE)) | |
else if (identical(obsmod, "bern")) | |
llcand <- sum(dbinom(Y, 1, lam.cand * cr * z, | |
log = TRUE)) | |
if (runif(1) < exp((llcand) - (ll))) { | |
ll <- llcand | |
lam0 <- lam0.cand | |
lam <- lam.cand | |
} | |
} | |
zUpsm <- zUps <- 0 | |
for (i in (nObs + 1):mmax) { | |
zcand <- ifelse(z[i] == 0, 1, 0) | |
if (identical(obsmod, "pois")) { | |
llz <- sum(dpois(Y[i, , ], lam[i, ] * cr[i] * | |
z[i], log = TRUE)) | |
llcandz <- sum(dpois(Y[i, , ], lam[i, ] * cr[i] * | |
zcand, log = TRUE)) | |
} | |
else if (identical(obsmod, "bern")) { | |
llz <- sum(dbinom(Y[i, , ], 1, lam[i, ] * cr[i] * | |
z[i], log = TRUE)) | |
llcandz <- sum(dbinom(Y[i, , ], 1, lam[i, ] * | |
cr[i] * zcand, log = TRUE)) | |
} | |
prior <- dbinom(z[i], 1, psim, log = TRUE) | |
prior.cand <- dbinom(zcand, 1, psim, log = TRUE) | |
if (runif(1) < exp((llcandz + prior.cand) - (llz + | |
prior))) { | |
z[i] <- zcand | |
zUpsm <- zUpsm + 1 | |
} | |
} | |
seen <- apply(Y > 0, 1, any) | |
for (i in (mmax + 1):(M + mmax)) { | |
if (seen[i]) | |
next | |
zcand <- ifelse(z[i] == 0, 1, 0) | |
if (identical(obsmod, "pois")) { | |
ll <- sum(dpois(Y[i, , ], lam[i, ] * z[i], log = TRUE)) | |
llcand <- sum(dpois(Y[i, , ], lam[i, ] * zcand, | |
log = TRUE)) | |
} | |
else if (identical(obsmod, "bern")) { | |
ll <- sum(dbinom(Y[i, , ], 1, lam[i, ] * z[i], | |
log = TRUE)) | |
llcand <- sum(dbinom(Y[i, , ], 1, lam[i, ] * | |
zcand, log = TRUE)) | |
} | |
prior <- dbinom(z[i], 1, psi, log = TRUE) | |
prior.cand <- dbinom(zcand, 1, psi, log = TRUE) | |
rat <- (llcand + prior.cand) - (ll + prior) | |
if (runif(1) < exp(rat)) { | |
z[i] <- zcand | |
zUps <- zUps + 1 | |
} | |
} | |
for (j in 1:J) { | |
zip <- lam[!marked, j] * z[!marked] | |
for (k in 1:K) { | |
if (n[j, k] == 0) { | |
Y[!marked, j, k] <- 0 | |
next | |
} | |
nUnknown <- n[j, k] | |
probs <- zip/sum(zip) | |
if (identical(obsmod, "pois")) | |
Y[!marked, j, k] <- rmultinom(1, nUnknown, | |
probs) | |
else if (identical(obsmod, "bern")) { | |
Y[!marked, j, k] <- 0 | |
guy <- sample((mmax + 1):(M + mmax), nUnknown, | |
prob = probs) | |
Y[guy, j, k] <- 1 | |
} | |
} | |
} | |
psim <- rbeta(1, 1 + sum(z[marked]), 1 + mmax - sum(z[marked])) | |
psi <- rbeta(1, 1 + sum(z[!marked]), 1 + M - sum(z[!marked])) | |
Sups <- 0 | |
for (i in 1:(M + mmax)) { | |
Scand <- c(rnorm(1, S[i, 1], delta[3]), rnorm(1, | |
S[i, 2], delta[3])) | |
inbox <- Scand[1] >= xlims[1] & Scand[1] <= xlims[2] & | |
Scand[2] >= ylims[1] & Scand[2] <= ylims[2] | |
if (!inbox) | |
next | |
dtmp <- sqrt((Scand[1] - X[, 1])^2 + (Scand[2] - | |
X[, 2])^2) | |
lam.cand <- lam0 * exp(-(dtmp * dtmp)/(2 * sigma * | |
sigma)) | |
if (identical(obsmod, "pois")) { | |
ll <- sum(dpois(Y[i, , ], lam[i, ] * cr[i] * | |
z[i], log = TRUE)) | |
llcand <- sum(dpois(Y[i, , ], lam.cand * cr[i] * | |
z[i], log = TRUE)) | |
} | |
else if (identical(obsmod, "bern")) { | |
ll <- sum(dbinom(Y[i, , ], 1, lam[i, ] * cr[i] * | |
z[i], log = TRUE)) | |
llcand <- sum(dbinom(Y[i, , ], 1, lam.cand * | |
cr[i] * z[i], log = TRUE)) | |
} | |
if (runif(1) < exp(llcand - ll)) { | |
ll <- llcand | |
S[i, ] <- Scand | |
lam[i, ] <- lam.cand | |
D[i, ] <- dtmp | |
Sups <- Sups + 1 | |
} | |
} | |
if (iter%%100 == 0) { | |
cat(" Acceptance rates\n") | |
cat(" z =", zUps/M, "\n") | |
cat(" zm =", zUpsm/mmax, "\n") | |
cat(" S =", Sups/(M + mmax), "\n") | |
} | |
out[iter, ] <- c(sigma, lam0, crat, psi, psim, sum(z[marked]), sum(z)) | |
# browser() | |
Slist[[iter]] <- S | |
Zlist[[iter]] <- zUps/M | |
Zmlist[[iter]] <- zUpsm/mmax | |
} | |
return(list(params = out, S = Slist, Z = Zlist, Zm = Zmlist)) | |
} | |
set.seed(2501) | |
#set input values | |
N=80 | |
lam0=0.5 | |
knownID=40 | |
rat=0.8 | |
sigma=0.5 | |
K=5 | |
#create grid and state space | |
coords<-seq(0,7, 1) | |
grid<-expand.grid(coords, coords) | |
trapmat<-as.matrix(grid) | |
buff<- 3*sigma | |
xl<-min(trapmat[,1])-buff | |
xu<-max(trapmat[,1])+buff | |
yl<-min(trapmat[,2])-buff | |
yu<-max(trapmat[,2])+buff | |
xlims=c(xl, xu) | |
ylims=c(yl,yu) | |
area<-(xu-xl)*(yu-yl) | |
#simulate data | |
dat<-sim.pID.data(N=N, K=K, sigma=sigma, lam0=lam0, knownID=knownID, | |
X=trapmat, xlims=xlims, ylims=ylims, obsmod= "pois", | |
nmarked="known",rat=1, tel =0, nlocs=0) | |
#create initial values function for scrPID, set M and tuning parameters | |
inits<-function(){list(S=cbind(runif(M, xlims[1], xlims[2]), | |
runif(M, ylims[1], ylims[2])), lam0=runif(1, 0.4, 0.6), | |
sigma=runif(1, 0.4, 0.6), psi=runif(1, 0.4, 0.6))} | |
M<-160 | |
delta=c(0.1, 0.01, 2) | |
n<-dat$n - apply(dat$Yknown, 2:3, sum) | |
inits<-function(){list(S=cbind(runif(M+mmax, xlims[1], xlims[2]), | |
runif(M+mmax, ylims[1], ylims[2])), lam0=runif(1, 0.4, 0.6), | |
sigma=runif(1, 0.4, 0.6), psi=runif(1, 0.4, 0.6), psim=runif(1, 0.4, 0.6))} | |
iobs<-which(apply(dat$Yknown>0,1,any)) | |
Yobs<-dat$Yknown[iobs,,] | |
mmax<-40 | |
mod<-scrPID.um2(n=n, X=trapmat, y=Yobs, M=M,mmax=mmax, obsmod = "pois", | |
niters=3, xlims=xlims, ylims=ylims, | |
inits=inits(), delta=delta) | |
> str(mod) | |
List of 4 | |
$ params: num [1:3, 1:7] 0.553 0.553 0.591 0.426 0.435 ... | |
..- attr(*, "dimnames")=List of 2 | |
.. ..$ : NULL | |
.. ..$ : chr [1:7] "sigma" "lam0" "c" "psi" ... | |
$ S :List of 3 | |
..$ : num [1:200, 1:2] -0.618 4.275 7.268 3.595 0.871 ... | |
..$ : num [1:200, 1:2] -0.618 4.275 7.268 3.595 2.415 ... | |
..$ : num [1:200, 1:2] -0.546 4.275 7.71 3.595 2.415 ... | |
$ Z :List of 3 | |
..$ : num 0.263 | |
..$ : num 0.156 | |
..$ : num 0.156 | |
$ Zm :List of 3 | |
..$ : num 0.2 | |
..$ : num 0.125 | |
..$ : num 0.2 |
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