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# Generate required random effects info----------------------------------------
# Sort-of drop-in replacement for lme4::mkReTrms
get_reTrms <- function(formula, data, newdata=NULL){
if(!has_random(formula)){
stop("No random effect terms in formula", call.=FALSE)
}
cnms <- get_cnms(formula)
# TODO: check these are factors
flist <- lapply(unique(names(cnms)), function(x){
out <- data[[x]]
if(!is.factor(out)) out <- factor(out)
out
})
names(flist) <- unique(names(cnms))
list(Z = get_Z(formula, data), cnms = cnms, flist=flist)
}
#Create Z random effects matrix from a formula, possibly using newdata---------
get_Z <- function(formula, data, newdata=NULL){
# If no random effects in formula, return an empty Matrix
if(!has_random(formula)){
if(is.null(newdata)){
return(Matrix::Matrix(matrix(0, nrow=nrow(data), ncol=0),sparse=TRUE))
} else{
return(Matrix::Matrix(matrix(0, nrow=nrow(newdata), ncol=0),sparse=TRUE))
}
}
# Get new formula
bars <- find_bars(formula)
new_form <- bars_to_formula(bars)
# Get partial Z for each bar expression
form_list <- lapply(1:length(bars), function(x) bars_to_formula(bars[x]))
Z_parts <- lapply(form_list, get_partial_Z, data=data, newdata=newdata)
# Create model frame
#mf <- model.frame(new_form, data, na.action=stats::na.pass)
#if(!is.null(newdata)){
# mf <- model.frame(stats::terms(mf), newdata, na.action=stats::na.pass,
# xlev=get_xlev(data, mf))
#}
# Create sparse Z matrix
#Z <- model.matrix(new_form, mf)
Z <- do.call(cbind, Z_parts)
colnames(Z) <- Z_colnames(formula, data)
Matrix::Matrix(Z, sparse=TRUE)
}
# Determine if formula has random effects specified----------------------------
has_random <- function(form){
length(find_bars(form)) > 0
}
# Find 'bar' random effect parts of formula (i.e., the (x|y) structures)-------
# Operates recursively
find_bars <- function(form){
out <- NULL
if(is.name(form)) return(NULL)
if(form[[1]] == as.name("(")) return(form)
if(is.call(form)){
out <- lapply(form, find_bars)
}
unlist(out)
}
# Convert bar components into new formula--------------------------------------
# E.g. ~x + (1|g) becomes ~g - 1
bars_to_formula <- function(bars){
bar_terms <- lapply(bars, bars_to_terms)
check_duplicate_terms(bar_terms)
as.formula(str2lang(paste("~", paste(bar_terms, collapse = " + "), "- 1")))
}
# Translate bar components into standard formula terms-------------------------
bars_to_terms <- function(bars){
info <- get_bar_info(bars)
new_terms <- sapply(info$LHS, function(x){
if(x == "1") return(info$RHS)
paste0(x, ":", info$RHS)
})
paste(new_terms, collapse=" + ")
}
# Organize information in a bar expression into a list-------------------------
get_bar_info <- function(bar){
out <- list(
operator = deparse(bar[[2]][[1]]),
LHS = terms_in_bar(bar, RHS=FALSE),
RHS = terms_in_bar(bar, RHS=TRUE)
)
check_bar_info(out)
}
terms_in_bar <- function(bars, RHS=FALSE){
bars_sub <- bars[[2]][[2]]
if(RHS) bars_sub <- bars[[2]][[3]]
form <- formula(substitute(~X, list(X=bars_sub)))
trms <- attr(terms(form), "term.labels")
int <- attr(terms(form), "intercept")
if(int == 1 & !RHS) trms <- c("1", trms)
trms
}
# Check bar info to make sure the expression are allowed-----------------------
# For example unmarked doesn't support correlated random effects with |
check_bar_info <- function(info){
if(info$operator == "|" & length(info$LHS) > 1){
stop("Correlated random effects not supported, use || instead of |", call.=FALSE)
}
if(any(grepl(":", info$RHS)) | any(grepl("/", info$RHS))){
stop("Nested random effects notation (: or /) not supported", call.=FALSE)
}
stopifnot(length(info$RHS) == 1)
info
}
# Check terms to make sure there aren't any duplicates-------------------------
# E.g. as a result of a formula like ~ (1|g) + (x||) where the intercept
# is also implied in the second bar expression
check_duplicate_terms <- function(bar_terms){
all_terms <- lapply(bar_terms, function(x){
unlist(strsplit(x, " + ", fixed=TRUE))
})
all_terms <- unlist(all_terms)
dups <- duplicated(all_terms)
if(any(dups)){
stop("Formula implies duplicate terms: ", paste0(all_terms[dups], collapse=", "),
call.=FALSE)
}
invisible()
}
# Get partial Z for a given bar expression-------------------------------------
get_partial_Z <- function(formula, data, newdata){
mf <- model.frame(formula, data, na.action=stats::na.pass)
if(!is.null(newdata)){
mf <- model.frame(stats::terms(mf), newdata, na.action=stats::na.pass,
xlev=get_xlev(data, mf))
}
model.matrix(formula, mf)
}
# Get levels of factor---------------------------------------------------------
# For use in specifying model frame
get_xlev <- function(data, model_frame){
fac_col <- data[, sapply(data, is.factor), drop=FALSE]
xlevs <- lapply(fac_col, levels)
xlevs[names(xlevs) %in% names(model_frame)]
}
# Generate colnames for Z to match what lme4::mkReTrms does--------------------
Z_colnames <- function(formula, data){
bars <- find_bars(formula)
info <- lapply(bars, get_bar_info)
groups <- sapply(info, function(x) x$RHS)
nreps <- sapply(info, function(x) length(x$LHS))
lvls <- lapply(1:length(groups), function(i){
group_dat <- data[[groups[i]]]
if(!is.factor(group_dat)) group_dat <- as.factor(group_dat)
rep(levels(group_dat), nreps[i])
})
unlist(lvls)
}
# Get 'cnms' - random effect names - as with lme4::mkReTrms--------------------
get_cnms <- function(formula){
bars <- find_bars(formula)
info <- lapply(bars, get_bar_info)
cnms <- lapply(info, function(x){
out <- lapply(x$LHS, function(y) ifelse(y == "1", "(Intercept)", y))
names(out) <- rep(x$RHS, length(out))
out
})
do.call(c, cnms)
}
# Get number of random effect SDs/variances------------------------------------
get_nrandom <- function(formula, data){
if(!has_random(formula)) return(as.array(0))
cnms <- get_cnms(formula)
out <- sapply(names(cnms), function(x){
length(unique(data[[x]]))
})
as.array(out)
}
# Get number of grouping variables---------------------------------------------
get_group_vars <- function(formula){
if(!has_random(formula)) return(0)
cnms <- get_cnms(formula)
length(cnms)
}
# Check if function has no support for random effects--------------------------
check_no_support <- function(formula_list){
has_bars <- any(sapply(formula_list, has_random))
if(has_bars){
stop("This function does not support random effects", call.=FALSE)
}
}
# Remove all bar components from a formula-------------------------------------
remove_bars <- function(formula){
s1 <- gsub("\\([^)]+\\|[^)]+\\) ?\\+?", "", deparse1(formula))
s2 <- gsub(" \\+ {0,}$", "", s1)
if(s2 == "~") return(~1)
as.formula(str2lang(s2))
}
sigma_names <- function(formula, data){
if(!has_random(formula)) return(NA_character_)
nms <- get_reTrms(formula, data)$cnms
nms <- paste0(unlist(nms), "|", names(nms))
nms <- gsub("(Intercept)", "1", nms, fixed=TRUE)
#paste0("sigma [", nms, "]")
nms
}
split_formula <- function(formula){
if(length(formula) != 3) stop("Double right-hand side formula required")
char <- lapply(formula, function(x){
paste(deparse(x), collapse="")
})
p1 <- as.formula(char[[2]])
p2 <- as.formula(paste("~", char[[3]]))
list(p1, p2)
}
is_tmb_fit <- function(mod){
if(!methods::.hasSlot(mod, "TMB")) return(FALSE)
!is.null(mod@TMB)
}
get_b_vector <- function(tmb_report, type){
#sdr <- TMB::sdreport(TMB)
bname <- paste0("b_",type)
bpar <- tmb_report$par.random
bpar <- bpar[grepl(bname, names(bpar))]
if(length(bpar)==0) return(NULL)
bpar
}
get_joint_cov <- function(tmb_report, type=NULL, remove_sigma=TRUE){
full <- tmb_report$jointPrecision
if(is.null(full)){
full <- tmb_report$cov.fixed
colnames(full) <- rownames(full) <- names(tmb_report$par)
} else {
full <- solve(full)
}
if(is.null(type)) return(full)
keep <- grepl(paste0("_",type), colnames(full))
out <- full[keep,keep,drop=FALSE]
if(!remove_sigma) return(out)
keep2 <- !grepl(paste0("lsigma_",type), colnames(out))
out <- out[keep2,keep2,drop=FALSE]
}
tmbfit_has_random <- function(mod, type){
paste0(type,"RE") %in% names(mod@estimates@estimates)
}
use_tmb_bootstrap <- function(mod, type, re.form){
is.null(re.form) && is_tmb_fit(mod) && tmbfit_has_random(mod, type)
}
# Gather information about grouping variables for a given submodel
get_randvar_info <- function(tmb_report, type, formula, data){
ngv <- get_group_vars(formula)
if(ngv == 0) return(list()) #Return blank list if there are no grouping variables
sigma_type <- paste0("lsigma_",type)
sigma_ind <- grepl(sigma_type, get_fixed_names(tmb_report))
sigma_est <- tmb_report$par.fixed[sigma_ind]
sigma_cov <- as.matrix(tmb_report$cov.fixed[sigma_ind,sigma_ind])
re <- get_reTrms(formula, data)
list(names=sigma_names(formula, data), estimates=sigma_est, covMat=sigma_cov,
invlink="exp", invlinkGrad="exp", n_obs=nrow(data),
n_levels=lapply(re$flist, function(x) length(levels(x))), cnms=re$cnms,
levels=colnames(re$Z))
}
get_fixed_names <- function(tmb_report){
out <- names(tmb_report$par.fixed)
if(is.null(out)) out <- 1:length(tmb_report$par.fixed)
out
}
print_randvar_info <- function(object){
group_info <- paste0(names(object$n_levels), ", ",
unlist(object$n_levels), collapse="; ")
val <- do.call(object$invlink, list(object$estimates))
disp <- data.frame(Groups=names(object$cnms), Name=unlist(object$cnms),
Variance=round(val^2,3), Std.Dev.=round(val,3))
cat("Random effects:\n")
print(disp, row.names=FALSE)
#below needs to be corrected for missing values at some point
#cat(paste0("Number of obs: ",object$n_obs,", groups: ",group_info,"\n"))
}
fit_TMB <- function(model, data, params, random,
starts, method, ...){
fixed_sub <- names(params)[!names(params) %in% random]
nfixed <- length(unlist(params[fixed_sub]))
list_fixed_only <- params[fixed_sub]
plengths <- sapply(list_fixed_only, length)
starts_order <- rep(fixed_sub, plengths)
if(!is.null(starts)){
if(length(starts) != nfixed){
stop(paste("The number of starting values should be", nfixed))
}
list_fixed_only <- params[fixed_sub]
list_fixed_only <- utils::relist(starts, list_fixed_only)
params <- replace(params, names(list_fixed_only), list_fixed_only)
}
tmb_mod <- TMB::MakeADFun(data = c(model = model, data),
parameters = params,
random = random,
silent=TRUE,
DLL = "unmarked_TMBExports")
tmb_mod$starts_order <- starts_order
opt <- optim(tmb_mod$par, fn=tmb_mod$fn, gr=tmb_mod$gr, method=method, ...)
sdr <- TMB::sdreport(tmb_mod, getJointPrecision=TRUE)
sdr$par <- tmb_mod$par
AIC = 2 * opt$value + 2 * nfixed
list(opt=opt, TMB=tmb_mod, sdr=sdr, AIC=AIC)
}
get_coef_info <- function(tmb_report, type, names, idx){
no_sigma <- !grepl("lsigma", get_fixed_names(tmb_report))
fixed <- tmb_report$par.fixed[no_sigma] #take out sigmas
fixed <- fixed[idx]
names(fixed) <- names
rand <- get_b_vector(tmb_report, type)
ests <- c(fixed, rand)
covMat <- get_joint_cov(tmb_report, type)
list(ests=ests, cov=covMat)
}
setMethod("sigma", "unmarkedEstimate", function(object, level=0.95, ...){
rinf <- object@randomVarInfo
if(length(rinf)==0){
stop("No random effects in this submodel", call.=FALSE)
}
z <- qnorm((1-level)/2, lower.tail = FALSE)
vals <- rinf$estimates
ses <- sqrt(diag(rinf$covMat))
lower <- vals - z*ses
upper <- vals + z*ses
Groups <- names(rinf$cnms)
Name <- unlist(rinf$cnms)
data.frame(Model=object@short.name, Groups=Groups, Name=Name, sigma=exp(vals),
lower=exp(lower), upper=exp(upper))
})
setMethod("sigma", "unmarkedFit", function(object, type, level=0.95, ...){
if(!missing(type)){
return(sigma(object[type], level=level))
}
ests <- object@estimates@estimates
has_rand <- sapply(ests, function(x) length(x@randomVarInfo)>0)
if(!any(has_rand)){
stop("No random effects in this model", call.=FALSE)
}
ests <- ests[has_rand]
out_list <- lapply(ests, sigma, level=level)
out <- do.call(rbind, out_list)
rownames(out) <- NULL
out
})
setGeneric("randomTerms", function(object, ...) standardGeneric("randomTerms"))
setMethod("randomTerms", "unmarkedEstimate", function(object, level=0.95, ...){
rv <- object@randomVarInfo
if(length(rv)==0){
stop("No random effects in this submodel", call.=FALSE)
}
Groups <- lapply(1:length(rv$cnms), function(x){
gn <- names(rv$cnms)[x]
rep(gn, rv$n_levels[[gn]])
})
Groups <- do.call(c, Groups)
Name <- lapply(1:length(rv$cnms), function(x){
gn <- names(rv$cnms)[x]
var <- rv$cnms[[x]]
rep(var, rv$n_levels[[gn]])
})
Name <- do.call(c, Name)
rv_idx <- !1:length(object@estimates) %in% object@fixed
b_var <- object@estimates[rv_idx]
b_se <- sqrt(diag(object@covMat[rv_idx,rv_idx,drop=FALSE]))
z <- qnorm((1-level)/2, lower.tail = FALSE)
lower <- b_var - z*b_se
upper <- b_var + z*b_se
data.frame(Model=object@short.name, Groups=Groups, Name=Name, Level=rv$levels,
Estimate=b_var, SE=b_se, lower=lower, upper=upper)
})
setMethod("randomTerms", "unmarkedFit", function(object, type, level=0.95, ...){
if(!missing(type)){
return(randomTerms(object[type], level))
}
has_random <- sapply(object@estimates@estimates,
function(x) length(x@randomVarInfo) > 0)
if(!any(has_random)){
stop("No random effects in this model", call.=FALSE)
}
keep <- object@estimates@estimates[has_random]
out <- lapply(keep, randomTerms, level=level)
out <- do.call(rbind, out)
rownames(out) <- NULL
out
})
get_ranef_inputs <- function(forms, datalist, dms, Zs){
stopifnot(!is.null(names(datalist)))
mods <- names(datalist)
ngv <- lapply(forms, get_group_vars)
names(ngv) <- paste0("n_group_vars_",mods)
ngroup <- mapply(get_nrandom, forms, datalist, SIMPLIFY=FALSE)
names(ngroup) <- paste0("n_grouplevels_",mods)
names(dms) <- paste0("X_", mods)
names(Zs) <- paste0("Z_", mods)
dat <- c(ngv, ngroup, dms, Zs)
beta <- lapply(dms, function(x) rep(0, ncol(x)))
names(beta) <- paste0("beta_", mods)
b <- lapply(ngroup, function(x) rep(0, sum(x)))
names(b) <- paste0("b_", mods)
lsigma <- lapply(ngv, function(x) rep(0, x))
names(lsigma) <- paste0("lsigma_", mods)
pars <- c(beta, b, lsigma)
rand_ef <- paste0(names(b))[sapply(forms, has_random)]
if(length(rand_ef) == 0) rand_ef <- NULL
list(data=dat, pars=pars, rand_ef=rand_ef)
}
add_covariates <- function(covs_long, covs_short, n){
if(is.null(covs_short)){
return(covs_long)
}
if(is.null(covs_long)){
covs_long <- data.frame(.dummy=rep(1, n))
} else {
stopifnot(nrow(covs_long) == n)
}
exp_factor <- nrow(covs_long) / nrow(covs_short)
stopifnot(exp_factor > 1)
rep_idx <- rep(1:nrow(covs_short), each=exp_factor)
to_add <- covs_short[rep_idx, ]
stopifnot(nrow(covs_long) == nrow(to_add))
cbind(covs_long, to_add)
}
vcov_TMB <- function(object, type, fixedOnly){
if(!missing(type)){
return(vcov(object[type], fixedOnly=fixedOnly))
}
v <- get_joint_cov(TMB::sdreport(object@TMB, getJointPrecision=TRUE))
no_sig <- !grepl("lsigma_",colnames(v))
v <- v[no_sig, no_sig]
colnames(v) <- rownames(v) <- names(coef(object, fixedOnly=FALSE))
if(fixedOnly){
no_re <- !grepl("b_", colnames(v))
v <- v[no_re, no_re]
}
v
}
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