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Fix(uncertainty): allow explicit MCMC and distribution paths; avoid o… #3663

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Fix(uncertainty): allow explicit MCMC and distribution paths; avoid o… #3663

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46 changes: 37 additions & 9 deletions modules/uncertainty/R/get.parameter.samples.R
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,14 @@
#'
#' @param settings PEcAn settings object
#' @param ensemble.size number of runs in model ensemble
#' @param posterior.files list of filenames to read from
#' @param posterior.files Either:
#' - a vector/list of length `length(settings$pfts)` with paths to posterior/ prior
#' distribution `.Rdata` files (backwards compatible behavior), OR
#' - a list of length `length(settings$pfts)`, where each element is itself a list
#' that may contain named elements `distribution` (path to `post.distns.Rdata` or
#' `prior.distns.Rdata`) and `mcmc` (path to `trait.mcmc*.Rdata`). When provided,
#' these files are used directly and PEcAn will not fall back to `pft$outdir`
#' to look for inputs. This avoids mixing read-only inputs in output directories.
#' @param ens.sample.method one of "halton", "sobol", "torus", "lhc", "uniform"
#' @export
#'
Expand All @@ -18,7 +25,9 @@ get.parameter.samples <- function(settings,
pft.names <- list()
outdirs <- list()

if (length(pfts) != length(posterior.files)) {
# Normalize to list for consistent handling (backwards compatible)
posterior_list <- as.list(posterior.files)
if (length(pfts) != length(posterior_list)) {
PEcAn.logger::logger.error(
"settings$pfts and posterior.files should be the same length"
)
Expand All @@ -36,11 +45,11 @@ get.parameter.samples <- function(settings,
)
}

for (i.pft in seq_along(pfts)) {
for (i.pft in seq_along(pfts)) {
# If no name given, use string "NULL" to warn user
pft.names[i.pft] <- settings$pfts[[i.pft]]$name %||% "NULL"

### Get output directory info
### Get output directory info (used for outputs and legacy fallbacks only)
if (!is.null(settings$pfts[[i.pft]]$outdir)) {
outdirs[i.pft] <- settings$pfts[[i.pft]]$outdir
} else {
Expand Down Expand Up @@ -68,10 +77,22 @@ get.parameter.samples <- function(settings,
for (i in seq_along(pft.names)) {
distns <- new.env()

## Load posteriors
if (!is.na(posterior.files[i])) {
# Per-PFT overrides (may be NA, a string path, or a list with
# $distribution and/or $mcmc entries)
pf_spec <- posterior_list[[i]]
dist_file <- NA
mcmc_file_arg <- NA
if (is.list(pf_spec)) {
dist_file <- pf_spec$distribution %||% NA
mcmc_file_arg <- pf_spec$mcmc %||% NA
} else {
dist_file <- pf_spec
}

## Load distribution (posterior/ prior) file
if (!is.na(dist_file)) {
# Load specified file
load(posterior.files[i], envir = distns)
load(dist_file, envir = distns)
if (is.null(distns$prior.distns) && !is.null(distns$post.distns)) {
distns$prior.distns <- distns$post.distns
}
Expand All @@ -88,7 +109,15 @@ get.parameter.samples <- function(settings,
}

### Load trait mcmc data (if exists, either from MA or PDA)
if (!is.null(settings$pfts[[i]]$posteriorid) && !is.null(con)) {
if (!is.na(mcmc_file_arg)) {
# Explicit path provided -> trust it and do not fall back to outdir
if (!file.exists(mcmc_file_arg)) {
PEcAn.logger::logger.severe("Specified MCMC file does not exist: ", mcmc_file_arg)
}
ma.results <- TRUE
load(mcmc_file_arg, envir = distns)
if (grepl("mcmc.pda", mcmc_file_arg)) independent <- FALSE
} else if (!is.null(settings$pfts[[i]]$posteriorid) && !is.null(con)) {
# first check if there are any files associated with posterior ids
files <- PEcAn.DB::dbfile.check("Posterior",
settings$pfts[[i]]$posteriorid,
Expand All @@ -101,7 +130,6 @@ get.parameter.samples <- function(settings,
ma.results <- TRUE
load(trait.mcmc.file, envir = distns)


# PDA samples are fitted together, to preserve correlations downstream
# let workflow know they should go together
if (grepl("mcmc.pda", trait.mcmc.file)) independent <- FALSE
Expand Down