all ci fixes

Author: S1DDHEY

base/db/R/get.trait.data.pft.R

@@ -29,7 +29,7 @@
 ##' }
 ##'
 ##' **Downstream contract:** The files `trait.data.Rdata` and
-##' `prior.distns.Rdata` are expected by \link[PEcAn.meta.analysis]{run.meta.analysis.pft}], which
+##' `prior.distns.Rdata` are expected by \code{\link[PEcAn.MA]{run.meta.analysis.pft}}, which
 ##' loads them from `pft$outdir`. This implicit file-based coupling means
 ##' the two functions must agree on directory path and object names. A future
 ##' refactoring goal is to pass these objects directly via function arguments

base/db/man/get.trait.data.pft.Rd

@@ -9,8 +9,8 @@
 #' @details
 #' **Upstream contract (reads from `settings$outdir`):**
 #' \describe{
-#'   \item{`samples.Rdata`}{Produced by `get.parameter.samples()` in
-#'     `PEcAn.uncertainty`. Contains 5 bundled objects: `trait.samples`,
+#'   \item{`samples.Rdata`}{Produced by \code{\link[PEcAn.uncertainty]{get.parameter.samples}}.
+#'     Contains 5 bundled objects: `trait.samples`,
 #'     `sa.samples`, `ensemble.samples`, `runs.samples`, `env.samples`.
 #'     This function loads `trait.samples` and `sa.samples` to build
 #'     model configuration files. If `input_design` contains a `param`
@@ -32,9 +32,9 @@
 #' }
 #'
 #' **Downstream contract:** The `sensitivity.samples.*.Rdata` and
-#' `ensemble.samples.*.Rdata` files are loaded by `get.results()` (in
-#' `PEcAn.uncertainty`) to match model outputs to their corresponding
-#' parameter sets. This implicit file-based coupling is a refactoring target.
+#' `ensemble.samples.*.Rdata` files are loaded by \code{\link[PEcAn.uncertainty]{get.results}}
+#'  to match model outputs to their corresponding
+#'  parameter sets. This implicit file-based coupling is a refactoring target.
 #'
 #' The default value for `posterior.files` is NA, in which case the
 #'    most recent posterior or prior (in that order) for the workflow is used.
@@ -47,7 +47,7 @@
 #' @param ensemble.size number of ensemble runs
 #' @param input_design Input design data.frame coordinating input files across
 #'   runs. Contains columns for each sampled input (met, param, etc.) with row
-#'   indices, as documented in `runModule.run.write.configs()`.
+#'   indices, as documented in \code{\link[PEcAn.workflow]{runModule.run.write.configs}}.
 #' @param write should the runs be written to the database?
 #' @param posterior.files Filenames for posteriors for drawing samples for
 #'   ensemble and sensitivity analysis (e.g. `post.distns.Rdata`, or

base/workflow/R/run.write.configs.R

@@ -186,17 +186,17 @@ check_consistent <- function(point, prior,
 #' #' Run Bayesian meta-analysis for a single PFT (file-based wrapper)
 #'
 #' @md
-#' Thin wrapper around [meta_analysis_standalone()] that reads trait data and
+#' Thin wrapper around \code{\link[PEcAn.MA]{meta_analysis_standalone}} that reads trait data and
 #' priors from disk, runs the meta-analysis, and saves results back to disk.
 #' Also registers result files in the BETYdb posteriors table.
 #'
 #' @details
 #' **Upstream contract (reads from `pft$outdir`):**
 #' \describe{
 #'   \item{`trait.data.Rdata`}{Named list of data frames produced by
-#'     [get.trait.data.pft()]. Loaded into `trait_env$trait.data`.}
+#'     \code{\link[PEcAn.DB]{get.trait.data.pft}}. Loaded into `trait_env$trait.data`.}
 #'   \item{`prior.distns.Rdata`}{Data frame of prior distributions produced by
-#'     [get.trait.data.pft()]. Loaded into `prior_env$prior.distns`.}
+#'     \code{\link[PEcAn.DB]{get.trait.data.pft}}. Loaded into `prior_env$prior.distns`.}
 #' }
 #'
 #' **File-based side effects (saved to `pft$outdir`):**
@@ -206,20 +206,20 @@ check_consistent <- function(point, prior,
 #'     JAGS. Each element has columns `beta.o` (overall mean) and optionally
 #'     `sd.o` (overall SD).}
 #'   \item{`post.distns.MA.Rdata`}{Contains `post.distns`: a data frame with
-#'     one row per trait and columns `distn`, `parama`, `paramb`, `n`
+#'     one row per trait and columns `distn`, `parama`, `paramb`, `n`}
 #'     summarizing the fitted posterior distribution.}
 #'   \item{`post.distns.Rdata`}{Symlink to `post.distns.MA.Rdata`.}
 #'   \item{`jagged.data.Rdata`}{Contains `jagged.data`: a named list of data
 #'     frames (one per trait) formatted for use in the JAGS meta-analysis
-#'     model (see [jagify()]).}
+#'     model (see \code{\link[PEcAn.MA]{jagify}}).}
 #' }
 #'
 #' **Downstream contract:** The files `trait.mcmc.Rdata` and
-#' `post.distns.Rdata` are expected by \link[PEcAn.uncertainty]{get.parameter.samples} (in
+#' `post.distns.Rdata` are expected by \code{\link[PEcAn.uncertainty]{get.parameter.samples}} (in
 #' `PEcAn.uncertainty`), which loads them to generate ensemble and sensitivity
 #' analysis samples.
 #'
-#' **Note:** The core computation is performed by [meta_analysis_standalone()],
+#' **Note:** The core computation is performed by \code{\link[PEcAn.MA]{meta_analysis_standalone}},
 #' which accepts and returns R objects directly — see its documentation for
 #' the pure-function interface.
 #'
@@ -352,8 +352,8 @@ run.meta.analysis.pft <- function(pft, iterations, random = TRUE, threshold = 1.
 ##' Run meta-analysis across all PFTs
 ##'
 ##' @md
-##' Iterates over a list of PFTs and runs [run.meta.analysis.pft()] for each
-##' one. This is the main entry point called by [runModule.run.meta.analysis()].
+##' Iterates over a list of PFTs and runs \code{\link[PEcAn.MA]{run.meta.analysis.pft}} for each
+##' one. This is the main entry point called by \code{\link[PEcAn.MA]{runModule.run.meta.analysis}}.
 ##'
 ##' This will use the following items from settings:
 ##' - `settings$pfts`
@@ -365,7 +365,7 @@ run.meta.analysis.pft <- function(pft, iterations, random = TRUE, threshold = 1.
 ##' @param database database connection parameters
 ##' @param update logical: Rerun the meta-analysis if result files already exist?
 ##' @param threshold Gelman-Rubin convergence diagnostic, passed on to
-##'   [pecan.ma.summary()]
+##'  \code{\link{pecan.ma.summary}}
 ##' @inheritParams meta_analysis_standalone
 ##' @inheritParams run.meta.analysis.pft
 ##'

base/workflow/man/run.write.configs.Rd

@@ -4,13 +4,13 @@
 #' Loads posterior distributions and MCMC chain results from disk, generates
 #' parameter samples for ensemble and sensitivity analysis runs, and optionally
 #' saves results to `samples.Rdata`. This is the backward-compatible wrapper
-#' that delegates computation to [get_parameter_samples()].
+#' that delegates computation to \code{\link[PEcAn.uncertainty]{get_parameter_samples}}.
 #'
 #' @details
 #' **Upstream contract (reads from each PFT's `outdir`):**
 #' \\describe{
 #'   \\item{`post.distns.Rdata` or `prior.distns.Rdata`}{Posterior (or prior)
-#'     distribution summaries produced by [run.meta.analysis.pft()]. A data
+#'     distribution summaries produced by \code{\link[PEcAn.MA]{run.meta.analysis.pft}}. A data
 #'     frame with columns `distn`, `parama`, `paramb`, `n`.}
 #'   \\item{`trait.mcmc.Rdata`}{(Optional) MCMC chain samples from the
 #'     meta-analysis. Named list of `mcmc.list` objects, one per trait.
@@ -35,9 +35,9 @@
 #'     }}
 #' }
 #'
-#' **Downstream contract:** `samples.Rdata` is loaded by [run.write.configs()]
+#' **Downstream contract:** `samples.Rdata` is loaded by \code{\link[PEcAn.workflow]{run.write.configs}}
 #' (in `PEcAn.workflow`) to generate model configuration files. It is also
-#' loaded by [get.results()] and [run.sensitivity.analysis()] to retrieve
+#' loaded by \code{\link[PEcAn.uncertainty]{get.results}} and \code{\link[PEcAn.uncertainty]{run.sensitivity.analysis}} to retrieve
 #' sample metadata for post-processing. This implicit file-based coupling is
 #' a refactoring target.
 #'

modules/meta.analysis/R/run.meta.analysis.R

@@ -3,7 +3,7 @@
 ##' @md
 ##' Loads sample metadata and run IDs from disk, reads model output for each
 ##' run, and saves parsed results for downstream analysis by
-##' [run.sensitivity.analysis()] and [run.ensemble.analysis()].
+##' \code{\link[PEcAn.uncertainty]{run.sensitivity.analysis}} and \code{\link[PEcAn.uncertainty]{run.ensemble.analysis}}.
 ##'
 ##' Output is placed in model output directory (`settings$outdir`).
 ##'
@@ -12,10 +12,10 @@
 ##' \describe{
 ##'   \item{`sensitivity.samples.<id>.Rdata` or `samples.Rdata`}{Loaded to
 ##'     obtain `sa.run.ids`, `pft.names`, `trait.names`, and `sa.samples` for
-##'     sensitivity analysis. Produced by [run.write.configs()].}
+##'     sensitivity analysis. Produced by \code{\link[PEcAn.workflow]{run.write.configs}}.}
 ##'   \item{`ensemble.samples.<id>.Rdata` or `samples.Rdata`}{Loaded to obtain
 ##'     `ens.run.ids`, `pft.names`, and `trait.names` for ensemble analysis.
-##'     Produced by [run.write.configs()].}
+##'     Produced by \code{\link[PEcAn.workflow]{run.write.configs}}.}
 ##' }
 ##'
 ##' **File-based side effects (saved to `settings$outdir`):**
@@ -30,8 +30,8 @@
 ##' }
 ##'
 ##' **Downstream contract:** `sensitivity.output.*.Rdata` is loaded by
-##' [run.sensitivity.analysis()]. `ensemble.output.*.Rdata` is loaded by
-##' [run.ensemble.analysis()]. Both use these files to compute diagnostics
+##' \code{\link[PEcAn.uncertainty]{run.sensitivity.analysis}}. `ensemble.output.*.Rdata` is loaded by
+##' \code{\link[PEcAn.uncertainty]{run.ensemble.analysis}}. Both use these files to compute diagnostics
 ##' and plots. This implicit file-based coupling is a refactoring target.
 ##'
 ##' @export

modules/meta.analysis/man/run.meta.analysis.Rd

@@ -9,7 +9,7 @@
 #' **Upstream contract (reads from `settings$outdir`):**
 #' \describe{
 #'   \item{`ensemble.output.<var>.<years>.<id>.Rdata`}{Produced by
-#'     [get.results()]. Contains `ensemble.output`: a numeric vector of
+#'     \code{\link[PEcAn.uncertainty]{get.results}}. Contains `ensemble.output`: a numeric vector of
 #'     model output values, one per ensemble member.}
 #' }
 #'
@@ -34,7 +34,7 @@
 #' @param ensemble.id database ID, taken from settings if not specified
 #' @param variable variable name to process, taken from settings if not specified
 #' @param start.year,end.year taken from settings if not specified
-#' @param ... additional arguments passed to [ensemble.ts()]
+#' @param ... additional arguments passed to \code{\link[PEcAn.uncertainty]{ensemble.ts}}
 #'
 #' @return Nothing (called for side effects). Creates ensemble plots as PDF
 #'   files and optionally saves time series analysis results.