From 0c3d0fc642c597a27fc66a170ab07e1edebeb6ea Mon Sep 17 00:00:00 2001
From: divne7022 <www.divinehome12@gmail.com>
Date: Mon, 10 Nov 2025 14:02:34 +0000
Subject: [PATCH 1/6] pass input_design param to write.sa.config and resolve
 the overwriting issue of sample.Rdata for multisite setting

---
 base/workflow/R/run.write.configs.R | 133 +++++++++++++++++++++++-----
 1 file changed, 109 insertions(+), 24 deletions(-)

diff --git a/base/workflow/R/run.write.configs.R b/base/workflow/R/run.write.configs.R
index 18756b4555..a2ac4ee381 100644
--- a/base/workflow/R/run.write.configs.R
+++ b/base/workflow/R/run.write.configs.R
@@ -51,7 +51,7 @@ run.write.configs <- function(settings, ensemble.size, input_design, write = TRU
       }
     )
   }
-
+  
   ## Which posterior to use?
   for (i in seq_along(settings$pfts)) {
     ## if posterior.files is specified us that
@@ -60,9 +60,9 @@ run.write.configs <- function(settings, ensemble.size, input_design, write = TRU
       if (!is.null(settings$pfts[[i]]$posteriorid)) {
         # TODO: sometimes `files` is a 0x0 tibble and other operations with it fail.
         files <- PEcAn.DB::dbfile.check("Posterior",
-          settings$pfts[[i]]$posteriorid,
-          con, settings$host$name,
-          return.all = TRUE
+                                        settings$pfts[[i]]$posteriorid,
+                                        con, settings$host$name,
+                                        return.all = TRUE
         )
         pid <- grep("post.distns.*Rdata", files$file_name) ## is there a posterior file?
         if (length(pid) == 0) {
@@ -97,12 +97,12 @@ run.write.configs <- function(settings, ensemble.size, input_design, write = TRU
       }
     } ## end else
   } ## end for loop over pfts
-
+  
   ## Sample parameters
   model <- settings$model$type
   scipen <- getOption("scipen")
   options(scipen = 12)
-
+  
   samples.file <- file.path(settings$outdir, "samples.Rdata")
   if (file.exists(samples.file)) {
     samples <- new.env()
@@ -126,17 +126,17 @@ run.write.configs <- function(settings, ensemble.size, input_design, write = TRU
   } else {
     PEcAn.logger::logger.error(samples.file, "not found, this file is required by the run.write.configs function")
   }
-
+  
   ## remove previous runs.txt
   if (overwrite && file.exists(file.path(settings$rundir, "runs.txt"))) {
     PEcAn.logger::logger.warn("Existing runs.txt file will be removed.")
     unlink(file.path(settings$rundir, "runs.txt"))
   }
-
+  
   PEcAn.utils::load.modelpkg(model)
-
+  
   ## Check for model-specific write configs
-
+  
   my.write.config <- paste0("write.config.", model)
   if (!exists(my.write.config)) {
     PEcAn.logger::logger.error(
@@ -145,22 +145,22 @@ run.write.configs <- function(settings, ensemble.size, input_design, write = TRU
       my.write.config
     )
   }
-
+  
   ## Prepare for model output.  Clean up any old config files (if exists)
   # TODO: shouldn't this check if the files exist before removing them?
   my.remove.config <- paste0("remove.config.", model)
   if (exists(my.remove.config)) {
     do.call(my.remove.config, args = list(settings$rundir, settings))
   }
-
+  
   # TODO RK : need to write to runs_inputs table
-
+  
   # Save names
   pft.names <- names(trait.samples)
   trait.names <- lapply(trait.samples, names)
-
+  
   ### NEED TO IMPLEMENT: Load Environmental Priors and Posteriors
-
+  
   ### Sensitivity Analysis
   if ("sensitivity.analysis" %in% names(settings)) {
     ### Write out SA config files
@@ -170,20 +170,21 @@ run.write.configs <- function(settings, ensemble.size, input_design, write = TRU
       quantile.samples = sa.samples,
       settings = settings,
       model = model,
+      input_design = input_design,
       write.to.db = write
     )
-
+    
     # Store output in settings and output variables
     runs.samples$sa <- sa.run.ids <- sa.runs$runs
     settings$sensitivity.analysis$ensemble.id <- sa.ensemble.id <- sa.runs$ensemble.id
-
+    
     # Save sensitivity analysis info
     fname <- PEcAn.uncertainty::sensitivity.filename(settings, "sensitivity.samples", "Rdata",
-      all.var.yr = TRUE, pft = NULL
+                                                     all.var.yr = TRUE, pft = NULL
     )
     save(sa.run.ids, sa.ensemble.id, sa.samples, pft.names, trait.names, file = fname)
   } ### End of SA
-
+  
   ### Write ENSEMBLE
   if ("ensemble" %in% names(settings)) {
     ens.runs <- PEcAn.uncertainty::write.ensemble.configs(
@@ -195,29 +196,113 @@ run.write.configs <- function(settings, ensemble.size, input_design, write = TRU
       input_design = input_design,
       write.to.db = write
     )
-
+    
     # Store output in settings and output variables
     runs.samples$ensemble <- ens.run.ids <- ens.runs$runs
     settings$ensemble$ensemble.id <- ens.ensemble.id <- ens.runs$ensemble.id
     ens.samples <- ensemble.samples # rename just for consistency
-
+    
     # Save ensemble analysis info
     fname <- PEcAn.uncertainty::ensemble.filename(settings, "ensemble.samples", "Rdata", all.var.yr = TRUE)
     save(ens.run.ids, ens.ensemble.id, ens.samples, pft.names, trait.names, file = fname)
   } else {
     PEcAn.logger::logger.info("not writing config files for ensemble, settings are NULL")
   } ### End of Ensemble
-
+  
   PEcAn.logger::logger.info("###### Finished writing model run config files #####")
   PEcAn.logger::logger.info("config files samples in ", file.path(settings$outdir, "run"))
+  
+  samples.file <- file.path(settings$outdir, "samples.Rdata")
+  
+  if (file.exists(samples.file)) {
+    existing_env <- new.env()
+    load(samples.file, envir = existing_env)
+    if (!is.null(existing_env$ensemble.samples)) {
+      for (pft_name in names(ensemble.samples)) {
+        if (pft_name %in% names(existing_env$ensemble.samples)) {
+          # combine parameter samples for same PFT across sites
+          ensemble.samples[[pft_name]] <- rbind(
+            existing_env$ensemble.samples[[pft_name]],
+            ensemble.samples[[pft_name]]
+          )
+        }
+        # New PFTs from current site are automatically preserved
+      }
+      
+      # preserves existing PFTs -- add PFTs that exist in file but not current site
+      for (existing_pft in names(existing_env$ensemble.samples)) {
+        if (!existing_pft %in% names(ensemble.samples)) {
+          ensemble.samples[[existing_pft]] <- existing_env$ensemble.samples[[existing_pft]]
+        }
+      }
+    }
+    
+    if (!is.null(existing_env$trait.samples)) {
+      trait.samples <- modifyList(existing_env$trait.samples, trait.samples)
+    }
+    
+    if (!is.null(existing_env$sa.samples)) {
+      sa.samples <- modifyList(existing_env$sa.samples, sa.samples)
+    }
+    
+    if (!is.null(existing_env$runs.samples)) {
+      if (!is.null(runs.samples$ensemble)) {
+        if (!is.null(existing_env$runs.samples$ensemble)) {
+          runs.samples$ensemble <- rbind(
+            existing_env$runs.samples$ensemble,
+            runs.samples$ensemble
+          )
+        }
+        # If existing is NULL, current ensemble data is preserved
+      } else if (!is.null(existing_env$runs.samples$ensemble)) {
+        # Current site has no ensemble, preserve existing
+        runs.samples$ensemble <- existing_env$runs.samples$ensemble
+      }
+      
+      # Merge SA runs
+      if (!is.null(runs.samples$sa)) {
+        if (!is.null(existing_env$runs.samples$sa)) {
+          for (pft_name in names(runs.samples$sa)) {
+            if (pft_name %in% names(existing_env$runs.samples$sa)) {
+              runs.samples$sa[[pft_name]] <- rbind(
+                existing_env$runs.samples$sa[[pft_name]],
+                runs.samples$sa[[pft_name]]
+              )
+            }
+          }
+          
+          for (existing_pft in names(existing_env$runs.samples$sa)) {
+            if (!existing_pft %in% names(runs.samples$sa)) {
+              runs.samples$sa[[existing_pft]] <- existing_env$runs.samples$sa[[existing_pft]]
+            }
+          }
+        }
+        # If existing SA is NULL, current SA data is preserved
+      } else if (!is.null(existing_env$runs.samples$sa)) {
+        # Current site has no SA, preserve existing
+        runs.samples$sa <- existing_env$runs.samples$sa
+      }
+    }
 
+    if (!is.null(existing_env$pft.names)) {
+      pft.names <- unique(c(existing_env$pft.names, pft.names))
+    }
+    
+    if (!is.null(existing_env$trait.names)) {
+      trait.names <- modifyList(existing_env$trait.names, trait.names)
+    }
+    
+  }
+  
   ### Save output from SA/Ensemble runs
   # A lot of this is duplicate with the ensemble/sa specific output above, but kept for backwards compatibility.
   save(ensemble.samples, trait.samples, sa.samples, runs.samples, pft.names, trait.names,
-    file = file.path(settings$outdir, "samples.Rdata")
+       file = samples.file
   )
-  PEcAn.logger::logger.info("parameter values for runs in ", file.path(settings$outdir, "samples.RData"))
+  
+  PEcAn.logger::logger.info("parameter values for runs in ", samples.file)
   options(scipen = scipen)
   invisible(settings)
   return(settings)
 }
+

From 18a35641c3f195e6d3c196bda8951ba7e26962a1 Mon Sep 17 00:00:00 2001
From: divne7022 <www.divinehome12@gmail.com>
Date: Mon, 10 Nov 2025 14:05:41 +0000
Subject: [PATCH 2/6] add input_design param for input coordination and
 enhancing README.txt to track all inputs used per run

---
 modules/uncertainty/R/sensitivity.R | 203 ++++++++++++++++++----------
 1 file changed, 132 insertions(+), 71 deletions(-)

diff --git a/modules/uncertainty/R/sensitivity.R b/modules/uncertainty/R/sensitivity.R
index 7caa635b8b..c94881f374 100644
--- a/modules/uncertainty/R/sensitivity.R
+++ b/modules/uncertainty/R/sensitivity.R
@@ -94,6 +94,7 @@ read.sa.output <- function(traits, quantiles, pecandir, outdir, pft.name = "",
 #'   by \code{settings$rundir} before writing to it?
 #' @param write.to.db logical: Record this run to BETY? If TRUE, uses connection
 #'   settings specified in \code{settings$database}
+#' @param input_design data.frame coordinating input files across runs
 #'
 #' @return list, containing $runs = data frame of runids,
 #'  and $ensemble.id = the ensemble ID for these runs.
@@ -101,11 +102,11 @@ read.sa.output <- function(traits, quantiles, pecandir, outdir, pft.name = "",
 #' @export
 #' @author David LeBauer, Carl Davidson
 write.sa.configs <- function(defaults, quantile.samples, settings, model,
-                             clean = FALSE, write.to.db = TRUE) {
+                             clean = FALSE, write.to.db = TRUE, input_design = NULL) {
   scipen <- getOption("scipen")
   options(scipen = 12)
   my.write.config <- paste("write.config.", model, sep = "")
-
+  
   if (write.to.db) {
     con <- try(PEcAn.DB::db.open(settings$database$bety), silent = TRUE)
     if (inherits(con, "try-error")) {
@@ -116,23 +117,23 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
   } else {
     con <- NULL
   }
-
+  
   # Get the workflow id
   if ("workflow" %in% names(settings)) {
     workflow.id <- settings$workflow$id
   } else {
     workflow.id <- -1
   }
-
+  
   # find all inputs that have an id
   inputs <- names(settings$run$inputs)
   inputs <- inputs[grepl(".id$", inputs)]
-
+  
   runs <- data.frame()
-
+  
   # Reading the site.pft specific tags from xml
   site.pfts.vec <- as.character(unlist(settings$run$site$site.pft))
-
+  
   if (!is.null(site.pfts.vec)) {
     # find the name of pfts defined in the body of pecan.xml
     defined.pfts <- as.character(unlist(purrr::map(settings$pfts, "name")))
@@ -151,8 +152,8 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
       )
     }
   }
-
-
+  
+  
   ## write median run
   MEDIAN <- "50"
   median.samples <- list()
@@ -160,14 +161,14 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
     median.samples[[i]] <- quantile.samples[[i]][MEDIAN, , drop  = FALSE]
   }
   names(median.samples) <- names(quantile.samples)
-
+  
   if (!is.null(con)) {
     # Note: ignores any existing run or ensemble ids in settings
     ensemble.id <- PEcAn.DB::db.query(paste0(
       "INSERT INTO ensembles (runtype, workflow_id) ",
       "VALUES ('sensitivity analysis', ", format(workflow.id, scientific = FALSE), ") ",
       "RETURNING id"), con = con)[["id"]]
-
+    
     paramlist <- paste0(
       "quantile=MEDIAN,trait=all,pft=",
       paste(lapply(settings$pfts, function(x) x[["name"]]), sep = ",")
@@ -176,15 +177,15 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
       "INSERT INTO runs ",
       "(model_id, site_id, start_time, finish_time, outdir, ensemble_id, parameter_list) ",
       "values ('",
-        settings$model$id, "', '",
-        settings$run$site$id, "', '",
-        settings$run$start.date, "', '",
-        settings$run$end.date, "', '",
-        settings$run$outdir, "', ",
-        ensemble.id, ", '",
-        paramlist, "') ",
+      settings$model$id, "', '",
+      settings$run$site$id, "', '",
+      settings$run$start.date, "', '",
+      settings$run$end.date, "', '",
+      settings$run$outdir, "', ",
+      ensemble.id, ", '",
+      paramlist, "') ",
       "RETURNING id"), con = con)[["id"]]
-
+    
     # associate posteriors with ensembles
     for (pft in defaults) {
       PEcAn.DB::db.query(
@@ -194,7 +195,7 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
         con = con
       )
     }
-
+    
     # associate inputs with runs
     if (!is.null(inputs)) {
       for (x in inputs) {
@@ -214,7 +215,7 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
     ensemble.id <- settings$sensitivity.analysis$ensemble.id %||% rlang::hash(settings)
   }
   medianrun <- run.id
-
+  
   # create folders (cleaning up old ones if needed)
   if (clean) {
     unlink(file.path(settings$rundir, run.id))
@@ -222,7 +223,49 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
   }
   dir.create(file.path(settings$rundir, run.id), recursive = TRUE)
   dir.create(file.path(settings$modeloutdir, run.id), recursive = TRUE)
-
+  
+  # I check to make sure the path under the met is a list.
+  # if it's specified what met needs to be used in 'met.id' under sensitivity
+  # analysis of pecan xml we used that otherwise, I use the first met.
+  if (is.list(settings$run$inputs$met$path)) {
+    # This checks for met.id tag in the settings under sensitivity analysis -
+    # if it's not there it creates it. Then it's gonna use what it created.
+    if (is.null(settings$sensitivity.analysis$met.id)) {
+      settings$sensitivity.analysis$met.id <- 1
+    }
+    settings$run$inputs$met$path <- settings$run$inputs$met$path[[settings$sensitivity.analysis$met.id]]
+  }
+  
+  # Apply input design coordination for median run
+  median_settings <- settings
+  if (!is.null(input_design)) {
+    # Coordinate inputs for median run (use first row)
+    for (input_tag in colnames(input_design)) {
+      if (input_tag != "param" && !is.null(median_settings$run$inputs[[input_tag]]$path)) {
+        input_paths <- median_settings$run$inputs[[input_tag]]$path
+        # Assume list structure (consistent with write.ensemble.configs)
+        if (length(input_paths) > 1) {
+          input_index <- input_design[[input_tag]][1]
+          median_settings$run$inputs[[input_tag]]$path <- input_paths[[input_index]]
+        }
+      }
+    }
+  }
+  
+  median_input_info <- ""
+  for (input_tag in names(median_settings$run$inputs)) {
+    input_data <- median_settings$run$inputs[[input_tag]]
+    
+    # At SA stage, path is ALWAYS a resolved string (thanks to input design)
+    if (!is.null(input_data) && !is.null(input_data$path)) {
+      median_input_info <- paste0(median_input_info, 
+                                  format(input_tag, width = 12, justify = "left"), 
+                                  ": ", 
+                                  input_data$path, 
+                                  "\n")
+    }
+  }
+  
   # write run information to disk TODO need to print list of pft names and trait
   # names
   cat("runtype     : sensitivity analysis\n",
@@ -236,7 +279,7 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
       "model id    : ", settings$model$id, "\n",
       "site        : ", settings$run$site$name, "\n",
       "site  id    : ", settings$run$site$id, "\n",
-      "met data    : ", settings$run$site$met, "\n",
+      median_input_info,
       "start date  : ", settings$run$start.date, "\n",
       "end date    : ", settings$run$end.date, "\n",
       "hostname    : ", settings$host$name, "\n",
@@ -244,26 +287,11 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
       "outdir      : ", file.path(settings$host$outdir, run.id), "\n",
       file = file.path(settings$rundir, run.id, "README.txt"),
       sep = "")
-
-
-  # I check to make sure the path under the met is a list.
-  # if it's specified what met needs to be used in 'met.id' under sensitivity
-  # analysis of pecan xml we used that otherwise, I use the first met.
-  if (is.list(settings$run$inputs$met$path)) {
-    # This checks for met.id tag in the settings under sensitivity analysis -
-    # if it's not there it creates it. Then it's gonna use what it created.
-    if (is.null(settings$sensitivity.analysis$met.id)) {
-      settings$sensitivity.analysis$met.id <- 1
-    }
-    settings$run$inputs$met$path <- settings$run$inputs$met$path[[settings$sensitivity.analysis$met.id]]
-
-  }
-
-
+  
   # write configuration
   do.call(my.write.config, args = list(defaults = defaults,
                                        trait.values = median.samples,
-                                       settings = settings,
+                                       settings = median_settings,
                                        run.id = run.id))
   cat(
     run.id,
@@ -271,20 +299,22 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
     sep = "\n",
     append = TRUE
   )
-
+  
+  run_index <- 1
+  
   ## loop over pfts
   runs <- list()
-  for (i in seq_along(names(quantile.samples))) {
-    pftname <- names(quantile.samples)[i]
+  for (pft_idx in seq_along(names(quantile.samples))) {
+    pftname <- names(quantile.samples)[pft_idx]
     if (pftname == "env") {
       next
     }
-
-    traits <- colnames(quantile.samples[[i]])
-    quantiles.str <- rownames(quantile.samples[[i]])
-
+    
+    traits <- colnames(quantile.samples[[pft_idx]])
+    quantiles.str <- rownames(quantile.samples[[pft_idx]])
+    
     runs[[pftname]] <- data.frame()
-
+    
     ## loop over variables
     for (trait in traits) {
       for (quantile.str in quantiles.str) {
@@ -293,29 +323,29 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
         } else {
           quantile <- as.numeric(quantile.str) / 100
           trait.samples <- median.samples
-          trait.samples[[i]][trait] <- quantile.samples[[i]][quantile.str, trait, drop = FALSE]
-
+          trait.samples[[pft_idx]][trait] <- quantile.samples[[pft_idx]][quantile.str, trait, drop = FALSE]
+          
           if (!is.null(con)) {
             paramlist <- paste0("quantile=", quantile.str, ",trait=", trait, ",pft=", pftname)
             insert_result <- PEcAn.DB::db.query(
               paste0(
                 "INSERT INTO runs (",
-                  "model_id, site_id, start_time, finish_time, outdir,",
-                  " ensemble_id, parameter_list) ",
+                "model_id, site_id, start_time, finish_time, outdir,",
+                " ensemble_id, parameter_list) ",
                 "values ('",
-                  settings$model$id, "', '",
-                  settings$run$site$id, "', '",
-                  settings$run$start.date, "', '",
-                  settings$run$end.date, "', '",
-                  settings$run$outdir, "', ",
-                  ensemble.id, ", '",
-                  paramlist,
+                settings$model$id, "', '",
+                settings$run$site$id, "', '",
+                settings$run$start.date, "', '",
+                settings$run$end.date, "', '",
+                settings$run$outdir, "', ",
+                ensemble.id, ", '",
+                paramlist,
                 "') ",
                 "RETURNING id"),
               con = con
             )
             run.id <- insert_result[["id"]]
-
+            
             # associate posteriors with ensembles
             for (pft in defaults) {
               PEcAn.DB::db.query(
@@ -326,7 +356,7 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
                 con = con
               )
             }
-
+            
             # associate inputs with runs
             if (!is.null(inputs)) {
               for (x in inputs) {
@@ -343,12 +373,15 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
               run.type = "SA",
               index = round(quantile, 3),
               trait = trait,
-              pft.name = names(trait.samples)[i],
+              pft.name = names(trait.samples)[pft_idx],
               site.id = settings$run$site$id
             )
           }
           runs[[pftname]][quantile.str, trait] <- run.id
-
+          
+          # Increment run counter
+          run_index <- run_index + 1
+          
           # create folders (cleaning up old ones if needed)
           if (clean) {
             unlink(file.path(settings$rundir, run.id))
@@ -356,12 +389,40 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
           }
           dir.create(file.path(settings$rundir, run.id), recursive = TRUE)
           dir.create(file.path(settings$modeloutdir, run.id), recursive = TRUE)
-
-          # write run information to disk
+          
+          # Apply input design coordination for SA runs
+          settings_copy <- settings
+          if (!is.null(input_design)) {
+            for (input_tag in colnames(input_design)) {
+              if (input_tag != "param" && !is.null(settings_copy$run$inputs[[input_tag]]$path)) {
+                input_paths <- settings_copy$run$inputs[[input_tag]]$path
+                if (length(input_paths) > 1) {
+                  input_index <- input_design[[input_tag]][run_index]
+                  settings_copy$run$inputs[[input_tag]]$path <- input_paths[[input_index]]
+                }
+              }
+            }
+          }
+          
+          
+          # Build dynamic input info string for SA run README
+          sa_input_info <- ""
+          for (input_tag in names(settings_copy$run$inputs)) {
+            input_data <- settings_copy$run$inputs[[input_tag]]
+            if (!is.null(input_data) && !is.null(input_data$path)) {
+              sa_input_info <- paste0(sa_input_info, 
+                                      format(input_tag, width = 12, justify = "left"), 
+                                      ": ", 
+                                      input_data$path, 
+                                      "\n")
+            }
+          }
+          
+          # write SA run information to disk
           cat("runtype     : sensitivity analysis\n",
               "workflow id : ", workflow.id, "\n",
               "ensemble id : ", ensemble.id, "\n",
-              "pft name    : ", names(trait.samples)[i], "\n",
+              "pft name    : ", names(trait.samples)[pft_idx], "\n",
               "quantile    : ", quantile.str, "\n",
               "trait       : ", trait, "\n",
               "run id      : ", run.id, "\n",
@@ -369,7 +430,7 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
               "model id    : ", settings$model$id, "\n",
               "site        : ", settings$run$site$name, "\n",
               "site  id    : ", settings$run$site$id, "\n",
-              "met data    : ", settings$run$site$met, "\n",
+              sa_input_info,
               "start date  : ", settings$run$start.date, "\n",
               "end date    : ", settings$run$end.date, "\n",
               "hostname    : ", settings$host$name, "\n",
@@ -377,12 +438,12 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
               "outdir      : ", file.path(settings$host$outdir, run.id), "\n",
               file = file.path(settings$rundir, run.id, "README.txt"),
               sep = "")
-
-
+          
+          
           # write configuration
           do.call(my.write.config, args = list(defaults = defaults,
                                                trait.values = trait.samples,
-                                               settings = settings,
+                                               settings = settings_copy,
                                                run.id))
           cat(
             run.id,
@@ -394,7 +455,7 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
       }
     }
   }
-
+  
   options(scipen = scipen)
   return(invisible(list(runs = runs, ensemble.id = ensemble.id)))
 } # write.sa.configs

From f075e4d7d0f9ad85ee340bbe01f7dca464988677 Mon Sep 17 00:00:00 2001
From: divne7022 <www.divinehome12@gmail.com>
Date: Mon, 10 Nov 2025 14:06:24 +0000
Subject: [PATCH 3/6] update .Rd

---
 modules/uncertainty/man/write.sa.configs.Rd | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/modules/uncertainty/man/write.sa.configs.Rd b/modules/uncertainty/man/write.sa.configs.Rd
index 545970713c..87227cff18 100644
--- a/modules/uncertainty/man/write.sa.configs.Rd
+++ b/modules/uncertainty/man/write.sa.configs.Rd
@@ -10,7 +10,8 @@ write.sa.configs(
   settings,
   model,
   clean = FALSE,
-  write.to.db = TRUE
+  write.to.db = TRUE,
+  input_design = NULL
 )
 }
 \arguments{
@@ -27,6 +28,8 @@ by \code{settings$rundir} before writing to it?}
 
 \item{write.to.db}{logical: Record this run to BETY? If TRUE, uses connection
 settings specified in \code{settings$database}}
+
+\item{input_design}{data.frame coordinating input files across runs}
 }
 \value{
 list, containing $runs = data frame of runids,

From f7b0c3a5870afb729bb91e07eaf502fa9cbc2643 Mon Sep 17 00:00:00 2001
From: divne7022 <www.divinehome12@gmail.com>
Date: Wed, 12 Nov 2025 09:16:52 +0000
Subject: [PATCH 4/6] fix indent, remove end-of-line whitespace and
 consolidated to a single env load

---
 base/workflow/R/run.write.configs.R | 144 +++++++++++++---------------
 1 file changed, 69 insertions(+), 75 deletions(-)

diff --git a/base/workflow/R/run.write.configs.R b/base/workflow/R/run.write.configs.R
index a2ac4ee381..17fd706cea 100644
--- a/base/workflow/R/run.write.configs.R
+++ b/base/workflow/R/run.write.configs.R
@@ -51,7 +51,7 @@ run.write.configs <- function(settings, ensemble.size, input_design, write = TRU
       }
     )
   }
-  
+
   ## Which posterior to use?
   for (i in seq_along(settings$pfts)) {
     ## if posterior.files is specified us that
@@ -60,9 +60,9 @@ run.write.configs <- function(settings, ensemble.size, input_design, write = TRU
       if (!is.null(settings$pfts[[i]]$posteriorid)) {
         # TODO: sometimes `files` is a 0x0 tibble and other operations with it fail.
         files <- PEcAn.DB::dbfile.check("Posterior",
-                                        settings$pfts[[i]]$posteriorid,
-                                        con, settings$host$name,
-                                        return.all = TRUE
+          settings$pfts[[i]]$posteriorid,
+          con, settings$host$name,
+          return.all = TRUE
         )
         pid <- grep("post.distns.*Rdata", files$file_name) ## is there a posterior file?
         if (length(pid) == 0) {
@@ -97,17 +97,22 @@ run.write.configs <- function(settings, ensemble.size, input_design, write = TRU
       }
     } ## end else
   } ## end for loop over pfts
-  
+
   ## Sample parameters
   model <- settings$model$type
   scipen <- getOption("scipen")
   options(scipen = 12)
-  
+
   samples.file <- file.path(settings$outdir, "samples.Rdata")
+  existing_data <- NULL
   if (file.exists(samples.file)) {
-    samples <- new.env()
-    load(samples.file, envir = samples) ## loads ensemble.samples, trait.samples, sa.samples, runs.samples, env.samples
-    trait.samples <- samples$trait.samples
+    existing_data <- new.env()
+    load(samples.file, envir = existing_data)
+    trait.samples <- existing_data$trait.samples
+    sa.samples <- existing_data$sa.samples
+    runs.samples <- existing_data$runs.samples
+
+    # Generate ensemble.samples for current site
     trait_sample_indices <- input_design[["param"]]
     ensemble.samples <- list()
     for (pft in names(trait.samples)) {
@@ -120,23 +125,21 @@ run.write.configs <- function(settings, ensemble.size, input_design, write = TRU
       )
       names(ensemble.samples[[pft]]) <- names(pft_traits)
     }
-    sa.samples <- samples$sa.samples
-    runs.samples <- samples$runs.samples
-    ## env.samples <- samples$env.samples
   } else {
-    PEcAn.logger::logger.error(samples.file, "not found, this file is required by the run.write.configs function")
+    # cannot proceed without sample.Rdata
+    PEcAn.logger::logger.severe(samples.file, "not found, this file is required by the run.write.configs function")
   }
-  
+
   ## remove previous runs.txt
   if (overwrite && file.exists(file.path(settings$rundir, "runs.txt"))) {
     PEcAn.logger::logger.warn("Existing runs.txt file will be removed.")
     unlink(file.path(settings$rundir, "runs.txt"))
   }
-  
+
   PEcAn.utils::load.modelpkg(model)
-  
+
   ## Check for model-specific write configs
-  
+
   my.write.config <- paste0("write.config.", model)
   if (!exists(my.write.config)) {
     PEcAn.logger::logger.error(
@@ -145,22 +148,22 @@ run.write.configs <- function(settings, ensemble.size, input_design, write = TRU
       my.write.config
     )
   }
-  
+
   ## Prepare for model output.  Clean up any old config files (if exists)
   # TODO: shouldn't this check if the files exist before removing them?
   my.remove.config <- paste0("remove.config.", model)
   if (exists(my.remove.config)) {
     do.call(my.remove.config, args = list(settings$rundir, settings))
   }
-  
+
   # TODO RK : need to write to runs_inputs table
-  
+
   # Save names
   pft.names <- names(trait.samples)
   trait.names <- lapply(trait.samples, names)
-  
+
   ### NEED TO IMPLEMENT: Load Environmental Priors and Posteriors
-  
+
   ### Sensitivity Analysis
   if ("sensitivity.analysis" %in% names(settings)) {
     ### Write out SA config files
@@ -173,18 +176,18 @@ run.write.configs <- function(settings, ensemble.size, input_design, write = TRU
       input_design = input_design,
       write.to.db = write
     )
-    
+
     # Store output in settings and output variables
     runs.samples$sa <- sa.run.ids <- sa.runs$runs
     settings$sensitivity.analysis$ensemble.id <- sa.ensemble.id <- sa.runs$ensemble.id
-    
+
     # Save sensitivity analysis info
     fname <- PEcAn.uncertainty::sensitivity.filename(settings, "sensitivity.samples", "Rdata",
-                                                     all.var.yr = TRUE, pft = NULL
+      all.var.yr = TRUE, pft = NULL
     )
     save(sa.run.ids, sa.ensemble.id, sa.samples, pft.names, trait.names, file = fname)
   } ### End of SA
-  
+
   ### Write ENSEMBLE
   if ("ensemble" %in% names(settings)) {
     ens.runs <- PEcAn.uncertainty::write.ensemble.configs(
@@ -196,111 +199,102 @@ run.write.configs <- function(settings, ensemble.size, input_design, write = TRU
       input_design = input_design,
       write.to.db = write
     )
-    
+
     # Store output in settings and output variables
     runs.samples$ensemble <- ens.run.ids <- ens.runs$runs
     settings$ensemble$ensemble.id <- ens.ensemble.id <- ens.runs$ensemble.id
     ens.samples <- ensemble.samples # rename just for consistency
-    
+
     # Save ensemble analysis info
     fname <- PEcAn.uncertainty::ensemble.filename(settings, "ensemble.samples", "Rdata", all.var.yr = TRUE)
     save(ens.run.ids, ens.ensemble.id, ens.samples, pft.names, trait.names, file = fname)
   } else {
     PEcAn.logger::logger.info("not writing config files for ensemble, settings are NULL")
   } ### End of Ensemble
-  
+
   PEcAn.logger::logger.info("###### Finished writing model run config files #####")
   PEcAn.logger::logger.info("config files samples in ", file.path(settings$outdir, "run"))
-  
-  samples.file <- file.path(settings$outdir, "samples.Rdata")
-  
-  if (file.exists(samples.file)) {
-    existing_env <- new.env()
-    load(samples.file, envir = existing_env)
-    if (!is.null(existing_env$ensemble.samples)) {
+
+  ## Use existing_data from earlier load
+  if (!is.null(existing_data)) {
+    # Merge ensemble.samples
+    if (!is.null(existing_data$ensemble.samples)) {
       for (pft_name in names(ensemble.samples)) {
-        if (pft_name %in% names(existing_env$ensemble.samples)) {
+        if (pft_name %in% names(existing_data$ensemble.samples)) {
           # combine parameter samples for same PFT across sites
           ensemble.samples[[pft_name]] <- rbind(
-            existing_env$ensemble.samples[[pft_name]],
+            existing_data$ensemble.samples[[pft_name]],
             ensemble.samples[[pft_name]]
           )
         }
         # New PFTs from current site are automatically preserved
       }
-      
       # preserves existing PFTs -- add PFTs that exist in file but not current site
-      for (existing_pft in names(existing_env$ensemble.samples)) {
+      for (existing_pft in names(existing_data$ensemble.samples)) {
         if (!existing_pft %in% names(ensemble.samples)) {
-          ensemble.samples[[existing_pft]] <- existing_env$ensemble.samples[[existing_pft]]
+          ensemble.samples[[existing_pft]] <- existing_data$ensemble.samples[[existing_pft]]
         }
       }
     }
-    
-    if (!is.null(existing_env$trait.samples)) {
-      trait.samples <- modifyList(existing_env$trait.samples, trait.samples)
+    # Merge trait.samples
+    if (!is.null(existing_data$trait.samples)) {
+      trait.samples <- modifyList(existing_data$trait.samples, trait.samples)
     }
-    
-    if (!is.null(existing_env$sa.samples)) {
-      sa.samples <- modifyList(existing_env$sa.samples, sa.samples)
+    # Merge sa.samples
+    if (!is.null(existing_data$sa.samples)) {
+      sa.samples <- modifyList(existing_data$sa.samples, sa.samples)
     }
-    
-    if (!is.null(existing_env$runs.samples)) {
+    # Merge runs.samples
+    if (!is.null(existing_data$runs.samples)) {
+      # Merge ensemble runs
       if (!is.null(runs.samples$ensemble)) {
-        if (!is.null(existing_env$runs.samples$ensemble)) {
+        if (!is.null(existing_data$runs.samples$ensemble)) {
           runs.samples$ensemble <- rbind(
-            existing_env$runs.samples$ensemble,
+            existing_data$runs.samples$ensemble,
             runs.samples$ensemble
           )
         }
-        # If existing is NULL, current ensemble data is preserved
-      } else if (!is.null(existing_env$runs.samples$ensemble)) {
+      } else if (!is.null(existing_data$runs.samples$ensemble)) {
         # Current site has no ensemble, preserve existing
-        runs.samples$ensemble <- existing_env$runs.samples$ensemble
+        runs.samples$ensemble <- existing_data$runs.samples$ensemble
       }
-      
       # Merge SA runs
       if (!is.null(runs.samples$sa)) {
-        if (!is.null(existing_env$runs.samples$sa)) {
+        if (!is.null(existing_data$runs.samples$sa)) {
           for (pft_name in names(runs.samples$sa)) {
-            if (pft_name %in% names(existing_env$runs.samples$sa)) {
+            if (pft_name %in% names(existing_data$runs.samples$sa)) {
               runs.samples$sa[[pft_name]] <- rbind(
-                existing_env$runs.samples$sa[[pft_name]],
+                existing_data$runs.samples$sa[[pft_name]],
                 runs.samples$sa[[pft_name]]
               )
             }
           }
-          
-          for (existing_pft in names(existing_env$runs.samples$sa)) {
+          for (existing_pft in names(existing_data$runs.samples$sa)) {
             if (!existing_pft %in% names(runs.samples$sa)) {
-              runs.samples$sa[[existing_pft]] <- existing_env$runs.samples$sa[[existing_pft]]
+              runs.samples$sa[[existing_pft]] <- existing_data$runs.samples$sa[[existing_pft]]
             }
           }
         }
-        # If existing SA is NULL, current SA data is preserved
-      } else if (!is.null(existing_env$runs.samples$sa)) {
+      } else if (!is.null(existing_data$runs.samples$sa)) {
         # Current site has no SA, preserve existing
-        runs.samples$sa <- existing_env$runs.samples$sa
+        runs.samples$sa <- existing_data$runs.samples$sa
       }
     }
-
-    if (!is.null(existing_env$pft.names)) {
-      pft.names <- unique(c(existing_env$pft.names, pft.names))
+    # Merge pft.names
+    if (!is.null(existing_data$pft.names)) {
+      pft.names <- unique(c(existing_data$pft.names, pft.names))
     }
-    
-    if (!is.null(existing_env$trait.names)) {
-      trait.names <- modifyList(existing_env$trait.names, trait.names)
+    # Merge trait.names
+    if (!is.null(existing_data$trait.names)) {
+      trait.names <- modifyList(existing_data$trait.names, trait.names)
     }
-    
   }
-  
   ### Save output from SA/Ensemble runs
   # A lot of this is duplicate with the ensemble/sa specific output above, but kept for backwards compatibility.
   save(ensemble.samples, trait.samples, sa.samples, runs.samples, pft.names, trait.names,
-       file = samples.file
+    file = file.path(settings$outdir, "samples.Rdata")
   )
-  
-  PEcAn.logger::logger.info("parameter values for runs in ", samples.file)
+  PEcAn.logger::logger.info("parameter values for runs in ", file.path(settings$outdir, "samples.RData"))
   options(scipen = scipen)
   invisible(settings)
   return(settings)

From 81f50f6ce6f91dcfcf2fff69c71ab5d88c7119b6 Mon Sep 17 00:00:00 2001
From: divne7022 <www.divinehome12@gmail.com>
Date: Wed, 12 Nov 2025 09:18:12 +0000
Subject: [PATCH 5/6] fix indent, remove end-of-line whitespace, remove auto
 linter and addcomments

---
 modules/uncertainty/R/sensitivity.R | 122 ++++++++++++++--------------
 1 file changed, 62 insertions(+), 60 deletions(-)

diff --git a/modules/uncertainty/R/sensitivity.R b/modules/uncertainty/R/sensitivity.R
index c94881f374..e7114e3cb2 100644
--- a/modules/uncertainty/R/sensitivity.R
+++ b/modules/uncertainty/R/sensitivity.R
@@ -106,7 +106,7 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
   scipen <- getOption("scipen")
   options(scipen = 12)
   my.write.config <- paste("write.config.", model, sep = "")
-  
+
   if (write.to.db) {
     con <- try(PEcAn.DB::db.open(settings$database$bety), silent = TRUE)
     if (inherits(con, "try-error")) {
@@ -117,23 +117,23 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
   } else {
     con <- NULL
   }
-  
+
   # Get the workflow id
   if ("workflow" %in% names(settings)) {
     workflow.id <- settings$workflow$id
   } else {
     workflow.id <- -1
   }
-  
+
   # find all inputs that have an id
   inputs <- names(settings$run$inputs)
   inputs <- inputs[grepl(".id$", inputs)]
-  
+
   runs <- data.frame()
-  
+
   # Reading the site.pft specific tags from xml
   site.pfts.vec <- as.character(unlist(settings$run$site$site.pft))
-  
+
   if (!is.null(site.pfts.vec)) {
     # find the name of pfts defined in the body of pecan.xml
     defined.pfts <- as.character(unlist(purrr::map(settings$pfts, "name")))
@@ -152,8 +152,8 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
       )
     }
   }
-  
-  
+
+
   ## write median run
   MEDIAN <- "50"
   median.samples <- list()
@@ -161,14 +161,14 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
     median.samples[[i]] <- quantile.samples[[i]][MEDIAN, , drop  = FALSE]
   }
   names(median.samples) <- names(quantile.samples)
-  
+
   if (!is.null(con)) {
     # Note: ignores any existing run or ensemble ids in settings
     ensemble.id <- PEcAn.DB::db.query(paste0(
       "INSERT INTO ensembles (runtype, workflow_id) ",
       "VALUES ('sensitivity analysis', ", format(workflow.id, scientific = FALSE), ") ",
       "RETURNING id"), con = con)[["id"]]
-    
+
     paramlist <- paste0(
       "quantile=MEDIAN,trait=all,pft=",
       paste(lapply(settings$pfts, function(x) x[["name"]]), sep = ",")
@@ -177,15 +177,15 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
       "INSERT INTO runs ",
       "(model_id, site_id, start_time, finish_time, outdir, ensemble_id, parameter_list) ",
       "values ('",
-      settings$model$id, "', '",
-      settings$run$site$id, "', '",
-      settings$run$start.date, "', '",
-      settings$run$end.date, "', '",
-      settings$run$outdir, "', ",
-      ensemble.id, ", '",
-      paramlist, "') ",
+        settings$model$id, "', '",
+        settings$run$site$id, "', '",
+        settings$run$start.date, "', '",
+        settings$run$end.date, "', '",
+        settings$run$outdir, "', ",
+        ensemble.id, ", '",
+        paramlist, "') ",
       "RETURNING id"), con = con)[["id"]]
-    
+
     # associate posteriors with ensembles
     for (pft in defaults) {
       PEcAn.DB::db.query(
@@ -195,7 +195,7 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
         con = con
       )
     }
-    
+
     # associate inputs with runs
     if (!is.null(inputs)) {
       for (x in inputs) {
@@ -215,7 +215,7 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
     ensemble.id <- settings$sensitivity.analysis$ensemble.id %||% rlang::hash(settings)
   }
   medianrun <- run.id
-  
+
   # create folders (cleaning up old ones if needed)
   if (clean) {
     unlink(file.path(settings$rundir, run.id))
@@ -223,7 +223,10 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
   }
   dir.create(file.path(settings$rundir, run.id), recursive = TRUE)
   dir.create(file.path(settings$modeloutdir, run.id), recursive = TRUE)
-  
+
+  ## select single met path for SA runs without input_design (backward compatibility)
+  ## when input_design is provided (recommended), it supersedes this selection
+  ## and allows different met files per SA run
   # I check to make sure the path under the met is a list.
   # if it's specified what met needs to be used in 'met.id' under sensitivity
   # analysis of pecan xml we used that otherwise, I use the first met.
@@ -235,7 +238,7 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
     }
     settings$run$inputs$met$path <- settings$run$inputs$met$path[[settings$sensitivity.analysis$met.id]]
   }
-  
+
   # Apply input design coordination for median run
   median_settings <- settings
   if (!is.null(input_design)) {
@@ -251,21 +254,20 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
       }
     }
   }
-  
+
   median_input_info <- ""
   for (input_tag in names(median_settings$run$inputs)) {
     input_data <- median_settings$run$inputs[[input_tag]]
-    
     # At SA stage, path is ALWAYS a resolved string (thanks to input design)
     if (!is.null(input_data) && !is.null(input_data$path)) {
-      median_input_info <- paste0(median_input_info, 
-                                  format(input_tag, width = 12, justify = "left"), 
-                                  ": ", 
-                                  input_data$path, 
+      median_input_info <- paste0(median_input_info,
+                                  format(input_tag, width = 12, justify = "left"),
+                                  ": ",
+                                  input_data$path,
                                   "\n")
     }
   }
-  
+
   # write run information to disk TODO need to print list of pft names and trait
   # names
   cat("runtype     : sensitivity analysis\n",
@@ -287,7 +289,8 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
       "outdir      : ", file.path(settings$host$outdir, run.id), "\n",
       file = file.path(settings$rundir, run.id, "README.txt"),
       sep = "")
-  
+
+
   # write configuration
   do.call(my.write.config, args = list(defaults = defaults,
                                        trait.values = median.samples,
@@ -299,9 +302,9 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
     sep = "\n",
     append = TRUE
   )
-  
+
   run_index <- 1
-  
+
   ## loop over pfts
   runs <- list()
   for (pft_idx in seq_along(names(quantile.samples))) {
@@ -309,12 +312,12 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
     if (pftname == "env") {
       next
     }
-    
+
     traits <- colnames(quantile.samples[[pft_idx]])
     quantiles.str <- rownames(quantile.samples[[pft_idx]])
-    
+
     runs[[pftname]] <- data.frame()
-    
+
     ## loop over variables
     for (trait in traits) {
       for (quantile.str in quantiles.str) {
@@ -324,28 +327,28 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
           quantile <- as.numeric(quantile.str) / 100
           trait.samples <- median.samples
           trait.samples[[pft_idx]][trait] <- quantile.samples[[pft_idx]][quantile.str, trait, drop = FALSE]
-          
+
           if (!is.null(con)) {
             paramlist <- paste0("quantile=", quantile.str, ",trait=", trait, ",pft=", pftname)
             insert_result <- PEcAn.DB::db.query(
               paste0(
                 "INSERT INTO runs (",
-                "model_id, site_id, start_time, finish_time, outdir,",
-                " ensemble_id, parameter_list) ",
+                  "model_id, site_id, start_time, finish_time, outdir,",
+                  " ensemble_id, parameter_list) ",
                 "values ('",
-                settings$model$id, "', '",
-                settings$run$site$id, "', '",
-                settings$run$start.date, "', '",
-                settings$run$end.date, "', '",
-                settings$run$outdir, "', ",
-                ensemble.id, ", '",
-                paramlist,
+                  settings$model$id, "', '",
+                  settings$run$site$id, "', '",
+                  settings$run$start.date, "', '",
+                  settings$run$end.date, "', '",
+                  settings$run$outdir, "', ",
+                  ensemble.id, ", '",
+                  paramlist,
                 "') ",
                 "RETURNING id"),
               con = con
             )
             run.id <- insert_result[["id"]]
-            
+
             # associate posteriors with ensembles
             for (pft in defaults) {
               PEcAn.DB::db.query(
@@ -356,7 +359,7 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
                 con = con
               )
             }
-            
+
             # associate inputs with runs
             if (!is.null(inputs)) {
               for (x in inputs) {
@@ -378,10 +381,10 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
             )
           }
           runs[[pftname]][quantile.str, trait] <- run.id
-          
+
           # Increment run counter
           run_index <- run_index + 1
-          
+
           # create folders (cleaning up old ones if needed)
           if (clean) {
             unlink(file.path(settings$rundir, run.id))
@@ -389,7 +392,7 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
           }
           dir.create(file.path(settings$rundir, run.id), recursive = TRUE)
           dir.create(file.path(settings$modeloutdir, run.id), recursive = TRUE)
-          
+
           # Apply input design coordination for SA runs
           settings_copy <- settings
           if (!is.null(input_design)) {
@@ -403,21 +406,20 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
               }
             }
           }
-          
-          
+
           # Build dynamic input info string for SA run README
           sa_input_info <- ""
           for (input_tag in names(settings_copy$run$inputs)) {
             input_data <- settings_copy$run$inputs[[input_tag]]
             if (!is.null(input_data) && !is.null(input_data$path)) {
-              sa_input_info <- paste0(sa_input_info, 
-                                      format(input_tag, width = 12, justify = "left"), 
-                                      ": ", 
-                                      input_data$path, 
+              sa_input_info <- paste0(sa_input_info,
+                                      format(input_tag, width = 12, justify = "left"),
+                                      ": ",
+                                      input_data$path,
                                       "\n")
             }
           }
-          
+
           # write SA run information to disk
           cat("runtype     : sensitivity analysis\n",
               "workflow id : ", workflow.id, "\n",
@@ -438,8 +440,8 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
               "outdir      : ", file.path(settings$host$outdir, run.id), "\n",
               file = file.path(settings$rundir, run.id, "README.txt"),
               sep = "")
-          
-          
+
+
           # write configuration
           do.call(my.write.config, args = list(defaults = defaults,
                                                trait.values = trait.samples,
@@ -455,7 +457,7 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
       }
     }
   }
-  
+
   options(scipen = scipen)
   return(invisible(list(runs = runs, ensemble.id = ensemble.id)))
 } # write.sa.configs

From 5dcfe5956565a9718f4b7882f7b49c4eea770c67 Mon Sep 17 00:00:00 2001
From: divne7022 <www.divinehome12@gmail.com>
Date: Wed, 12 Nov 2025 09:30:19 +0000
Subject: [PATCH 6/6] add explicit namespace to modifyList calls

---
 base/workflow/R/run.write.configs.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/base/workflow/R/run.write.configs.R b/base/workflow/R/run.write.configs.R
index 17fd706cea..849efd3c92 100644
--- a/base/workflow/R/run.write.configs.R
+++ b/base/workflow/R/run.write.configs.R
@@ -238,11 +238,11 @@ run.write.configs <- function(settings, ensemble.size, input_design, write = TRU
     }
     # Merge trait.samples
     if (!is.null(existing_data$trait.samples)) {
-      trait.samples <- modifyList(existing_data$trait.samples, trait.samples)
+      trait.samples <- utils::modifyList(existing_data$trait.samples, trait.samples)
     }
     # Merge sa.samples
     if (!is.null(existing_data$sa.samples)) {
-      sa.samples <- modifyList(existing_data$sa.samples, sa.samples)
+      sa.samples <- utils::modifyList(existing_data$sa.samples, sa.samples)
     }
     # Merge runs.samples
     if (!is.null(existing_data$runs.samples)) {
@@ -286,7 +286,7 @@ run.write.configs <- function(settings, ensemble.size, input_design, write = TRU
     }
     # Merge trait.names
     if (!is.null(existing_data$trait.names)) {
-      trait.names <- modifyList(existing_data$trait.names, trait.names)
+      trait.names <- utils::modifyList(existing_data$trait.names, trait.names)
     }
   }
   ### Save output from SA/Ensemble runs