Fix duplicate youngAge term in the spread formula

NEWS.md

@@ -1,5 +1,11 @@
 # fireSense_dataPrepFit (development version)
 
+- `prepare_SpreadFit()` built the spread formula's RHS as `climate + youngAgeTxt + vegCols`, but `vegCols`
+  (derived from `fireSenseVegData`) already includes a `youngAge` column whenever
+  `fireSenseUtils::fireSenseCovariatesCreate()` finds young forest or non-forest pixels. The formula then
+  listed `youngAge` twice; `terms()` silently drops the duplicate, leaving one fewer distinct term than the
+  covariates actually used downstream. `youngAgeTxt` and the spread climate variable are now excluded from
+  `vegCols` before building the RHS. Version 1.2.0.9013.
 - `prepare_SpreadFitFire_Vector()` filtered `spreadFirePolys` by pixel size only, while `spreadFirePoints`
   was filtered with `escapedFires()` (pixel size and `escapeSizeHa`, PR #44). A fire between one pixel and
   `escapeSizeHa` then survived in the polygons but not the points, and `fireSenseUtils::harmonizeFireData()`

fireSense_dataPrepFit.R

@@ -8,7 +8,7 @@ defineModule(sim, list(
     person(c("Alex", "M"), "Chubaty", role = "ctb", email = "achubaty@for-cast.ca")
   ),
   childModules = character(0),
-  version = list(fireSense_dataPrepFit = "1.2.0.9012"),
+  version = list(fireSense_dataPrepFit = "1.2.0.9013"),
   timeframe = as.POSIXlt(c(NA, NA)),
   timeunit = "year",
   citation = list("citation.bib"),
@@ -771,8 +771,13 @@ prepare_SpreadFit <- function(sim) {
                                             round(sim$spreadClimateSelection$auc, 2), collapse = ", "))
   }
 
+  ## vegCols can already contain "youngAge" (added by fireSenseUtils::fireSenseCovariatesCreate()
+  ## when there are young non-forest/forest pixels) and, in principle, the spread climate variable
+  ## name; both are also added explicitly below, so they must be excluded here or the formula lists
+  ## them twice and terms() silently drops the duplicate, leaving one fewer term than parameters.
+  vegColsForRHS <- setdiff(vegCols, c(youngAgeTxt, sim$climateVariablesForFire$spread))
   RHS <- paste(paste0(sim$climateVariablesForFire$spread, collapse = " + "), youngAgeTxt,
-               paste0(vegCols, collapse = " + "), sep =  " + ")
+               paste0(vegColsForRHS, collapse = " + "), sep =  " + ")
 
   ## this is a funny way to get years but avoids years with 0 fires
   allYears <- unname(unlist(mod$allYears))

tests/testthat/test-spreadFormulaYoungAgeOnce.R

@@ -0,0 +1,39 @@
+## fireSense_dataPrepFit.R ~774 (prepare_SpreadFit()): the spread formula's RHS was built as
+## `climate + youngAgeTxt + vegCols`, but vegCols already includes a "youngAge" column whenever
+## fireSenseUtils::fireSenseCovariatesCreate() finds young forest/non-forest pixels (real cache
+## entries for ELFs 14.3 and 14.4, 2026-09-27). R's terms() silently drops the duplicate, so the
+## resulting formula has one fewer distinct term than the raw covariate list that downstream code
+## (the fitted parameter bounds) is built from.
+
+test_that("the spread formula lists a veg-table youngAge column once, not twice", {
+  body <- body(prepare_SpreadFit)
+  stmts <- as.list(body)[-1]
+  txt <- vapply(stmts, function(s) paste(deparse(s), collapse = " "), character(1))
+
+  ## pull just the statements that build vegCols and the formula's RHS out of prepare_SpreadFit,
+  ## in their original order, and eval them against a small fabricated fireSenseVegData -- the
+  ## rest of that function (fire buffering, climate rasters, ...) is irrelevant to this defect
+  patterns <- c("^nonVegColnames <-", "^vegCols <- setdiff", "^dropCols <-",
+                "^if \\(length\\(dropCols\\)", "^vegColsForRHS <-", "^RHS <-",
+                "^if \\(is\\.null\\(sim\\$fireSense_spreadFormula\\)\\)")
+  idx <- sort(unique(unlist(lapply(patterns, grep, x = txt))))
+  expect_true(length(idx) >= 5) # sanity: these statements are still present in prepare_SpreadFit
+
+  env <- new.env(parent = environment(prepare_SpreadFit))
+  env$sim <- new.env()
+  env$sim$climateVariablesForFire <- list(spread = "CMD")
+  env$sim$fireSense_spreadFormula <- NULL
+  ## the shape fireSenseVegData has after joinFireBuffersToVeg() and setnames(..., "buffer",
+  ## "burned"): a youngAge column that is not all-zero, as in ELFs 14.3/14.4
+  env$fireSenseVegData <- data.table::data.table(
+    pixelID = 1:10, ids = 1L, burned = rep(0:1, 5), year = 2010L,
+    fuelA = c(rep(0, 5), rep(1, 5)), youngAge = c(rep(1, 3), rep(0, 7))
+  )
+
+  for (i in idx) eval(stmts[[i]], env)
+
+  rhsTerms <- trimws(strsplit(env$RHS, "\\+")[[1]])
+  expect_identical(anyDuplicated(rhsTerms), 0L)
+  expect_identical(length(rhsTerms), length(env$vegCols) + 1L) # +1 for the climate variable
+  expect_identical(env$sim$fireSense_spreadFormula, "~ 0 + CMD + youngAge + fuelA")
+})