1. Add full @param descriptions for adjust.biomass.LPJGUESS, `AbvGr…

…ndWood`, `TotalCarbon`;

2. Fix the hard code `npatches <- 5` in `read_state.R`

models/lpjguess/R/adjust.biomass.LPJGUESS.R

@@ -6,13 +6,13 @@
 ##' adjustments to the litter pools.
 ##' 
 ##' @param individual A nested list which encapsulates an LPJ-GUESS 'Individual' as read from a binary state file
-##' @param rel.change A numeric by which to scale the density and C and N pools
+##' @param biomass.inc A numeric value specifying the biomass increment to be applied.
 ##' @param sla The SLA (specific leaf area) (per PFT parameter)
-##' @param k_latosa The leaf area to sapwood area ratio (per PFT parameter)
-##' @param k_allom2,k_allom3, Allometry coefficients (per PFT parameters)
 ##' @param wooddens Wood density (kgC/m^2) (per PFT parameter)
-##' @param crownarea_max Maximum allowed crown area (m^2)  (per PFT parameter)
 ##' @param lifeform An integer code for the lifeform of this individual (cohort): 1 = Tree, 2 = Grass
+##' @param k_latosa The leaf area to sapwood area ratio (per PFT parameter)
+##' @param k_allom2,k_allom3, Allometry coefficients (per PFT parameters)
+##' @param trace Logical; if TRUE, prints details of biomass adjustment process.
 ##' 
 ##' The changes in C pools are determined by the allocation.  The changes in the N pools are designed to 
 ##' maintain the pre-exisiing C:N ratios, so N is just scaled using the updated C with the initial C:N ratio.
@@ -27,7 +27,7 @@
 ##' @keywords internal
 ##' @return the scaled 'individual' (the initial nested list with update values)
 ##' @author Matthew Forrest
-adjust.biomass.LPJGUESS <- function(individual, biomass.inc,  sla, wooddens, lifeform, k_latosa, k_allom2, k_allom3, trace = TRUE){
+adjust.biomass.LPJGUESS <- function(individual, biomass.inc, sla, wooddens, lifeform, k_latosa, k_allom2, k_allom3, trace = TRUE){
 
   # dummy input values to the allocation function below
   # note that they are not actually updated by the function, the updated values are in the returned list

models/lpjguess/R/read_state.R

@@ -480,10 +480,10 @@ read_binary_LPJGUESS <- function(outdir, version = "PalEON"){
   paramh_name <- paste0("parameters.", version, ".h") 
   paramh_in   <- readLines(con = system.file(paramh_name, package = "PEcAn.LPJGUESS"), n = -1)
 
-  ### these are the values read from params.ins, passed to this fcn
-  #paramsins <- readLines(file.path(rundir, "params.ins"), n = -1)
-  #npatches  <- as.numeric(gsub(".*([0-9]+).*$", "\\1", paramsins[grepl("npatch", paramsins, fixed = TRUE)]))
-  npatches  <- 5
+  ## these are the values read from params.ins, passed to this fcn
+  paramsins <- readLines(file.path(rundir, "params.ins"), n = -1)
+  npatches  <- as.numeric(gsub(".*([0-9]+).*$", "\\1", paramsins[grepl("npatch", paramsins, fixed = TRUE)]))
+  #npatches  <- 5
 
   ######################################
   ## read meta.bin

models/lpjguess/R/update.state.LPJGUESS.R

@@ -1,5 +1,11 @@
-##'  Calculate Above Ground Woody Biomass
-
+##' @title AbvGrndWood
+##'
+##' @description Calculates the above-ground woody biomass of an LPJ-GUESS individual.
+##'
+##' @param individual A nested list representing an LPJ-GUESS individual from a binary state file.
+##' @param include.debt Logical; if TRUE, includes carbon mass debt in the calculation.
+##'
+##' @return A numeric value representing the above-ground woody biomass (kgC/m²).
 ##' @keywords internal
 AbvGrndWood <- function(individual, include.debt = TRUE){
 
@@ -15,8 +21,14 @@ AbvGrndWood <- function(individual, include.debt = TRUE){
 
 }
 
-##'  Calculate Above Ground Woody Biomass
-
+##' @title TotalCarbon
+##'
+##' @description Calculates the total carbon content of an LPJ-GUESS individual.
+##'
+##' @param individual A nested list representing an LPJ-GUESS individual from a binary state file.
+##' @param include.debt Logical; if TRUE, includes carbon mass debt in the calculation.
+##'
+##' @return A numeric value representing the total carbon content (kgC/m²).
 ##' @keywords internal
 TotalCarbon <- function(individual, include.debt = TRUE){