Update news and documentation files

DESCRIPTION

@@ -35,7 +35,7 @@ Description: Wrapper of the C++ model FATE. FATE is a vegetation model based on
         1) gather, prepare and format data to be used with FATE ;
         2) run FATE simulation(s)
         3) process and analyze data produced by FATE.
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Encoding: UTF-8
 NeedsCompilation: yes
 License:

R/PRE_FATE.params_PFGlight.R

@@ -50,12 +50,11 @@
 ##'   \code{H} (herbaceous), \code{C} (chamaephyte) or \code{P} (phanerophyte) 
 ##'   for now \cr \cr}
 ##'   
-##'   \item{(\emph{shade_factor})}{an \code{integer} between \code{1} and 
-##'   \code{Inf} corresponding to an index of shade quantity to weight PFG 
-##'   abundance and transform it into light resources (\emph{e.g. if two PFG 
-##'   have shade factors of \code{1} and \code{5} respectively, for the same 
-##'   abundances, the second PFG will produce 5 times more shade than the first 
-##'   one}) \cr \cr}
+##'   \item{(\emph{shade_factor})}{a value corresponding to an index of shade 
+##'   quantity to weight PFG abundance and transform it into light resources 
+##'   (\emph{e.g. if two PFG have shade factors of \code{1} and \code{5} 
+##'   respectively, for the same abundances, the second PFG will produce 5 
+##'   times more shade than the first one}) \cr \cr}
 ##'   
 ##'   \item{(\emph{active_germ_low})}{an \code{integer} between \code{0} and 
 ##'   \code{100} corresponding to the proportion of seeds that will germinate for 
@@ -381,8 +380,6 @@ PRE_FATE.params_PFGlight = function(
     if (sum(colnames(mat.PFG.light) == "shade_factor") == 1)
     {
       .testParam_NAvalues.m("mat.PFG.light$shade_factor", mat.PFG.light$shade_factor)
-      .testParam_notInteger.m("mat.PFG.light$shade_factor", mat.PFG.light$shade_factor)
-      .testParam_notBetween.m("mat.PFG.light$shade_factor", mat.PFG.light$shade_factor, 0, Inf)
     }
     if (sum(colnames(mat.PFG.light) == "light_need") == 1)
     {

R/PRE_FATE.params_PFGsuccession.R

@@ -91,16 +91,16 @@
 ##'   Two methods to define these abundances are available :
 ##'   \itemize{
 ##'     \item from \strong{predefined rules} (using \code{type}, 
-##'     \code{MAX_STRATUM}) : \cr \cr
+##'     \code{HEIGHT}) : \cr \cr
 ##'     \tabular{rcccc}{
-##'       \strong{MAX_STRATUM} \tab \strong{1} \tab \strong{2} \tab 
-##'       \strong{3} \tab \strong{+}\cr
-##'       \strong{\code{H} (herbaceous)} \tab \code{3} \tab \code{3} \tab 
-##'       \code{2} \tab \code{2} \cr
-##'       \strong{\code{C} (chamaephyte)} \tab \code{3} \tab \code{2} \tab 
-##'       \code{2} \tab \code{1} \cr
-##'       \strong{\code{P} (phanerophyte)} \tab \code{3} \tab \code{2} \tab 
-##'       \code{1} \tab \code{1}
+##'       \strong{HEIGHT} \tab \strong{<20cm} \tab \strong{<50cm} \tab 
+##'       \strong{<150cm} \tab \strong{>150cm}\cr
+##'       \strong{\code{H} (herbaceous)} \tab \code{100} \tab \code{100} \tab 
+##'       \code{50} \tab \code{50} \cr
+##'       \strong{\code{C} (chamaephyte)} \tab \code{100} \tab \code{50} \tab 
+##'       \code{50} \tab \code{10} \cr
+##'       \strong{\code{P} (phanerophyte)} \tab \code{100} \tab \code{50} \tab 
+##'       \code{10} \tab \code{10}
 ##'     }
 ##'     \item from \strong{user data} : \cr
 ##'       \emph{with the values contained within the \code{max_abundance} 
@@ -113,12 +113,12 @@
 ##'   contribute to shade half less}) than mature individuals \cr \cr
 ##'   Two methods to define these sizes are available :
 ##'   \itemize{
-##'     \item from \strong{predefined rules} (using \code{type}, \code{MAX_STRATUM}) 
+##'     \item from \strong{predefined rules} (using \code{type}, \code{HEIGHT}) 
 ##'     : \cr \cr
 ##'     
 ##'     \tabular{rcccc}{
-##'       \strong{MAX_STRATUM} \tab \strong{1} \tab \strong{2} \tab 
-##'       \strong{3} \tab \strong{+}\cr
+##'       \strong{HEIGHT} \tab \strong{<20cm} \tab \strong{<50cm} \tab 
+##'       \strong{<10m} \tab \strong{>10m}\cr
 ##'       \strong{\code{H} (herbaceous)} \tab \code{100\%} \tab \code{80\%} 
 ##'       \tab \code{50\%} \tab \code{50\%} \cr
 ##'       \strong{\code{C} (chamaephyte)} \tab \code{100\%} \tab \code{50\%} 
@@ -170,9 +170,7 @@
 ##'   \item{MATURITY}{PFG maturity age \emph{(in years)}}
 ##'   \item{LONGEVITY}{PFG life span \emph{(in years)}}
 ##'   \item{MAX_STRATUM}{maximum height stratum that the PFG can reach}
-##'   \item{MAX_ABUNDANCE}{maximum abundance / space (quantitative) that the 
-##'   PFG is able to produce / occupy \cr \emph{(\code{1}: Low \code{2}: 
-##'   Medium \code{3}: High)}}
+##'   \item{MAX_ABUND}{maximum abundance of mature individuals that the PFG can reach}
 ##'   \item{IMM_SIZE}{PFG immature relative size \emph{(integer between \code{0}  
 ##'   and \code{100}\%)}}
 ##'   \item{CHANG_STR_AGES}{ages at which the PFG goes in the upper stratum 
@@ -384,7 +382,6 @@ PRE_FATE.params_PFGsuccession = function(
     if (sum(colnames(mat.PFG.succ) == "max_abundance") == 1)
     {
       .testParam_NAvalues.m("mat.PFG.succ$max_abundance", mat.PFG.succ$max_abundance)
-      .testParam_notInValues.m("mat.PFG.succ$max_abundance", mat.PFG.succ$max_abundance, 1:3)
     }
     if (sum(colnames(mat.PFG.succ) == "potential_fecundity") == 1)
     {
@@ -511,7 +508,6 @@ PRE_FATE.params_PFGsuccession = function(
   ##  = maximum abundance of mature PFG
   ##  = carrying capacity proxy in terms of number of individuals
   ## Defined according to the number of strata potentially occupied by a PFG
-  ## 3 levels : 1 = Low, 2 = Medium or 3 = High
   if (sum(colnames(mat.PFG.succ) == "max_abundance") == 1)
   {
     MAX_ABUNDANCE = mat.PFG.succ$max_abundance
@@ -520,18 +516,17 @@ PRE_FATE.params_PFGsuccession = function(
     ## herbaceous are small and can be numerous (high number of individuals)
     ## chamaephytes can produce medium number of individuals
     ## phanerophytes can produce small number of individuals
-    ## all plants in first stratum can produce high number of individuals
-    ## plants other than herbaceous in stratum 2 can produce medium number of individuals
-    ## herbaceous in stratum > 2 can produce medium number of individuals
-    ## chamaephytes in stratum > 3 can produce small number of individuals
+    ## all plants < 20cm can produce high number of individuals
+    ## herbaceous > 20cm & other plants < 20cm can produce medium number of individuals
+    ## plants > 150cm can produce small number of individuals
     MAX_ABUNDANCE = rep(NA, no.PFG)
-    MAX_ABUNDANCE[which(mat.PFG.succ$type == "H")] = 3
-    MAX_ABUNDANCE[which(mat.PFG.succ$type == "C")] = 2
-    MAX_ABUNDANCE[which(mat.PFG.succ$type == "P")] = 1
-    MAX_ABUNDANCE[which(MAX_STRATUM == 1)] = 3
-    MAX_ABUNDANCE[which(MAX_STRATUM == 2 & mat.PFG.succ$type != "H")] = 2
-    MAX_ABUNDANCE[which(MAX_STRATUM > 2 & mat.PFG.succ$type == "H")] = 2
-    MAX_ABUNDANCE[which(MAX_STRATUM > 3 & mat.PFG.succ$type == "C")] = 1
+    MAX_ABUNDANCE[which(mat.PFG.succ$type == "H")] = 100
+    MAX_ABUNDANCE[which(mat.PFG.succ$type == "C")] = 50
+    MAX_ABUNDANCE[which(mat.PFG.succ$type == "P")] = 10
+    MAX_ABUNDANCE[which(mat.PFG.succ$type == "H" & mat.PFG.succ$height > 50)] = 50
+    MAX_ABUNDANCE[which(mat.PFG.succ$type != "H" & mat.PFG.succ$height < 50)] = 50
+    MAX_ABUNDANCE[which(mat.PFG.succ$height > 150)] = 10
+    MAX_ABUNDANCE[which(mat.PFG.succ$height < 20)] = 100
   }
 
   #############################################################################
@@ -543,20 +538,20 @@ PRE_FATE.params_PFGsuccession = function(
     IMM_SIZE = mat.PFG.succ$immature_size
   } else
   {
-    ## immature herbaceous contribute to shade in the same way than mature herbaceous
-    ## immature chamaephytes contribute to shade half less than mature herbaceous
+    ## immature herbaceous contribute to shade in the same way than mature
+    ## immature chamaephytes contribute to shade half less than mature
     ## immature phanerophytes contribute to shade only by 10 % of their full capacity
-    ## intermediate percentage for herbaceous in stratum 2
-    ## intermediate percentage for herbaceous in stratum > 2
-    ## immature chamaephytes in 1st stratum contribute to shade in the same way than mature chamaephytes
-    ## immature phanerophytes with height < 10m contribute to shade half less than mature phanerophytes
+    ## intermediate percentage for herbaceous in stratum > 20cm & < 50cm
+    ## immature herbaceous with height > 50cm contribute to shade half less than mature
+    ## immature chamaephytes < 20cm contribute to shade in the same way than mature
+    ## immature phanerophytes with height < 10m contribute to shade half less than mature
     IMM_SIZE = rep(100, no.PFG)
     IMM_SIZE[which(mat.PFG.succ$type == "H")] = 100
     IMM_SIZE[which(mat.PFG.succ$type == "C")] = 50
     IMM_SIZE[which(mat.PFG.succ$type == "P")] = 10
-    IMM_SIZE[which(mat.PFG.succ$type == "H" & MAX_STRATUM == 2)] = 80
-    IMM_SIZE[which(mat.PFG.succ$type == "H" & MAX_STRATUM > 2)] = 50
-    IMM_SIZE[which(mat.PFG.succ$type == "C" & MAX_STRATUM == 1)] = 100
+    IMM_SIZE[which(mat.PFG.succ$type == "H" & mat.PFG.succ$height > 20)] = 80
+    IMM_SIZE[which(mat.PFG.succ$type == "H" & mat.PFG.succ$height > 50)] = 50
+    IMM_SIZE[which(mat.PFG.succ$type == "C" & mat.PFG.succ$height < 20)] = 100
     IMM_SIZE[which(mat.PFG.succ$type == "P" & mat.PFG.succ$height < 1000)] = 50
   }
 

README.md

@@ -43,7 +43,9 @@ library(devtools)
 devtools::install_github(repo="leca-dev/RFate")
 </pre>
 
-**Note :** `RFate` is currently having problems compiling on Windows with RTools4.3 <i class="fa-solid fa-triangle-exclamation"></i>
+**Note :** v1.3.5 changes `MAX_ABUND` parameters <i class="fa-solid fa-triangle-exclamation"></i>
+
+**Note :** v1.3.4 is compiling on Windows with R 4.4.0 RTools44 <i class="fa-solid fa-triangle-exclamation"></i>
 
 **Note :** v1.3.1 changes scale from `0:10` to `0:100` <br/> for `IMM_SIZE`, `ACTIVE_GERM`, `LIGHT_TOL`, `SOIL_TOL`, `PROP_KILLED`, `ACTIVATED_SEED`, `FATES` parameters <i class="fa-solid fa-triangle-exclamation"></i>
 

vignettes/fate_tutorial_3_MODULES.Rmd

@@ -53,9 +53,6 @@ SEEDING_DURATION 300
 SEEDING_TIMESTEP 1
 SEEDING_INPUT 100
 POTENTIAL_FECUNDITY 10
-MAX_ABUND_LOW 100
-MAX_ABUND_MEDIUM 500
-MAX_ABUND_HIGH 8000
 </pre>
 
 The number of computer resources can also be given :
@@ -104,8 +101,7 @@ TYPE P
 HEIGHT 1200
 MATURITY 45
 LONGEVITY 451
-MAX_STRATUM 5
-MAX_ABUNDANCE 3
+MAX_ABUNDANCE 100
 IMM_SIZE 10
 CHANG_STR_AGES 0 14 38 110 344
 SEED_POOL_LIFE 0 0
@@ -114,6 +110,7 @@ SEED_DORMANCY 0
 
 The maximum number of seeds produced each year can also be specified per PFG :
 <pre class = "grey">
+MAX_STRATUM 5
 POTENTIAL_FECUNDITY 50
 </pre>
 
@@ -404,8 +401,8 @@ RESPR_AGE 0 0 3 26 0 0 3 26
 FATES 60 0 20 0 50 0 60 0 20 0 50 0 10 0 20 0
 PROP_KILLED 0 0
 ACTIVATED_SEED 0 0
-THRESHOLD_MOD -11.50406848
-THRESHOLD_SEV -12.3335733
+DROUGHT_THRESH_MOD -11.50406848
+DROUGHT_THRESH_SEV -12.3335733
 COUNTER_RECOVERY 1
 COUNTER_SENS 3
 COUNTER_CUM 3

vignettes/news.Rmd

@@ -44,6 +44,20 @@ Refinements to the model, and integration of the `C++` code within an `R` packag
 
 <br/> <br/>
 
+#### Version 1.3.5 (june 2024)
+
+- 1.3.5 :
+    + do not need dispersal to have seeding
+    + transform `SHADE_FACTOR` from int to double
+    + remove `MAX_ABUND_LOW`, `MAX_ABUND_MEDIUM`, `MAX_ABUND_HIGH` in global parameters
+    + addition of `MAX_ABUND` parameter within PFG succession files (see [FATE tutorial - Modules](fate_tutorial_3_MODULES.html))
+    + update `DROUGHT` module code
+- 1.3.4 : 
+    + switch between int / unsigned to remove warnings (*compilation*)
+    + change variable names (from `m_Dispersed` to `m_IsSeeded`, `MaxRecruit` to `Light/SoilActiveGerm`, `m_DormBreaks` to `m_ActiveSeeds`)
+    + change PFG parameter names related to drought (see [FATE tutorial - Modules](fate_tutorial_3_MODULES.html))
+    + update `Makevars.win` and `winlibs` to compile on Windows with R 4.4.0 and RTools44
+
 #### Version 1.3.3 (november 2023) 
 
 - 1.3.3 : addition of `DIST_PROB` and `DIST_PAIR` parameters within `DIST` module (see [FATE tutorial - Modules](fate_tutorial_3_MODULES.html))