From 92a695c1a5b7476c4c433a31a6f1581c707dd0da Mon Sep 17 00:00:00 2001 From: MayaGueguen Date: Fri, 29 Oct 2021 10:24:16 +0200 Subject: [PATCH 01/20] Trying to couple RangeShiftR with RFate --- DESCRIPTION | 6 +++--- R/UTILS.loadPackage.R | 1 + 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index b9a9d5c..b1bfe9b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: RFate Type: Package Title: FATE with R -Version: 1.0.1 -Date: 2021-06-14 +Version: 1.0.2 +Date: 2021-09-27 Authors@R: c(person("Wilfried", "Thuiller", role = "aut" , email = "wilfried.thuiller@univ-grenoble-alpes.fr"), person("Damien", "Georges", role = "aut"), @@ -59,6 +59,6 @@ Suggests: testthat, covr, knitr, markdown, rmarkdown -LinkingTo: Rcpp, RcppThread, BH (>= 1.75.0-0) +LinkingTo: Rcpp, RcppThread, BH (>= 1.75.0-0), RangeShiftR VignetteBuilder: knitr, rmarkdown Language: en-US diff --git a/R/UTILS.loadPackage.R b/R/UTILS.loadPackage.R index 6359c4b..914cc99 100644 --- a/R/UTILS.loadPackage.R +++ b/R/UTILS.loadPackage.R @@ -80,5 +80,6 @@ .onUnload = function (libpath) { + library.dynam.unload("RangeShiftR", libpath) library.dynam.unload("RFate", libpath) } From 7e4bafebbc25c40bfc8467e9d818b5bb006cd7b2 Mon Sep 17 00:00:00 2001 From: MayaGueguen Date: Tue, 23 Nov 2021 14:28:14 +0100 Subject: [PATCH 02/20] Add first version of FATE_RS function --- R/FATE_RS.R | 120 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 120 insertions(+) create mode 100644 R/FATE_RS.R diff --git a/R/FATE_RS.R b/R/FATE_RS.R new file mode 100644 index 0000000..6415368 --- /dev/null +++ b/R/FATE_RS.R @@ -0,0 +1,120 @@ +### HEADER ##################################################################### +##' @title S +##' +##' @name FATE_RS +##' +##' @author Maya Guéguen +##' +##' +##' @description ... +##' +##' +##' @keywords RangeShifter +##' +##' @export +##' +##' @importFrom RangeShiftR RunRS readPop +##' @importFrom raster stack rasterFromXYZ writeRaster +##' +## END OF HEADER ############################################################### + + +FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.level = 2 + , name.simulation.RS, params.RS + , year.start, year.end, year.step) +{ + ## + argument pour savoir si on commence par FATE ou RS + + ## LOOP over simulation years + for (ye in seq(year.start, year.end, 1)) + { + .setParam(params.lines = abs.simulParam + , flag = "SAVING_DIR" + , flag.split = "^--.*--$" + , value = paste0(name.simulation, "/RESULTS/SIMUL_YEAR_", ye, "")) + + ## Run FATE ################################################################################### + FATE(simulParam = abs.simulParam, no_CPU = opt.no_CPU, verboseLevel = verbose.level) + + ## Get resulting FATE vegetation maps ######################################################### + ## Get results directories ------------------------------------------------ + GLOB_DIR = .getGraphics_results(name.simulation = name.simulation + , abs.simulParam = abs.simulParam) + + ## Get number of PFGs ----------------------------------------------------- + ## Get PFG names ---------------------------------------------------------- + GLOB_SIM = .getGraphics_PFG(name.simulation = name.simulation + , abs.simulParam = abs.simulParam) + + ## Get raster mask -------------------------------------------------------- + GLOB_MASK = .getGraphics_mask(name.simulation = name.simulation + , abs.simulParam = abs.simulParam) + + ## UNZIP the raster saved ------------------------------------------------- + raster.perPFG.allStrata = .getRasterNames(year.step, "allStrata", "ABUND", GLOB_DIR) + .unzip(folder_name = GLOB_DIR$dir.output.perPFG.allStrata + , list_files = raster.perPFG.allStrata + , no_cores = opt.no_CPU) + + ## GET PFG abundance maps (all strata) ------------------------------ + file_name = paste0(GLOB_DIR$dir.output.perPFG.allStrata + , "Abund_YEAR_" + , year.step + , "_" + , GLOB_SIM$PFG + , "_STRATA_all.tif") + gp = GLOB_SIM$PFG[which(file.exists(file_name))] + file_name = file_name[which(file.exists(file_name))] + + if (length(file_name) > 0) + { + ras.PFG = stack(file_name) * GLOB_MASK$ras.mask + names(ras.PFG) = gp + } else + { + stop(paste0("Missing data!\n The folder " + , GLOB_DIR$dir.output.perPFG.allStrata + , " does not contain adequate files")) + } + + ## Transform them into habitat map ############################################################ + + ## Transform them into RS species distribution map ############################################ + + ## Update RS disp-cost and patch maps ######################################################### + + ## Run RangeShifter ########################################################################### + RunRS(RSparams = params.RS, dirpath = name.simulation.RS) + + ## Get resulting RS species density ########################################################### + ## Code from RangeShiftR help + # read population output file into a dataframe + pop_df <- readPop(s = params.RS, dirpath = name.simulation.RS) + + # Make stack of different raster layers for each year and for only one repetition (Rep==0): + pop_wide_rep0 <- reshape(subset(pop_df, Rep == 0)[, c('Year', 'x', 'y', 'NInd')] + , timevar = 'Year' + , v.names = c('NInd') + , idvar = c('x', 'y') + , direction = 'wide') + + # use raster package to make a raster from the data frame + stack_years_rep0 <- rasterFromXYZ(pop_wide_rep0) + name.dist = paste0(name.simulation, "/DATA/MASK/MASK_DIST_YEAR_", ye, ".tif") + writeRaster(stack_years_rep0, filename = name.dist) + + ## Update FATE disturbance maps ############################################################### + .setParam(params.lines = abs.simulParam + , flag = "DIST_MASK" + , flag.split = "^--.*--$" + , value = paste0(name.simulation, "/DATA/MASK/MASK_DIST_YEAR_", ye, ".tif")) + + ## Update FATE simulation to load ############################################################# + .setParam(params.lines = abs.simulParam + , flag = "SAVED_STATE" + , flag.split = "^--.*--$" + , value = "XXX") + + } +} + From adb0c2e576e3dcb84882b7829e8dbd05a6b515df Mon Sep 17 00:00:00 2001 From: MayaGueguen Date: Tue, 30 Nov 2021 12:52:37 +0100 Subject: [PATCH 03/20] Remove ALIEN.no parameter --- R/PRE_FATE.params_globalParameters.R | 12 +---- .../PRE_FATE.params_globalParameters.html | 20 +++------ man/PRE_FATE.params_globalParameters.Rd | 6 --- .../test-PRE_FATE.params_globalParameters.R | 44 ++----------------- .../test-PRE_FATE.params_simulParameters.R | 1 - 5 files changed, 11 insertions(+), 72 deletions(-) diff --git a/R/PRE_FATE.params_globalParameters.R b/R/PRE_FATE.params_globalParameters.R index bd1e786..c09abd0 100644 --- a/R/PRE_FATE.params_globalParameters.R +++ b/R/PRE_FATE.params_globalParameters.R @@ -124,8 +124,6 @@ ##' @param doAliens default \code{FALSE}. \cr If \code{TRUE}, invasive plant ##' introduction is activated in the \code{FATE} simulation, and associated ##' parameters are required -##' @param ALIEN.no (\emph{optional}) \cr an \code{integer} corresponding to the -##' number of introductions ##' @param ALIEN.freq (\emph{optional}) \cr a \code{vector} of \code{integer} ##' corresponding to the frequency of each introduction (\emph{in years}) ##' @param doFire default \code{FALSE}. \cr If \code{TRUE}, fire @@ -435,7 +433,6 @@ ##' introduction areas. \cr If the habitat suitability filter is on, ##' suitability maps will also be needed for these new groups. ##' \describe{ -##' \item{ALIEN.no}{the number of different introductions} ##' \item{ALIEN.freq}{the frequency of each introduction (\emph{in years})} ##' } ##' } @@ -642,7 +639,6 @@ ##' ##' \itemize{ ##' \item DO_ALIENS_INTRODUCTION -##' \item ALIENS_NO ##' \item ALIENS_FREQ ##' } ##' @@ -768,7 +764,6 @@ PRE_FATE.params_globalParameters = function( , doDrought = FALSE , DROUGHT.no_sub = 4 , doAliens = FALSE - , ALIEN.no , ALIEN.freq = 1 , doFire = FALSE , FIRE.no @@ -862,11 +857,10 @@ PRE_FATE.params_globalParameters = function( } if (doAliens) { - .testParam_notInteger.m("ALIEN.no", ALIEN.no) .testParam_notInteger.m("ALIEN.freq", ALIEN.freq) - if (length(ALIEN.freq) != ALIEN.no){ + if (length(ALIEN.freq) != required.no_PFG){ stop(paste0("Wrong type of data!\n `ALIEN.freq` must contain as many " - , "values as the number of introductions (`ALIEN.no`)")) + , "values as the number of PFG (`required.no_PFG`)")) } } if (doFire) @@ -1012,10 +1006,8 @@ PRE_FATE.params_globalParameters = function( if (doAliens) { params.ALIEN = list(as.numeric(doAliens) - , ALIEN.no , ALIEN.freq) names.params.list.ALIEN = c("DO_ALIENS_INTRODUCTION" - , "ALIENS_NO" , "ALIENS_FREQ") } else { diff --git a/docs/reference/PRE_FATE.params_globalParameters.html b/docs/reference/PRE_FATE.params_globalParameters.html index d41c784..8c5dc4f 100644 --- a/docs/reference/PRE_FATE.params_globalParameters.html +++ b/docs/reference/PRE_FATE.params_globalParameters.html @@ -75,7 +75,7 @@ RFate - 1.0.1 + 1.0.2 @@ -83,7 +83,7 @@
  • - +
    • @@ -127,21 +127,21 @@
  • - + Build PFG
  • - + Build parameter files
  • - + Build graphics @@ -158,7 +158,7 @@
  • - + Reference @@ -246,7 +246,6 @@

    Create Global_parameters parameter file for a FATE doDrought = FALSE, DROUGHT.no_sub = 4, doAliens = FALSE, - ALIEN.no, ALIEN.freq = 1, doFire = FALSE, FIRE.no, @@ -487,11 +486,6 @@

    Arg

    default FALSE.
    If TRUE, invasive plant introduction is activated in the FATE simulation, and associated parameters are required

    - - - ALIEN.no -

    (optional)
    an integer corresponding to the -number of introductions

    ALIEN.freq @@ -679,7 +673,6 @@

    Value

    If the simulation includes aliens introduction :

    • DO_ALIENS_INTRODUCTION

      • -

    • ALIENS_NO

    • ALIENS_FREQ

    @@ -901,7 +894,6 @@

    Details introduction areas.
    If the habitat suitability filter is on, suitability maps will also be needed for these new groups.
    -
    ALIEN.no

    the number of different introductions

    ALIEN.freq

    the frequency of each introduction (in years)

    FIRE

    = to influence plant mortality and / or resprouting according to PFG tolerances to these events (see diff --git a/man/PRE_FATE.params_globalParameters.Rd b/man/PRE_FATE.params_globalParameters.Rd index c70f136..b296022 100644 --- a/man/PRE_FATE.params_globalParameters.Rd +++ b/man/PRE_FATE.params_globalParameters.Rd @@ -42,7 +42,6 @@ PRE_FATE.params_globalParameters( doDrought = FALSE, DROUGHT.no_sub = 4, doAliens = FALSE, - ALIEN.no, ALIEN.freq = 1, doFire = FALSE, FIRE.no, @@ -210,9 +209,6 @@ to the number of way a PFG could react to a drought disturbance} introduction is activated in the \code{FATE} simulation, and associated parameters are required} -\item{ALIEN.no}{(\emph{optional}) \cr an \code{integer} corresponding to the -number of introductions} - \item{ALIEN.freq}{(\emph{optional}) \cr a \code{vector} of \code{integer} corresponding to the frequency of each introduction (\emph{in years})} @@ -373,7 +369,6 @@ If the simulation includes \emph{aliens introduction} : \itemize{ \item DO_ALIENS_INTRODUCTION - \item ALIENS_NO \item ALIENS_FREQ } @@ -624,7 +619,6 @@ file, and if so, some additional parameters will be required : introduction areas. \cr If the habitat suitability filter is on, suitability maps will also be needed for these new groups. \describe{ - \item{ALIEN.no}{the number of different introductions} \item{ALIEN.freq}{the frequency of each introduction (\emph{in years})} } } diff --git a/tests/testthat/test-PRE_FATE.params_globalParameters.R b/tests/testthat/test-PRE_FATE.params_globalParameters.R index ed003c3..c4cd734 100644 --- a/tests/testthat/test-PRE_FATE.params_globalParameters.R +++ b/tests/testthat/test-PRE_FATE.params_globalParameters.R @@ -723,38 +723,6 @@ test_that("PRE_FATE.params_globalParameters gives error with wrong data : DROUGH , "`DROUGHT.no_sub` must be an integer > 0") }) -## INPUTS -test_that("PRE_FATE.params_globalParameters gives error with wrong data : ALIEN.no", { - - ## TEST ALIEN.no : integer - expect_error(PRE_FATE.params_globalParameters(name.simulation = "FATE_simulation" - , required.no_PFG = 5 - , required.no_strata = 2 - , required.max_abund_low = 3000 - , required.max_abund_medium = 5000 - , required.max_abund_high = 9000 - , doAliens = T - , ALIEN.no = NA) - , "`ALIEN.no` must be an integer > 0") - expect_error(PRE_FATE.params_globalParameters(name.simulation = "FATE_simulation" - , required.no_PFG = 5 - , required.no_strata = 2 - , required.max_abund_low = 3000 - , required.max_abund_medium = 5000 - , required.max_abund_high = 9000 - , doAliens = T - , ALIEN.no = NULL) - , "`ALIEN.no` must be an integer > 0") - expect_error(PRE_FATE.params_globalParameters(name.simulation = "FATE_simulation" - , required.no_PFG = 5 - , required.no_strata = 2 - , required.max_abund_low = 3000 - , required.max_abund_medium = 5000 - , required.max_abund_high = 9000 - , doAliens = T - , ALIEN.no = "") - , "`ALIEN.no` must be an integer > 0") -}) ## INPUTS test_that("PRE_FATE.params_globalParameters gives error with wrong data : ALIEN.freq", { @@ -766,9 +734,8 @@ test_that("PRE_FATE.params_globalParameters gives error with wrong data : ALIEN. , required.max_abund_low = 3000 , required.max_abund_medium = 5000 , required.max_abund_high = 9000 - , doAliens = T - , ALIEN.no = 2) - , "`ALIEN.freq` must contain as many values as the number of introductions (`ALIEN.no`)" + , doAliens = T) + , "`ALIEN.freq` must contain as many values as the number of PFG (`required.no_PFG`)" , fixed = TRUE) expect_error(PRE_FATE.params_globalParameters(name.simulation = "FATE_simulation" , required.no_PFG = 5 @@ -777,7 +744,6 @@ test_that("PRE_FATE.params_globalParameters gives error with wrong data : ALIEN. , required.max_abund_medium = 5000 , required.max_abund_high = 9000 , doAliens = T - , ALIEN.no = 2 , ALIEN.freq = NA) , "`ALIEN.freq` must be an integer > 0") expect_error(PRE_FATE.params_globalParameters(name.simulation = "FATE_simulation" @@ -787,7 +753,6 @@ test_that("PRE_FATE.params_globalParameters gives error with wrong data : ALIEN. , required.max_abund_medium = 5000 , required.max_abund_high = 9000 , doAliens = T - , ALIEN.no = 2 , ALIEN.freq = NULL) , "`ALIEN.freq` must be an integer > 0") expect_error(PRE_FATE.params_globalParameters(name.simulation = "FATE_simulation" @@ -797,7 +762,6 @@ test_that("PRE_FATE.params_globalParameters gives error with wrong data : ALIEN. , required.max_abund_medium = 5000 , required.max_abund_high = 9000 , doAliens = T - , ALIEN.no = 2 , ALIEN.freq = "") , "`ALIEN.freq` must be an integer > 0") @@ -809,9 +773,8 @@ test_that("PRE_FATE.params_globalParameters gives error with wrong data : ALIEN. , required.max_abund_medium = 5000 , required.max_abund_high = 9000 , doAliens = T - , ALIEN.no = 2 , ALIEN.freq = 2) - , "`ALIEN.freq` must contain as many values as the number of introductions (`ALIEN.no`)" + , "`ALIEN.freq` must contain as many values as the number of PFG (`required.no_PFG`)" , fixed = TRUE) }) @@ -1706,7 +1669,6 @@ test_that("PRE_FATE.params_globalParameters gives correct output : scenario modu , required.max_abund_medium = 5000 , required.max_abund_high = 9000 , doAliens = TRUE - , ALIEN.no = 10 , ALIEN.freq = rep(1, 10)) , "The parameter file FATE_simulation/DATA/GLOBAL_PARAMETERS/Global_parameters_V1.txt has been successfully created !") diff --git a/tests/testthat/test-PRE_FATE.params_simulParameters.R b/tests/testthat/test-PRE_FATE.params_simulParameters.R index c11018a..6e01f88 100644 --- a/tests/testthat/test-PRE_FATE.params_simulParameters.R +++ b/tests/testthat/test-PRE_FATE.params_simulParameters.R @@ -116,7 +116,6 @@ test_that("PRE_FATE.params_simulParameters gives error with wrong data : folders , doDrought = TRUE , DROUGHT.no_sub = 2 , doAliens = TRUE - , ALIEN.no = 1 , ALIEN.freq = 1 , doFire = TRUE , FIRE.no = 1 From f251fa7d62a3a568b4e6a97e891cf1290a43bcd1 Mon Sep 17 00:00:00 2001 From: MayaGueguen Date: Tue, 30 Nov 2021 12:58:35 +0100 Subject: [PATCH 04/20] Update PRE_FATE.speciesDistanceOverlap to allow categorical variables --- NAMESPACE | 1 + R/PRE_FATE.speciesDistanceOverlap.R | 4 ++-- R/UTILS.package_ecospat.R | 4 ++-- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index 0891e0a..cba6e41 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -64,6 +64,7 @@ importFrom(R.utils,gunzip) importFrom(R.utils,gzip) importFrom(RColorBrewer,brewer.pal) importFrom(Rcpp,sourceCpp) +importFrom(ade4,dudi.hillsmith) importFrom(ade4,dudi.pca) importFrom(ade4,dudi.pco) importFrom(ade4,inertia.dudi) diff --git a/R/PRE_FATE.speciesDistanceOverlap.R b/R/PRE_FATE.speciesDistanceOverlap.R index 941792b..3303754 100644 --- a/R/PRE_FATE.speciesDistanceOverlap.R +++ b/R/PRE_FATE.speciesDistanceOverlap.R @@ -79,7 +79,7 @@ ##' ##' @importFrom stats as.dist ##' @importFrom methods as -##' @importFrom ade4 dudi.pca suprow +##' @importFrom ade4 dudi.hillsmith suprow ##' @importFrom raster raster extension ##' @importFrom phyloclim niche.overlap ##' @@ -118,7 +118,7 @@ PRE_FATE.speciesDistanceOverlap = function(mat.overlap.option, mat.overlap.objec } ## Calculate PCA for all environment - pca.env = dudi.pca(tab.env, scannf = F, nf = 2) + pca.env = dudi.hillsmith(tab.env, scannf = F, nf = 2) scores.env = pca.env$li ## Calculate overlap matrix diff --git a/R/UTILS.package_ecospat.R b/R/UTILS.package_ecospat.R index 041b2b0..35c7e48 100644 --- a/R/UTILS.package_ecospat.R +++ b/R/UTILS.package_ecospat.R @@ -72,7 +72,7 @@ ecospat.kd = function (x, ext, R = 100, th = 0, env.mask = c(), method = "adehab x.dens <- kernelUD(SpatialPoints(xr[, 1:2]), h = "href", grid = mask, kern = "bivnorm") x.dens <- raster(xmn = ext[1], xmx = ext[2], ymn = ext[3], ymx = ext[4], matrix(x.dens$ud, nrow = R)) if (!is.null(th)) { - th.value <- quantile(extract(x.dens, x), th) + th.value <- quantile(extract(x.dens, x), th, na.rm = TRUE) x.dens[x.dens < th.value] <- 0 } if (!is.null(env.mask)) { @@ -86,7 +86,7 @@ ecospat.kd = function (x, ext, R = 100, th = 0, env.mask = c(), method = "adehab } if (!is.null(th)) { xr <- sapply(x, findInterval, x.dens$x) - th.value <- quantile(x.dens$y[xr], th) + th.value <- quantile(x.dens$y[xr], th, na.rm = TRUE) sprm <- which(x.dens$y < th.value) x.dens$y[sprm] <- 0 } From fa08ce0e8cc88bd26f76235b44cc261760aa0b0c Mon Sep 17 00:00:00 2001 From: MayaGueguen Date: Thu, 27 Jan 2022 09:11:28 +0100 Subject: [PATCH 05/20] Doc update --- docs/reference/FATE.html | 12 +- docs/reference/FATE_RS.html | 251 ++++++++++++++++++ docs/reference/POST_FATE.binaryMaps.html | 12 +- .../POST_FATE.graphic_evolutionCoverage.html | 12 +- .../POST_FATE.graphic_evolutionPixels.html | 12 +- .../POST_FATE.graphic_evolutionStability.html | 12 +- docs/reference/POST_FATE.graphic_mapPFG.html | 12 +- .../POST_FATE.graphic_mapPFGvsHS.html | 12 +- ...OST_FATE.graphic_validationStatistics.html | 12 +- docs/reference/POST_FATE.graphics.html | 12 +- docs/reference/POST_FATE.relativeAbund.html | 12 +- .../POST_FATE.temporalEvolution.html | 12 +- .../PRE_FATE.abundBraunBlanquet.html | 12 +- .../PRE_FATE.params_PFGdispersal.html | 12 +- .../PRE_FATE.params_PFGdisturbance.html | 12 +- .../reference/PRE_FATE.params_PFGdrought.html | 12 +- docs/reference/PRE_FATE.params_PFGlight.html | 12 +- docs/reference/PRE_FATE.params_PFGsoil.html | 12 +- .../PRE_FATE.params_PFGsuccession.html | 12 +- .../PRE_FATE.params_changingYears.html | 12 +- .../PRE_FATE.params_multipleSet.html | 16 +- .../PRE_FATE.params_savingYears.html | 12 +- .../PRE_FATE.params_simulParameters.html | 12 +- docs/reference/PRE_FATE.selectDominant.html | 12 +- .../reference/PRE_FATE.skeletonDirectory.html | 12 +- .../PRE_FATE.speciesClustering_step1.html | 20 +- .../PRE_FATE.speciesClustering_step2.html | 12 +- .../PRE_FATE.speciesClustering_step3.html | 12 +- docs/reference/PRE_FATE.speciesDistance.html | 16 +- .../PRE_FATE.speciesDistanceCombine.html | 16 +- .../PRE_FATE.speciesDistanceOverlap.html | 12 +- .../PRE_FATE.speciesDistanceTraits.html | 16 +- docs/reference/RFATE.html | 12 +- docs/reference/SAVE_FATE.step1_PFG.html | 12 +- .../reference/SAVE_FATE.step2_parameters.html | 12 +- docs/reference/beta.pair.html | 14 +- docs/reference/cluster.stats.html | 14 +- docs/reference/designLHD.html | 16 +- docs/reference/divLeinster.html | 12 +- docs/reference/dot-adaptMaps.html | 12 +- docs/reference/dot-createParams.html | 12 +- docs/reference/dot-getCutoff.html | 12 +- docs/reference/dot-getELLIPSE.html | 12 +- docs/reference/dot-getOS.html | 12 +- docs/reference/dot-getParam.html | 12 +- docs/reference/dot-loadData.html | 12 +- docs/reference/dot-loadPackage.html | 12 +- docs/reference/dot-scaleMaps.html | 12 +- docs/reference/dot-setParam.html | 12 +- docs/reference/dot-setPattern.html | 12 +- docs/reference/dot-unzip_ALL.html | 12 +- docs/reference/dunn.html | 14 +- docs/reference/ecospat.niche.overlap.html | 12 +- docs/reference/index.html | 12 +- 54 files changed, 586 insertions(+), 335 deletions(-) create mode 100644 docs/reference/FATE_RS.html diff --git a/docs/reference/FATE.html b/docs/reference/FATE.html index 41740b0..2e7e3e1 100644 --- a/docs/reference/FATE.html +++ b/docs/reference/FATE.html @@ -72,7 +72,7 @@ RFate - 1.0.1 + 1.0.2 @@ -80,7 +80,7 @@

    • - +
      • @@ -124,21 +124,21 @@
    • - + Build PFG
    • - + Build parameter files
    • - + Build graphics @@ -155,7 +155,7 @@
    • - + Reference diff --git a/docs/reference/FATE_RS.html b/docs/reference/FATE_RS.html new file mode 100644 index 0000000..e3bd081 --- /dev/null +++ b/docs/reference/FATE_RS.html @@ -0,0 +1,251 @@ + + + + + + + + +S — FATE_RS • RFate + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      +
      + + + + +
      + +
      +
      +
      +

      S

      + Source: R/FATE_RS.R + +
      + +
      +

      ...

      +
      + + 
      FATE_RS(
+  name.simulation,
+  file.simulParam,
+  opt.no_CPU = 1,
+  verbose.level = 2,
+  name.simulation.RS,
+  params.RS,
+  year.start,
+  year.end,
+  year.step
+)
      + + +

      Author

      + +

      Maya Guéguen

      + +
      + +
      + + + +
      + + + + + + + + diff --git a/docs/reference/POST_FATE.binaryMaps.html b/docs/reference/POST_FATE.binaryMaps.html index 38f20a1..367a347 100644 --- a/docs/reference/POST_FATE.binaryMaps.html +++ b/docs/reference/POST_FATE.binaryMaps.html @@ -75,7 +75,7 @@ RFate - 1.0.1 + 1.0.2 @@ -83,7 +83,7 @@
      • - +
        • @@ -127,21 +127,21 @@
      • - + Build PFG
      • - + Build parameter files
      • - + Build graphics @@ -158,7 +158,7 @@
      • - + Reference diff --git a/docs/reference/POST_FATE.graphic_evolutionCoverage.html b/docs/reference/POST_FATE.graphic_evolutionCoverage.html index afd9cf0..4b87ab3 100644 --- a/docs/reference/POST_FATE.graphic_evolutionCoverage.html +++ b/docs/reference/POST_FATE.graphic_evolutionCoverage.html @@ -78,7 +78,7 @@ RFate - 1.0.1 + 1.0.2 @@ -86,7 +86,7 @@
        • - +
          • @@ -130,21 +130,21 @@
        • - + Build PFG
        • - + Build parameter files
        • - + Build graphics @@ -161,7 +161,7 @@
        • - + Reference diff --git a/docs/reference/POST_FATE.graphic_evolutionPixels.html b/docs/reference/POST_FATE.graphic_evolutionPixels.html index 4d69c07..015a851 100644 --- a/docs/reference/POST_FATE.graphic_evolutionPixels.html +++ b/docs/reference/POST_FATE.graphic_evolutionPixels.html @@ -77,7 +77,7 @@ RFate - 1.0.1 + 1.0.2 @@ -85,7 +85,7 @@
          • - +
            • @@ -129,21 +129,21 @@
          • - + Build PFG
          • - + Build parameter files
          • - + Build graphics @@ -160,7 +160,7 @@
          • - + Reference diff --git a/docs/reference/POST_FATE.graphic_evolutionStability.html b/docs/reference/POST_FATE.graphic_evolutionStability.html index f618274..af3b2b1 100644 --- a/docs/reference/POST_FATE.graphic_evolutionStability.html +++ b/docs/reference/POST_FATE.graphic_evolutionStability.html @@ -76,7 +76,7 @@ RFate - 1.0.1 + 1.0.2 @@ -84,7 +84,7 @@
            • - +
              • @@ -128,21 +128,21 @@
            • - + Build PFG
            • - + Build parameter files
            • - + Build graphics @@ -159,7 +159,7 @@
            • - + Reference diff --git a/docs/reference/POST_FATE.graphic_mapPFG.html b/docs/reference/POST_FATE.graphic_mapPFG.html index caaa400..650a2f0 100644 --- a/docs/reference/POST_FATE.graphic_mapPFG.html +++ b/docs/reference/POST_FATE.graphic_mapPFG.html @@ -78,7 +78,7 @@ RFate - 1.0.1 + 1.0.2 @@ -86,7 +86,7 @@
              • - +
                • @@ -130,21 +130,21 @@
              • - + Build PFG
              • - + Build parameter files
              • - + Build graphics @@ -161,7 +161,7 @@
              • - + Reference diff --git a/docs/reference/POST_FATE.graphic_mapPFGvsHS.html b/docs/reference/POST_FATE.graphic_mapPFGvsHS.html index bd41fcd..072d0ac 100644 --- a/docs/reference/POST_FATE.graphic_mapPFGvsHS.html +++ b/docs/reference/POST_FATE.graphic_mapPFGvsHS.html @@ -78,7 +78,7 @@ RFate - 1.0.1 + 1.0.2 @@ -86,7 +86,7 @@
                • - +
                  • @@ -130,21 +130,21 @@
                • - + Build PFG
                • - + Build parameter files
                • - + Build graphics @@ -161,7 +161,7 @@
                • - + Reference diff --git a/docs/reference/POST_FATE.graphic_validationStatistics.html b/docs/reference/POST_FATE.graphic_validationStatistics.html index b8cd851..6414a13 100644 --- a/docs/reference/POST_FATE.graphic_validationStatistics.html +++ b/docs/reference/POST_FATE.graphic_validationStatistics.html @@ -78,7 +78,7 @@ RFate - 1.0.1 + 1.0.2 @@ -86,7 +86,7 @@
                  • - +
                    • @@ -130,21 +130,21 @@
                  • - + Build PFG
                  • - + Build parameter files
                  • - + Build graphics @@ -161,7 +161,7 @@
                  • - + Reference diff --git a/docs/reference/POST_FATE.graphics.html b/docs/reference/POST_FATE.graphics.html index f4fc54c..cc83146 100644 --- a/docs/reference/POST_FATE.graphics.html +++ b/docs/reference/POST_FATE.graphics.html @@ -79,7 +79,7 @@ RFate - 1.0.1 + 1.0.2 @@ -87,7 +87,7 @@
                    • - +
                      • @@ -131,21 +131,21 @@
                    • - + Build PFG
                    • - + Build parameter files
                    • - + Build graphics @@ -162,7 +162,7 @@
                    • - + Reference diff --git a/docs/reference/POST_FATE.relativeAbund.html b/docs/reference/POST_FATE.relativeAbund.html index 2ee81d5..5bbb9ed 100644 --- a/docs/reference/POST_FATE.relativeAbund.html +++ b/docs/reference/POST_FATE.relativeAbund.html @@ -76,7 +76,7 @@ RFate - 1.0.1 + 1.0.2 @@ -84,7 +84,7 @@
                      • - +
                        • @@ -128,21 +128,21 @@
                      • - + Build PFG
                      • - + Build parameter files
                      • - + Build graphics @@ -159,7 +159,7 @@
                      • - + Reference diff --git a/docs/reference/POST_FATE.temporalEvolution.html b/docs/reference/POST_FATE.temporalEvolution.html index f9a41e9..8d0d463 100644 --- a/docs/reference/POST_FATE.temporalEvolution.html +++ b/docs/reference/POST_FATE.temporalEvolution.html @@ -77,7 +77,7 @@ RFate - 1.0.1 + 1.0.2 @@ -85,7 +85,7 @@
                        • - +
                          • @@ -129,21 +129,21 @@
                        • - + Build PFG
                        • - + Build parameter files
                        • - + Build graphics @@ -160,7 +160,7 @@
                        • - + Reference diff --git a/docs/reference/PRE_FATE.abundBraunBlanquet.html b/docs/reference/PRE_FATE.abundBraunBlanquet.html index d3ae094..5ecfd26 100644 --- a/docs/reference/PRE_FATE.abundBraunBlanquet.html +++ b/docs/reference/PRE_FATE.abundBraunBlanquet.html @@ -74,7 +74,7 @@ RFate - 1.0.1 + 1.0.2 @@ -82,7 +82,7 @@
                          • - +
                            • @@ -126,21 +126,21 @@
                          • - + Build PFG
                          • - + Build parameter files
                          • - + Build graphics @@ -157,7 +157,7 @@
                          • - + Reference diff --git a/docs/reference/PRE_FATE.params_PFGdispersal.html b/docs/reference/PRE_FATE.params_PFGdispersal.html index 9aaa17c..9c9ee93 100644 --- a/docs/reference/PRE_FATE.params_PFGdispersal.html +++ b/docs/reference/PRE_FATE.params_PFGdispersal.html @@ -76,7 +76,7 @@ RFate - 1.0.1 + 1.0.2 @@ -84,7 +84,7 @@
                            • - +
                              • @@ -128,21 +128,21 @@
                            • - + Build PFG
                            • - + Build parameter files
                            • - + Build graphics @@ -159,7 +159,7 @@
                            • - + Reference diff --git a/docs/reference/PRE_FATE.params_PFGdisturbance.html b/docs/reference/PRE_FATE.params_PFGdisturbance.html index 28bbb5b..bea9cb5 100644 --- a/docs/reference/PRE_FATE.params_PFGdisturbance.html +++ b/docs/reference/PRE_FATE.params_PFGdisturbance.html @@ -76,7 +76,7 @@ RFate - 1.0.1 + 1.0.2 @@ -84,7 +84,7 @@
                              • - +
                                • @@ -128,21 +128,21 @@
                              • - + Build PFG
                              • - + Build parameter files
                              • - + Build graphics @@ -159,7 +159,7 @@
                              • - + Reference diff --git a/docs/reference/PRE_FATE.params_PFGdrought.html b/docs/reference/PRE_FATE.params_PFGdrought.html index 78b7e04..1d69ffa 100644 --- a/docs/reference/PRE_FATE.params_PFGdrought.html +++ b/docs/reference/PRE_FATE.params_PFGdrought.html @@ -76,7 +76,7 @@ RFate - 1.0.1 + 1.0.2 @@ -84,7 +84,7 @@
                                • - +
                                  • @@ -128,21 +128,21 @@
                                • - + Build PFG
                                • - + Build parameter files
                                • - + Build graphics @@ -159,7 +159,7 @@
                                • - + Reference diff --git a/docs/reference/PRE_FATE.params_PFGlight.html b/docs/reference/PRE_FATE.params_PFGlight.html index 4d98efc..e22e3f6 100644 --- a/docs/reference/PRE_FATE.params_PFGlight.html +++ b/docs/reference/PRE_FATE.params_PFGlight.html @@ -74,7 +74,7 @@ RFate - 1.0.1 + 1.0.2 @@ -82,7 +82,7 @@
                                  • - +
                                    • @@ -126,21 +126,21 @@
                                  • - + Build PFG
                                  • - + Build parameter files
                                  • - + Build graphics @@ -157,7 +157,7 @@
                                  • - + Reference diff --git a/docs/reference/PRE_FATE.params_PFGsoil.html b/docs/reference/PRE_FATE.params_PFGsoil.html index d94ed8b..f0dc7b9 100644 --- a/docs/reference/PRE_FATE.params_PFGsoil.html +++ b/docs/reference/PRE_FATE.params_PFGsoil.html @@ -74,7 +74,7 @@ RFate - 1.0.1 + 1.0.2 @@ -82,7 +82,7 @@
                                    • - +
                                      • @@ -126,21 +126,21 @@
                                    • - + Build PFG
                                    • - + Build parameter files
                                    • - + Build graphics @@ -157,7 +157,7 @@
                                    • - + Reference diff --git a/docs/reference/PRE_FATE.params_PFGsuccession.html b/docs/reference/PRE_FATE.params_PFGsuccession.html index d3104d7..bb77dbd 100644 --- a/docs/reference/PRE_FATE.params_PFGsuccession.html +++ b/docs/reference/PRE_FATE.params_PFGsuccession.html @@ -74,7 +74,7 @@ RFate - 1.0.1 + 1.0.2 @@ -82,7 +82,7 @@
                                      • - +
                                        • @@ -126,21 +126,21 @@
                                      • - + Build PFG
                                      • - + Build parameter files
                                      • - + Build graphics @@ -157,7 +157,7 @@
                                      • - + Reference diff --git a/docs/reference/PRE_FATE.params_changingYears.html b/docs/reference/PRE_FATE.params_changingYears.html index 96c5132..bfc5fd3 100644 --- a/docs/reference/PRE_FATE.params_changingYears.html +++ b/docs/reference/PRE_FATE.params_changingYears.html @@ -77,7 +77,7 @@ RFate - 1.0.1 + 1.0.2 @@ -85,7 +85,7 @@
                                        • - +
                                          • @@ -129,21 +129,21 @@
                                        • - + Build PFG
                                        • - + Build parameter files
                                        • - + Build graphics @@ -160,7 +160,7 @@
                                        • - + Reference diff --git a/docs/reference/PRE_FATE.params_multipleSet.html b/docs/reference/PRE_FATE.params_multipleSet.html index 282cc78..376234a 100644 --- a/docs/reference/PRE_FATE.params_multipleSet.html +++ b/docs/reference/PRE_FATE.params_multipleSet.html @@ -76,7 +76,7 @@ RFate - 1.0.1 + 1.0.2 @@ -84,7 +84,7 @@
                                          • - +
                                            • @@ -128,21 +128,21 @@
                                          • - + Build PFG
                                          • - + Build parameter files
                                          • - + Build graphics @@ -159,7 +159,7 @@
                                          • - + Reference @@ -287,7 +287,7 @@

                                            Arg

                                            (optional) default NULL.
                                            An integer to be given to set.seed function, in order to fix the produced results if needed, as -designLHD is also a random value generator

                                            +designLHD is also a random value generator

                                            opt.percent_maxAbund @@ -506,7 +506,7 @@

                                            Details drawn in order to explore the whole space of combinations.

                                            See also

                                            -

                                            designLHD, +

                                            designLHD, PRE_FATE.skeletonDirectory, PRE_FATE.params_globalParameters, PRE_FATE.params_PFGsuccession, diff --git a/docs/reference/PRE_FATE.params_savingYears.html b/docs/reference/PRE_FATE.params_savingYears.html index 180bd7c..c6bcd50 100644 --- a/docs/reference/PRE_FATE.params_savingYears.html +++ b/docs/reference/PRE_FATE.params_savingYears.html @@ -75,7 +75,7 @@ RFate - 1.0.1 + 1.0.2

                                            @@ -83,7 +83,7 @@
                                            @@ -83,7 +83,7 @@
                                            • - +
                                              • @@ -127,21 +127,21 @@
                                            • - + Build PFG
                                            • - + Build parameter files
                                            • - + Build graphics @@ -158,7 +158,7 @@
                                            • - + Reference diff --git a/docs/reference/PRE_FATE.selectDominant.html b/docs/reference/PRE_FATE.selectDominant.html index 8685da5..a8d4809 100644 --- a/docs/reference/PRE_FATE.selectDominant.html +++ b/docs/reference/PRE_FATE.selectDominant.html @@ -73,7 +73,7 @@ RFate - 1.0.1 + 1.0.2 @@ -81,7 +81,7 @@
                                              • - +
                                                • @@ -125,21 +125,21 @@
                                              • - + Build PFG
                                              • - + Build parameter files
                                              • - + Build graphics @@ -156,7 +156,7 @@
                                              • - + Reference diff --git a/docs/reference/PRE_FATE.skeletonDirectory.html b/docs/reference/PRE_FATE.skeletonDirectory.html index 3e22d6b..7d0f345 100644 --- a/docs/reference/PRE_FATE.skeletonDirectory.html +++ b/docs/reference/PRE_FATE.skeletonDirectory.html @@ -73,7 +73,7 @@ RFate - 1.0.1 + 1.0.2 @@ -81,7 +81,7 @@
                                                • - +
                                                  • @@ -125,21 +125,21 @@
                                                • - + Build PFG
                                                • - + Build parameter files
                                                • - + Build graphics @@ -156,7 +156,7 @@
                                                • - + Reference diff --git a/docs/reference/PRE_FATE.speciesClustering_step1.html b/docs/reference/PRE_FATE.speciesClustering_step1.html index 949f0da..1d984ad 100644 --- a/docs/reference/PRE_FATE.speciesClustering_step1.html +++ b/docs/reference/PRE_FATE.speciesClustering_step1.html @@ -75,7 +75,7 @@ RFate - 1.0.1 + 1.0.2 @@ -83,7 +83,7 @@
                                                  • - +
                                                    • @@ -127,21 +127,21 @@
                                                  • - + Build PFG
                                                  • - + Build parameter files
                                                  • - + Build graphics @@ -158,7 +158,7 @@
                                                  • - + Reference @@ -328,8 +328,8 @@

                                                    See a

                                                    hclust, cutree, -cluster.stats, -dunn, +cluster.stats, +dunn, PRE_FATE.speciesDistance, PRE_FATE.speciesClustering_step2

                                                    Author

                                                    @@ -358,11 +358,11 @@

                                                    Examp if (FALSE) { require(foreach) require(ggplot2) -require(ggdendro) +require(ggdendro) pp = foreach(x = names(sp.CLUST$clust.dendrograms)) %do% { hc = sp.CLUST$clust.dendrograms[[x]] - pp = ggdendrogram(hc, rotate = TRUE) + + pp = ggdendrogram(hc, rotate = TRUE) + labs(title = paste0('Hierarchical clustering based on species distance ' , ifelse(length(names(sp.CLUST$clust.dendrograms)) > 1 , paste0('(group ', x, ')') diff --git a/docs/reference/PRE_FATE.speciesClustering_step2.html b/docs/reference/PRE_FATE.speciesClustering_step2.html index 1c90364..fd1514d 100644 --- a/docs/reference/PRE_FATE.speciesClustering_step2.html +++ b/docs/reference/PRE_FATE.speciesClustering_step2.html @@ -75,7 +75,7 @@ RFate - 1.0.1 + 1.0.2 @@ -83,7 +83,7 @@
                                                    • - +
                                                      • @@ -127,21 +127,21 @@
                                                    • - + Build PFG
                                                    • - + Build parameter files
                                                    • - + Build graphics @@ -158,7 +158,7 @@
                                                    • - + Reference diff --git a/docs/reference/PRE_FATE.speciesClustering_step3.html b/docs/reference/PRE_FATE.speciesClustering_step3.html index 5cce1f2..67ea3e8 100644 --- a/docs/reference/PRE_FATE.speciesClustering_step3.html +++ b/docs/reference/PRE_FATE.speciesClustering_step3.html @@ -77,7 +77,7 @@ RFate - 1.0.1 + 1.0.2 @@ -85,7 +85,7 @@
                                                      • - +
                                                        • @@ -129,21 +129,21 @@
                                                      • - + Build PFG
                                                      • - + Build parameter files
                                                      • - + Build graphics @@ -160,7 +160,7 @@
                                                      • - + Reference diff --git a/docs/reference/PRE_FATE.speciesDistance.html b/docs/reference/PRE_FATE.speciesDistance.html index 9523fc3..8a31690 100644 --- a/docs/reference/PRE_FATE.speciesDistance.html +++ b/docs/reference/PRE_FATE.speciesDistance.html @@ -76,7 +76,7 @@ RFate - 1.0.1 + 1.0.2 @@ -84,7 +84,7 @@
                                                        • - +
                                                          • @@ -128,21 +128,21 @@
                                                        • - + Build PFG
                                                        • - + Build parameter files
                                                        • - + Build graphics @@ -159,7 +159,7 @@
                                                        • - + Reference @@ -388,11 +388,11 @@

                                                          Examp str(sp.DIST) if (FALSE) { -require(foreach); require(ggplot2); require(ggdendro) +require(foreach); require(ggplot2); require(ggdendro) pp = foreach(x = names(sp.DIST$mat.ALL)) %do% { hc = hclust(sp.DIST$mat.ALL[[x]]) - pp = ggdendrogram(hc, rotate = TRUE) + + pp = ggdendrogram(hc, rotate = TRUE) + labs(title = paste0('Hierarchical clustering based on species distance ' , ifelse(length(names(sp.DIST$mat.ALL)) > 1 , paste0('(group ', x, ')') diff --git a/docs/reference/PRE_FATE.speciesDistanceCombine.html b/docs/reference/PRE_FATE.speciesDistanceCombine.html index 6c77f5c..d4064a0 100644 --- a/docs/reference/PRE_FATE.speciesDistanceCombine.html +++ b/docs/reference/PRE_FATE.speciesDistanceCombine.html @@ -73,7 +73,7 @@ RFate - 1.0.1 + 1.0.2 @@ -81,7 +81,7 @@
                                                          • - +
                                                            • @@ -125,21 +125,21 @@
                                                          • - + Build PFG
                                                          • - + Build parameter files
                                                          • - + Build graphics @@ -156,7 +156,7 @@
                                                          • - + Reference @@ -316,9 +316,9 @@

                                                            Examp , is.corr = FALSE, title = names(list.DIST)[li]) } -require(foreach); require(ggplot2); require(ggdendro) +require(foreach); require(ggplot2); require(ggdendro) hc = hclust(as.dist(sp.DIST.n)) -pp = ggdendrogram(hc, rotate = TRUE) + +pp = ggdendrogram(hc, rotate = TRUE) + labs(title = 'Hierarchical clustering based on species distances') plot(pp) } diff --git a/docs/reference/PRE_FATE.speciesDistanceOverlap.html b/docs/reference/PRE_FATE.speciesDistanceOverlap.html index 14c0030..b25f12a 100644 --- a/docs/reference/PRE_FATE.speciesDistanceOverlap.html +++ b/docs/reference/PRE_FATE.speciesDistanceOverlap.html @@ -73,7 +73,7 @@ RFate - 1.0.1 + 1.0.2 @@ -81,7 +81,7 @@
                                                            • - +
                                                              • @@ -125,21 +125,21 @@
                                                            • - + Build PFG
                                                            • - + Build parameter files
                                                            • - + Build graphics @@ -156,7 +156,7 @@
                                                            • - + Reference diff --git a/docs/reference/PRE_FATE.speciesDistanceTraits.html b/docs/reference/PRE_FATE.speciesDistanceTraits.html index 3140184..5d44a0c 100644 --- a/docs/reference/PRE_FATE.speciesDistanceTraits.html +++ b/docs/reference/PRE_FATE.speciesDistanceTraits.html @@ -73,7 +73,7 @@ RFate - 1.0.1 + 1.0.2 @@ -81,7 +81,7 @@
                                                              • - +
                                                                • @@ -125,21 +125,21 @@
                                                              • - + Build PFG
                                                              • - + Build parameter files
                                                              • - + Build graphics @@ -156,7 +156,7 @@
                                                              • - + Reference @@ -307,11 +307,11 @@

                                                                Examp str(DIST.traits) if (FALSE) { -require(foreach); require(ggplot2); require(ggdendro) +require(foreach); require(ggplot2); require(ggdendro) pp = foreach(x = names(DIST.traits)) %do% { hc = hclust(as.dist(DIST.traits[[x]])) - pp = ggdendrogram(hc, rotate = TRUE) + + pp = ggdendrogram(hc, rotate = TRUE) + labs(title = paste0('Hierarchical clustering based on species distance ' , ifelse(length(names(DIST.traits)) > 1 , paste0('(group ', x, ')') diff --git a/docs/reference/RFATE.html b/docs/reference/RFATE.html index 4e78348..0fc225b 100644 --- a/docs/reference/RFATE.html +++ b/docs/reference/RFATE.html @@ -77,7 +77,7 @@ RFate - 1.0.0 + 1.0.2 @@ -85,7 +85,7 @@
                                                                • - +
                                                                  • @@ -129,21 +129,21 @@
                                                                • - + Build PFG
                                                                • - + Build parameter files
                                                                • - + Build graphics @@ -160,7 +160,7 @@
                                                                • - + Reference diff --git a/docs/reference/SAVE_FATE.step1_PFG.html b/docs/reference/SAVE_FATE.step1_PFG.html index 3b00032..84c1ae4 100644 --- a/docs/reference/SAVE_FATE.step1_PFG.html +++ b/docs/reference/SAVE_FATE.step1_PFG.html @@ -73,7 +73,7 @@ RFate - 1.0.1 + 1.0.2 @@ -81,7 +81,7 @@
                                                                  • - +
                                                                    • @@ -125,21 +125,21 @@
                                                                  • - + Build PFG
                                                                  • - + Build parameter files
                                                                  • - + Build graphics @@ -156,7 +156,7 @@
                                                                  • - + Reference diff --git a/docs/reference/SAVE_FATE.step2_parameters.html b/docs/reference/SAVE_FATE.step2_parameters.html index c405cc1..d22e9d4 100644 --- a/docs/reference/SAVE_FATE.step2_parameters.html +++ b/docs/reference/SAVE_FATE.step2_parameters.html @@ -73,7 +73,7 @@ RFate - 1.0.1 + 1.0.2 @@ -81,7 +81,7 @@
                                                                    • - +
                                                                      • @@ -125,21 +125,21 @@
                                                                    • - + Build PFG
                                                                    • - + Build parameter files
                                                                    • - + Build graphics @@ -156,7 +156,7 @@
                                                                    • - + Reference diff --git a/docs/reference/beta.pair.html b/docs/reference/beta.pair.html index 4601b4a..602e71d 100644 --- a/docs/reference/beta.pair.html +++ b/docs/reference/beta.pair.html @@ -72,7 +72,7 @@ RFate - 1.0.1 + 1.0.2 @@ -80,7 +80,7 @@
                                                                      • - +
                                                                        • @@ -124,21 +124,21 @@
                                                                      • - + Build PFG
                                                                      • - + Build parameter files
                                                                      • - + Build graphics @@ -155,7 +155,7 @@
                                                                      • - + Reference @@ -225,7 +225,7 @@

                                                                        Arg

                                                                        See also

                                                                        -

                                                                        beta.pair

                                                                        +

                                                                        beta.pair

                                                                        @@ -80,7 +80,7 @@
                                                                        • - +
                                                                          • @@ -124,21 +124,21 @@
                                                                        • - + Build PFG
                                                                        • - + Build parameter files
                                                                        • - + Build graphics @@ -155,7 +155,7 @@
                                                                        • - + Reference @@ -307,7 +307,7 @@

                                                                          Arg

                                                                          See also

                                                                          -

                                                                          cluster.stats

                                                                          +

                                                                          cluster.stats

                                                                          @@ -80,7 +80,7 @@
                                                                          • - +
                                                                            • @@ -124,21 +124,21 @@
                                                                          • - + Build PFG
                                                                          • - + Build parameter files
                                                                          • - + Build graphics @@ -155,7 +155,7 @@
                                                                          • - + Reference @@ -261,13 +261,13 @@

                                                                            Arg control -

                                                                            list of controls: see designLHD

                                                                            +

                                                                            list of controls: see designLHD

                                                                            See also

                                                                            -

                                                                            designLHD

                                                                            +

                                                                            designLHD

                                                                            @@ -82,7 +82,7 @@
                                                                            • - +
                                                                              • @@ -126,21 +126,21 @@
                                                                            • - + Build PFG
                                                                            • - + Build parameter files
                                                                            • - + Build graphics @@ -157,7 +157,7 @@
                                                                            • - + Reference diff --git a/docs/reference/dot-adaptMaps.html b/docs/reference/dot-adaptMaps.html index d5e391a..e2af401 100644 --- a/docs/reference/dot-adaptMaps.html +++ b/docs/reference/dot-adaptMaps.html @@ -76,7 +76,7 @@ RFate - 1.0.1 + 1.0.2 @@ -84,7 +84,7 @@
                                                                              • - +
                                                                                • @@ -128,21 +128,21 @@
                                                                              • - + Build PFG
                                                                              • - + Build parameter files
                                                                              • - + Build graphics @@ -159,7 +159,7 @@
                                                                              • - + Reference diff --git a/docs/reference/dot-createParams.html b/docs/reference/dot-createParams.html index 2c80040..40bfbdb 100644 --- a/docs/reference/dot-createParams.html +++ b/docs/reference/dot-createParams.html @@ -73,7 +73,7 @@ RFate - 1.0.1 + 1.0.2 @@ -81,7 +81,7 @@
                                                                                • - +
                                                                                  • @@ -125,21 +125,21 @@
                                                                                • - + Build PFG
                                                                                • - + Build parameter files
                                                                                • - + Build graphics @@ -156,7 +156,7 @@
                                                                                • - + Reference diff --git a/docs/reference/dot-getCutoff.html b/docs/reference/dot-getCutoff.html index a615e96..5975d96 100644 --- a/docs/reference/dot-getCutoff.html +++ b/docs/reference/dot-getCutoff.html @@ -74,7 +74,7 @@ RFate - 1.0.1 + 1.0.2 @@ -82,7 +82,7 @@
                                                                                  • - +
                                                                                    • @@ -126,21 +126,21 @@
                                                                                  • - + Build PFG
                                                                                  • - + Build parameter files
                                                                                  • - + Build graphics @@ -157,7 +157,7 @@
                                                                                  • - + Reference diff --git a/docs/reference/dot-getELLIPSE.html b/docs/reference/dot-getELLIPSE.html index 49cae35..6cad15e 100644 --- a/docs/reference/dot-getELLIPSE.html +++ b/docs/reference/dot-getELLIPSE.html @@ -72,7 +72,7 @@ RFate - 1.0.1 + 1.0.2 @@ -80,7 +80,7 @@
                                                                                    • - +
                                                                                      • @@ -124,21 +124,21 @@
                                                                                    • - + Build PFG
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                                                                                                          • - + Reference From 3c252a656243147b0ac2e88e750143dd8f547d04 Mon Sep 17 00:00:00 2001 From: MayaGueguen Date: Thu, 27 Jan 2022 09:12:06 +0100 Subject: [PATCH 06/20] Correct check of parameters within FATE --- src/FG.h | 2 +- src/SimulMap.cpp | 174 +++++++++++++++++++++++++++++++++++++--------- src/main_rcpp.cpp | 39 ----------- 3 files changed, 142 insertions(+), 73 deletions(-) diff --git a/src/FG.h b/src/FG.h index 09eb8c0..16de0cb 100644 --- a/src/FG.h +++ b/src/FG.h @@ -97,7 +97,7 @@ class FG double m_SoilContrib; /*!< Contribution of PFG to refill soil nutriment resources (kind of litter index) */ double m_SoilLow; /*!< Contribution of PFG to refill soil nutriment resources (kind of litter index) */ double m_SoilHigh; /*!< Contribution of PFG to refill soil nutriment resources (kind of litter index) */ - vector m_SoilActiveGerm; /*!< Proportion of Active seeds able to germinate considering light resources [Rcount] */ + vector m_SoilActiveGerm; /*!< Proportion of Active seeds able to germinate considering soil nutriment resources [Rcount] */ vector< vector > m_SoilTolerance; /*!< Is FG survived considering available soil nutriment resources [LScount][Rcount] */ /* Disturbance response */ diff --git a/src/SimulMap.cpp b/src/SimulMap.cpp index 76cc5b8..4d1ad92 100644 --- a/src/SimulMap.cpp +++ b/src/SimulMap.cpp @@ -1483,46 +1483,115 @@ void SimulMap::UpdateSimulationParameters(FOPL file_of_params) GSP old_glob_params(m_glob_params); /* read new global parameters file */ + logg.info("*** REBUILDING Global simulation parameters..."); m_glob_params = GSP(file_of_params.getGlobSimulParams()); - /* check some parameters compatibility */ + /* check some parameters compatibility (between SAVED_STATE and "new" global parameter file) */ if (old_glob_params.getNoFG() != m_glob_params.getNoFG()) { - logg.error("!!! Number of functional groups involved in saved object (", - old_glob_params.getNoFG(), - ") is incompatible with new parameters (", - m_glob_params.getNoFG(), ")!"); + logg.error("!!! Number of functional groups involved in saved object (", old_glob_params.getNoFG(), + ") is incompatible with new parameters (", m_glob_params.getNoFG(), ")!"); } - if (old_glob_params.getDoHabSuitability() != m_glob_params.getDoHabSuitability()) + if (old_glob_params.getNoStrata() != m_glob_params.getNoStrata()) { - logg.error("!!! Succession model involved in saved object (", - old_glob_params.getDoHabSuitability(), - ") is incompatible with new parameters (", - m_glob_params.getDoHabSuitability(), ")!"); + logg.error("!!! Number of strata involved in saved object (", old_glob_params.getNoStrata(), + ") is incompatible with new parameters (", m_glob_params.getNoStrata(), ")!"); } - if (old_glob_params.getNoStrata() != m_glob_params.getNoStrata()) + if (m_glob_params.getDoDisturbances()) + { + if (old_glob_params.getNoDist() != m_glob_params.getNoDist()) + { + logg.error("!!! Number of disturbances involved in saved object (", old_glob_params.getNoDist(), + ") is incompatible with new parameters (", m_glob_params.getNoDist(), ")!"); + } + if (old_glob_params.getNoDistSub() != m_glob_params.getNoDistSub()) + { + logg.error("!!! Number of way to be influenced by disturbances involved in saved object (", old_glob_params.getNoDistSub(), + ") is incompatible with new parameters (", m_glob_params.getNoDistSub(), ")!"); + } + } + if (m_glob_params.getDoDroughtDisturbances()) + { + if (old_glob_params.getNoDroughtSub() != m_glob_params.getNoDroughtSub()) + { + logg.error("!!! Number of way to be influenced by drought disturbances involved in saved object (", old_glob_params.getNoDroughtSub(), + ") is incompatible with new parameters (", m_glob_params.getNoDroughtSub(), ")!"); + } + } + if (m_glob_params.getDoFireDisturbances()) + { + if (old_glob_params.getNoFireDist() != m_glob_params.getNoFireDist()) + { + logg.error("!!! Number of fire disturbances involved in saved object (", old_glob_params.getNoFireDist(), + ") is incompatible with new parameters (", m_glob_params.getNoFireDist(), ")!"); + } + if (old_glob_params.getNoFireDistSub() != m_glob_params.getNoFireDistSub()) + { + logg.error("!!! Number of way to be influenced by fire disturbances involved in saved object (", old_glob_params.getNoFireDistSub(), + ") is incompatible with new parameters (", m_glob_params.getNoFireDistSub(), ")!"); + } + } + /* end of check parameters compatibility */ + + /* check some parameters compatibility (between "new" global and simul parameter files) */ + int noFG = m_glob_params.getNoFG(); + if (noFG != file_of_params.getFGLifeHistory().size()) + { + logg.error("!!! Parameters NO_PFG (", noFG, ") and --PFG_PARAMS_LIFE_HISTORY-- (", + file_of_params.getFGLifeHistory().size(), ") do not match in term of number!"); + } + if (m_glob_params.getDoLightInteraction() && noFG != file_of_params.getFGLight().size()) { - logg.error("!!! Number of strata involved in saved object (", - old_glob_params.getNoStrata(), - ") is incompatible with new parameters (", - m_glob_params.getNoStrata(), ")!"); + logg.error("!!! Parameters NO_PFG (", noFG, ") and --PFG_PARAMS_LIGHT-- (", + file_of_params.getFGLight().size(), ") do not match in term of number!"); } - if (old_glob_params.getNoDist() != m_glob_params.getNoDist()) + if (m_glob_params.getDoSoilInteraction() && noFG != file_of_params.getFGSoil().size()) { - logg.error("!!! Number of disturbances involved in saved object (", - old_glob_params.getNoDist(), - ") is incompatible with new parameters (", - m_glob_params.getNoDist(), ")!"); + logg.error("!!! Parameters NO_PFG (", noFG, ") and --PFG_PARAMS_SOIL-- (", + file_of_params.getFGSoil().size(), ") do not match in term of number!"); } - if (old_glob_params.getNoDistSub() != m_glob_params.getNoDistSub()) + if (m_glob_params.getDoDispersal() && noFG != file_of_params.getFGDispersal().size()) { - logg.error("!!! Number of way to be influence by disturbances involved in saved object (", - old_glob_params.getNoDistSub(), - ") is incompatible with new parameters (", - m_glob_params.getNoDistSub(), ")"); + logg.error("!!! Parameters NO_PFG (", noFG, ") and --PFG_PARAMS_DISPERSAL-- (", + file_of_params.getFGDispersal().size(), ") do not match in term of number!"); + } + if (m_glob_params.getDoDisturbances() && noFG != file_of_params.getFGDisturbance().size()) + { + logg.error("!!! Parameters NO_PFG (", noFG, ") and --PFG_PARAMS_DISTURBANCES-- (", + file_of_params.getFGDisturbance().size(), ") do not match in term of number!"); + } + if (m_glob_params.getDoDroughtDisturbances() && noFG != file_of_params.getFGDrought().size()) + { + logg.error("!!! Parameters NO_PFG (", noFG, ") and --PFG_PARAMS_DROUGHT-- (", + file_of_params.getFGDrought().size(), ") do not match in term of number!"); + } + if (m_glob_params.getDoFireDisturbances() && noFG != file_of_params.getFGFire().size()) + { + logg.error("!!! Parameters NO_PFG (", noFG, ") and --PFG_PARAMS_FIRE-- (", + file_of_params.getFGFire().size(), ") do not match in term of number!"); + } + if (m_glob_params.getDoHabSuitability() && noFG != file_of_params.getFGMapsHabSuit().size()) + { + logg.error("!!! Parameters NO_PFG (", noFG, ") and --PFG_MASK_HABSUIT-- (", + file_of_params.getFGMapsHabSuit().size(), ") do not match in term of number!"); + } + if (m_glob_params.getDoAliensIntroduction() && noFG != file_of_params.getFGMapsAliens().size()) + { + logg.error("!!! Parameters NO_PFG (", noFG, ") and --PFG_MASK_ALIENS-- (", + file_of_params.getFGMapsAliens().size(), ") do not match in term of number!"); } /* end of check parameters compatibility */ + /* check for parameters file */ + file_of_params.checkCorrectParams(m_glob_params.getDoLightInteraction(), + m_glob_params.getDoHabSuitability(), + m_glob_params.getDoDispersal(), + m_glob_params.getDoDisturbances(), + m_glob_params.getDoSoilInteraction(), + m_glob_params.getDoFireDisturbances(), + m_glob_params.getDoDroughtDisturbances(), + m_glob_params.getDoAliensIntroduction()); + /* update fg environmental suitability conditions if needed */ if (file_of_params.getFGMapsHabSuit()[0] != "0") { // some new initial envsuit conditions given @@ -1576,6 +1645,45 @@ void SimulMap::UpdateSimulationParameters(FOPL file_of_params) } } + /* build simulation fire disturbances masks */ + // if (m_glob_params.getDoFireDisturbances()) + // { + // if (m_glob_params.getFireIgnitMode()==5) + // { + // logg.info("> build simulation fire disturbances masks..."); + // if (m_glob_params.getNoFireDist() == file_of_params.getMaskFire().size()) + // { + // vector< vector< int > > fireMap; // fire disturbances masks + // fireMap.reserve(m_glob_params.getNoFireDist()); + // for (int dist_id=0; dist_id( file_of_params.getMaskFire()[dist_id], 0.0, 1.0 ) ); + // } + // m_FireMap = SpatialStack(m_Coord_ptr, fireMap); + // } else + // { + // logg.error("!!! Parameters FIRE_NO and --FIRE_MASK-- ", + // "do not match in term of number!"); + // } + // } else + // { + // m_FireMap = SpatialStack(m_Coord_ptr, emptyMapInt); + // } + // + // /* build fire masks */ + // logg.info("> build fire masks..."); + // if (m_glob_params.getFirePropMode()==4) + // { + // m_DroughtMap = SpatialMap(m_Coord_ptr, ReadMask( file_of_params.getMaskDrought(), 0.0, 1.0 ) ); + // m_ElevationMap = SpatialMap(m_Coord_ptr, ReadMask( file_of_params.getMaskElevation()) ); + // m_SlopeMap = SpatialMap(m_Coord_ptr, ReadMask( file_of_params.getMaskSlope()) ); + // } + // + // /* build TSLF mask (study area) */ + // logg.info("> build TSLF mask (study area)..."); + // m_TslfMap = SpatialMap(m_Coord_ptr, ReadMask( file_of_params.getMask(), 0.0, 1.0 ) ); + // } + /* build aliens introduction masks */ if (file_of_params.getFGMapsAliens()[0] != "0") { @@ -1763,10 +1871,10 @@ void SimulMap::SaveRasterAbund(string saveDir, int year, string prevFile) delete [] abunValues2; } // end loop on PFG - if (!positiveVal12) - { - logg.error("!!! ALL PFG DIED! Stopping simulation."); - } + // if (!positiveVal12 && year > m_glob_params.getSeedingDuration()) + // { + // logg.error("!!! ALL PFG DIED! Stopping simulation."); + // } } if (m_glob_params.getDoSavingStratum()) @@ -1829,10 +1937,10 @@ void SimulMap::SaveRasterAbund(string saveDir, int year, string prevFile) delete [] abunValues3; } // end loop on Stratum*/ - if (!positiveVal33) - { - logg.error("!!! ALL PFG DIED! Stopping simulation."); - } + // if (!positiveVal33 && year > m_glob_params.getSeedingDuration()) + // { + // logg.error("!!! ALL PFG DIED! Stopping simulation."); + // } } } diff --git a/src/main_rcpp.cpp b/src/main_rcpp.cpp index 53871be..411cb8b 100644 --- a/src/main_rcpp.cpp +++ b/src/main_rcpp.cpp @@ -478,45 +478,6 @@ int FATE(std::string simulParam, int no_CPU = 1, int verboseLevel = 0) GSP glob_params = GSP(file_of_params.getGlobSimulParams()); int noFG = glob_params.getNoFG(); logg.info("*** REBUILDING Functional groups..."); - if (noFG != file_of_params.getFGLifeHistory().size()) - { - logg.error("!!! Parameters NO_PFG (", noFG, - ") and --PFG_PARAMS_LIFE_HISTORY-- (", - file_of_params.getFGLifeHistory().size(), - ") do not match in term of number!"); - } - if (glob_params.getDoDispersal() && - noFG != file_of_params.getFGDispersal().size()) - { - logg.error("!!! Parameters NO_PFG (", noFG, - ") and --PFG_PARAMS_DISPERSAL-- (", - file_of_params.getFGDispersal().size(), - ") do not match in term of number!"); - } - if (glob_params.getDoDisturbances() && - noFG != file_of_params.getFGDisturbance().size()) - { - logg.error("!!! Parameters NO_PFG (", noFG, - ") and --PFG_PARAMS_DISTURBANCES-- (", - file_of_params.getFGDisturbance().size(), - ") do not match in term of number!"); - } - if (glob_params.getDoFireDisturbances() && - noFG != file_of_params.getFGFire().size()) - { - logg.error("!!! Parameters NO_PFG (", noFG, - ") and --PFG_PARAMS_FIRE-- (", - file_of_params.getFGFire().size(), - ") do not match in term of number!"); - } - if (glob_params.getDoDroughtDisturbances() && - noFG != file_of_params.getFGDrought().size()) - { - logg.error("!!! Parameters NO_PFG (", noFG, - ") and --PFG_PARAMS_DROUGHT-- (", - file_of_params.getFGDrought().size(), - ") do not match in term of number!"); - } vector fg_vec_tmp; for (int fg_id=0; fg_id Date: Tue, 1 Mar 2022 13:13:54 +0100 Subject: [PATCH 07/20] Add PPM part in FATE_RS (get vegetation maps and predict ppm) Not done yet --- R/FATE_RS.R | 75 ++++++++++++++++++++++++++++++++++++++------- src/RcppExports.cpp | 1 + 2 files changed, 65 insertions(+), 11 deletions(-) diff --git a/R/FATE_RS.R b/R/FATE_RS.R index 6415368..0a47fc6 100644 --- a/R/FATE_RS.R +++ b/R/FATE_RS.R @@ -20,6 +20,7 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.level = 2 + # , TRANS.PFG_var, TRANS.ras.var, mod.obj , name.simulation.RS, params.RS , year.start, year.end, year.step) { @@ -41,11 +42,6 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev GLOB_DIR = .getGraphics_results(name.simulation = name.simulation , abs.simulParam = abs.simulParam) - ## Get number of PFGs ----------------------------------------------------- - ## Get PFG names ---------------------------------------------------------- - GLOB_SIM = .getGraphics_PFG(name.simulation = name.simulation - , abs.simulParam = abs.simulParam) - ## Get raster mask -------------------------------------------------------- GLOB_MASK = .getGraphics_mask(name.simulation = name.simulation , abs.simulParam = abs.simulParam) @@ -61,9 +57,9 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev , "Abund_YEAR_" , year.step , "_" - , GLOB_SIM$PFG + , TRANS.PFG_var , "_STRATA_all.tif") - gp = GLOB_SIM$PFG[which(file.exists(file_name))] + gp = TRANS.PFG_var[which(file.exists(file_name))] file_name = file_name[which(file.exists(file_name))] if (length(file_name) > 0) @@ -77,15 +73,70 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev , " does not contain adequate files")) } - ## Transform them into habitat map ############################################################ + ## Combine with other variables ############################################################### + ras.all = stack(ras.PFG, TRANS.ras.var) + + env.data = as.data.frame(ras.all) + env.data = na.exclude(env.data) + for(pfg in TRANS.PFG_var) { + env.data[which(env.data[, pfg] < 0), pfg] = 0 + } + + ### Create all explanatory variables (with interactions between vegetation and environment) + mess = paste0(c(paste0("env.data$", names(TRANS.ras.var)) + , paste0("sqrt(env.data$", TRANS.PFG_var, ")")), collapse = ", ") + eval(parse(text = paste0("X.des = poly(", mess, ", degree = 2, raw = TRUE)"))) + col_power_1 = which(str_count(colnames(X.des), "1") == 1) + col_power_2 = which(str_count(colnames(X.des), "1") == 0) + col_inter_var1 = grep("^1.", colnames(X.des)) + col_inter_var2 = grep("^0.1.", colnames(X.des)) + col_toKeep = sort(unique(c( + col_power_1, col_power_2, col_inter_var1, col_inter_var2 + ))) + X.des = X.des[, col_toKeep] + + ### Change explanatory variables into images + ux = sort(unique(TRANS.quad[, 1])) #x ordinates + uy = sort(unique(TRANS.quad[, 2])) #y ordinates + nx = length(ux) + ny = length(uy) + col.ref = match(TRANS.quad[, 1], ux) # indice de l'abscisse de quad dans ux + row.ref = match(TRANS.quad[, 2], uy) + + int.list = list() + for (n in 1:dim(X.des)[2]) { + all.vec = rep(NA, max(row.ref) * max(col.ref)) + vec.ref = (col.ref - 1) * max(row.ref) + row.ref + all.vec[vec.ref] = X.des[, n] + int.list[[n]] = im(matrix(all.vec, max(row.ref), max(col.ref), dimnames = list(uy, ux)), + xcol = ux, + yrow = uy) + } + names(int.list) = paste0("V", 1:dim(X.des)[2]) ## Transform them into RS species distribution map ############################################ + mod.pred = predict(TRANS.ppm, covariates = int.list, ngrid = c(ny, nx)) + ras.pred = raster(mod.pred) + ras.quality = ras.pred / max(na.exclude(values(ras.pred))) * 100 + tmp = log(ras.quality) + abs(min(log(ras.quality)[], na.rm = TRUE)) + ras.log = tmp / max(tmp[], na.rm = TRUE) * 100 + + # name.distrib = paste0(name.simulation.RS, "BLABLABLA.asc") + # writeRaster(ras.log, filename = name.distrib) + ## SAVE as ASCII, voir script Emmanuel ? + + ## Update RS disp-cost maps ################################################################### + + + ## Update RS patch maps ####################################################################### + ## ADD script - ## Update RS disp-cost and patch maps ######################################################### ## Run RangeShifter ########################################################################### RunRS(RSparams = params.RS, dirpath = name.simulation.RS) + ## RENAME output with year + ## Get resulting RS species density ########################################################### ## Code from RangeShiftR help # read population output file into a dataframe @@ -100,14 +151,16 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev # use raster package to make a raster from the data frame stack_years_rep0 <- rasterFromXYZ(pop_wide_rep0) - name.dist = paste0(name.simulation, "/DATA/MASK/MASK_DIST_YEAR_", ye, ".tif") + ## MISSING conversion into 0-1 scale (what is the max Nind for which the dist is max ?) + ## parameter user-defined ? + name.dist = paste0(name.simulation, "/DATA/MASK/MASK_DIST_YEAR_", ye + 1, ".tif") writeRaster(stack_years_rep0, filename = name.dist) ## Update FATE disturbance maps ############################################################### .setParam(params.lines = abs.simulParam , flag = "DIST_MASK" , flag.split = "^--.*--$" - , value = paste0(name.simulation, "/DATA/MASK/MASK_DIST_YEAR_", ye, ".tif")) + , value = paste0(name.simulation, "/DATA/MASK/MASK_DIST_YEAR_", ye + 1, ".tif")) ## Update FATE simulation to load ############################################################# .setParam(params.lines = abs.simulParam diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp index a09c958..9fc0157 100644 --- a/src/RcppExports.cpp +++ b/src/RcppExports.cpp @@ -1,6 +1,7 @@ // Generated by using Rcpp::compileAttributes() -> do not edit by hand // Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393 +#include #include using namespace Rcpp; From 4b49b13b0fa1ebfe0f68f6cf75473bcc65d1a33a Mon Sep 17 00:00:00 2001 From: MayaGueguen Date: Tue, 1 Mar 2022 14:17:55 +0100 Subject: [PATCH 08/20] Add in FATE_RS script about patches creation --- R/FATE_RS.R | 67 +++++++++++++++++++++++++++++++++-------------------- 1 file changed, 42 insertions(+), 25 deletions(-) diff --git a/R/FATE_RS.R b/R/FATE_RS.R index 0a47fc6..e372fc1 100644 --- a/R/FATE_RS.R +++ b/R/FATE_RS.R @@ -20,8 +20,10 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.level = 2 - # , TRANS.PFG_var, TRANS.ras.var, mod.obj + , PPM.names_PFG, PPM.ras_env, PPM.quad, PPM.mod + , PATCH.threshold = 80, PATCH.buffer = 500, PATCH.min_m2 = 300000 , name.simulation.RS, params.RS + , POP.carrying_capacity , year.start, year.end, year.step) { ## + argument pour savoir si on commence par FATE ou RS @@ -36,7 +38,7 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev ## Run FATE ################################################################################### FATE(simulParam = abs.simulParam, no_CPU = opt.no_CPU, verboseLevel = verbose.level) - + ## Get resulting FATE vegetation maps ######################################################### ## Get results directories ------------------------------------------------ GLOB_DIR = .getGraphics_results(name.simulation = name.simulation @@ -57,9 +59,9 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev , "Abund_YEAR_" , year.step , "_" - , TRANS.PFG_var + , PPM.names_PFG , "_STRATA_all.tif") - gp = TRANS.PFG_var[which(file.exists(file_name))] + gp = PPM.names_PFG[which(file.exists(file_name))] file_name = file_name[which(file.exists(file_name))] if (length(file_name) > 0) @@ -74,17 +76,17 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev } ## Combine with other variables ############################################################### - ras.all = stack(ras.PFG, TRANS.ras.var) + ras.all = stack(ras.PFG, PPM.ras_env) env.data = as.data.frame(ras.all) env.data = na.exclude(env.data) - for(pfg in TRANS.PFG_var) { + for(pfg in PPM.names_PFG) { env.data[which(env.data[, pfg] < 0), pfg] = 0 } ### Create all explanatory variables (with interactions between vegetation and environment) - mess = paste0(c(paste0("env.data$", names(TRANS.ras.var)) - , paste0("sqrt(env.data$", TRANS.PFG_var, ")")), collapse = ", ") + mess = paste0(c(paste0("env.data$", names(PPM.ras_env)) + , paste0("sqrt(env.data$", PPM.names_PFG, ")")), collapse = ", ") eval(parse(text = paste0("X.des = poly(", mess, ", degree = 2, raw = TRUE)"))) col_power_1 = which(str_count(colnames(X.des), "1") == 1) col_power_2 = which(str_count(colnames(X.des), "1") == 0) @@ -96,12 +98,12 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev X.des = X.des[, col_toKeep] ### Change explanatory variables into images - ux = sort(unique(TRANS.quad[, 1])) #x ordinates - uy = sort(unique(TRANS.quad[, 2])) #y ordinates + ux = sort(unique(PPM.quad[, 1])) #x ordinates + uy = sort(unique(PPM.quad[, 2])) #y ordinates nx = length(ux) ny = length(uy) - col.ref = match(TRANS.quad[, 1], ux) # indice de l'abscisse de quad dans ux - row.ref = match(TRANS.quad[, 2], uy) + col.ref = match(PPM.quad[, 1], ux) # indice de l'abscisse de quad dans ux + row.ref = match(PPM.quad[, 2], uy) int.list = list() for (n in 1:dim(X.des)[2]) { @@ -115,13 +117,13 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev names(int.list) = paste0("V", 1:dim(X.des)[2]) ## Transform them into RS species distribution map ############################################ - mod.pred = predict(TRANS.ppm, covariates = int.list, ngrid = c(ny, nx)) + mod.pred = predict(PPM.mod, covariates = int.list, ngrid = c(ny, nx)) ras.pred = raster(mod.pred) ras.quality = ras.pred / max(na.exclude(values(ras.pred))) * 100 tmp = log(ras.quality) + abs(min(log(ras.quality)[], na.rm = TRUE)) ras.log = tmp / max(tmp[], na.rm = TRUE) * 100 - # name.distrib = paste0(name.simulation.RS, "BLABLABLA.asc") + # name.distrib = paste0(name.simulation.RS, "BLABLABLA_YEAR_", ye, ".asc") # writeRaster(ras.log, filename = name.distrib) ## SAVE as ASCII, voir script Emmanuel ? @@ -129,7 +131,23 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev ## Update RS patch maps ####################################################################### - ## ADD script + ras.patch = ras.log > PATCH.threshold # defining patches + ras.patch[ras.patch[] < 1] = NA # keep only patches + + pol.patch = rasterToPolygons(ras.patch, dissolve = TRUE) # converting into polygons + pol.patch = disaggregate(pol.patch) # separating into multiple polygons + + pol.patch = st_as_sf(pol.patch) + pol.patch_buffer = st_buffer(pol.patch, dist = PATCH.buffer) + pol.patch_buffer = st_union(pol.patch_buffer) # merging overlapping polygons + pol.patch_buffer = ms_explode(pol.patch_buffer) # separating into multiple polygons + + pol.patch_buffer$area_m2 = as.numeric(st_area(pol.patch_buffer)) # ne marche pas chez Emmanuel -> on passe ? 'area()' + pol.patch_buffer = pol.patch_buffer[which(pol.patch_buffer$area_m2 > PATCH.min_m2)] # excluding too small patches + + # st_write(pol.patch_buffer + # , paste0("tampons", PATCH.buffer, "m_suit_HS", threshold_habquality, "percent_filtre", PATCH.min_m2 / 10000, "ha_Lambert93") + # , dsn = "Output_Patches_3methodes", driver = "ESRI Shapefile") ## Run RangeShifter ########################################################################### @@ -140,22 +158,21 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev ## Get resulting RS species density ########################################################### ## Code from RangeShiftR help # read population output file into a dataframe - pop_df <- readPop(s = params.RS, dirpath = name.simulation.RS) + pop_df = readPop(s = params.RS, dirpath = name.simulation.RS) # Make stack of different raster layers for each year and for only one repetition (Rep==0): - pop_wide_rep0 <- reshape(subset(pop_df, Rep == 0)[, c('Year', 'x', 'y', 'NInd')] - , timevar = 'Year' - , v.names = c('NInd') - , idvar = c('x', 'y') - , direction = 'wide') + pop_wide_rep0 = reshape(subset(pop_df, Rep == 0)[, c('Year', 'x', 'y', 'NInd')] + , timevar = 'Year' + , v.names = c('NInd') + , idvar = c('x', 'y') + , direction = 'wide') # use raster package to make a raster from the data frame - stack_years_rep0 <- rasterFromXYZ(pop_wide_rep0) - ## MISSING conversion into 0-1 scale (what is the max Nind for which the dist is max ?) - ## parameter user-defined ? + stack_years_rep0 = rasterFromXYZ(pop_wide_rep0) + stack_years_rep0 = stack_years_rep0 / POP.carrying_capacity name.dist = paste0(name.simulation, "/DATA/MASK/MASK_DIST_YEAR_", ye + 1, ".tif") writeRaster(stack_years_rep0, filename = name.dist) - + ## Update FATE disturbance maps ############################################################### .setParam(params.lines = abs.simulParam , flag = "DIST_MASK" From f49db0f80a310fa8ff24667acf64b28d01937bc4 Mon Sep 17 00:00:00 2001 From: MayaGueguen Date: Thu, 10 Mar 2022 09:07:59 +0100 Subject: [PATCH 09/20] Add modifications to FATE_RS (saving ascii maps) --- R/FATE_RS.R | 58 +++++++++++++++++++++++++++++++++++++++++------------ 1 file changed, 45 insertions(+), 13 deletions(-) diff --git a/R/FATE_RS.R b/R/FATE_RS.R index e372fc1..dcc09b9 100644 --- a/R/FATE_RS.R +++ b/R/FATE_RS.R @@ -20,10 +20,10 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.level = 2 - , PPM.names_PFG, PPM.ras_env, PPM.quad, PPM.mod + , PPM.names_PFG, PPM.ras_env, PPM.xy, PPM.mod , PATCH.threshold = 80, PATCH.buffer = 500, PATCH.min_m2 = 300000 , name.simulation.RS, params.RS - , POP.carrying_capacity + , POP.carrying_capacity = 0.115 , year.start, year.end, year.step) { ## + argument pour savoir si on commence par FATE ou RS @@ -98,12 +98,12 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev X.des = X.des[, col_toKeep] ### Change explanatory variables into images - ux = sort(unique(PPM.quad[, 1])) #x ordinates - uy = sort(unique(PPM.quad[, 2])) #y ordinates + ux = sort(unique(PPM.xy[, 1])) #x ordinates + uy = sort(unique(PPM.xy[, 2])) #y ordinates nx = length(ux) ny = length(uy) - col.ref = match(PPM.quad[, 1], ux) # indice de l'abscisse de quad dans ux - row.ref = match(PPM.quad[, 2], uy) + col.ref = match(PPM.xy[, 1], ux) # indice de l'abscisse de quad dans ux + row.ref = match(PPM.xy[, 2], uy) int.list = list() for (n in 1:dim(X.des)[2]) { @@ -123,9 +123,6 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev tmp = log(ras.quality) + abs(min(log(ras.quality)[], na.rm = TRUE)) ras.log = tmp / max(tmp[], na.rm = TRUE) * 100 - # name.distrib = paste0(name.simulation.RS, "BLABLABLA_YEAR_", ye, ".asc") - # writeRaster(ras.log, filename = name.distrib) - ## SAVE as ASCII, voir script Emmanuel ? ## Update RS disp-cost maps ################################################################### @@ -142,12 +139,39 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev pol.patch_buffer = st_union(pol.patch_buffer) # merging overlapping polygons pol.patch_buffer = ms_explode(pol.patch_buffer) # separating into multiple polygons - pol.patch_buffer$area_m2 = as.numeric(st_area(pol.patch_buffer)) # ne marche pas chez Emmanuel -> on passe ? 'area()' + pol.patch_buffer$area_m2 = as.numeric(st_area(pol.patch_buffer)) pol.patch_buffer = pol.patch_buffer[which(pol.patch_buffer$area_m2 > PATCH.min_m2)] # excluding too small patches - # st_write(pol.patch_buffer - # , paste0("tampons", PATCH.buffer, "m_suit_HS", threshold_habquality, "percent_filtre", PATCH.min_m2 / 10000, "ha_Lambert93") - # , dsn = "Output_Patches_3methodes", driver = "ESRI Shapefile") + st_write(pol.patch_buffer + , paste0("tampons", PATCH.buffer, "m_suit_HS", PATCH.threshold, "percent_filtre", PATCH.min_m2 / 10000, "ha_Lambert93") + , dsn = paste0(name.simulation.RS, "Inputs"), driver = "ESRI Shapefile") + + + ## SAVE HS RASTER MAP AS ASCII ################################################################ + ras.patch_buffer = rasterize(pol.patch_buffer, ras.log) + ras.log[which(is.na(ras.patch_buffer[]))] = NA + + val.log = ras.log[] + val.log[is.na(val.log)] = -9 + val.log = as.character(val.log) + seq_linestarts <- seq(from = nrow(ras.log), to = ncell(ras.log) - nrow(ras.log) + 1, by = nrow(ras.log)) + val.log[seq_linestarts] = paste0(val.log[seq_linestarts], "\n") # delineating rows for future character string + cha.log = paste(val.log, collapse = ' ') # concatenating in 1 character + cha.log = gsub("\n ", "\n", cha.log) # removing blank from line starts + + file.rename(from = paste0(name.simulation.RS, "Inputs/LandscapeFile_HabSuit_ChamoisBauges.txt") + , to = paste0(name.simulation.RS, "Inputs/LandscapeFile_HabSuit_ChamoisBauges_YEAR_", ye - 1, ".txt")) + + fileConn <- file(paste0(name.simulation.RS, "Inputs/LandscapeFile_HabSuit_ChamoisBauges.txt") + writeLines(c(paste("ncols", ncol(ras.log), sep = " "), + paste("nrows", nrow(ras.log), sep = " "), + paste("xllcorner", extent(ras.log)[1], sep = " "), + paste("yllcorner", extent(ras.log)[3], sep = " "), + paste("cellsize", resolution(ras.log)[1], sep = " "), + "NODATA_value -9", + cha.log), + fileConn) + close(fileConn) ## Run RangeShifter ########################################################################### @@ -166,10 +190,18 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev , v.names = c('NInd') , idvar = c('x', 'y') , direction = 'wide') + tmp_ncells = reshape(subset(pop_df, Rep == 0)[, c('Year', 'x', 'y', 'Ncells')] + , timevar = 'Year' + , v.names = c('Ncells') + , idvar = c('x', 'y') + , direction = 'wide') # use raster package to make a raster from the data frame stack_years_rep0 = rasterFromXYZ(pop_wide_rep0) + stack_ncells = rasterFromXYZ(tmp_ncells) + stack_years_rep0 = stack_years_rep0 / stack_ncells stack_years_rep0 = stack_years_rep0 / POP.carrying_capacity + stack_years_rep0[which(stack_years_rep0[] > 1)] = 1 name.dist = paste0(name.simulation, "/DATA/MASK/MASK_DIST_YEAR_", ye + 1, ".tif") writeRaster(stack_years_rep0, filename = name.dist) From 1bb9345c54433d6210a6390f1b940f7a30f87109 Mon Sep 17 00:00:00 2001 From: MayaGueguen Date: Thu, 10 Mar 2022 09:14:21 +0100 Subject: [PATCH 10/20] Update FATE_RS (rename files) --- R/FATE_RS.R | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/R/FATE_RS.R b/R/FATE_RS.R index dcc09b9..58098ec 100644 --- a/R/FATE_RS.R +++ b/R/FATE_RS.R @@ -184,6 +184,9 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev # read population output file into a dataframe pop_df = readPop(s = params.RS, dirpath = name.simulation.RS) + file.rename(from = paste0(name.simulation.RS, "Outputs/Batch1_Sim1_Land1_Pop.txt") + , to = paste0(name.simulation.RS, "Outputs/Batch1_Sim1_Land1_Pop_YEAR_", ye, ".txt")) + # Make stack of different raster layers for each year and for only one repetition (Rep==0): pop_wide_rep0 = reshape(subset(pop_df, Rep == 0)[, c('Year', 'x', 'y', 'NInd')] , timevar = 'Year' @@ -215,7 +218,7 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev .setParam(params.lines = abs.simulParam , flag = "SAVED_STATE" , flag.split = "^--.*--$" - , value = "XXX") + , value = paste0("SIMUL_YEAR_", ye)) } } From 95b10ec33aca9a56595cba0ea543a7f6332d4c0c Mon Sep 17 00:00:00 2001 From: MayaGueguen Date: Tue, 15 Mar 2022 10:30:05 +0100 Subject: [PATCH 11/20] Add in FATE_RS code for cost map part --- R/FATE_RS.R | 62 +++++++++++++++++++++++++++++++++++++++++++++-------- 1 file changed, 53 insertions(+), 9 deletions(-) diff --git a/R/FATE_RS.R b/R/FATE_RS.R index 58098ec..b2d4574 100644 --- a/R/FATE_RS.R +++ b/R/FATE_RS.R @@ -14,7 +14,12 @@ ##' @export ##' ##' @importFrom RangeShiftR RunRS readPop -##' @importFrom raster stack rasterFromXYZ writeRaster +##' @importFrom raster stack rasterFromXYZ writeRaster rasterToPolygons disaggregate rasterize +##' @importFrom sf st_as_sf st_buffer st_union st_area st_write +##' @importFrom rmapshaper ms_explode +##' @importFrom spatstat im predict +##' @importFrom stringr str_count +##' @importFrom scales rescale ##' ## END OF HEADER ############################################################### @@ -22,6 +27,7 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.level = 2 , PPM.names_PFG, PPM.ras_env, PPM.xy, PPM.mod , PATCH.threshold = 80, PATCH.buffer = 500, PATCH.min_m2 = 300000 + , COST.ras_elev, COST.ras_barr, COST.wei = c(0.43, 0.53, 0.04), COST.range = c(1, 10) , name.simulation.RS, params.RS , POP.carrying_capacity = 0.115 , year.start, year.end, year.step) @@ -54,7 +60,7 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev , list_files = raster.perPFG.allStrata , no_cores = opt.no_CPU) - ## GET PFG abundance maps (all strata) ------------------------------ + ## GET PFG abundance maps (all strata) ------------------------------------ file_name = paste0(GLOB_DIR$dir.output.perPFG.allStrata , "Abund_YEAR_" , year.step @@ -97,7 +103,7 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev ))) X.des = X.des[, col_toKeep] - ### Change explanatory variables into images + ### Change explanatory variables into images ------------------------------ ux = sort(unique(PPM.xy[, 1])) #x ordinates uy = sort(unique(PPM.xy[, 2])) #y ordinates nx = length(ux) @@ -122,10 +128,7 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev ras.quality = ras.pred / max(na.exclude(values(ras.pred))) * 100 tmp = log(ras.quality) + abs(min(log(ras.quality)[], na.rm = TRUE)) ras.log = tmp / max(tmp[], na.rm = TRUE) * 100 - - - ## Update RS disp-cost maps ################################################################### - + ## Update RS patch maps ####################################################################### ras.patch = ras.log > PATCH.threshold # defining patches @@ -162,7 +165,7 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev file.rename(from = paste0(name.simulation.RS, "Inputs/LandscapeFile_HabSuit_ChamoisBauges.txt") , to = paste0(name.simulation.RS, "Inputs/LandscapeFile_HabSuit_ChamoisBauges_YEAR_", ye - 1, ".txt")) - fileConn <- file(paste0(name.simulation.RS, "Inputs/LandscapeFile_HabSuit_ChamoisBauges.txt") + fileConn <- file(paste0(name.simulation.RS, "Inputs/LandscapeFile_HabSuit_ChamoisBauges.txt")) writeLines(c(paste("ncols", ncol(ras.log), sep = " "), paste("nrows", nrow(ras.log), sep = " "), paste("xllcorner", extent(ras.log)[1], sep = " "), @@ -174,10 +177,51 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev close(fileConn) + ## Update RS disp-cost maps ################################################################### + ## Function to rescale habitat suitability maps + fun_rescale = function(a = 1, b = 100, ras, ext) { + mini = min(values(ras), na.rm = TRUE) + maxi = max(values(ras), na.rm = TRUE) + res = (((b - a) * (ras - mini)) / (maxi - mini)) + a + res = mask(res, ext) + return(res) + } + + ras.log_ = fun_rescale(a = a, b = b, ras = ras.log, ext = ras.log) + ras.HS = fun_rescale(a = a, b = b, ras = 100 + (-1 * ras.log_) ^ 1, ext = ras.log_) + + # Compute cost map -------------------------------------------------------- + ras.cost <- COST.wei[1] * ras.HS + COST.wei[2] * COST.ras_elev + COST.wei[3] * COST.ras_barr + ras.cost[] <- rescale(ras.cost[], c(COST.range[1], COST.range[2])) + ras.cost[] <- round(ras.cost[]) # round for SMS module + + ## SAVE COST RASTER MAP AS ASCII ############################################################## + val.cost = ras.cost[] + val.cost[is.na(val.cost)] = -9 + val.cost = as.character(val.cost) + seq_linestarts <- seq(from = nrow(ras.cost), to = ncell(ras.cost) - nrow(ras.cost) + 1, by = nrow(ras.cost)) + val.cost[seq_linestarts] = paste0(val.cost[seq_linestarts], "\n") # delineating rows for future character string + cha.cost = paste(val.cost, collapse = ' ') # concatenating in 1 character + cha.cost = gsub("\n ", "\n", cha.cost) # removing blank from line starts + + file.rename(from = paste0(name.simulation.RS, "Inputs/LandscapeFile_CostMap_ChamoisBauges.txt") + , to = paste0(name.simulation.RS, "Inputs/LandscapeFile_CostMap_ChamoisBauges_YEAR_", ye - 1, ".txt")) + + fileConn <- file(paste0(name.simulation.RS, "Inputs/LandscapeFile_CostMap_ChamoisBauges.txt")) + writeLines(c(paste("ncols", ncol(ras.cost), sep = " "), + paste("nrows", nrow(ras.cost), sep = " "), + paste("xllcorner", extent(ras.cost)[1], sep = " "), + paste("yllcorner", extent(ras.cost)[3], sep = " "), + paste("cellsize", resolution(ras.cost)[1], sep = " "), + "NODATA_value -9", + cha.cost), + fileConn) + close(fileConn) + + ## Run RangeShifter ########################################################################### RunRS(RSparams = params.RS, dirpath = name.simulation.RS) - ## RENAME output with year ## Get resulting RS species density ########################################################### ## Code from RangeShiftR help From f58ab5d4640f4c13c9e21e3db856551fc897e38a Mon Sep 17 00:00:00 2001 From: MayaGueguen Date: Wed, 16 Mar 2022 10:12:17 +0100 Subject: [PATCH 12/20] Correct file.simulParam in FATE_RS --- R/FATE_RS.R | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/R/FATE_RS.R b/R/FATE_RS.R index b2d4574..77cf98c 100644 --- a/R/FATE_RS.R +++ b/R/FATE_RS.R @@ -37,22 +37,22 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev ## LOOP over simulation years for (ye in seq(year.start, year.end, 1)) { - .setParam(params.lines = abs.simulParam + .setParam(params.lines = file.simulParam , flag = "SAVING_DIR" , flag.split = "^--.*--$" , value = paste0(name.simulation, "/RESULTS/SIMUL_YEAR_", ye, "")) ## Run FATE ################################################################################### - FATE(simulParam = abs.simulParam, no_CPU = opt.no_CPU, verboseLevel = verbose.level) + FATE(simulParam = file.simulParam, no_CPU = opt.no_CPU, verboseLevel = verbose.level) ## Get resulting FATE vegetation maps ######################################################### ## Get results directories ------------------------------------------------ GLOB_DIR = .getGraphics_results(name.simulation = name.simulation - , abs.simulParam = abs.simulParam) + , abs.simulParam = file.simulParam) ## Get raster mask -------------------------------------------------------- GLOB_MASK = .getGraphics_mask(name.simulation = name.simulation - , abs.simulParam = abs.simulParam) + , abs.simulParam = file.simulParam) ## UNZIP the raster saved ------------------------------------------------- raster.perPFG.allStrata = .getRasterNames(year.step, "allStrata", "ABUND", GLOB_DIR) @@ -253,13 +253,13 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev writeRaster(stack_years_rep0, filename = name.dist) ## Update FATE disturbance maps ############################################################### - .setParam(params.lines = abs.simulParam + .setParam(params.lines = file.simulParam , flag = "DIST_MASK" , flag.split = "^--.*--$" , value = paste0(name.simulation, "/DATA/MASK/MASK_DIST_YEAR_", ye + 1, ".tif")) ## Update FATE simulation to load ############################################################# - .setParam(params.lines = abs.simulParam + .setParam(params.lines = file.simulParam , flag = "SAVED_STATE" , flag.split = "^--.*--$" , value = paste0("SIMUL_YEAR_", ye)) From f8dc6155e57107af22910dc13ace924b1d29f3fe Mon Sep 17 00:00:00 2001 From: MayaGueguen Date: Thu, 24 Mar 2022 16:03:59 +0100 Subject: [PATCH 13/20] Update creation of RS landscape and parameters --- R/FATE_RS.R | 33 +++++++++++++++++++++------------ 1 file changed, 21 insertions(+), 12 deletions(-) diff --git a/R/FATE_RS.R b/R/FATE_RS.R index 77cf98c..432ff4b 100644 --- a/R/FATE_RS.R +++ b/R/FATE_RS.R @@ -28,7 +28,7 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev , PPM.names_PFG, PPM.ras_env, PPM.xy, PPM.mod , PATCH.threshold = 80, PATCH.buffer = 500, PATCH.min_m2 = 300000 , COST.ras_elev, COST.ras_barr, COST.wei = c(0.43, 0.53, 0.04), COST.range = c(1, 10) - , name.simulation.RS, params.RS + , RS.name_simul, RS.dens_dep, RS.sim, RS.demo, RS.disp, RS.init , POP.carrying_capacity = 0.115 , year.start, year.end, year.step) { @@ -147,7 +147,7 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev st_write(pol.patch_buffer , paste0("tampons", PATCH.buffer, "m_suit_HS", PATCH.threshold, "percent_filtre", PATCH.min_m2 / 10000, "ha_Lambert93") - , dsn = paste0(name.simulation.RS, "Inputs"), driver = "ESRI Shapefile") + , dsn = paste0(RS.name_simul, "Inputs"), driver = "ESRI Shapefile") ## SAVE HS RASTER MAP AS ASCII ################################################################ @@ -162,10 +162,10 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev cha.log = paste(val.log, collapse = ' ') # concatenating in 1 character cha.log = gsub("\n ", "\n", cha.log) # removing blank from line starts - file.rename(from = paste0(name.simulation.RS, "Inputs/LandscapeFile_HabSuit_ChamoisBauges.txt") - , to = paste0(name.simulation.RS, "Inputs/LandscapeFile_HabSuit_ChamoisBauges_YEAR_", ye - 1, ".txt")) + file.rename(from = paste0(RS.name_simul, "Inputs/LandscapeFile_HabSuit.txt") + , to = paste0(RS.name_simul, "Inputs/LandscapeFile_HabSuit_YEAR_", ye - 1, ".txt")) - fileConn <- file(paste0(name.simulation.RS, "Inputs/LandscapeFile_HabSuit_ChamoisBauges.txt")) + fileConn <- file(paste0(RS.name_simul, "Inputs/LandscapeFile_HabSuit.txt")) writeLines(c(paste("ncols", ncol(ras.log), sep = " "), paste("nrows", nrow(ras.log), sep = " "), paste("xllcorner", extent(ras.log)[1], sep = " "), @@ -204,10 +204,10 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev cha.cost = paste(val.cost, collapse = ' ') # concatenating in 1 character cha.cost = gsub("\n ", "\n", cha.cost) # removing blank from line starts - file.rename(from = paste0(name.simulation.RS, "Inputs/LandscapeFile_CostMap_ChamoisBauges.txt") - , to = paste0(name.simulation.RS, "Inputs/LandscapeFile_CostMap_ChamoisBauges_YEAR_", ye - 1, ".txt")) + file.rename(from = paste0(RS.name_simul, "Inputs/LandscapeFile_CostMap.txt") + , to = paste0(RS.name_simul, "Inputs/LandscapeFile_CostMap_YEAR_", ye - 1, ".txt")) - fileConn <- file(paste0(name.simulation.RS, "Inputs/LandscapeFile_CostMap_ChamoisBauges.txt")) + fileConn <- file(paste0(RS.name_simul, "Inputs/LandscapeFile_CostMap.txt")) writeLines(c(paste("ncols", ncol(ras.cost), sep = " "), paste("nrows", nrow(ras.cost), sep = " "), paste("xllcorner", extent(ras.cost)[1], sep = " "), @@ -220,16 +220,25 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev ## Run RangeShifter ########################################################################### - RunRS(RSparams = params.RS, dirpath = name.simulation.RS) + RS.land = ImportedLandscape(LandscapeFile = "LandscapeFile_HabSuit.txt", + Resolution = resolution(ras.log), + HabPercent = TRUE, # continuous values for habitat quality (and not discrete) + K_or_DensDep = RS.dens_dep, + PatchFile = "PatchFile.txt", + CostsFile = "LandscapeFile_CostMap.txt") + + RS.params = RSsim(simul = RS.sim, land = RS.land, demog = RS.demo, dispersal = RS.disp, init = RS.init) + + RunRS(RSparams = RS.params, dirpath = RS.name_simul) ## Get resulting RS species density ########################################################### ## Code from RangeShiftR help # read population output file into a dataframe - pop_df = readPop(s = params.RS, dirpath = name.simulation.RS) + pop_df = readPop(s = RS.params, dirpath = RS.name_simul) - file.rename(from = paste0(name.simulation.RS, "Outputs/Batch1_Sim1_Land1_Pop.txt") - , to = paste0(name.simulation.RS, "Outputs/Batch1_Sim1_Land1_Pop_YEAR_", ye, ".txt")) + file.rename(from = paste0(RS.name_simul, "Outputs/Batch1_Sim1_Land1_Pop.txt") + , to = paste0(RS.name_simul, "Outputs/Batch1_Sim1_Land1_Pop_YEAR_", ye, ".txt")) # Make stack of different raster layers for each year and for only one repetition (Rep==0): pop_wide_rep0 = reshape(subset(pop_df, Rep == 0)[, c('Year', 'x', 'y', 'NInd')] From 3afbba728b1ff6421762f3963164d6d70319995e Mon Sep 17 00:00:00 2001 From: MayaGueguen Date: Fri, 25 Mar 2022 12:11:08 +0100 Subject: [PATCH 14/20] Save patch buffer raster into ASCII Change filenames into ImportedLandscape function --- R/FATE_RS.R | 41 ++++++++++++++++++++++++++++++++--------- 1 file changed, 32 insertions(+), 9 deletions(-) diff --git a/R/FATE_RS.R b/R/FATE_RS.R index 432ff4b..151f0e1 100644 --- a/R/FATE_RS.R +++ b/R/FATE_RS.R @@ -145,15 +145,38 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev pol.patch_buffer$area_m2 = as.numeric(st_area(pol.patch_buffer)) pol.patch_buffer = pol.patch_buffer[which(pol.patch_buffer$area_m2 > PATCH.min_m2)] # excluding too small patches - st_write(pol.patch_buffer - , paste0("tampons", PATCH.buffer, "m_suit_HS", PATCH.threshold, "percent_filtre", PATCH.min_m2 / 10000, "ha_Lambert93") - , dsn = paste0(RS.name_simul, "Inputs"), driver = "ESRI Shapefile") - - - ## SAVE HS RASTER MAP AS ASCII ################################################################ + ## Change into raster ras.patch_buffer = rasterize(pol.patch_buffer, ras.log) + ## Set Habitat Suitability out of patches to NA ras.log[which(is.na(ras.patch_buffer[]))] = NA + ## SAVE PATCH into ASCII + val.buf = ras.patch_buffer[] + val.buf[is.na(val.buf)] = -9 + val.buf = as.character(val.buf) + seq_linestarts <- seq(from = nrow(ras.patch_buffer) + , to = ncell(ras.patch_buffer) - nrow(ras.patch_buffer) + 1 + , by = nrow(ras.patch_buffer)) + val.buf[seq_linestarts] = paste0(val.buf[seq_linestarts], "\n") # delineating rows for future character string + cha.buf = paste(val.buf, collapse = ' ') # concatenating in 1 character + cha.buf = gsub("\n ", "\n", cha.buf) # removing blank from line starts + + file.rename(from = paste0(RS.name_simul, "Inputs/PatchFile.txt") + , to = paste0(RS.name_simul, "Inputs/PatchFile_YEAR_", ye - 1, ".txt")) + + fileConn <- file(paste0(RS.name_simul, "Inputs/PatchFile.txt")) + writeLines(c(paste("ncols", ncol(ras.patch_buffer), sep = " "), + paste("nrows", nrow(ras.patch_buffer), sep = " "), + paste("xllcorner", extent(ras.patch_buffer)[1], sep = " "), + paste("yllcorner", extent(ras.patch_buffer)[3], sep = " "), + paste("cellsize", resolution(ras.patch_buffer)[1], sep = " "), + "NODATA_value -9", + cha.buf), + fileConn) + close(fileConn) + + + ## SAVE HS RASTER MAP AS ASCII ################################################################ val.log = ras.log[] val.log[is.na(val.log)] = -9 val.log = as.character(val.log) @@ -220,12 +243,12 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev ## Run RangeShifter ########################################################################### - RS.land = ImportedLandscape(LandscapeFile = "LandscapeFile_HabSuit.txt", + RS.land = ImportedLandscape(LandscapeFile = paste0(RS.name_simul, "Inputs/LandscapeFile_HabSuit.txt"), Resolution = resolution(ras.log), HabPercent = TRUE, # continuous values for habitat quality (and not discrete) K_or_DensDep = RS.dens_dep, - PatchFile = "PatchFile.txt", - CostsFile = "LandscapeFile_CostMap.txt") + PatchFile = paste0(RS.name_simul, "Inputs/PatchFile.txt"), + CostsFile = paste0(RS.name_simul, "Inputs/LandscapeFile_CostMap.txt")) RS.params = RSsim(simul = RS.sim, land = RS.land, demog = RS.demo, dispersal = RS.disp, init = RS.init) From 29d470b9d365b20938e2a7ba128b012f59a94184 Mon Sep 17 00:00:00 2001 From: MayaGueguen Date: Mon, 28 Mar 2022 15:07:06 +0200 Subject: [PATCH 15/20] Update reading of population output file into FATE_RS --- R/FATE_RS.R | 22 ++++++---------------- 1 file changed, 6 insertions(+), 16 deletions(-) diff --git a/R/FATE_RS.R b/R/FATE_RS.R index 151f0e1..70c22c2 100644 --- a/R/FATE_RS.R +++ b/R/FATE_RS.R @@ -256,29 +256,19 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev ## Get resulting RS species density ########################################################### - ## Code from RangeShiftR help # read population output file into a dataframe pop_df = readPop(s = RS.params, dirpath = RS.name_simul) + pop_df = pop_df[which(pop_df$Rep == 0 & pop_df$Year == 1), ] file.rename(from = paste0(RS.name_simul, "Outputs/Batch1_Sim1_Land1_Pop.txt") , to = paste0(RS.name_simul, "Outputs/Batch1_Sim1_Land1_Pop_YEAR_", ye, ".txt")) # Make stack of different raster layers for each year and for only one repetition (Rep==0): - pop_wide_rep0 = reshape(subset(pop_df, Rep == 0)[, c('Year', 'x', 'y', 'NInd')] - , timevar = 'Year' - , v.names = c('NInd') - , idvar = c('x', 'y') - , direction = 'wide') - tmp_ncells = reshape(subset(pop_df, Rep == 0)[, c('Year', 'x', 'y', 'Ncells')] - , timevar = 'Year' - , v.names = c('Ncells') - , idvar = c('x', 'y') - , direction = 'wide') - - # use raster package to make a raster from the data frame - stack_years_rep0 = rasterFromXYZ(pop_wide_rep0) - stack_ncells = rasterFromXYZ(tmp_ncells) - stack_years_rep0 = stack_years_rep0 / stack_ncells + stack_years_rep0 = ras.patch_buffer + stack_years_rep0[which(!is.na(stack_years_rep0[]))] = 0 + for (pp in 1:nrow(pop_df)) { + stack_years_rep0[which(ras.patch_buffer[] == pop_df$PatchID[pp])] = pop_df$NInd[pp] / pop_df$Ncells[pp] + } stack_years_rep0 = stack_years_rep0 / POP.carrying_capacity stack_years_rep0[which(stack_years_rep0[] > 1)] = 1 name.dist = paste0(name.simulation, "/DATA/MASK/MASK_DIST_YEAR_", ye + 1, ".tif") From cb83932bbe6ddf72da42fdf77caa80f10d3d7932 Mon Sep 17 00:00:00 2001 From: MayaGueguen Date: Mon, 28 Mar 2022 16:03:04 +0200 Subject: [PATCH 16/20] Correct in FATE_RS update of dist mask --- R/FATE_RS.R | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/R/FATE_RS.R b/R/FATE_RS.R index 70c22c2..0ff1417 100644 --- a/R/FATE_RS.R +++ b/R/FATE_RS.R @@ -275,10 +275,17 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev writeRaster(stack_years_rep0, filename = name.dist) ## Update FATE disturbance maps ############################################################### + dist.files = .getParam(params.lines = file.simulParam + , flag = "DIST_MASK" + , flag.split = "^--.*--$" + , is.num = FALSE) + dist.files[1] = paste0(name.simulation, "/DATA/MASK/MASK_DIST_YEAR_", ye + 1, ".tif") + .setParam(params.lines = file.simulParam , flag = "DIST_MASK" , flag.split = "^--.*--$" - , value = paste0(name.simulation, "/DATA/MASK/MASK_DIST_YEAR_", ye + 1, ".tif")) + , value = dist.files) + ## Update FATE simulation to load ############################################################# .setParam(params.lines = file.simulParam From 85350d58ea8e3888cf650b4e2c694a0b68598130 Mon Sep 17 00:00:00 2001 From: MayaGueguen Date: Tue, 29 Mar 2022 15:37:54 +0200 Subject: [PATCH 17/20] Correct change of SAVED_STATE in FATE_RS --- R/FATE_RS.R | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/R/FATE_RS.R b/R/FATE_RS.R index 0ff1417..4781d98 100644 --- a/R/FATE_RS.R +++ b/R/FATE_RS.R @@ -288,10 +288,17 @@ FATE_RS = function(name.simulation, file.simulParam, opt.no_CPU = 1, verbose.lev ## Update FATE simulation to load ############################################################# + year.save = readLines(.getParam(params.lines = file.simulParam + , flag = "SAVING_YEARS_OBJECTS" + , flag.split = "^--.*--$" + , is.num = FALSE)) + file.rename(from = paste0(GLOB_DIR$dir.save, "SimulMap_", year.save[1], ".sav") + , to = paste0(GLOB_DIR$dir.save, "SimulMap_STEP_YEAR_", ye, ".sav")) + .setParam(params.lines = file.simulParam , flag = "SAVED_STATE" , flag.split = "^--.*--$" - , value = paste0("SIMUL_YEAR_", ye)) + , value = paste0(GLOB_DIR$dir.save, "SimulMap_STEP_YEAR_", ye, ".sav")) } } From e2d8a9ba541e71ed39865775c4b86004ce9ef3a0 Mon Sep 17 00:00:00 2001 From: MayaGueguen Date: Mon, 25 Apr 2022 14:33:12 +0200 Subject: [PATCH 18/20] Add opt.no_clust_max in PRE_FATE.speciesClustering_step1 --- R/PRE_FATE.speciesClustering_step1.R | 4 ++-- man/PRE_FATE.speciesClustering_step1.Rd | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/R/PRE_FATE.speciesClustering_step1.R b/R/PRE_FATE.speciesClustering_step1.R index 42aaf87..468f392 100644 --- a/R/PRE_FATE.speciesClustering_step1.R +++ b/R/PRE_FATE.speciesClustering_step1.R @@ -193,7 +193,7 @@ ## END OF HEADER ############################################################### -PRE_FATE.speciesClustering_step1 = function(mat.species.DIST) +PRE_FATE.speciesClustering_step1 = function(mat.species.DIST, opt.no_clust_max = 15) { ############################################################################# @@ -376,7 +376,7 @@ PRE_FATE.speciesClustering_step1 = function(mat.species.DIST) ## Calculated for each group, and varying the number of clusters min_no_species_in_group = sapply(mat.species.DIST, function(x) ncol(as.matrix(x))) - min_no_species_in_group = sapply(min_no_species_in_group, function(x) min(x, 15)) + min_no_species_in_group = sapply(min_no_species_in_group, function(x) min(x, opt.no_clust_max)) combi = foreach(group = 1:length(group_names), .combine = "rbind") %do% { expand.grid(no.clusters = 2:(min_no_species_in_group[group] - 1), GROUP = group) } diff --git a/man/PRE_FATE.speciesClustering_step1.Rd b/man/PRE_FATE.speciesClustering_step1.Rd index 0774681..a60607f 100644 --- a/man/PRE_FATE.speciesClustering_step1.Rd +++ b/man/PRE_FATE.speciesClustering_step1.Rd @@ -4,7 +4,7 @@ \alias{PRE_FATE.speciesClustering_step1} \title{Create clusters based on dissimilarity matrix} \usage{ -PRE_FATE.speciesClustering_step1(mat.species.DIST) +PRE_FATE.speciesClustering_step1(mat.species.DIST, opt.no_clust_max = 15) } \arguments{ \item{mat.species.DIST}{a \code{dist} object, or a \code{list} of From fa0202dfbdb2cdd452907d783ff1543ab2e7676c Mon Sep 17 00:00:00 2001 From: MayaGueguen Date: Mon, 25 Apr 2022 14:33:55 +0200 Subject: [PATCH 19/20] Add opt.min.noMat in PRE_FATE.speciesDistanceCombine --- R/PRE_FATE.speciesDistanceCombine.R | 39 ++++++++++++++++++++------ man/PRE_FATE.speciesDistanceCombine.Rd | 5 ++++ 2 files changed, 36 insertions(+), 8 deletions(-) diff --git a/R/PRE_FATE.speciesDistanceCombine.R b/R/PRE_FATE.speciesDistanceCombine.R index 2111f2d..bfba4cd 100644 --- a/R/PRE_FATE.speciesDistanceCombine.R +++ b/R/PRE_FATE.speciesDistanceCombine.R @@ -10,6 +10,9 @@ ##' ##' @param list.mat.dist a \code{list} of matrices containing dissimilarity ##' distance values between each pair of species. +##' @param opt.min.noMat (\emph{optional}) default \code{length(list.mat.dist)}. \cr +##' An \code{integer} corresponding to the minimal number of distance matrices for +##' which each species should have values ##' @param opt.normal (\emph{optional}) default \code{TRUE}. \cr ##' If \code{TRUE}, all given distance matrices will be normalized ##' (see \href{PRE_FATE.speciesDistanceCombine#details}{\code{Details}}) @@ -118,6 +121,7 @@ PRE_FATE.speciesDistanceCombine = function(list.mat.dist + , opt.min.noMat = length(list.mat.dist) , opt.normal = TRUE , opt.weights = NULL ){ @@ -212,15 +216,20 @@ PRE_FATE.speciesDistanceCombine = function(list.mat.dist cat("\n Comparison of matrix' dimensions : \n") combi = combn(1:no_mat, 2) - inti_all = unique(unlist(names_species)) - for(x in 1:ncol(combi)){ - inti = intersect(names_species[[combi[1, x]]], names_species[[combi[2, x]]]) - inti_all = intersect(inti_all, inti) - cat("\n> Matrices ", names_mat[combi[1, x]], "-", names_mat[combi[2, x]], ": " - , length(inti), "species in common") - } - cat("\n Number of species with values for all matrices : ", length(inti_all)) + + inti_all = table(unlist(names_species)) + inti_all = names(inti_all)[which(inti_all >= opt.min.noMat)] + cat("\n Number of species with values for at least", opt.min.noMat, " matrices : ", length(inti_all)) cat("\n") + # inti_all = unique(unlist(names_species)) + # for(x in 1:ncol(combi)){ + # inti = intersect(names_species[[combi[1, x]]], names_species[[combi[2, x]]]) + # inti_all = intersect(inti_all, inti) + # cat("\n> Matrices ", names_mat[combi[1, x]], "-", names_mat[combi[2, x]], ": " + # , length(inti), "species in common") + # } + # cat("\n Number of species with values for all matrices : ", length(inti_all)) + # cat("\n") names_species.toKeep = inti_all } @@ -246,6 +255,20 @@ PRE_FATE.speciesDistanceCombine = function(list.mat.dist }) } + ## Fill missing species whith NA if there is any + mat.dist = lapply(mat.dist, function(x) { + if (ncol(x) < length(names_species.toKeep)) { + tmp.col = colnames(x) + tmp.row = rownames(x) + miss = setdiff(names_species.toKeep, colnames(x)) + x = cbind(x, matrix(rep(NA, length(miss) * nrow(x)), ncol = length(miss))) + x = rbind(x, matrix(rep(NA, length(miss) * ncol(x)), nrow = length(miss))) + colnames(x) = c(tmp.col, miss) + rownames(x) = c(tmp.row, miss) + } + return(x) + }) + ## Multiply each distance matrix by its weight mat.species.DIST = lapply(1:no_mat, function(x) { tmp = as.matrix(mat.dist[[x]]) diff --git a/man/PRE_FATE.speciesDistanceCombine.Rd b/man/PRE_FATE.speciesDistanceCombine.Rd index c32d6a8..f251ff7 100644 --- a/man/PRE_FATE.speciesDistanceCombine.Rd +++ b/man/PRE_FATE.speciesDistanceCombine.Rd @@ -6,6 +6,7 @@ \usage{ PRE_FATE.speciesDistanceCombine( list.mat.dist, + opt.min.noMat = length(list.mat.dist), opt.normal = TRUE, opt.weights = NULL ) @@ -14,6 +15,10 @@ PRE_FATE.speciesDistanceCombine( \item{list.mat.dist}{a \code{list} of matrices containing dissimilarity distance values between each pair of species.} +\item{opt.min.noMat}{(\emph{optional}) default \code{length(list.mat.dist)}. \cr +An \code{integer} corresponding to the minimal number of distance matrices for +which each species should have values} + \item{opt.normal}{(\emph{optional}) default \code{TRUE}. \cr If \code{TRUE}, all given distance matrices will be normalized (see \href{PRE_FATE.speciesDistanceCombine#details}{\code{Details}})} From f3bdf0369eabbca397ab285b8329e584ab166470 Mon Sep 17 00:00:00 2001 From: MayaGueguen Date: Mon, 25 Apr 2022 14:42:05 +0200 Subject: [PATCH 20/20] Add doc files --- DESCRIPTION | 2 +- man/FATE_RS.Rd | 41 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 42 insertions(+), 1 deletion(-) create mode 100644 man/FATE_RS.Rd diff --git a/DESCRIPTION b/DESCRIPTION index b1bfe9b..2d2aa69 100644 --- a/DESCRIPTION +++ b/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: 7.1.1 +RoxygenNote: 7.1.2 Encoding: UTF-8 NeedsCompilation: yes License: diff --git a/man/FATE_RS.Rd b/man/FATE_RS.Rd new file mode 100644 index 0000000..983d466 --- /dev/null +++ b/man/FATE_RS.Rd @@ -0,0 +1,41 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/FATE_RS.R +\name{FATE_RS} +\alias{FATE_RS} +\title{S} +\usage{ +FATE_RS( + name.simulation, + file.simulParam, + opt.no_CPU = 1, + verbose.level = 2, + PPM.names_PFG, + PPM.ras_env, + PPM.xy, + PPM.mod, + PATCH.threshold = 80, + PATCH.buffer = 500, + PATCH.min_m2 = 3e+05, + COST.ras_elev, + COST.ras_barr, + COST.wei = c(0.43, 0.53, 0.04), + COST.range = c(1, 10), + RS.name_simul, + RS.dens_dep, + RS.sim, + RS.demo, + RS.disp, + RS.init, + POP.carrying_capacity = 0.115, + year.start, + year.end, + year.step +) +} +\description{ +... +} +\author{ +Maya Guéguen +} +\keyword{RangeShifter}