Load a dataset

Source: R/UTILS.loadData.R

This function loads one of the available datasets :

Champsaur_PFG

elements to create Plant Functional Groups (PFG) over Champsaur valley, in Ecrins National Park (PNE)

Champsaur_params

all necessary files to build the FATE simulation folder as well as the parameter files

Champsaur_simul_[...]

simulation folder and outputs obtained from FATE simulation

Champsaur_results_[...]

results obtained from outputs and POST_FATE functions 

.loadData(data.name, format.name)

Arguments

data.name

a string corresponding to the name of the dataset that will be loaded

format.name

a string corresponding to the downloading format way (either RData or 7z)

Value

Note : references to habitat refer to habitat map and classes from CESBIO2018. Some class gathering has been made, as follow :

  • 0 - Other : 0, 21, 22, 23

  • 1 - Urban : 1, 2, 3, 4

  • 2 - Crops : 5, 6, 7, 8, 9, 10, 11, 12

  • 3 - Prairies : 13

  • 4 - Orchards, vineyards : 14, 15

  • 5 - Deciduous forests : 16

  • 6 - Coniferous forests : 17

  • 7 - Natural grasslands : 18

  • 8 - Woody heathlands : 19

  • 9 - Mineral surfaces : 20



#########################################################
 >>> Champsaur_PFG
#########################################################

A list object with 18 elements to help building the Plant Functional Group :

name.dataset

Champsaur

sp.observations

a data.frame of dimension 127257 x 6
containing releves data about plant species in Champsaur
to be used with the PRE_FATE.selectDominant function

  • sites : sites ID

  • species : species ID

  • abundBB : Braun-Blanquet abundance

  • abund : relative abundance obtained from the abund_BB column with the PRE_FATE.abundBraunBlanquet function

  • habitat : habitat classes (gathered) from CESBIO2018

  • TYPE : type of records, exhaustive (COMMUNITY) or single occurrences (OCCURRENCE)

rules.selectDominant

a vector containing parameters to be given to the PRE_FATE.selectDominant function
(doRuleA, rule.A1, rule.A2_quantile, doRuleB, rule.B1_percentage, rule.B1_number, rule.B2, doRuleC)

sp.SELECT

a list obtained from the PRE_FATE.selectDominant function run with sp.observations and rules.selectDominant

sp.traits

a data.frame of dimension 250 x 23
containing traits for dominant species
to be used with the PRE_FATE.speciesDistance function

  • species : species ID

  • GROUP : rough generalization of Raunkier life-forms (Phanerophyte, Chamaephyte, Herbaceous)

  • MATURITY / LONGEVITY / HEIGHT / LDMC / LNC / SEEDM / SLA : numerical values

  • LONGEVITY_log / HEIGHT_log / LDMC_log / LNC_log / SEEDM_log / SLA_log : log-transformed numerical values

  • DISPERSAL / LIGHT / NITROGEN / NITROGEN_TOLERANCE / MOISTURE / GRAZ_MOW_TOLERANCE / HABITAT / STRATEGY : categorical values

sp.traits.P

a data.frame of dimension 20 x 9
a subset of sp.traits (LONGEVITY_log / HEIGHT_log / SEEDM_log / SLA_log / DISPERSAL / LIGHT / NITROGEN) for Phanerophyte dominant species
to be used with the PRE_FATE.speciesDistance function

sp.traits.C

a data.frame of dimension 38 x 6
a subset of sp.traits (HEIGHT_log / SEEDM_log / LIGHT / NITROGEN) for Chamaephyte dominant species
to be used with the PRE_FATE.speciesDistance function

sp.traits.H

a data.frame of dimension 192 x 7
a subset of sp.traits (HEIGHT_log / LDMC_log / LNC_log / SLA_log / LIGHT) for Herbaceous dominant species
to be used with the PRE_FATE.speciesDistance function

mat.habitat

matrix of dimension 240 x 240
containing habitat dissimilarity distance (1 - Schoeners' D, obtained with gowdis) for dominant species
to be used with the PRE_FATE.speciesDistance function

tab.dom.PA

matrix of dimension 13654 x 264
containing dominant species occurrences and absences (obtained from sp.SELECT object and absences corrected with the TYPE information of sp.observations), to build mat.overlap

tab.env

matrix of dimension 13590 x 5
containing environmental values (bio1, bio12, slope, dem, CESBIO2018) for sites, to build mat.overlap

mat.overlap

matrix of dimension 244 x 244
containing niche overlap distance (1 - Schoeners' D, obtained with ecospat.niche.overlap) for dominant species
to be used with the PRE_FATE.speciesDistance function

sp.DIST.P

a list obtained from the PRE_FATE.speciesDistance function run for Phanerophyte dominant species with mat.habitat, mat.overlap and sp.traits.P parameters

sp.DIST.C

a list obtained from the PRE_FATE.speciesDistance function run for Chamaephyte dominant species with mat.habitat, mat.overlap and sp.traits.C parameters

sp.DIST.H

a list obtained from the PRE_FATE.speciesDistance function run for Herbaceous dominant species with mat.habitat, mat.overlap and sp.traits.H parameters

PFG.species

data.frame of dimension 224 x 5
containing dominant species information relative to PFG
obtained from the PRE_FATE.speciesClustering_step2 function

  • PFG : name of assigned Plant Functional Group

  • DETERMINANT : is the species kept as determinant species within the PFG ?
    (see PRE_FATE.speciesClustering_step2 function for details)

  • species : species ID

  • species_name : species name (taxonomic)

  • species_genus : species genus (taxonomic)

PFG.traits

data.frame of dimension 15 x 12
containing traits for plant functional groups
obtained from the PRE_FATE.speciesClustering_step3 function

  • PFG : Plant Functional Group short name

  • no.species : number of species within each group

  • maturity : MEAN age of maturity

  • longevity : MEAN age of lifespan

  • height : MEAN height (cm)

  • light : MEDIAN Landolt indicator value for light preference (from 1 to 5)

  • dispersal : MEDIAN classes (from 1 to 7) based on dispersal distances and types (Vittoz & Engler)

  • soil_contrib : MEAN Landolt indicator value for nitrogen preference (from 1 to 5)

  • soil_tol_min : MIN tolerance value for nitrogen preference (based on Landolt indicators, from 1 to 5)

  • soil_tol_max : MAX tolerance value for nitrogen preference (based on Landolt indicators, from 1 to 5)

  • LDMC : MEAN LDMC

  • LNC : MEAN LNC

PFG.PA

data.frame of dimension 13654 x 15
containing PFG occurrences and absences obtained from tab.dom.PA object and the PRE_FATE.speciesClustering_step3 function



#########################################################
 >>> Champsaur_params
#########################################################

A list object with 12 elements to help building the simulation files and folders to run a FATE simulation :

name.dataset

Champsaur

tab.occ

a data.frame of dimension 13590 x 15
containing presence / absence (NA, 0 or 1) values per site for each PFG

tab.env

a data.frame of dimension 13590 x 5
containing environmental values (bio1, bio12, slope, dem, CESBIO2018) for each site

tab.xy

a data.frame of dimension 13590 x 2
containing coordinates for each site

stk.var

a stack object of dimension 358 x 427 with a resolution of 100m and ETRS89 projection, containing 3 layers with environmental values (bio1, slope, CESBIO2018) and to be used to produce PFG SDM

tab.SUCC

a data.frame of dimension 15 x 5
containing PFG characteristics (type, height, maturity, longevity)
to be used with the PRE_FATE.params_PFGsuccession function

tab.DISP

a data.frame of dimension 15 x 4
containing PFG characteristics (d50, d99, ldd)
to be used with the PRE_FATE.params_PFGdispersal function

tab.DIST

a data.frame of dimension 15 x 3
containing PFG characteristics (nameDist, strategy_tol)
to be used with the PRE_FATE.params_PFGdisturbance function

tab.LIGHT

a data.frame of dimension 15 x 3
containing PFG characteristics (type, strategy_tol)
to be used with the PRE_FATE.params_PFGlight function

tab.SOIL

a data.frame of dimension 15 x 5
containing PFG characteristics (type, soil_contrib, soil_tol_min, soil_tol_max)
to be used with the PRE_FATE.params_PFGsoil function

stk.wmean

a stack object of dimension 358 x 427 with a resolution of 100m and ETRS89 projection, containing 15 layers with habitat suitability values (between 0 and 1) for each PFG

stk.mask

a stack object of dimension 358 x 427 with a resolution of 100m and ETRS89 projection, containing 4 mask layers with binary values (0 or 1) or categorical values (habitat) to be used in a FATE simulation :

  • Champsaur : simulation map, where occurs succession

  • noDisturb : perturbation map, when there is none

  • mowing : perturbation map, where occurs mowing

  • habitat : habitat map, from CESBIO2018 (gathered)



#########################################################
 >>> Champsaur_simul_[...]
#########################################################

A 7z file containing one FATE simulation result folder.
4 simulations are available :

  1. a simulation with only basic modules activated :
    CORE (succession) module, dispersal module, and habitat suitability module

  2. the same as V1 + the light module

  3. the same as V1 + the soil module

  4. the same as V1 + the light and soil modules



#########################################################
 >>> Champsaur_results_[...]
#########################################################

A 7z file containing .csv and .pdf files obtained from the corresponding FATE simulation result folder (4 simulations available) with the help of POST_FATE functions.

Author

Maya Guéguen