4  Les covariables

4.1 Question internes

• Faut-il intégrer des scripts pour récupérer certaines covariables –> peut-être à fournir en annexe
• Où héberger la pile de covariables que nous allons utiliser? –> tout dépend de leur poids. Sur une AOBOX ou un nextcloud
• Faut-il présenter toutes les covariables? Avec quel niveau de détail? –> présenter les groupes de covariables. Méanmoins il ne semble important que les gens sachent ce qu’ils utilisent.

Nom de la variable	Description	Type	Groupe de covariable DSM	Source
bioX	18 bioclimatic variables (X means the id of the bioclimatic variable, eg bio1, bio2, etc.)	continuous	Climate	Wordclim
bdforet	Land use for forest areas only	categorical	organism	Data from the French forest database (version 1 (2006 data) IGN BDForêt)
PC1_NDVI	Principal component of a stack of combined NDVI images for a dry and wet period	continuous	organism	SentinelII Loiseau et al
NDVI	Principal component of a set of NDVI images during dry and wet periods	continuous	organism
clc90	Corine Land Cover 1990	categorical	organism	Corine Land Cover
clc00	Corine Land Cover 2000	categorical	organism	Corine Land Cover
clc06	Corine Land Cover 2006	categorical	organism	Corine Land Cover
clc18	Corine Land Cover 2018	categorical	organism	Corine Land Cover
ecoclim	Land use from the ECOCLIMAP II database	continuous	Parental Material
graviAL2000	Gravimetric data from the BRGM	continuous	Parental Material	BRGM
graviBg2000	Gravimetric data from the BRGM	continuous	Parental Material	BRGM
graviG2000	Gravimetric data from the BRGM	continuous	Parental Material	BRGM
mrrtf	Multi-resolution Ridge Top Flatness index	continuous	Relief	dem derivative
cti	Compound Topographic Index (calculated with the Geomorphometric and Gradient Metrics Toolbox)	continuous	Relief	dem derivative
curv_long	Longitudinal curvature	continuous	Relief	dem derivative
curv_trans	Transversal curvature	continuous	Relief	dem derivative
curvature	Mean curvature	continuous	Relief	dem derivative
dissection	Describes dissection in a continuous raster surface within rectangular or circular window index	continuous	Relief	dem derivative
eros	Estimated erosion rates in Europe	continuous	Relief	Cerdan et al
exposition	Exposition	continuous	Relief
flow_acc	Flow accumulation	continuous	Relief
flow_dir	Flow direction	categorical	Relief
hli	Heat Load Index (A southwest-facing slope should have warmer temperatures than a southeast-facing slope, even though the amount of solar radiation they receive is equivalent)	continuous	Relief
flow_length	Flow length	continuous	Relief
mrvbf	Multi-resolution Valley Bottom Flatness index	continuous	Relief
roughness	Represents the roughness in a continuous raster within a specified window	continuous	Relief
ruprh1	Available water capacity (mm, “réserve utile”, or RU, in French). Calculated by Wosten pedotransfer function	continuous	Soil
slopeascos	Slope sinus transformations	continuous	Relief
slopeastrasp	Slope TRASP (Topographic Radiation Aspect Index) transformations	continuous	Relief
srr	Surface relief ratio	continuous	Relief
pHIFN	Combined predictions of pH from large datasets of soil test results for arable land areas and from interpreted pH from indicator plants for forest areas	continuous	Soil	French Forest Institute
soil1	Dominant soil type of the SMU of the European Soil Map at 1/1,000,000 scale	continuous	Soil	European Soil Map at 1/1,000,000 scale
arg1	Dominant topsoil clay content of the European Soil Map at 1/1,000,000 scale	continuous	Soil	European Soil Map at 1/1,000,000 scale
profsolMillion	Dominant soil depth of the European Soil Map at 1/1,000,000 scale	continuous	Soil	European Soil Map at 1/1,000,000 scale
mat11	Dominant parental material level 1 of the European Soil Map at 1/1,000,000 scale	continuous	Soil	European Soil Map at 1/1,000,000 scale
lim1	Dominant topsoil silt content of the European Soil Map at 1/1,000,000 scale	continuous	Soil	European Soil Map at 1/1,000,000 scale
sab1	Dominant topsoil sand content of the European Soil Map at 1/1,000,000 scale	continuous	Soil	European Soil Map at 1/1,000,000 scale
linear_aspect	Transforms circular aspect to a linear variable	continuous	Relief
idpr	Network Development and Persistence Index	continuous	Relief
srtm	Elevation from SRTM DEM	continuous	Relief
FBS_B12	Mosaic of Sentinel 2 images, Spectral band B12, Sentinel 2 sensor, from March 1 to April 30 in 2016 and 2017 and from November 1 to December 31 in 2016	continuous	Soil	ScienceDirect
FBS_B2	Mosaic of Sentinel 2 images, Spectral band B2	continuous	Soil	ScienceDirect
FBS_B4	Mosaic of Sentinel 2 images, Spectral band B4, Sentinel 2 sensor	continuous	Soil	ScienceDirect
FBS_CalcRIND	Mosaic of Sentinel 2 images, Carbonate Index	continuous	Soil	ScienceDirect
FBS_ClayRIND	Mosaic of Sentinel 2 images, Clay response, Sentinel 2 sensor indices	continuous	Soil	ScienceDirect
FBS_ColIND	Mosaic of Sentinel 2 images, Coloration Index (CI)	continuous	Soil	ScienceDirect
FBS_FeIND	Mosaic of Sentinel 2 images, Ferrous Iron (FeI)	continuous	Soil	ScienceDirect
FBS_HueIND	Mosaic of Sentinel 2 images, Hue Index (HI)	continuous	Soil	ScienceDirect
class_aspect	Classifies aspect into discrete classes (calculated with the Geomorphometric and Gradient Metrics Toolbox)	categorical	Relief	Data from DEM and derived attributes
Modis2001_01_01.Land_Cover_Type_1.tif	MODIS Land Cover Type (MCD12Q1) - Annual global land cover types at 500m resolution. Year in the title.	categorical	organism	NASA LP DAAC - Mark Friedl, Damien Sulla-Menashe. 2018.
Modis2001_01_01.Npp_1km.tif	MODIS Net Primary Production (NPP) for CONUS - Estimates NPP using MODIS surface reflectance. Year in the title.	continuous	organism	Robinson et al. 2018 - Remote Sensing in Ecology and Conservation.
Modis2002_01_01.Land_Cover_Type_1.tif	MODIS Land Cover Type (MCD12Q1) - Annual global land cover types at 500m resolution. Year in the title.	categorical	organism	NASA LP DAAC
Modis2002_01_01.Npp_1km.tif	MODIS Net Primary Production (NPP) for CONUS - Estimates NPP using MODIS surface reflectance. Year in the title.	continuous	organism	Robinson et al. 2018
Modis2003_01_01.Land_Cover_Type_1.tif	MODIS Land Cover Type (MCD12Q1) - Annual global land cover types at 500m resolution. Year in the title.	categorical	organism	NASA LP DAAC
Modis2003_01_01.Npp_1km.tif	MODIS Net Primary Production (NPP) for CONUS - Estimates NPP using MODIS surface reflectance. Year in the title.	continuous	organism	Robinson et al. 2018
Modis2004_01_01.Land_Cover_Type_1.tif	MODIS Land Cover Type (MCD12Q1) - Annual global land cover types at 500m resolution. Year in the title.	categorical	organism	NASA LP DAAC
Modis2004_01_01.Npp_1km.tif	MODIS Net Primary Production (NPP) for CONUS - Estimates NPP using MODIS surface reflectance. Year in the title.	continuous	organism	Robinson et al. 2018
Modis2005_01_01.Land_Cover_Type_1.tif	MODIS Land Cover Type (MCD12Q1) - Annual global land cover types at 500m resolution. Year in the title.	categorical	organism	NASA LP DAAC
Modis2005_01_01.Npp_1km.tif	MODIS Net Primary Production (NPP) for CONUS - Estimates NPP using MODIS surface reflectance. Year in the title.	continuous	organism	Robinson et al. 2018
Modis2006_01_01.Land_Cover_Type_1.tif	MODIS Land Cover Type (MCD12Q1) - Annual global land cover types at 500m resolution. Year in the title.	categorical	organism	NASA LP DAAC
Modis2006_01_01.Npp_1km.tif	MODIS Net Primary Production (NPP) for CONUS - Estimates NPP using MODIS surface reflectance. Year in the title.	continuous	organism	Robinson et al. 2018
Modis2007_01_01.Land_Cover_Type_1.tif	MODIS Land Cover Type (MCD12Q1) - Annual global land cover types at 500m resolution. Year in the title.	categorical	organism	NASA LP DAAC
Modis2007_01_01.Npp_1km.tif	MODIS Net Primary Production (NPP) for CONUS - Estimates NPP using MODIS surface reflectance. Year in the title.	continuous	organism	Robinson et al. 2018
Modis2008_01_01.Land_Cover_Type_1.tif	MODIS Land Cover Type (MCD12Q1) - Annual global land cover types at 500m resolution. Year in the title.	categorical	organism	NASA LP DAAC
Modis2008_01_01.Npp_1km.tif	MODIS Net Primary Production (NPP) for CONUS - Estimates NPP using MODIS surface reflectance. Year in the title.	continuous	organism	[Robinson et al.

==> CE TABLEAU EST TROP PEU LISIBLE. POSSIBLE D’ALEMIORER SA MISE EN FORME ?

4.2 Initialisation

library(sf)

Linking to GEOS 3.12.2, GDAL 3.11.4, PROJ 9.4.1; sf_use_s2() is TRUE

library(terra)

terra 1.9.6

library(httr)
library(ggplot2)
library(tidyterra)

Attachement du package : 'tidyterra'

L'objet suivant est masqué depuis 'package:stats':

    filter

pts_sf <- readRDS("donnees/sorties/pointsSpline.rds") 
bbox <- st_bbox(pts_sf)  # Étendue des points

4.3 Importation des covariables

4.3.1 Modèle numérique d’altitude

Le Modlèle Numérique d’Altitude (MNA) est obtenu via les services Copernicus.

# Définir l'étendue + résolution (ex: 10m)
ext <- ext(bbox["xmin"], bbox["xmax"], bbox["ymin"], bbox["ymax"])
# Convertit l'étendue de la zone d'étude (bbox) en un polygone
poly_l93 <- st_as_sfc(bbox)

4.3.2 Chargement des cartes des covariables

covariables <- terra::rast("donnees/covariables/clipped_raster_stack.tif")

# Exploration des données : nuage de points (plot) des 6 premières covariables
terra::plot(covariables, y = 1:6)

4.3.3 Extraction des points et graphique, exemple de la température

require(ggplot2)
X <- terra::extract(covariables, vect(pts_sf))
variables_categorielles <- c("Modis2006_01_01.Land_Cover_Type_1",            "clc90" ,
"Modis2009_01_01.Land_Cover_Type_1", "Modis2011_01_01.Land_Cover_Type_1",
"TMN_rgf93", "PJE_rgf93", "PDE_rgf93")
variables_quantitatives <- setdiff(names(X), variables_categorielles)[-1]
X[, variables_categorielles] <- lapply(X[, variables_categorielles], as.factor)

ggplot() +
    tidyterra::geom_spatvector(
    data = vect(cbind(pts_sf,X)),
    aes(color = tmean),
    size = 2
  ) +
  scale_color_viridis_c()

4.3.4 Inspection des covariables

GGally::ggpairs(
  data = X,
  columns = variables_quantitatives,
  title = "Correlation entre la variables quantitatives",
  upper = list(continuous = GGally::wrap("cor", size = 3)),
  lower = list(continuous = GGally::wrap("smooth", alpha = 0.3, linewidth = 0.3)) , #,  mapping = aes(color = children_fac)
  progress = FALSE
)

Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2

Warning: Removed 3 rows containing non-finite outside the scale range
(`stat_density()`).

Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
Removed 3 rows containing missing values
Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
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Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
Removed 3 rows containing missing values
Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
Removed 3 rows containing missing values

Warning in geom_point(...): Ignoring unknown parameters: `linewidth`

Warning: Removed 3 rows containing non-finite outside the scale range
(`stat_smooth()`).

Warning: Removed 3 rows containing missing values or values outside the scale range
(`geom_point()`).

Warning: Removed 3 rows containing non-finite outside the scale range
(`stat_density()`).

Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
Removed 3 rows containing missing values
Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
Removed 3 rows containing missing values
Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
Removed 3 rows containing missing values

Warning in geom_point(...): Ignoring unknown parameters: `linewidth`

Warning: Removed 3 rows containing non-finite outside the scale range
(`stat_smooth()`).

Warning: Removed 3 rows containing missing values or values outside the scale range
(`geom_point()`).

Warning in geom_point(...): Ignoring unknown parameters: `linewidth`

Warning: Removed 3 rows containing non-finite outside the scale range
(`stat_smooth()`).

Warning: Removed 3 rows containing missing values or values outside the scale range
(`geom_point()`).

Warning: Removed 3 rows containing non-finite outside the scale range
(`stat_density()`).

Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
Removed 3 rows containing missing values
Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
Removed 3 rows containing missing values

Warning in geom_point(...): Ignoring unknown parameters: `linewidth`

Warning: Removed 3 rows containing non-finite outside the scale range
(`stat_smooth()`).

Warning: Removed 3 rows containing missing values or values outside the scale range
(`geom_point()`).

Warning in geom_point(...): Ignoring unknown parameters: `linewidth`

Warning: Removed 3 rows containing non-finite outside the scale range
(`stat_smooth()`).

Warning: Removed 3 rows containing missing values or values outside the scale range
(`geom_point()`).

Warning in geom_point(...): Ignoring unknown parameters: `linewidth`

Warning: Removed 3 rows containing non-finite outside the scale range
(`stat_smooth()`).

Warning: Removed 3 rows containing missing values or values outside the scale range
(`geom_point()`).

Warning: Removed 3 rows containing non-finite outside the scale range
(`stat_density()`).

Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
Removed 3 rows containing missing values

Warning in geom_point(...): Ignoring unknown parameters: `linewidth`

Warning: Removed 3 rows containing non-finite outside the scale range
(`stat_smooth()`).

Warning: Removed 3 rows containing missing values or values outside the scale range
(`geom_point()`).

Warning in geom_point(...): Ignoring unknown parameters: `linewidth`

Warning: Removed 3 rows containing non-finite outside the scale range
(`stat_smooth()`).

Warning: Removed 3 rows containing missing values or values outside the scale range
(`geom_point()`).

Warning in geom_point(...): Ignoring unknown parameters: `linewidth`

Warning: Removed 3 rows containing non-finite outside the scale range
(`stat_smooth()`).

Warning: Removed 3 rows containing missing values or values outside the scale range
(`geom_point()`).

Warning in geom_point(...): Ignoring unknown parameters: `linewidth`

Warning: Removed 3 rows containing non-finite outside the scale range
(`stat_smooth()`).

Warning: Removed 3 rows containing missing values or values outside the scale range
(`geom_point()`).

Warning: Removed 3 rows containing non-finite outside the scale range
(`stat_density()`).

GGally::ggpairs(data = X,   
                columns = variables_quantitatives, 
                title = "Correlation entre la variables quantitatives",  progress = FALSE

                )

Warning: Removed 3 rows containing non-finite outside the scale range
(`stat_density()`).

Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
Removed 3 rows containing missing values
Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
Removed 3 rows containing missing values
Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
Removed 3 rows containing missing values
Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
Removed 3 rows containing missing values

Warning: Removed 3 rows containing missing values or values outside the scale range
(`geom_point()`).

Warning: Removed 3 rows containing non-finite outside the scale range
(`stat_density()`).

Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
Removed 3 rows containing missing values
Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
Removed 3 rows containing missing values
Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
Removed 3 rows containing missing values

Warning: Removed 3 rows containing missing values or values outside the scale range
(`geom_point()`).
Removed 3 rows containing missing values or values outside the scale range
(`geom_point()`).

Warning: Removed 3 rows containing non-finite outside the scale range
(`stat_density()`).

Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
Removed 3 rows containing missing values
Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
Removed 3 rows containing missing values

Warning: Removed 3 rows containing missing values or values outside the scale range
(`geom_point()`).
Removed 3 rows containing missing values or values outside the scale range
(`geom_point()`).
Removed 3 rows containing missing values or values outside the scale range
(`geom_point()`).

Warning: Removed 3 rows containing non-finite outside the scale range
(`stat_density()`).

Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
Removed 3 rows containing missing values

Warning: Removed 3 rows containing missing values or values outside the scale range
(`geom_point()`).
Removed 3 rows containing missing values or values outside the scale range
(`geom_point()`).
Removed 3 rows containing missing values or values outside the scale range
(`geom_point()`).
Removed 3 rows containing missing values or values outside the scale range
(`geom_point()`).

Warning: Removed 3 rows containing non-finite outside the scale range
(`stat_density()`).