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get_gbif_data(), which downloads the occurrence records of
a species for a region of interest with the public GBIF search API (no
account needed) and returns them as sf points.habitat(), add_habitat() and
add_nohabitat() gain a priority argument,
stored in a new priority column of the habitat
object. In habitat_raster(), overlapping features are
stacked by priority and the pixel takes the value of the top one, so the
result no longer depends on the order of the add_*() calls.
By default each new layer goes on top of the previous ones, as
before.habitat(), add_habitat() and
add_nohabitat() gain a touches argument,
stored in a new touches column. With
touches = TRUE, lines and polygons fill every pixel they
touch in habitat_raster(), which keeps hedgerows, rivers or
roads continuous; with touches = FALSE, polygons fill the
pixels whose centre they cover.habitat_raster() now
accepts points, lines and polygons in the same habitat
object.priority and
touches on a watercourse of the Metaleurop landscape.get_ocsge(), a single entry point to get the OCS-GE of a
region of interest, with a source argument.
source = "ign" calls the new
get_ocsge_data_ign(), which downloads the per-department
GeoPackages of the IGN Géoplateforme (no API key), keeps them in a cache
directory and lets you choose the vintage with year.
source = "fgb" calls get_ocsge_data_fgb(),
unchanged. Extracting the IGN archives needs the archive
package or the 7z command line tool.ref_ocsge_eunis, a ranked correspondence between the 14
OCS-GE cover classes (CS), optionally refined by land use
(US), and the 45 EUNIS Level 2 classes, with the share of
each match measured on the Metaleurop site.ocsge_species_dict now has rows for 47 (cover, use) pairs
(code_us) in addition to the 14 covers, derived from
eunis_species_dict through ref_ocsge_eunis.
join_ocsge_species() gains a us_col argument:
when the polygons carry the land use, they take the scores of their
(cover, use) pair, and of their cover otherwise. New dataset
ocsge_us_metaleurop, the OCS-GE of the Metaleurop site with
cover and use.touches defaults to TRUE, whereas
habitat_raster() used to fill the pixels whose centre is
covered by a polygon, and the pixels of a thin line. Existing rasters
therefore change: features are drawn larger. Set
touches = FALSE to get the previous result, in particular
for layers of contiguous polygons such as a land cover map.ocsge_species_dict rebuilt with the columns of
eunis_species_dict: weight_global
becomes suitability, weight_movement becomes
permeability, weight_breeding and the
species-level columns (sppID, taxon_group,
habitat_breadth, specialization,
confidence, in_france) are added, and cover
codes are written without space ("CS2.2.1"). The scores
themselves changed: they follow an anchored scale, are lower on classes
that are not habitat, and movement accounts for flight.
resistance is now on a 1-100 logarithmic scale derived from
permeability (it was a 1-10 score): code that rescaled it,
or tested resistance == 10, must be updated (use
permeability == 0 for impassable classes).nom_espece renamed
species_name in ocsge_species_dict
and eunis_species_dict.plot_species_habitat() now expects
suitability instead of weight_global, and
draws resistance on a log scale.habitat_raster() no longer fails on an empty
habitat object.get_eunis_data() returned the raster upside down (north
and south swapped), because the image exported by the EEA service
carries no georeferencing. The image is now georeferenced before being
read. The Metaleurop layer shipped in
inst/extdata/eunis_metaleurop_L2.tif was rebuilt; rasters
obtained with earlier versions must be downloaded again.get_eunis_data() now takes service_url = NULL
by default (the EEA service, as before), the examples of
habitat_raster() and plot() for habitat
objects are run, and the vignette figures are lighter.calibrate_simple() checked for the wrong compiled model
before sampling.dispersal(method = "omniscape") reports its progress
with message() instead of cat().soil_variogram(),
fit_soil_variogram(), soil_vgm(),
krige_soil() (ordinary kriging or kriging with external
drift), cv_soil() (random or spatial-block
cross-validation), kernel_smooth_soil() (Gaussian smoothing
reusing compute_kernel()), soil_grid() and
source_covariates() (distance / wind covariates around a
point source). New dataset soil_metaleurop (595 soil Cd,
Pb, Zn samples) and new article “Soil contamination maps by
kriging”.get_eunis_data() to download EUNIS Level 1 / Level 2 land
cover rasters for a region of interest from the EEA Ecosystem Type Map
v3.1 service, and new lookup dataset ref_eunis.plot() for
trophic objects gains link weights and custom colors.remotes::install_github("Qonfluens/spacemodR").intake() function has been completely redesigned and
renamed to flux() to better reflect the mathematical and
ecological concept of transfer rates.flux() and chain specific
rules using the new add_flux() function.flux() (used within the
transfer() function) has been renamed to avoid conflicts
with the new main API.add_flux() function: Allows for
adding transfer rules in a readable, sequential manner (e.g.,
add_flux(from = "soil", to = "plant", value = ~ 10^x / 32)).add_flux(), if
the source compartment (from) is not specified, the rule
(value) is automatically applied to all links pointing to
the target compartment (to).flux()
function now features an explicit default parameter. It is
highly recommended to use 1 (full transfer) or
0 (no transfer) instead of NA to prevent the
propagation of missing values during subsequent model calculations.rlang_error (replacement has length zero) in
spacemodel raster layer sub-assignment within the Tutorial
vignette.DBFunc_BirdFuncDat dataset to pass CRAN checks.no visible binding for global variable
(weight_global, weight_foraging,
resistance).roxygen2 documentation for internal
datasets: FmrBT, DBFunc_MamFuncDat, and
DBFunc_BirdFuncDat.Food_Intake vignette into
professional scientific English.pkgdown website structure to use a clean
3-tier navigation system (Quick Start, Core Guides, Example Zoo).Food_Intake module and dataset integration
(FmrBT, EltonTraits) to compute Daily Food Intake (DFI).Omniscape_Connectivity tutorial with
real-world spatial data for the Wood Mouse (Apodemus
sylvaticus).spacemodel class for merging raster
stacks and trophic networks.transfer and dispersal modeling
functions.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.