High-Performance Open-Source Archive
tempdir() now follows
the pattern ‘mapme-data-…’ for better visibilitydelay, indicating the interval between
successive retries, has been added to the mapme_options()
functionmapme_options() function arguments
delay and retries now command the GDAL
configuration options GDAL_HTTP_RETRY_DELAY and
GDAL_HTTP_MAX_RETRY, so it is not necessary to set them
using Sys.setenv() (see 441)get_nelson_et_al() to cope with Figshare
asynchronous download mechanism (474)get_humanfootprint() to accept years up to
2024get_acled() to align with the new ACLED API
version (440)get_acled() function.fetch_resource() to include
GDAL options in the list of resources it failed to fetchget_mcd64a1() and
get_nasa_srtm(), that download data from Microsoft
Planetary Computer, now use a more efficient URL signing scheme, which
should reduce the risk of hitting the rate limitations (see 441)get_gfw_treecover() and get_gfw_lossyear()
updated to version “GFC-2024-v1.12” (416)calc_treecover_area(),
calc_treecover_area_and_emissions() and
calc_treecoverloss_emissions() updated to include the year
2024 (416)get_esalandcover() has been adapted to download data
from a new source in a format compatible with the previous version (430)calc_treecover_area() to return zero area and
not NULL when tree cover < min_cover (413)get_teow() now requires users to manually download the
file (450).has_internet() now delegates to
curl::has_internet().check_system_requirements() that checks
on package load if system requirements (GDAL and PROJ versions) are met,
and warns if notutils::compareVersion() instead of simple ‘<’ to
check the GDAL system library version.fetch_resource() now correctly takes
into account the resources that could not be retrieved and reports them
(433)check_namespace() functionnormalizePath() is used so it works
correctly on Windows (446)calc_treecover_area() to correctly handle the
full tree cover (100%) (451)get_biodiversity_intactness_index(),
get_iucn(), and get_key_biodiversity_areas()
now use spds_exists() to check if input files existget_chelsa() now supports precipitation layers for
2019get_chelsa() to
https://os.zhdk.cloud.switch.ch/chelsav2/GLOBAL/monthly/prspds_exist() and make_footprints() now use
normalizePath() allowing better handling of relative file
pathsthe sf_col attribute value is now retained
throughout the portfolio checks and chunking routines
.raster_bbox() now only uses the
cornerCoordinates output from gdalinfo to
derive a bounding box (385)
bounding boxes for raster and vector resources are now derived
via st_as_sfc(st_bbox(x)) to ensure that they are oriented
correctly when using S2 (377
and 385)
get_nasa_srtm() now uses GDAL’s VSI path option
pc_url_signing=yes to sign URLs from Microsoft Planetary
Computer (383).read_vector() now copies input GPKG to a
directory with write permissions to avoid CRAN check failures when
included in a read only directoryget_acled()calc_fatalities_acled()calc_fatalities_ucdp() (renamed)calc_exposed_population_acled()calc_exposed_population_ucdp() (renamed)calc_fatalities_ucdp() now returns a sparse timeseries,
e.g. asset-months with now fatalities are omitted.portfolio_wide() throwing an error when single
assets with NULL values are presentcalc_mangroves_area() returned NULL if invalid
geometries were encountered Now it tries to repair geometries and return
the area of valid geometries (375).get_intersection() now assumes both x and
tindex to be represented by oriented rings on the sphere
(378)get_accessibility_2000() (365,
@fBedecarrats)calc_traveltime_2000() (365,
@fBedecarrats)get_gsw_timseries() and
calc_gsw_timeseries() to write to temporal directory of the
R session to fix CRAN errors (370,
@karpfen)prep_resources() received additional argument
mode to get control over the reading mode (e.g. portfolio
or asset)
resources based on WorldClim now support selecting the spatial resolution and cover the historical timeseries starting from 1960 (302)
assets are now chunked into sub-components prior to indicator calculation thus parallelization now is applied to a single level (322)
chunk_size now is properly set to 100,000 ha as per
documentation (before it was set to 10,000 ha) (324)
setting chunk_size=NULL is now allowed and skips
chunking (331)
treecover indicators now trough a message if landscapemetrics is not installed (325)
setting outdir via mapme_options() now
probes the destination by trying to write a GTiff file and errors if
unsuccessful (335)
code previously using httr now uses
httr2 (330)
new resources:
new indicators:
calc_slope() (355,
@fBedecarrats)calc_ipbes_biomes() (345)calc_humanfootprint() (341)calc_gsw_time_series() (354,
@karpfen)calc_species_richness() (359)calc_exposed_population() (321)calc_precipitation_chelsa() (318)calc_key_biodiversity_area() (349,
@karpfen)calc_biodiversity_intactness_index() (351,
@karpfen)calc_vul_carbon(), calc_man_carbon(), and
calc_irr_carbon() (339)calc_deforestation_drivers() (300)write_portfolio() now drops indicators with only NULL
values instead of throwing an error (303)get_ucdp_ged() now adds SRS infos to the footprints
object (313)worldpop resource on
Windows (319).check_portfolio() now checks if assetid
has unique values and only overrides them if this in not the case (305).read_raster() now reads values into memory and removes
VRT files on-exit (311).fetch_resources() now honours both creation and
opening options (315)httr calls are replaced with the respective
httr2 equivalents (329)gfw_lossyear resource to v20240402
which entails emission data between 2000 - 2023nasa_firms resource and associated
active_fire_counts indicatormcd64a1 resource and burned_area
indicatormapme.biodiveristy now leverages GDAL for data I/O
meaning that all GDAL readable source data sets and writable
destinations are now supportedREADME.md now includes a section on how to set up
cloud-storages to use as a destination for resource datawrite_portfolio() now again serializes to a two-table
GeoPackage and re-introduces read_portfolio() (294)datetime column values are now encoded as
POSIXctmake_footprints() to ease the process of
creating footprints for resource functionsspds_exists() for resource function to check if
a data source is existsget_*() functions are now required to return footprint
objects indicating the spatial extent of each elements and pointing
towards a GDAL readable data source in the source
columngdal_translate to write data from source to
destinationtbl_dfget_gfw_emissions()get_chirps() now allows to specify the years for which
to download CHIRPS resourcescalc_precipitation_chirps() now only returns
precipitation sumsactive_fire_properties since
resources can now be retrieved using prep_resources() (see
below)prep_resources() to prepare resources for
single assetsportfolio_long() and
portfolio_wide() to automatically unnest indicator columns
and change the data layout to either long or widewrite_portfolio() to serialize
portfolios to GDAL supported spatial formats in either long or wide
format and deprecates read_portfolio()chunk_size to
mapme_options() to control the size for which polygons are
split and processed in chunks'MULTIPOLYGON' and automatically
combines the results based on an aggregation functionportfolio_long() instead of
tidyr::unnest()datetime, variable, unit and
valuechirps and nasa_grace resources
updatedmapme_check_connection (262)gfw_treecover and gfw_lossyear resources
updated to v1.11 (277,
@fBedecarrats)gfw_lossyear layer (273)curl, stringr, and
tidyselect as dependenciesprogressr and rvest from
Imports to SuggestsSPEI from Suggestsavailable_resources() and
available_indicators()mapme_options() to add fine-control of the
packages behaviourinit_portfolio() in favour of
mapme_options()check_available_years()check_namespace()download_or_skip()check_engine()check_stats()select_engine()make_global_grid()unzip_and_remove()st_make_valid() from
.read_vector().The argument add_resources to
init_portfolio() is deprecated. This means that
get_resources() has to be run in every new R session to
make resource available for further processing (219).
Rasters are now cropped to the spatial extent of an asset with
setting snap="out", thus delivering a slightly bigger
extent (212).
Speed improvements for GFW indicators (up to x10 for larger
rasters) now require R package exactextractr to be
installed. Also, it is advised to have the R package
landscapemetrics installed to gain the full computation
speed improvement.
calc_indicators() checks for 0-length tibbles (196,
199,
215)..read_raster_source() now uses a simplified logic to
cover all cases (e.g. single tiles, tiled rasters with and without
temporal dimension, single temporal rasters) (211).snap="out" by default (212)..read_raster_source() now projects assets in case their
CRS differs from the portfolio (213).sf objects instead of being written to disk
(219)..read_raster_source() now applies a precision
round-trip of 5 decimal point to match rasters with slight changes in
their spatial extent (217).register_resource() and
register_indicator() now issue warnings for
resources/indicators with names already registered and overwrites them
(220).added new resource called ucdp_ged providing a
database of violent conflict from 1989 to today
added a new indicator called fatalities aggregating
number of deaths by type of conflict on a monthly time scale based on
the ucdp_ged resource.
Added a new resource called fritz_et_al providing a
raster layer of deforestation
added a new resource called fritz_et_al providing a
raster layer of deforestation drivers in tropical forests based on Fritz
et al. (2022)
added a new indicator called deforestation_drivers
using the fritz_et_al resource to obtain information on the
absolute and relative area driving forest losses in assets for the
period 2008-2019
added two new exported functions register_resource()
and register_indicator() which allow users to register
custom functions for resources/indicators
added a new vignette for the web-version of the package only informing about how to obtain wide-output from indicators
added a new vignette for the web-version for a custom analysis of the NASA FIRMS resource in the example section
added the data for years 2017-2020 to the Global Mangrove Watch resource
Changed the parallel backend to the future package. Parallel processing is now implemented by furrr::future_map() on the asset level within the calc_indicators() function. User code is now required to set up a plan() to enable parallel processing. The function call needs to be wrapped on the user side with progressr::with_progress() to show a progress bar.
mapme.biodiversity no longer sets terra’s temporal directory for
you. Instead you have to call terra::terraOptions()
manually
esalandcover indicator now returns the value per each
land cover class exactly once (177)disabled running examples on CRAN
disabled tests for get_* functions on CRAN
terra engines now use get() to resolve
the requested zonal statistic function
applying tidyverse coding style to existing code (156, @karpfen)
extensive re-factoring of vector-raster zonal statistic engines (150)
extensive re-writing of testing infrastructure for indicator functions omitting the usage of snapshot tests as far as possible (142)
rundir and todisk arguments removed
from indicator functions since they were of no practical use
instead of a resource and indicator backlog, resources and indicators are now registered to .pkgenv and queried there during runtime. This also allows users to register custom resources/indicator functions
removed deprecation warnings for old resource/indicator name
on MacOS s2-based calculations are now enabled so users can expect the package to return numerically equivalent results on any operating system (131)
the online source for the nasa_srtm resource shows
an expired SSL certificate since November 2022. The
get_resources() function now includes an error and
instructions how to disable SSL certification at a users own risk. The
websites maintainers have been contacted and asked to renew the
certification. (131)
GFW resources are now updated to use the latest version allowing analysis for the additional year of 2021 (123, @fBedecarrats)
GFW indicators now accept numeric min_size argument
allowing to specify fractional covers (110)
fire indicators now allow the simultaneous calculation of indicators based on MODIS and VIIRS. Before users had to chose between one of the instruments for each analysis (126)
case when one or multiple assets return NA instead of a tibble is now properly tested and handled (101)
Rasters are no longer temporary written to disk to omit a bug caused by applying mask/classify to an already existing raster file (108, @Jo-Schie)
Bug with soilproperties set to NA caused by the function to return a data.frame instead of a tibble was fixed (116)
both, treecoverloss_emissions and
treecover_area_and_emissions now return 0 instead of NaN
for observation years where now forest loss occurred (120)
.make_global_grid() now specifies the CRS when
constructing the bounding box and returns the grid in the specified CRS
instead of Lat/Lon (113)
.calc_active_fire_properties now uses st_coordinates
to retrieve locations of fires (119,
@DavisVaughan)
tests for MacOS have been re-enabled (131)
tests for downloading nasa_srtm resource are skipped
because the SSL certificate of the online source has expired (131)
extensive renaming of resources and indicators. These are handled gracefully until the next release (i.e. a warning is issued and names are replaced):
resources:
treecover2000 ->
gfw_treecover
lossyear -> gfw_lossyear
greenhouse -> gfw_emissions
traveltime -> nelson_et_al
nasagrace -> nasa_grace
mintemperature ->
worldclim_min_temperature
maxtemperature ->
worldclim_max_temperature
precipitation ->
worldclim_precipitation
ecoregions -> teow
mangrove -> gmw
srtmdem -> nasa_srtm
indicators:
treecover -> treecover_area
emissions ->
treecoverloss_emissions
treeloss ->
treecover_area_and_emissions
chirpsprec ->
precipitation_chirps
accessibility -> traveltime
popcount ->
population_count
wctmin ->
temperature_min_wc
wctmax ->
temperature_max_wc
wcprec -> precipitation_wc
gmw -> mangroves_area
teow -> ecoregion
init_portfolio() now sets the testing
attribute to FALSE by default.get_<resource>() functions now return filenames
early if testing is set to TRUE.calc_<indicator>() examples now copy files to the
R temporal directory and are wrapped in try() to avoid
errors/warnings on CRAN if an internet resource is not available.calc_tri() and
calc_elevation() are now disabled on CRAN because of the
responsiveness of CIGAR servers.NEWS.md file to track changes to the
package.init_portfolio() is used to initialize a portfolio
object. The input must be an sf object where all geometries are of type
POLYGONget_resources()calc_indicators()write_portfolio()read_portfolio(). If users wish to download additional
resources or calculate indicators, init_portfolio() has to
be called again.
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