calc_fatalities_ucdp() now returns a sparse timeseries, e.g. asset-months with now fatalities are omitted.
Bug fixes
fixes portfolio_wide() throwing an error when single assets with NULL values are present
calc_mangroves_area() returned NULL if invalid geometries were encountered Now it tries to repair geometries and return the area of valid geometries (#375)
Internal
.get_intersection() now assumes both x andtindex to be represented by oriented rings on the sphere (#378)
mapme.biodiversity 0.9.1
General
new resources:
get_accessibility_2000() (#365, @fBedecarrats)
new indicators:
calc_traveltime_2000() (#365, @fBedecarrats)
Internal
adjusts test for get_gsw_timseries() andcalc_gsw_timeseries() to write to temporal directory of the R session to fix CRAN errors (#370, @karpfen)
mapme.biodiversity 0.9.0
General
prep_resources() received additional argumentmode 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)
fixes transforming asset to the CRS of raster dataset incalc_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)
uses binary writing mode for worldpop resource on Windows (#319)
Internal
.check_portfolio() now checks if assetidhas 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 honors both creation and opening options (#315)
httr calls are replaced with the respectivehttr2 equivalents (#329)
mapme.biodiversity 0.8.0
General
updates gfw_lossyear resource to v20240402which entails emission data between 2000 - 2023
removes the nasa_firms resource and associatedactive_fire_counts indicator
adds mcd64a1 resource and burned_areaindicator
mapme.biodiveristy now leverages GDAL for data I/O meaning that all GDAL readable source data sets and writable destinations are now supported
README.md now includes a section on how to set up cloud-storages to use as a destination for resource data
The quickstart vignette now uses GFW data as example data
chunking is now applied based on the area of an assets bounding box instead of its own area
write_portfolio() now again serializes to a two-table GeoPackage and re-introduces read_portfolio() (#294)
datetime column values are now encoded asPOSIXct
Internal
exports make_footprints() to ease the process of creating footprints for resource functions
exports spds_exists() for resource function to check if a data source is exists
get_*() 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 sourcecolumn
in case a user-specified destination is found, the package now usesgdal_translate to write data from source to destination
tests for long-running examples and tests are skipped on GA and CRAN
fixes a bug in checking if a portfolio inherits fromtbl_df
mapme.biodiversity 0.7.0
Bug fixes
fixes bug with wrong tile paths returned byget_gfw_emissions()
Breaking changes
introduces a standardized output format for indicators, see #240 for more information
get_chirps() now allows to specify the years for which to download CHIRPS resources
calc_precipitation_chirps() now only returns precipitation sums
deprecation of indicator active_fire_properties since resources can now be retrieved using prep_resources() (see below)
General
exports prep_resources() to prepare resources for single assets
exports portfolio_long() andportfolio_wide() to automatically un-nest indicator columns and change the data layout to either long or wide
changes the behavior of write_portfolio() to serialize portfolios to GDAL supported spatial formats in either long or wide format and deprecates read_portfolio()
introduces option chunk_size tomapme_options() to control the size for which polygons are split and processed in chunks
allows assets of type 'MULTIPOLYGON' and automatically combines the results based on an aggregation function
indicator examples now use portfolio_long() instead oftidyr::unnest()
Internal
indicator functions must now return tibbles with columns nameddatetime, variable, unit andvalue
inner-level indicator functions must now specify a statistic for aggregation of chunks
chirps and nasa_grace resources updated
check for internet connectivity can now be disabled via environment variable mapme_check_connection (#262)
gfw_treecover and gfw_lossyear resources updated to v1.11 (#277, @fBedecarrats)
GFW indicators now automatically detect the maximum years based on the gfw_lossyear layer (#273)
drops curl, stringr, andtidyselect as dependencies
moves progressr and rvest fromImports to Suggests
drops SPEI from Suggests
mapme.biodiversity 0.6.0
Breaking changes
introduces a new UI based on closures for resources and indicators, see #240 for more information
General
improves output of available_resources() andavailable_indicators()
introduces mapme_options() to add fine-control of the packages behaviour
deprecates init_portfolio() in favor ofmapme_options()
exports helper functions for third parties to extend the package for custom resources and indicators:
check_available_years()
check_namespace()
download_or_skip()
check_engine()
check_stats()
select_engine()
make_global_grid()
unzip_and_remove()
New features
added Global Surface Water resources and respective indicators (#235, @karpfen)
Internal
removed st_make_valid() from.read_vector().
mapme.biodiversity 0.5.0
General
Quickstart vignette uses the WorldPop resource instead of CHIRPS, not relying on a working internet connection (#230).
New features
GFW resources and indicators include latest GFC-2022-v1.10 version (#203).
Raster resources with a CRS different from WGS84 are now supported (#213).
Breaking changes
The argument add_resources toinit_portfolio() is deprecated. This means thatget_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 packagelandscapemetrics installed to gain the full computation speed improvement.
Bug Fixes
calc_indicators() checks for 0-length tibbles (#196, #199, #215).
Fix bug with reading rasters with temporal dimensions (#209).
All raster cells touching a polygon are now returned (#208).
Internal
.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).
Rasters are cropped using snap="out" by default (#212).
.read_raster_source() now projects assets in case their CRS differs from the portfolio (#213).
tile indices for raster resources are now appended to the portfolio attributes as 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() andregister_indicator() now issue warnings for resources/indicators with names already registered and overwrites them (#220).
mapme.biodiversity 0.4.0
New features
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_driversusing 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
Breaking changes
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
Bug Fixes
esalandcover indicator now returns the value per each land cover class exactly once (#177)
Internal
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
mapme.biodiversity 0.3.0
Breaking changes
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. Theget_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)
New features
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)
Bug fixes
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 andtreecover_area_and_emissions now return 0 instead of NaN for observation years where now forest loss occurred (#120)
Internal
.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)
mapme.biodiversity 0.2.1
Bug fixes
fixes a serious bug that occurred for tiled resources when multiple assets are within the same tile resulting in returning the same tile multiple times
Internal
tests to catch above mentioned bug have been introduced for tiled resources
mapme.biodiversity 0.2.0
Breaking changes
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
New features
new resource(s):
nasa_firms
new indicator(s):
active_fire_properties
active_fire_counts
Internal
adapted download routine to GMW v3 (#80)
removed data.table from imports
Bug fixes
fixing issue #84 concerning intersection of tiled datasets (#86,@Jo-Schie)
mapme.biodiversity 0.1.2
Internal
unit tests have been silenced in order to be more informative for reverse dependency checks
checks for tile availability reactivated for SRTM
fixed notes due to uninitialized variables in TEOW and biome indicators
mapme.biodiversity 0.1.1
Internal
init_portfolio() now sets the testingattribute 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.
examples for calc_tri() andcalc_elevation() are now disabled on CRAN because of the responsiveness of CIGAR servers.
mapme.biodiversity 0.1.0
Breaking changes
renamed ‘.assetid’ to ‘assetid’ (#22)
New features
None
Internal
ensures that tests and examples adhere to CRAN policies of only writing to the temporal directory (#22).
mapme.biodiversity 0.0.1
Initial release
Added a NEWS.md file to track changes to the package.
initial supported resources are:
ecoregions
esalandcover
greenhouse
lossyear
mangrove
nasagrace
soilgrids
srtmdem
traveltime
treecover
worldclim
worldpop
initial supported indicators are:
acessibility
biome
chirpsprec
drought_indicator
elevation
emissions
gmw
landcover
popcount
soilproperties
teow
treecover
treeloss
tri
wcprec
wctmax
wctmin
init_portfolio() is used to initialize a portfolio object. The input must be an sf object where all geometries are of typePOLYGON
users can request the download of one or more resources viaget_resources()
users can request the processing of an indicator viacalc_indicators()
indicators are added to the portfolio object as nested list columns
a processed portfolio object can be exported as a GeoPackage viawrite_portfolio()
a portfolio saved to disk as a GeoPackage can be read back into R via read_portfolio(). If users wish to download additional resources or calculate indicators, init_portfolio() has to be called again.
Parallelization using multiple cores on the host machine is disabled on Windows
on MacOS, the s2 engine for spherical geometric vector operations is disabled and lwgeom is used instead.
Internal
Introduced absolute URLS in userguide.Rmd pointing to the online documentation (#59)
tags added to all exported functions explaining what is the output/side effect (#59)
using requireNamespace() instead of installed.packages() to check if packages listed in SUGGEST are loadable (#58)