Changelog
Source:NEWS.md
mapme.biodiversity (development version)
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:
Internal
- removed
st_make_valid()
from.read_vector()
.
mapme.biodiversity 0.5.0
CRAN release: 2024-01-08
General
- Quickstart vignette uses the WorldPop resource instead of CHIRPS, not relying on a working internet connection (#230).
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.
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
CRAN release: 2023-08-28
New features
added new resource called
ucdp_ged
providing a database of violent conflict from 1989 to todayadded a new indicator called
fatalities
aggregating number of deaths by type of conflict on a monthly time scale based on theucdp_ged
resource.Added a new resource called
fritz_et_al
providing a raster layer of deforestationadded 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 thefritz_et_al
resource to obtain information on the absolute and relative area driving forest losses in assets for the period 2008-2019added two new exported functions
register_resource()
andregister_indicator()
which allow users to register custom functions for resources/indicatorsadded 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 useget()
to resolve the requested zonal statistic functionapplying 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
andtodisk
arguments removed from indicator functions since they were of no practical useinstead 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
CRAN release: 2023-01-21
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
CRAN release: 2022-09-09
mapme.biodiversity 0.2.0
CRAN release: 2022-08-23
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
mapme.biodiversity 0.1.1
CRAN release: 2022-05-02
Internal
-
init_portfolio()
now sets thetesting
attribute to FALSE by default. -
get_<resource>()
functions now return filenames early iftesting
is set to TRUE. -
calc_<indicator>()
examples now copy files to the R temporal directory and are wrapped intry()
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
CRAN release: 2022-04-27
Breaking changes
- renamed ‘.assetid’ to ‘assetid’ (#22)
Internal
- ensures that tests and examples adhere to CRAN policies of only writing to the temporal directory (#22).
mapme.biodiversity 0.0.1
CRAN release: 2022-04-19
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 via
get_resources()
- users can request the processing of an indicator via
calc_indicators()
- indicators are added to the portfolio object as nested list columns
- a processed portfolio object can be exported as a GeoPackage via
write_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.