From 5423e54814e7038d72fcdf00871602714ff77d69 Mon Sep 17 00:00:00 2001 From: goergen95 Date: Tue, 27 Aug 2024 11:27:10 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20mapme-in?= =?UTF-8?q?itiative/mapme.indicators@2b12798f17f3fc86a744b8e9c38107901d853?= =?UTF-8?q?300=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- index.html | 4 ++++ pkgdown.yml | 2 +- search.json | 2 +- 3 files changed, 6 insertions(+), 2 deletions(-) diff --git a/index.html b/index.html index 5ba85a2..e728d1d 100644 --- a/index.html +++ b/index.html @@ -48,6 +48,10 @@

mapme.indicators

+
+

[!IMPORTANT]
+This respository is now ARCHIVED. Resource and indicator functions have been transferred to mapme.biodiversity.

+

Introduction

diff --git a/pkgdown.yml b/pkgdown.yml index 733d487..2a7f055 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 3.1.11 pkgdown: 2.1.0 pkgdown_sha: ~ articles: {} -last_built: 2024-08-27T04:13Z +last_built: 2024-08-27T11:27Z urls: reference: https://mapme-initiative.github.io/mapme.indicators/reference article: https://mapme-initiative.github.io/mapme.indicators/articles diff --git a/search.json b/search.json index 046651e..9ea6c8a 100644 --- a/search.json +++ b/search.json @@ -1 +1 @@ -[{"path":"https://mapme-initiative.github.io/mapme.indicators/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2023 mapme.indicators authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Darius . Görgen. Author, maintainer.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Görgen D (2024). mapme.indicators: Extension resources indicators mapme.biodiversity. R package version 0.0.4.9002.","code":"@Manual{, title = {mapme.indicators: Extension resources and indicators for mapme.biodiversity}, author = {Darius A. Görgen}, year = {2024}, note = {R package version 0.0.4.9002}, }"},{"path":[]},{"path":"https://mapme-initiative.github.io/mapme.indicators/index.html","id":"introduction","dir":"","previous_headings":"","what":"Introduction","title":"Extension resources and indicators for mapme.biodiversity","text":"package currently work--progress. going used develop new resources/indicators mapme.biodiversity undergoing number functionality changes. learn ongoing changes current status, please visit announcement issue. branch seeing links mapme.biodiversity v0.8.0. update resource/indicator functions developed new version released. reaching milestones mapme.biodiversity, decide whether move resources/indicators developed main package resources/indicators moved .","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Extension resources and indicators for mapme.biodiversity","text":"Please run following code install required packages:","code":"remotes::install_version(\"mapme.biodiversity\", version = \"0.8.0\") remotes::install_github(\"mapme-initiative/mapme.indicators\")"},{"path":"https://mapme-initiative.github.io/mapme.indicators/index.html","id":"resources-and-indicators","dir":"","previous_headings":"","what":"Resources and Indicators","title":"Extension resources and indicators for mapme.biodiversity","text":"package adds new resources indicators. ready--use workflow based  mapme.biodiversity. package loaded R session via library(mapme.indicators), new resources associated indicators registered available workflows. table gives overview implemented planned resources/indicators:","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/biodiversity_intactness_index.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Biodiversity Intactness Index — biodiversity_intactness_index","title":"Calculate Biodiversity Intactness Index — biodiversity_intactness_index","text":"function calculates mean biodiversity intactness index region. variable modeled average abundance originally-present species, relative abundance intact ecosystem. Please refer Newbold et al. (2016) details, please cite using data.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/biodiversity_intactness_index.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Biodiversity Intactness Index — biodiversity_intactness_index","text":"","code":"calc_biodiversity_intactness_index() get_biodiversity_intactness_index(path = NULL)"},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/biodiversity_intactness_index.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Calculate Biodiversity Intactness Index — biodiversity_intactness_index","text":"function returning tibble aggregated biodiversity intactness index.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/biodiversity_intactness_index.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Calculate Biodiversity Intactness Index — biodiversity_intactness_index","text":"https://data.nhm.ac.uk/dataset/global-map---biodiversity-intactness-index--newbold-et-al-2016-science","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/biodiversity_intactness_index.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Biodiversity Intactness Index — biodiversity_intactness_index","text":"path character vector biodiversity intactness index ASCII file.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/biodiversity_intactness_index.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Biodiversity Intactness Index — biodiversity_intactness_index","text":"function returns character vector file paths.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/biodiversity_intactness_index.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate Biodiversity Intactness Index — biodiversity_intactness_index","text":"required resources indicator : biodiversity_intactness_index use data mapme workflows, manually download global data set point towards file path local machine. Please find available data source link given .","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/biodiversity_intactness_index.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate Biodiversity Intactness Index — biodiversity_intactness_index","text":"Tim Newbold; Lawrence Hudson; Andy Arnell; Sara Contu et al. (2016). Global map Biodiversity Intactness Index, Newbold et al. (2016) Science [Data set]. Natural History Museum. doi:10.5519/0009936","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_indicators.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate carbon statistics — carbon_indicators","title":"Calculate carbon statistics — carbon_indicators","text":"functions allow calculated statistics based harmonized carbon layers 2010 2018 Noon et al. (2022).","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_indicators.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate carbon statistics — carbon_indicators","text":"","code":"calc_irr_carbon( type = c(\"total\", \"soil\", \"biomass\", \"all\"), engine = \"extract\", stats = \"mean\" ) calc_man_carbon( type = c(\"total\", \"soil\", \"biomass\", \"all\"), engine = \"extract\", stats = \"mean\" ) calc_vul_carbon( type = c(\"total\", \"soil\", \"biomass\", \"all\"), engine = \"extract\", stats = \"mean\" )"},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_indicators.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate carbon statistics — carbon_indicators","text":"type One \"total\", \"soil\", \"biomass\", \"\". Determines data layer statistics calculated. engine preferred processing functions either one \"zonal\", \"extract\" \"exactextract\" character. stats Function applied compute statistics polygons either one multiple inputs character. Supported statistics : \"mean\", \"median\", \"sd\", \"min\", \"max\", \"sum\", \"var\".","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_indicators.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate carbon statistics — carbon_indicators","text":"function returns tibble column statistic rows every year type carbon.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_indicators.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate carbon statistics — carbon_indicators","text":"required resources indicators : carbon_resources Irrecoverable carbon amount carbon , lost today, recovered 2050. can calculated - -ground carbon, total amount carbon, layers. Manageable carbon amount carbon , principle, manageable human activities, e.g. release atmosphere can prevented. can calculated - -ground carbon, total amount carbon, layers. Vulnerable carbon amount carbon released typical land conversion activity. can calculated - -ground carbon, total amount carbon, layers.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_resources.html","id":null,"dir":"Reference","previous_headings":"","what":"Carbon Layers — carbon_resources","title":"Carbon Layers — carbon_resources","text":"resource part publication Noon et al. (2022) \"Mapping irrecoverable carbon Earth’s ecosystems\". publication differentiates 3 different kinds carbon varying degrees manageability humans. three layers available ground carbon, well layer combining two.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_resources.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Carbon Layers — carbon_resources","text":"","code":"get_irr_carbon() get_vul_carbon() get_man_carbon()"},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_resources.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Carbon Layers — carbon_resources","text":"https://zenodo.org/records/4091029","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_resources.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Carbon Layers — carbon_resources","text":"function returns character vector file paths.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_resources.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Carbon Layers — carbon_resources","text":"may required increase timeout option successfully download theses layers source location via e.g. options(timeout = 600). Irrecoverable carbon defined amount carbon, , lost today, recovered mid 21st century (within 30 years, considering publication date). Vulnerable carbon defined amount carbon lost hypothetical typical conversion event (without including information probability event actually occurring). Manageable carbon defined land areas, expect cyrosols, carbon loss driven direct land-use conversion halted climate change impacts affecting area can potentially directly mitigated adaptive management.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_resources.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Carbon Layers — carbon_resources","text":"Noon, M.L., Goldstein, ., Ledezma, J.C. et al. Mapping irrecoverable carbon Earth’s ecosystems. Nat Sustain 5, 37–46 (2022). https://doi.org/10.1038/s41893-021-00803-6","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/gsw_time_series.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Global Surface Water Time Series — gsw_time_series","title":"Calculate Global Surface Water Time Series — gsw_time_series","text":"function calculates total area global surface water time series data, separated following classes: function constructs necessary data URLs given data set, version polygon downloads processing mapme.biodiversity package.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/gsw_time_series.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Global Surface Water Time Series — gsw_time_series","text":"","code":"calc_gsw_time_series(years = 1984:2021) get_gsw_time_series(years, version = \"LATEST\")"},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/gsw_time_series.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Calculate Global Surface Water Time Series — gsw_time_series","text":"function returning tibble time series global surface water data classes.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/gsw_time_series.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Calculate Global Surface Water Time Series — gsw_time_series","text":"Raw Data: https://jeodpp.jrc.ec.europa.eu/ftp/jrc-opendata/GSWE/YearlyClassification/LATEST/tiles/","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/gsw_time_series.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Global Surface Water Time Series — gsw_time_series","text":"years Numeric vector years process 1984 2021. Default: 1984:2021. version Version data set process. Available options (VER1-0, VER2-0, VER3-0, VER4-0, VER5-0 LATEST) Default: LATEST. Choosing LATEST result latest available version.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/gsw_time_series.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Global Surface Water Time Series — gsw_time_series","text":"function returns character vector file paths.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/gsw_time_series.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate Global Surface Water Time Series — gsw_time_series","text":"Observation: possible determine whether pixel water (may case frozen areas polar night extreme latitudes). Permanent Water: Water detected twelve months per year combination permanent observation. Seasonal Water: Water water detected. Water: Water detected. required resources indicator : gsw_time_series available surface water classes given pixel following: Observation: possible determine whether pixel water (may case frozen areas polar night extreme latitudes). Permanent Water: Water detected twelve months per year combination permanent observation. Seasonal Water: Water water detected. Water: Water detected.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/gsw_time_series.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate Global Surface Water Time Series — gsw_time_series","text":"Global Surface Water Explorer: https://global-surface-water.appspot.com/ Data Users Guide: https://storage.cloud.google.com/global-surface-water/downloads_ancillary/DataUsersGuidev2021.pdf Research Article: https://www.nature.com/articles/nature20584","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/humanfootprint.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate human footprint statistics — humanfootprint","title":"Calculate human footprint statistics — humanfootprint","text":"Human footprint data measures pressure imposed natural environment different dimensions human actions. theoretical maximum value, representing highest level human pressure, 50. routine allows extract zonal statistics human footprint data. resource part publication Mu et al. (2022) \"global record annual terrestrial Human Footprint dataset 2000 2018\". calculated based 8 variables representing human pressures natural ecosystems collected yearly cadence 2000 2020 sampled 1km spatial resolution. variables used expansion built environments (expressed percentage built-areas within grid cell), population density (aggregated gridd cell), nighttime lights, crop pasture lands, roads railways (excluding trails minor roads), navigable waterways (compares waterways nighttime lights dataset). human footprint calculated based weighting scheme proposed Venter et al. (2016), assigning pixel value 0 50, 50 representing theoretical value highest human pressure.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/humanfootprint.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate human footprint statistics — humanfootprint","text":"","code":"calc_humanfootprint(engine = \"extract\", stats = \"mean\") get_humanfootprint(years = 2000:2020)"},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/humanfootprint.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Calculate human footprint statistics — humanfootprint","text":"https://figshare.com/articles/figure/An_annual_global_terrestrial_Human_Footprint_dataset_from_2000_to_2018/16571064","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/humanfootprint.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate human footprint statistics — humanfootprint","text":"engine preferred processing functions either one \"zonal\", \"extract\" \"exactextract\" character. stats Function applied compute statistics polygons either one multiple inputs character. Supported statistics : \"mean\", \"median\", \"sd\", \"min\", \"max\", \"sum\" \"var\". years numeric vector indicating years download human footprint data, defaults 2000:2020.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/humanfootprint.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate human footprint statistics — humanfootprint","text":"function returns tibble column statistic row every requested year. function returns character vector file paths.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/humanfootprint.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate human footprint statistics — humanfootprint","text":"required resources indicator : humanfootprint may required increase timeout option successfully download theses layers source location via e.g. options(timeout = 600).","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/humanfootprint.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate human footprint statistics — humanfootprint","text":"Mu, H., Li, X., Wen, Y. et al. global record annual terrestrial Human Footprint dataset 2000 2018. Sci Data 9, 176 (2022). doi:10.1038/s41597-022-01284-8","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/ipbes.html","id":null,"dir":"Reference","previous_headings":"","what":"Terrestrial and Aquatic Biomes — ipbes","title":"Terrestrial and Aquatic Biomes — ipbes","text":"resource part Global Assessment Report Biodiversity Ecosystem Services represents division Earth's surface several subcategories. classification differentiates biomes anthromes. Biomes differentiated terrestrial aquatic biomes.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/ipbes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Terrestrial and Aquatic Biomes — ipbes","text":"","code":"get_ipbes_biomes()"},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/ipbes.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Terrestrial and Aquatic Biomes — ipbes","text":"https://zenodo.org/records/3975694","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/ipbes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Terrestrial and Aquatic Biomes — ipbes","text":"function returns character vector file paths.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/ipbes.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Terrestrial and Aquatic Biomes — ipbes","text":"Terrestrial biomes include: Tropical subtropical dry humid forests Temperate boreal forests woodlands Mediterranean forests, woodlands scrub Tundra High Mountain habitats Tropical subtropical savannas grasslands Temperate Grasslands Deserts xeric shrublands Wetlands – peatlands, mires, bogs Aquatic biomes include: Cryosphere Aquaculture areas Inland surface waters water bodies/freshwater Shelf ecosystems (neritic intertidal/littoral zone) Open ocean pelagic systems (euphotic zone)","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/ipbes.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Terrestrial and Aquatic Biomes — ipbes","text":"IPBES (2019): Summary policymakers global assessment report biodiversity ecosystem services Intergovernmental Science-Policy Platform Biodiversity Ecosystem Services. S. Díaz, J. Settele, E. S. Brondízio, H. T. Ngo, M. Guèze, J. Agard, . Arneth, P. Balvanera, K. . Brauman, S. H. M. Butchart, K. M. . Chan, L. . Garibaldi, K. Ichii, J. Liu, S. M. Subramanian, G. F. Midgley, P. Miloslavich, Z. Molnár, D. Obura, . Pfaff, S. Polasky, . Purvis, J. Razzaque, B. Reyers, R. Roy Chowdhury, Y. J. Shin, . J. Visseren-Hamakers, K. J. Willis, C. N. Zayas (eds.). IPBES secretariat, Bonn, Germany. 56 pages. https://doi.org/10.5281/zenodo.3553579","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/ipbes_biome_stats.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate areal statistics for IBPES Biomes — ipbes_biome_stats","title":"Calculate areal statistics for IBPES Biomes — ipbes_biome_stats","text":"indicator calculates areal distribution different biome classes within asset based IBPES biomes dataset.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/ipbes_biome_stats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate areal statistics for IBPES Biomes — ipbes_biome_stats","text":"","code":"calc_ipbes_biomes()"},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/ipbes_biome_stats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate areal statistics for IBPES Biomes — ipbes_biome_stats","text":"function returns tibble columns class name, absolute relative coverage within asset.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/ipbes_biome_stats.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate areal statistics for IBPES Biomes — ipbes_biome_stats","text":"required resources indicator : ipbes","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/iucn.html","id":null,"dir":"Reference","previous_headings":"","what":"IUCN Red List of Threatened Species — iucn","title":"IUCN Red List of Threatened Species — iucn","text":"resource part spatial data set Red List Threatened Species released IUCN. free use non-commercial licence. commercial uses, request sent Integrated Biodiversity Assessment Tool (IBAT).","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/iucn.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"IUCN Red List of Threatened Species — iucn","text":"","code":"get_iucn(paths = NULL)"},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/iucn.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"IUCN Red List of Threatened Species — iucn","text":"https://www.iucnredlist.org/resources/-spatial-downloads","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/iucn.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"IUCN Red List of Threatened Species — iucn","text":"paths character vector respective species range files GTiff format. Note, theses files downloaded manually.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/iucn.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"IUCN Red List of Threatened Species — iucn","text":"function returns sf footprint object.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/iucn.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"IUCN Red List of Threatened Species — iucn","text":"use data mapme workflows, manually download global data set point towards file path local machine. Please find available data source link given .","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/iucn.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"IUCN Red List of Threatened Species — iucn","text":"IUCN (2024). IUCN Red List Threatened Species. https://www.iucnredlist.org. doi:10.1038/s41597-022-01284-8","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/key_biodiversity_areas.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Key Biodiversity Areas — key_biodiversity_areas","title":"Calculate Key Biodiversity Areas — key_biodiversity_areas","text":"function calculates total area key biodiversity areas given input polygon. variable contains outlines key biodiversity areas. areas represent sites specific importance nature conservation efforts.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/key_biodiversity_areas.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Key Biodiversity Areas — key_biodiversity_areas","text":"","code":"calc_key_biodiversity_area() get_key_biodiversity_areas(path = NULL)"},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/key_biodiversity_areas.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Calculate Key Biodiversity Areas — key_biodiversity_areas","text":"function returning tibble key biodiversity area overlap","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/key_biodiversity_areas.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Calculate Key Biodiversity Areas — key_biodiversity_areas","text":"https://www.keybiodiversityareas.org/kba-data","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/key_biodiversity_areas.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Key Biodiversity Areas — key_biodiversity_areas","text":"path character vector key biodiversity areas gpkg file. Note, file downloaded manually.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/key_biodiversity_areas.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Key Biodiversity Areas — key_biodiversity_areas","text":"function returns character vector file paths.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/key_biodiversity_areas.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate Key Biodiversity Areas — key_biodiversity_areas","text":"required resources indicator : key_biodiversity_areas use data mapme workflows, manually download global data set point towards file path local machine. Please find available data source link given .","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/key_biodiversity_areas.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate Key Biodiversity Areas — key_biodiversity_areas","text":"BirdLife International (2024). World Database Key Biodiversity Areas. Developed KBA Partnership: BirdLife International, International Union Conservation Nature, Amphibian Survival Alliance, Conservation International, Critical Ecosystem Partnership Fund, Global Environment Facility, Re:wild, NatureServe, Rainforest Trust, Royal Society Protection Birds, Wildlife Conservation Society World Wildlife Fund. Available www.keybiodiversityareas.org.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/species_richness.html","id":null,"dir":"Reference","previous_headings":"","what":"Species richness based on IUCN raster data — species_richness","title":"Species richness based on IUCN raster data — species_richness","text":"Species richness counts number potential species intersecting polygon grouped IUCN threat categorization. Note, indicator function requires manual download respective raster files.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/species_richness.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Species richness based on IUCN raster data — species_richness","text":"","code":"calc_species_richness(engine = \"extract\", stats = \"mean\")"},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/species_richness.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Species richness based on IUCN raster data — species_richness","text":"engine preferred processing functions either one \"zonal\", \"extract\" \"exactextract\" character. stats Function applied compute statistics polygons either one multiple inputs character. Supported statistics : \"mean\", \"median\", \"sd\", \"min\", \"max\", \"sum\" \"var\".","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/species_richness.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Species richness based on IUCN raster data — species_richness","text":"function returns indicator tibble IUCN layers specified statistics variable respective values value.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/species_richness.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Species richness based on IUCN raster data — species_richness","text":"specific meaning species richness indicator depends supplied raster file. required resources indicator : iucn","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/news/index.html","id":"mapmeindicators-development-version","dir":"Changelog","previous_headings":"","what":"mapme.indicators (development version)","title":"mapme.indicators (development version)","text":"carbon statistics now calculated based carbon per pixel instead area fixes bug get_hfp() re-downloaded resources even present datetime extraction carbon, species_richness humanfootprint extraction robust","code":""}] +[{"path":"https://mapme-initiative.github.io/mapme.indicators/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2023 mapme.indicators authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Darius . Görgen. Author, maintainer.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Görgen D (2024). mapme.indicators: Extension resources indicators mapme.biodiversity. R package version 0.0.4.9002.","code":"@Manual{, title = {mapme.indicators: Extension resources and indicators for mapme.biodiversity}, author = {Darius A. Görgen}, year = {2024}, note = {R package version 0.0.4.9002}, }"},{"path":"https://mapme-initiative.github.io/mapme.indicators/index.html","id":"mapmeindicators","dir":"","previous_headings":"","what":"Extension resources and indicators for mapme.biodiversity","title":"Extension resources and indicators for mapme.biodiversity","text":"[!IMPORTANT] respository now ARCHIVED. Resource indicator functions transferred mapme.biodiversity.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/index.html","id":"introduction","dir":"","previous_headings":"","what":"Introduction","title":"Extension resources and indicators for mapme.biodiversity","text":"package currently work--progress. going used develop new resources/indicators mapme.biodiversity undergoing number functionality changes. learn ongoing changes current status, please visit announcement issue. branch seeing links mapme.biodiversity v0.8.0. update resource/indicator functions developed new version released. reaching milestones mapme.biodiversity, decide whether move resources/indicators developed main package resources/indicators moved .","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Extension resources and indicators for mapme.biodiversity","text":"Please run following code install required packages:","code":"remotes::install_version(\"mapme.biodiversity\", version = \"0.8.0\") remotes::install_github(\"mapme-initiative/mapme.indicators\")"},{"path":"https://mapme-initiative.github.io/mapme.indicators/index.html","id":"resources-and-indicators","dir":"","previous_headings":"","what":"Resources and Indicators","title":"Extension resources and indicators for mapme.biodiversity","text":"package adds new resources indicators. ready--use workflow based  mapme.biodiversity. package loaded R session via library(mapme.indicators), new resources associated indicators registered available workflows. table gives overview implemented planned resources/indicators:","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/biodiversity_intactness_index.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Biodiversity Intactness Index — biodiversity_intactness_index","title":"Calculate Biodiversity Intactness Index — biodiversity_intactness_index","text":"function calculates mean biodiversity intactness index region. variable modeled average abundance originally-present species, relative abundance intact ecosystem. Please refer Newbold et al. (2016) details, please cite using data.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/biodiversity_intactness_index.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Biodiversity Intactness Index — biodiversity_intactness_index","text":"","code":"calc_biodiversity_intactness_index() get_biodiversity_intactness_index(path = NULL)"},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/biodiversity_intactness_index.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Calculate Biodiversity Intactness Index — biodiversity_intactness_index","text":"function returning tibble aggregated biodiversity intactness index.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/biodiversity_intactness_index.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Calculate Biodiversity Intactness Index — biodiversity_intactness_index","text":"https://data.nhm.ac.uk/dataset/global-map---biodiversity-intactness-index--newbold-et-al-2016-science","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/biodiversity_intactness_index.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Biodiversity Intactness Index — biodiversity_intactness_index","text":"path character vector biodiversity intactness index ASCII file.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/biodiversity_intactness_index.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Biodiversity Intactness Index — biodiversity_intactness_index","text":"function returns character vector file paths.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/biodiversity_intactness_index.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate Biodiversity Intactness Index — biodiversity_intactness_index","text":"required resources indicator : biodiversity_intactness_index use data mapme workflows, manually download global data set point towards file path local machine. Please find available data source link given .","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/biodiversity_intactness_index.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate Biodiversity Intactness Index — biodiversity_intactness_index","text":"Tim Newbold; Lawrence Hudson; Andy Arnell; Sara Contu et al. (2016). Global map Biodiversity Intactness Index, Newbold et al. (2016) Science [Data set]. Natural History Museum. doi:10.5519/0009936","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_indicators.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate carbon statistics — carbon_indicators","title":"Calculate carbon statistics — carbon_indicators","text":"functions allow calculated statistics based harmonized carbon layers 2010 2018 Noon et al. (2022).","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_indicators.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate carbon statistics — carbon_indicators","text":"","code":"calc_irr_carbon( type = c(\"total\", \"soil\", \"biomass\", \"all\"), engine = \"extract\", stats = \"mean\" ) calc_man_carbon( type = c(\"total\", \"soil\", \"biomass\", \"all\"), engine = \"extract\", stats = \"mean\" ) calc_vul_carbon( type = c(\"total\", \"soil\", \"biomass\", \"all\"), engine = \"extract\", stats = \"mean\" )"},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_indicators.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate carbon statistics — carbon_indicators","text":"type One \"total\", \"soil\", \"biomass\", \"\". Determines data layer statistics calculated. engine preferred processing functions either one \"zonal\", \"extract\" \"exactextract\" character. stats Function applied compute statistics polygons either one multiple inputs character. Supported statistics : \"mean\", \"median\", \"sd\", \"min\", \"max\", \"sum\", \"var\".","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_indicators.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate carbon statistics — carbon_indicators","text":"function returns tibble column statistic rows every year type carbon.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_indicators.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate carbon statistics — carbon_indicators","text":"required resources indicators : carbon_resources Irrecoverable carbon amount carbon , lost today, recovered 2050. can calculated - -ground carbon, total amount carbon, layers. Manageable carbon amount carbon , principle, manageable human activities, e.g. release atmosphere can prevented. can calculated - -ground carbon, total amount carbon, layers. Vulnerable carbon amount carbon released typical land conversion activity. can calculated - -ground carbon, total amount carbon, layers.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_resources.html","id":null,"dir":"Reference","previous_headings":"","what":"Carbon Layers — carbon_resources","title":"Carbon Layers — carbon_resources","text":"resource part publication Noon et al. (2022) \"Mapping irrecoverable carbon Earth’s ecosystems\". publication differentiates 3 different kinds carbon varying degrees manageability humans. three layers available ground carbon, well layer combining two.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_resources.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Carbon Layers — carbon_resources","text":"","code":"get_irr_carbon() get_vul_carbon() get_man_carbon()"},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_resources.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Carbon Layers — carbon_resources","text":"https://zenodo.org/records/4091029","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_resources.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Carbon Layers — carbon_resources","text":"function returns character vector file paths.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_resources.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Carbon Layers — carbon_resources","text":"may required increase timeout option successfully download theses layers source location via e.g. options(timeout = 600). Irrecoverable carbon defined amount carbon, , lost today, recovered mid 21st century (within 30 years, considering publication date). Vulnerable carbon defined amount carbon lost hypothetical typical conversion event (without including information probability event actually occurring). Manageable carbon defined land areas, expect cyrosols, carbon loss driven direct land-use conversion halted climate change impacts affecting area can potentially directly mitigated adaptive management.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/carbon_resources.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Carbon Layers — carbon_resources","text":"Noon, M.L., Goldstein, ., Ledezma, J.C. et al. Mapping irrecoverable carbon Earth’s ecosystems. Nat Sustain 5, 37–46 (2022). https://doi.org/10.1038/s41893-021-00803-6","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/gsw_time_series.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Global Surface Water Time Series — gsw_time_series","title":"Calculate Global Surface Water Time Series — gsw_time_series","text":"function calculates total area global surface water time series data, separated following classes: function constructs necessary data URLs given data set, version polygon downloads processing mapme.biodiversity package.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/gsw_time_series.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Global Surface Water Time Series — gsw_time_series","text":"","code":"calc_gsw_time_series(years = 1984:2021) get_gsw_time_series(years, version = \"LATEST\")"},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/gsw_time_series.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Calculate Global Surface Water Time Series — gsw_time_series","text":"function returning tibble time series global surface water data classes.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/gsw_time_series.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Calculate Global Surface Water Time Series — gsw_time_series","text":"Raw Data: https://jeodpp.jrc.ec.europa.eu/ftp/jrc-opendata/GSWE/YearlyClassification/LATEST/tiles/","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/gsw_time_series.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Global Surface Water Time Series — gsw_time_series","text":"years Numeric vector years process 1984 2021. Default: 1984:2021. version Version data set process. Available options (VER1-0, VER2-0, VER3-0, VER4-0, VER5-0 LATEST) Default: LATEST. Choosing LATEST result latest available version.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/gsw_time_series.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Global Surface Water Time Series — gsw_time_series","text":"function returns character vector file paths.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/gsw_time_series.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate Global Surface Water Time Series — gsw_time_series","text":"Observation: possible determine whether pixel water (may case frozen areas polar night extreme latitudes). Permanent Water: Water detected twelve months per year combination permanent observation. Seasonal Water: Water water detected. Water: Water detected. required resources indicator : gsw_time_series available surface water classes given pixel following: Observation: possible determine whether pixel water (may case frozen areas polar night extreme latitudes). Permanent Water: Water detected twelve months per year combination permanent observation. Seasonal Water: Water water detected. Water: Water detected.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/gsw_time_series.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate Global Surface Water Time Series — gsw_time_series","text":"Global Surface Water Explorer: https://global-surface-water.appspot.com/ Data Users Guide: https://storage.cloud.google.com/global-surface-water/downloads_ancillary/DataUsersGuidev2021.pdf Research Article: https://www.nature.com/articles/nature20584","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/humanfootprint.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate human footprint statistics — humanfootprint","title":"Calculate human footprint statistics — humanfootprint","text":"Human footprint data measures pressure imposed natural environment different dimensions human actions. theoretical maximum value, representing highest level human pressure, 50. routine allows extract zonal statistics human footprint data. resource part publication Mu et al. (2022) \"global record annual terrestrial Human Footprint dataset 2000 2018\". calculated based 8 variables representing human pressures natural ecosystems collected yearly cadence 2000 2020 sampled 1km spatial resolution. variables used expansion built environments (expressed percentage built-areas within grid cell), population density (aggregated gridd cell), nighttime lights, crop pasture lands, roads railways (excluding trails minor roads), navigable waterways (compares waterways nighttime lights dataset). human footprint calculated based weighting scheme proposed Venter et al. (2016), assigning pixel value 0 50, 50 representing theoretical value highest human pressure.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/humanfootprint.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate human footprint statistics — humanfootprint","text":"","code":"calc_humanfootprint(engine = \"extract\", stats = \"mean\") get_humanfootprint(years = 2000:2020)"},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/humanfootprint.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Calculate human footprint statistics — humanfootprint","text":"https://figshare.com/articles/figure/An_annual_global_terrestrial_Human_Footprint_dataset_from_2000_to_2018/16571064","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/humanfootprint.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate human footprint statistics — humanfootprint","text":"engine preferred processing functions either one \"zonal\", \"extract\" \"exactextract\" character. stats Function applied compute statistics polygons either one multiple inputs character. Supported statistics : \"mean\", \"median\", \"sd\", \"min\", \"max\", \"sum\" \"var\". years numeric vector indicating years download human footprint data, defaults 2000:2020.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/humanfootprint.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate human footprint statistics — humanfootprint","text":"function returns tibble column statistic row every requested year. function returns character vector file paths.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/humanfootprint.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate human footprint statistics — humanfootprint","text":"required resources indicator : humanfootprint may required increase timeout option successfully download theses layers source location via e.g. options(timeout = 600).","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/humanfootprint.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate human footprint statistics — humanfootprint","text":"Mu, H., Li, X., Wen, Y. et al. global record annual terrestrial Human Footprint dataset 2000 2018. Sci Data 9, 176 (2022). doi:10.1038/s41597-022-01284-8","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/ipbes.html","id":null,"dir":"Reference","previous_headings":"","what":"Terrestrial and Aquatic Biomes — ipbes","title":"Terrestrial and Aquatic Biomes — ipbes","text":"resource part Global Assessment Report Biodiversity Ecosystem Services represents division Earth's surface several subcategories. classification differentiates biomes anthromes. Biomes differentiated terrestrial aquatic biomes.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/ipbes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Terrestrial and Aquatic Biomes — ipbes","text":"","code":"get_ipbes_biomes()"},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/ipbes.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Terrestrial and Aquatic Biomes — ipbes","text":"https://zenodo.org/records/3975694","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/ipbes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Terrestrial and Aquatic Biomes — ipbes","text":"function returns character vector file paths.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/ipbes.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Terrestrial and Aquatic Biomes — ipbes","text":"Terrestrial biomes include: Tropical subtropical dry humid forests Temperate boreal forests woodlands Mediterranean forests, woodlands scrub Tundra High Mountain habitats Tropical subtropical savannas grasslands Temperate Grasslands Deserts xeric shrublands Wetlands – peatlands, mires, bogs Aquatic biomes include: Cryosphere Aquaculture areas Inland surface waters water bodies/freshwater Shelf ecosystems (neritic intertidal/littoral zone) Open ocean pelagic systems (euphotic zone)","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/ipbes.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Terrestrial and Aquatic Biomes — ipbes","text":"IPBES (2019): Summary policymakers global assessment report biodiversity ecosystem services Intergovernmental Science-Policy Platform Biodiversity Ecosystem Services. S. Díaz, J. Settele, E. S. Brondízio, H. T. Ngo, M. Guèze, J. Agard, . Arneth, P. Balvanera, K. . Brauman, S. H. M. Butchart, K. M. . Chan, L. . Garibaldi, K. Ichii, J. Liu, S. M. Subramanian, G. F. Midgley, P. Miloslavich, Z. Molnár, D. Obura, . Pfaff, S. Polasky, . Purvis, J. Razzaque, B. Reyers, R. Roy Chowdhury, Y. J. Shin, . J. Visseren-Hamakers, K. J. Willis, C. N. Zayas (eds.). IPBES secretariat, Bonn, Germany. 56 pages. https://doi.org/10.5281/zenodo.3553579","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/ipbes_biome_stats.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate areal statistics for IBPES Biomes — ipbes_biome_stats","title":"Calculate areal statistics for IBPES Biomes — ipbes_biome_stats","text":"indicator calculates areal distribution different biome classes within asset based IBPES biomes dataset.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/ipbes_biome_stats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate areal statistics for IBPES Biomes — ipbes_biome_stats","text":"","code":"calc_ipbes_biomes()"},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/ipbes_biome_stats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate areal statistics for IBPES Biomes — ipbes_biome_stats","text":"function returns tibble columns class name, absolute relative coverage within asset.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/ipbes_biome_stats.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate areal statistics for IBPES Biomes — ipbes_biome_stats","text":"required resources indicator : ipbes","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/iucn.html","id":null,"dir":"Reference","previous_headings":"","what":"IUCN Red List of Threatened Species — iucn","title":"IUCN Red List of Threatened Species — iucn","text":"resource part spatial data set Red List Threatened Species released IUCN. free use non-commercial licence. commercial uses, request sent Integrated Biodiversity Assessment Tool (IBAT).","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/iucn.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"IUCN Red List of Threatened Species — iucn","text":"","code":"get_iucn(paths = NULL)"},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/iucn.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"IUCN Red List of Threatened Species — iucn","text":"https://www.iucnredlist.org/resources/-spatial-downloads","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/iucn.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"IUCN Red List of Threatened Species — iucn","text":"paths character vector respective species range files GTiff format. Note, theses files downloaded manually.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/iucn.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"IUCN Red List of Threatened Species — iucn","text":"function returns sf footprint object.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/iucn.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"IUCN Red List of Threatened Species — iucn","text":"use data mapme workflows, manually download global data set point towards file path local machine. Please find available data source link given .","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/iucn.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"IUCN Red List of Threatened Species — iucn","text":"IUCN (2024). IUCN Red List Threatened Species. https://www.iucnredlist.org. doi:10.1038/s41597-022-01284-8","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/key_biodiversity_areas.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Key Biodiversity Areas — key_biodiversity_areas","title":"Calculate Key Biodiversity Areas — key_biodiversity_areas","text":"function calculates total area key biodiversity areas given input polygon. variable contains outlines key biodiversity areas. areas represent sites specific importance nature conservation efforts.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/key_biodiversity_areas.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Key Biodiversity Areas — key_biodiversity_areas","text":"","code":"calc_key_biodiversity_area() get_key_biodiversity_areas(path = NULL)"},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/key_biodiversity_areas.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Calculate Key Biodiversity Areas — key_biodiversity_areas","text":"function returning tibble key biodiversity area overlap","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/key_biodiversity_areas.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Calculate Key Biodiversity Areas — key_biodiversity_areas","text":"https://www.keybiodiversityareas.org/kba-data","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/key_biodiversity_areas.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Key Biodiversity Areas — key_biodiversity_areas","text":"path character vector key biodiversity areas gpkg file. Note, file downloaded manually.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/key_biodiversity_areas.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Key Biodiversity Areas — key_biodiversity_areas","text":"function returns character vector file paths.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/key_biodiversity_areas.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate Key Biodiversity Areas — key_biodiversity_areas","text":"required resources indicator : key_biodiversity_areas use data mapme workflows, manually download global data set point towards file path local machine. Please find available data source link given .","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/key_biodiversity_areas.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate Key Biodiversity Areas — key_biodiversity_areas","text":"BirdLife International (2024). World Database Key Biodiversity Areas. Developed KBA Partnership: BirdLife International, International Union Conservation Nature, Amphibian Survival Alliance, Conservation International, Critical Ecosystem Partnership Fund, Global Environment Facility, Re:wild, NatureServe, Rainforest Trust, Royal Society Protection Birds, Wildlife Conservation Society World Wildlife Fund. Available www.keybiodiversityareas.org.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/species_richness.html","id":null,"dir":"Reference","previous_headings":"","what":"Species richness based on IUCN raster data — species_richness","title":"Species richness based on IUCN raster data — species_richness","text":"Species richness counts number potential species intersecting polygon grouped IUCN threat categorization. Note, indicator function requires manual download respective raster files.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/species_richness.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Species richness based on IUCN raster data — species_richness","text":"","code":"calc_species_richness(engine = \"extract\", stats = \"mean\")"},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/species_richness.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Species richness based on IUCN raster data — species_richness","text":"engine preferred processing functions either one \"zonal\", \"extract\" \"exactextract\" character. stats Function applied compute statistics polygons either one multiple inputs character. Supported statistics : \"mean\", \"median\", \"sd\", \"min\", \"max\", \"sum\" \"var\".","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/species_richness.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Species richness based on IUCN raster data — species_richness","text":"function returns indicator tibble IUCN layers specified statistics variable respective values value.","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/reference/species_richness.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Species richness based on IUCN raster data — species_richness","text":"specific meaning species richness indicator depends supplied raster file. required resources indicator : iucn","code":""},{"path":"https://mapme-initiative.github.io/mapme.indicators/news/index.html","id":"mapmeindicators-development-version","dir":"Changelog","previous_headings":"","what":"mapme.indicators (development version)","title":"mapme.indicators (development version)","text":"carbon statistics now calculated based carbon per pixel instead area fixes bug get_hfp() re-downloaded resources even present datetime extraction carbon, species_richness humanfootprint extraction robust","code":""}]