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elgabbaselgabbas
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Fix Road processing
1 parent 51bdfa3 commit 9f3c89d

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lines changed

‎R/mod_prepare_data.R‎

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@@ -157,7 +157,10 @@ mod_prepare_data <- function(
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include_backtrace = TRUE)
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}
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data_sp <- ecokit::load_as(data_sp) %>%
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dplyr::arrange(ias_id)
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dplyr::arrange(ias_id) %>%
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dplyr::mutate(
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ias_id = stringr::str_pad(ias_id, pad = "0", width = 4),
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ias_id = paste0("sp_", ias_id))
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if (hab_abb == "0") {
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hab_column <- NULL

‎vignettes/workflow_1_overview.R‎

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@@ -11,3 +11,85 @@ knitr::opts_chunk$set(
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c("<style>", readLines("style.css"), "</style>") %>%
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cat(sep = "\n")
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## -----------------------------------------------------------------------------
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DT <- tibble::tribble(
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~Abbreviation, ~`Habitat Type`, ~Description,
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"1", "Forests", "closed vegetation dominated by deciduous or evergreen trees",
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"2", "Open forests", "woodlands with canopy openings created by environmental stress or disturbance, including forest edges",
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"3", "Scrub", "shrublands maintained by environmental stress (aridity) or disturbance",
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"4a", "Natural grasslands", "grasslands maintained by climate (aridity, unevenly distributed precipitation), herbivores or environmental stress (aridity, instability or toxicity of substrate)",
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"4b", "Human-maintained grasslands", "grasslands dependent on regular human-induced management (mowing, grazing by livestock, artificial burning)",
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"10", "Wetlands", "sites with the permanent or seasonal influence of moisture, ranging from oligotrophic to eutrophic",
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"12a", "Ruderal habitats", "anthropogenically disturbed or eutrophicated sites, where the anthropogenic disturbance or fertilization is typically a side-product and not the aim of the management",
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"12b", "Agricultural habitats", "synanthropic habitats directly associated with growing of agricultural products, thus dependent on specific type of management (ploughing, fertilization)")
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DT %>%
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knitr::kable(format = "html") %>%
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kableExtra::kable_styling(
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c("basic", "condensed", "hover"), font_size = 16, full_width = TRUE)
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## -----------------------------------------------------------------------------
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DT <- tibble::tribble(
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~Variable, ~Category, ~Description, ~"Default value",
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"DP_R_bioreg_interim", "Biogeographical regions", "Directory path to biogeographical regions interim data", "datasets/interim/biogeoregions",
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"DP_R_bioreg_processed", "Biogeographical regions", "Directory path to biogeographical regions processed data", "datasets/processed/biogeoregions",
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"DP_R_bioreg_raw", "Biogeographical regions", "Directory path to biogeographical regions raw data", "datasets/raw/biogeoregions",
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"DP_R_bioreg_url", "Biogeographical regions", "URL for downloading biogeographical regions data", "https://www.eea.europa.eu/en/datahub/datahubitem-view/11db8d14-f167-4cd5-9205-95638dfd9618",
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"DP_R_chelsa_links", "CHELSA", "Directory path containing CHELSA download links", "references/chelsa/dwnload_links",
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"DP_R_chelsa_processed", "CHELSA", "Directory path to processed CHELSA data", "datasets/processed/chelsa",
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"DP_R_chelsa_raw", "CHELSA", "Directory path to raw CHELSA data", "datasets/raw/chelsa",
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"DP_R_chelsa_url", "CHELSA", "Base URL for CHELSA data", "https://os.zhdk.cloud.switch.ch/chelsav2/GLOBAL",
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"DP_R_clc_crosswalk", "CLC", "Path to a text file containing custom cross-walk between CLC values at level 3 and their corresponding values for *EUNIS* and *SynHab* habitat types", "references/CrossWalk.txt",
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"DP_R_clc_processed", "CLC", "Directory path to processed CLC data", "datasets/processed/corine",
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"DP_R_clc_tif", "CLC", "Path to the input CLC tif file", "datasets/raw/corine/u2018_clc2018_v2020_20u1_raster100m/DATA/U2018_CLC2018_V2020_20u1.tif",
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"DP_R_lumi_cpu", "HPC", "LUMI project number for CPU computations", "project_465001857",
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"DP_R_lumi_gpu", "HPC", "LUMI project number for GPU computations", "project_465001857",
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"DP_R_lumi_gpu_check", "HPC", "File path to a python script for reporting if the GPU was used in the running SLURM job", "references/LUMI_Check_GPU.py",
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"DP_R_country_codes", "Misc", "Path to a file containing countries ISO codes", "references/country_codes.csv",
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"DP_R_country_boundaries", "Misc", "Path to `RData` file containing country boundaries", "references/EU_boundaries_sf.RData",
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"DP_R_model_root_path", "Models", "Directory path for model fitting", "datasets/processed/model_fitting",
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"DP_R_railway_interim", "Railways", "Directory path to interim railways data", "datasets/interim/railway",
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"DP_R_railway_processed", "Railways", "Directory path to processed railways data", "datasets/processed/railway",
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"DP_R_railway_raw", "Railways", "Directory path to raw railways data", "datasets/raw/railway",
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"DP_R_railway_url", "Railways", "URL for railways data", "https://download.geofabrik.de/",
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"DP_R_grid_processed", "Reference grid", "Directory path for reference grid (resulted from processing CLC data)", "datasets/processed/grid",
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"DP_R_grid_raw", "Reference grid", "Directory path for reference grid (original)", "references/grid",
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"DP_R_rivers_interim", "Rivers", "Directory path to interim rivers data", "datasets/interim/rivers",
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"DP_R_rivers_processed", "Rivers", "Directory path to processed rivers data", "datasets/processed/rivers",
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"DP_R_rivers_raw", "Rivers", "Directory path to raw rivers data", "datasets/raw/rivers",
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"DP_R_rivers_zip", "Rivers", "Path to zip file containing river data", "datasets/raw/rivers/EU_hydro_gpkg_eu.zip",
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"DP_R_roads_interim", "Roads", "Directory path to interim roads data", "datasets/interim/roads",
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"DP_R_roads_processed", "Roads", "Directory path to processed roads data", "datasets/processed/roads",
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"DP_R_roads_raw", "Roads", "Directory path to raw roads data", "datasets/raw/roads",
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"DP_R_roads_url", "Roads", "URL for the Global Roads Inventory Project (GRIP) data", "https://dataportaal.pbl.nl/downloads/GRIP4/GRIP4_Region4_vector_fgdb.zip",
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"DP_R_efforts_interim", "Sampling efforts", "Directory path to interim sampling efforts data", "datasets/interim/sampling_efforts",
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"DP_R_efforts_processed", "Sampling efforts", "Directory path to processed sampling efforts data", "datasets/processed/sampling_efforts",
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"DP_R_efforts_raw", "Sampling efforts", "Directory path to raw sampling efforts data", "datasets/raw/sampling_efforts",
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"DP_R_easin_interim", "Species distribution", "Directory path to EASIN data", "datasets/interim/EASIN",
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"DP_R_easin_processed", "Species distribution", "Directory path to processed EASIN data", "datasets/processed/EASIN",
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"DP_R_easin_summary", "Species distribution", "Directory path to summary of processed EASIN data", "datasets/processed/EASIN/Summary",
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"DP_R_easin_taxa_url", "Species distribution", "URL for EASIN API for downloading taxa list", "https://easin.jrc.ec.europa.eu/apixg/catxg",
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"DP_R_easin_data_url", "Species distribution", "URL for EASIN API for downloading species data", "https://easin.jrc.ec.europa.eu/apixg/geoxg",
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"DP_R_elter_processed", "Species distribution", "Path to `RData` containing processed eLTER presence-absence data", "datasets/processed/naps_pa/elter_naps.RData",
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"DP_R_elter_raw", "Species distribution", "Path to `rds` file containing processed and standardized eLTER data", "references/elter_data_gbif_2024-02-07.rds",
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"DP_R_gbif_interim", "Species distribution", "Directory path to interim GBIF data", "datasets/interim/GBIF",
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"DP_R_gbif_processed", "Species distribution", "Directory path to processed GBIF data", "datasets/processed/GBIF",
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"DP_R_gbif_raw", "Species distribution", "Directory path to raw GBIF data", "datasets/raw/gbif",
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"DP_R_pa", "Species distribution", "Directory path to species-specific presence-absence data", "datasets/processed/naps_pa",
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"DP_R_hab_affinity", "Taxa information", "Path to `rds` file containing species affinity to habitat types", "references/taxon-habitat-combined_2024-02-07.rds",
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"DP_R_taxa_country", "Taxa information", "Path to excel file containing the number of grid cells per species and country", "references/cell_count_per_species_and_country_2024-01-30-IA-VK-MG.xlsx",
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"DP_R_taxa_easin", "Taxa information", "Path to `rds` file containing EASIN standardized taxonomy", "references/easin_taxon-list-gbif_2024-02-07.rds",
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"DP_R_opendap_url", "", "Path to OpENDAP server for the `IASDT`", "http://opendap.biodt.eu/ias-pdt/") %>%
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dplyr::mutate(
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Variable = paste0("<cc>", Variable, "</cc>"),
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Category = NULL,
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`Default value` = paste0("<i>", `Default value`, "</i>"))
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DT %>%
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knitr::kable(format = "html", escape = FALSE) %>%
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kableExtra::kable_styling(
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c("basic", "condensed", "hover"), font_size = 16, full_width = TRUE) %>%
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kableExtra::column_spec(column = 1, extra_css = "white-space: nowrap;") %>%
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kableExtra::column_spec(column = 2, width = "25em")
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‎vignettes/workflow_1_overview.html‎

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‎vignettes/workflow_2_abiotic_data.R‎

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## -----------------------------------------------------------------------------
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library(kableExtra)
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library(knitr)
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library(tibble)
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knitr::opts_chunk$set(
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collapse = TRUE, comment = "#>", eval = FALSE, warning = FALSE,
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message = FALSE, dev = "ragg_png", dpi = 300, tidy = "styler",
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out.width = "100%", fig.show = "hold", echo = FALSE)
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## -----------------------------------------------------------------------------
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c("<style>", readLines("style.css"), "</style>") %>%
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cat(sep = "\n")
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## -----------------------------------------------------------------------------
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DT <- tibble::tribble(
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~`Climate model`, ~Institution,
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"mpi-esm1-2-hr", "Max Planck Institute for Meteorology, Germany",
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"ipsl-cm6a-lr", "Institut Pierre Simon Laplace, France",
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"ukesm1-0-ll", "Met Office Hadley Centre, UK",
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"gfdl-esm4", "National Oceanic and Atmospheric Administration, USA",
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"mri-esm2-0", "Meteorological Research Institute, Japan") %>%
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dplyr::mutate(`Climate model` = paste0(`Climate model`, "<tab0>"))
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DT %>%
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knitr::kable(format = "html", escape = FALSE, align = "l") %>%
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kableExtra::kable_styling(
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c("basic", "condensed", "hover"), font_size = 16, full_width = TRUE) %>%
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kableExtra::add_indent(
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positions = seq_len(nrow(DT)), level_of_indent = 2) %>%
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kableExtra::column_spec(
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column = 1, extra_css = "white-space: nowrap;", width_min = "3in")
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## -----------------------------------------------------------------------------
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DT <- tibble::tribble(
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~"Shared Socioeconomic Pathway", ~Description,
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"ssp126", "SSP1-RCP2.6 climate as simulated by the GCMs",
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"ssp370", "SSP3-RCP7 climate as simulated by the GCMs",
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"ssp585", "SSP5-RCP8.5 climate as simulated by the GCMs") %>%
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dplyr::mutate(
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`Shared Socioeconomic Pathway` = paste0(
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`Shared Socioeconomic Pathway`, "<tab0>"))
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DT %>%
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knitr::kable(format = "html", escape = FALSE, align = "l") %>%
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kableExtra::kable_styling(
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c("basic", "condensed", "hover"), font_size = 16, full_width = TRUE) %>%
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kableExtra::add_indent(
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positions = seq_len(nrow(DT)), level_of_indent = 2) %>%
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kableExtra::column_spec(
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column = 1, extra_css = "white-space: nowrap;", width_min = "3in")
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‎vignettes/workflow_2_abiotic_data.html‎

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‎vignettes/workflow_3_biotic_data.R‎

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## -----------------------------------------------------------------------------
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library(kableExtra)
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library(knitr)
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library(tibble)
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knitr::opts_chunk$set(
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collapse = TRUE, comment = "#>", eval = FALSE, warning = FALSE,
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message = FALSE, dev = "ragg_png", dpi = 300, tidy = "styler",
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out.width = "100%", fig.show = "hold", echo = FALSE)
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## -----------------------------------------------------------------------------
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c("<style>", readLines("style.css"), "</style>") %>%
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cat(sep = "\n")
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## -----------------------------------------------------------------------------
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DT <- tibble::tribble(
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~"class", ~"order", ~`# species`,
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"Liliopsida", "Acorales", 2,
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"Liliopsida", "Alismatales", 9,
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"Liliopsida", "Arecales", 5,
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"Liliopsida", "Asparagales", 75,
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"Liliopsida", "Commelinales", 4,
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"Liliopsida", "Liliales", 6,
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"Liliopsida", "Poales", 168,
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"Liliopsida", "Zingiberales", 7,
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"Lycopodiopsida", "Selaginellales", 1,
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"Magnoliopsida", "Apiales", 15,
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"Magnoliopsida", "Asterales", 150,
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"Magnoliopsida", "Boraginales", 10,
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"Magnoliopsida", "Brassicales", 14,
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"Magnoliopsida", "Caryophyllales", 144,
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"Magnoliopsida", "Celastrales", 4,
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"Magnoliopsida", "Cornales", 10,
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"Magnoliopsida", "Cucurbitales", 6,
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"Magnoliopsida", "Dipsacales", 19,
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"Magnoliopsida", "Ericales", 40,
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"Magnoliopsida", "Escalloniales", 1,
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"Magnoliopsida", "Fabales", 52,
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"Magnoliopsida", "Fagales", 20,
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"Magnoliopsida", "Garryales", 1,
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"Magnoliopsida", "Gentianales", 9,
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"Magnoliopsida", "Geraniales", 9,
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"Magnoliopsida", "Gunnerales", 1,
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"Magnoliopsida", "Lamiales", 65,
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"Magnoliopsida", "Laurales", 1,
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"Magnoliopsida", "Magnoliales", 1,
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"Magnoliopsida", "Malpighiales", 42,
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"Magnoliopsida", "Malvales", 10,
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"Magnoliopsida", "Myrtales", 75,
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"Magnoliopsida", "Oxalidales", 19,
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"Magnoliopsida", "Piperales", 3,
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"Magnoliopsida", "Proteales", 4,
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"Magnoliopsida", "Ranunculales", 27,
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"Magnoliopsida", "Rosales", 124,
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"Magnoliopsida", "Sapindales", 24,
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"Magnoliopsida", "Saxifragales", 38,
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"Magnoliopsida", "Solanales", 52,
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"Magnoliopsida", "Vitales", 9,
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"Pinopsida", "Pinales", 46,
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"Polypodiopsida", "Cyatheales", 1,
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"Polypodiopsida", "Equisetales", 1,
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"Polypodiopsida", "Polypodiales", 13,
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"Polypodiopsida", "Schizaeales", 1)
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knitr::kable(
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cbind(DT[1:23,], DT[24:46,]), format = "html",
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align = "l", escape = FALSE) %>%
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kableExtra::column_spec(c(1, 2, 4, 5), width_min = "1.4in") %>%
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kableExtra::column_spec(c(3, 6), width_min = "1.2in") %>%
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kableExtra::kable_styling(
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c("basic", "condensed", "hover"), font_size = 16,
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position = "center", full_width = TRUE)
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‎vignettes/workflow_3_biotic_data.html‎

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