Pieter Huybrechts PietrH
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| # Finding species that are only a single dataset and nowhere else: human | |
| # observations edition | |
| if(file.exists("query_results/0024071-251009101135966.zip")) { | |
| species_per_dataset <- | |
| readr::read_delim("query_results/0024071-251009101135966.zip") | |
| } else { | |
| species_per_dataset <- | |
| rgbif::occ_download_get("0024071-251009101135966") |> | |
| rgbif::occ_download_import() |
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| # Passerines in South America | |
| # Data read from GBIF occurrence download (SQL QUERY) | |
| pas_sa <- | |
| rgbif::occ_download_get("0028483-251009101135966") |> | |
| rgbif::occ_download_import() |> | |
| dplyr::filter(!is.na(month)) | |
| # Identify the 3 most common genera ------------------------------------- | |
| common_genera <- pas_sa |> |
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| # Get all rato data as a flat csv | |
| if(!rlang::is_installed("ratatouille", version = "1.0.4")){ | |
| pak::pak("inbo/ratatouille") | |
| } | |
| library(ratatouille) | |
| # To run this function you need to store your RATO database credentials as env variables, as RATO_USER and RATO_PWD, otherwise you'll get an error. | |
| all_rato_data <- ratatouille() |
PietrH
/ return_default_value.R
Created
August 11, 2025 11:42
Get default value for a function argument in R
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| return_default <- function(my_param = 50){ | |
| rlang::eval_bare(formals(rlang::caller_fn(0))[["my_param"]]) | |
| } |
PietrH
/ object_name_message.R
Created
June 26, 2025 10:31
Use object name (symbol) in cli message in R
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| object_name_message <- function(x){ | |
| cli::cli_inform("The object you passed is called {substitute(x)}") | |
| } | |
| object_name_message(letters) |
PietrH
/ create_zenodo_release_versions.R
Created
April 17, 2025 13:30
Add old github repo releases to Zenodo
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| repo <- "my_org/my_repo" | |
| zenodo_token <- "token from url in webhook page of repo" | |
| repo_response <- | |
| httr2::request("https://api.github.com/repos") %>% | |
| httr2::req_url_path_append(repo) %>% | |
| httr2::req_perform() %>% | |
| httr2::resp_body_json() | |
| release_response <- |
PietrH
/ ripple_shuffle.R
Last active
March 31, 2025 14:04
Ripple shuffle a vector in R so the order is: [first, last, second, second to last ...]
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| ripple_shuffle <- function(object) { | |
| purrr::map( | |
| seq(1, length(object) / 2), | |
| ~ c( | |
| purrr::chuck(object, .x), | |
| purrr::chuck(object, length(object) - .x + 1) | |
| ) | |
| ) %>% | |
| unlist() | |
| } |
PietrH
/ create_inat_leaflet_map.R
Last active
January 30, 2025 15:02
Example usage of iNaturalist API to create leaflet map for a taxon within radius of a point
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| get_inat_obs_radius <- function(taxon_id, lat, lng, radius) { | |
| api_response <- httr2::request( | |
| "https://api.inaturalist.org/v1/observations/" | |
| ) %>% | |
| httr2::req_url_query( | |
| taxon_id = taxon_id, | |
| lat = lat, | |
| lng = lng, | |
| radius = radius | |
| ) %>% |
PietrH
/ get_etn_stats.R
Last active
January 27, 2025 14:53
Get a number of stats for a few ETN projects
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| library(dplyr) | |
| # Ensure ETN API-beta version | |
| remotes::install_github("inbo/[email protected]") | |
| library(etn) | |
| # Get number of detections, species and animals for lifewatch presentation | |
| project_codes_to_investigate <- c( | |
| "2010_PHD_REUBENS", | |
| "2011_RIVIERPRIK", | |
| "2012_LEOPOLDKANAAL", |
PietrH
/ find_allele_per_gene.R
Last active
January 2, 2025 14:08
Find the closest gene per allele for every chromosome
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| # We are trying to find the closest allele per gene | |
| ## You could possibly do this with this package as well: | |
| ## https://bioconductor.org/packages/release/bioc/vignettes/GenomicRanges/inst/doc/GenomicRangesIntroduction.html#finding-the-nearest-genomic-position-in-granges-objects | |
| library(dplyr) # A Grammar of Data Manipulation | |
| library(assertthat) # Easy Pre and Post Assertions | |
| # Some example data |
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