Pieter Huybrechts PietrH
PietrH
/ no_connection.arg.R
Created
January 23, 2026 09:11
Example of etn without connection argument
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| library(etn) | |
| # Creating a connection object will result in a warning and not result in a | |
| # connection object | |
| my_con <- connect_to_etn() | |
| #> Warning: `connect_to_etn()` was deprecated in etn 2.3.0. | |
| #> ℹ You will be prompted for credentials instead. | |
| #> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was | |
| #> generated. |
PietrH
/ connection_deprecated.R
Created
January 23, 2026 09:04
Example of etn with deprecated connection argument
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| library(etn) | |
| # Creating a connection object will result in a warning and not result in a | |
| # connection object | |
| my_con <- connect_to_etn() | |
| #> Warning: `connect_to_etn()` was deprecated in etn 2.3.0. | |
| #> ℹ You will be prompted for credentials instead. | |
| #> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was | |
| #> generated. | |
| class(my_con) |
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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 | |
| ) %>% |
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