add read abiotic ranges function

NAMESPACE

@@ -13,6 +13,7 @@ export(n2khab_options)
 export(read_GRTSmh)
 export(read_GRTSmh_base4frac)
 export(read_GRTSmh_diffres)
+export(read_abiotic_ranges)
 export(read_admin_areas)
 export(read_ecoregions)
 export(read_env_pressures)

R/read_abiotic_ranges.R

@@ -0,0 +1,98 @@
+#' Read favourable abiotic ranges for vegetation types of Flanders
+#'
+#' The function will download the data from a Zenodo deposit to a temporary
+#' folder and read the data back into the current R session.
+#' The original source for the data is the report 10.21436/inbor.19362510.
+#'
+#' @param doi A doi string. The default DOI string will resolve to the latest
+#' version of the data in the Zenodo deposit.
+#' If you want a specific version, please consult the Zenodo deposits web page
+#' to obtain the version-specific DOI.
+#'
+#' @return A `data.frame`.
+#'
+#' The table contains 950 rows and 19 columns.
+#' The first row is a column header and represents the variable name.
+#' The following list provides a brief description for each variable:
+#'
+#' `Habitatsubtype`: Natura 2000 (sub)type habitat code
+#'
+#' `Subtype`: code/name of possible vegetation variants.
+#' For aquatic types, the Flemish water type is listed
+#' (according to Water Framework Directive-Integrated Water Policy Objectives)
+#'
+#' `Milieucompartiment`: soil, groundwater, inundation water (flooding with
+#' water of external origin), water column/surface water, air
+#'
+#' `Variabele`: name of the environmental variable.
+#'
+#' `Afkorting`: abbreviation used for the environmental variable
+#'
+#' `Eenheid`: unit used for the environmental variable
+#'
+#' `Toetswijze bepaling`: for aquatic types, measurements are first summarized
+#'  using certain statistics such as percentiles, mean, etc. (in accordance with
+#'  Water Framework Directive-Integrated Water Policy Objectives)
+#'
+#' `Teken`: range type
+#' - LL-UL: lower limit-upper limit
+#' - 10-90 perc: 10-90 percentile values
+#' - min-max: minimum - maximum
+#' - < - >: less than - greater than
+#'
+#' `Abiotisch bereik`: overall measurement range of an environmental variable
+#'  within which a habitat type can function sustainably:
+#' - `Abiotisch bereik`: range as text field
+#' - `Waarde1` - `Waarde2`: lower and upper limit as text field
+#' - `WaardeNum1` - `WaardeNum2`: lower and upper limit as numerical value
+#'  (where conversion was possible)
+#'
+#' `N gunstig`: number of test plots in favorable conservation status used for
+#' the calculation. The definition of favorable conservation status is based on
+#' Oosterlynck et al. (2020, version 3).
+#'
+#' `Status`: source and method by which the range was derived:
+#' - Dp: ranges calculated with INBO data, prediction intervals, local
+#'   conservation status (LCS) known
+#' - Dt: ranges determined using Titan method (Baker & King 2010), LCS unknown
+#' - Dk: ranges calculated with INBO data, quantiles, insufficient data to
+#'   calculate prediction intervals
+#' - Lg: ranges derived from literature (LCS clearly indicated)
+#' - Lk: ranges derived from literature (LCS derived, based on site
+#'   characteristics)
+#'
+#' `Referentie`: references based on which the abiotic range was determined
+#'
+#' `Opmerking`: remarks
+#'
+#' `Wijziging`: whether this record has been modified compared to Van Calster
+#' et al. (2020) and how
+#'
+#' @export
+#'
+#' @references
+#' - Van Calster H., Cools N., De Keersmaeker L., Denys L., Herr C., Leyssen A.,
+#' Provoost S., Vanderhaeghe F., Vandevoorde B., Wouters J. en M. Raman (2020).
+#' Gunstige abiotische bereiken voor vegetatietypes in Vlaanderen. Rapporten van
+#' het Instituut voor Natuur- en Bosonderzoek 2020 (44). Instituut voor Natuur-
+#' en Bosonderzoek, Brussel. DOI: doi.org/10.21436/inbor.19362510D
+#' - Oosterlynck P., De Saeger S., Leyssen A., Provoost S., Thomaes A.,
+#' Vandevoorde B., Wouters J., & Paelinckx D. (2020). Criteria voor de
+#' beoordeling van de lokale staat van instandhouding van de Natura2000
+#' habitattypen in Vlaanderen. Rapporten van het Instituut voor Natuur- en
+#' Bosonderzoek 2020 (27). Instituut voor Natuur- en Bosonderzoek, Brussel.
+#' DOI: doi.org/10.21436/inbor.14061248
+#'
+#' @examples
+#' \dontrun{
+#' far <- read_abiotic_ranges()
+#' }
+read_abiotic_ranges <- function(doi = "10.5281/zenodo.10533791") {
+  td <- tempdir()
+  download_zenodo(doi = doi, path = td, quiet = TRUE)
+  file <- list.files(path = td, pattern = "txt$")
+  far <- read.delim(
+    file = file.path(td, file), header = TRUE, sep = "\t", dec = ","
+  )
+  return(far)
+}