diff --git a/NAMESPACE b/NAMESPACE index 245aa95..372cc25 100644 --- a/NAMESPACE +++ b/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) diff --git a/R/read_abiotic_ranges.R b/R/read_abiotic_ranges.R new file mode 100644 index 0000000..70e5f8b --- /dev/null +++ b/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) +} diff --git a/man/read_abiotic_ranges.Rd b/man/read_abiotic_ranges.Rd new file mode 100644 index 0000000..5ecd929 --- /dev/null +++ b/man/read_abiotic_ranges.Rd @@ -0,0 +1,97 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/read_abiotic_ranges.R +\name{read_abiotic_ranges} +\alias{read_abiotic_ranges} +\title{Read favourable abiotic ranges for vegetation types of Flanders} +\usage{ +read_abiotic_ranges(doi = "10.5281/zenodo.10533791") +} +\arguments{ +\item{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.} +} +\value{ +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 +} +\description{ +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. +} +\examples{ +\dontrun{ +far <- read_abiotic_ranges() +} +} +\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 +}