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Update read_watersurfaces for version 2024 #191

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Update read_watersurfaces for version 2024 #191

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7be670e
Bump dev version number
florisvdh Oct 7, 2024
6110cd1
read_watersurfaces: update doc for v 2024
cecileherr Dec 11, 2024
08b3655
read_watersurfaces: replace mutate_if _at by across
cecileherr Dec 11, 2024
b706a0b
read_watersurfaces: adapt foor v2024
cecileherr Dec 11, 2024
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: n2khab
Title: Providing Preprocessed Reference Data for Flemish Natura 2000 Habitat Analyses
Version: 0.11.0
Version: 0.11.0.9000
Authors@R: c(
person("Floris", "Vanderhaeghe", email = "floris.vanderhaeghe@inbo.be", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6378-6229")),
person("Toon", "Westra", email = "toon.westra@inbo.be", role = c("aut"), comment = c(ORCID = "0000-0003-2478-9459")),
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1 change: 1 addition & 0 deletions NAMESPACE
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Expand Up @@ -60,6 +60,7 @@ importFrom(dplyr,mutate)
importFrom(dplyr,mutate_at)
importFrom(dplyr,mutate_if)
importFrom(dplyr,n)
importFrom(dplyr,na_if)
importFrom(dplyr,pull)
importFrom(dplyr,recode)
importFrom(dplyr,relocate)
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2 changes: 2 additions & 0 deletions NEWS.md
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
# n2khab (development version)

# n2khab 0.11.0 (2024-10-03)

## Support for new data source versions
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139 changes: 96 additions & 43 deletions R/read_habitatdata.R
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Expand Up @@ -448,7 +448,7 @@ read_watersurfaces_hab <-

#' Return the data source \code{watersurfaces} as an \code{sf} polygon layer
#'
#' Returns the raw data source \code{watersurfaces} (Scheers et al., 2022)
#' Returns the raw data source \code{watersurfaces} (Leyssen et al., 2024)
#' as a standardized \code{sf} polygon layer
#' (tidyverse-styled, internationalized) in the Belgian Lambert 72 CRS
#' (EPSG-code \href{https://epsg.io/31370}{31370}).
Expand All @@ -462,7 +462,7 @@ read_watersurfaces_hab <-
#' is the version corresponding to the \code{file} (note that the \code{version}
#' defaults to the latest version).
#'
#' See Scheers et al. (2022) for an elaborate explanation of the data source
#' See Leyssen et al. (2024) for an elaborate explanation of the data source
#' and its attributes.
#'
#' @param file Optional string. An absolute or relative file path of
Expand Down Expand Up @@ -499,19 +499,23 @@ read_watersurfaces_hab <-
#' \item \code{polygon_id}: code of the polygon;
#' \item \code{wfd_code}: optional; Flemish code of the water body with
#' regard to the Water Framework Directive (WFD);
#' \item \code{hyla_code}: optional; code of the watersurface according to the
#' Flemish working group 'Hyla', a working group on amphibians & reptiles;
#' \item \code{hyla_code}: optional (only v1.2 and earlier); code of the
#' watersurface according to the Flemish working group 'Hyla', a working group
#' on amphibians & reptiles;
#' \item \code{name}: name of the watersurface;
#' \item \code{area_name}: name of the area;
#' \item \code{wfd_type}: type code according to the Flemish WFD typology
#' (Denys, 2009);
#' \item \code{wfd_type_alternative}: alternative type code according to the
#' Flemish WFD typology, in case there is a gradient between different types
#' (only version 2024);
#' \item \code{wfd_type_certain}: Logical.
#' Is there high confidence about the \code{wfd_type} determination?
#' \item \code{depth_class}: class of water depth;
#' \item \code{connectivity}: connectivity class;
#' \item \code{usage}: usage class;
#' \item \code{water_level_management}: water-level management class (not in
#' older versions).
#' \item \code{water_level_management}: water-level management class (only
#' since v1.2).
#' }
#'
#' @family functions involved in processing the 'watersurfaces' data source
Expand All @@ -524,10 +528,10 @@ read_watersurfaces_hab <-
#' wateren in Vlaanderen.
#' Rapporten van het Instituut voor Natuur- en Bosonderzoek INBO.R.2009.34.
#' Instituut voor Natuur- en Bosonderzoek, Brussel.
#' \item Scheers K., Smeekens V., Wils C., Packet J., Leyssen A. & Denys L.
#' (2022). Watervlakken versie 1.2: Polygonenkaart van stilstaand water in
#' Vlaanderen. Uitgave 2022. Instituut voor Natuur- en Bosonderzoek.
#' \doi{10.21436/inbor.87014272}.
#' \item Leyssen A., Scheers K., Packet J., Van Hecke F., Wils C. (2024).
#' Watervlakken 2024: Polygonenkaart van stilstaand water in
#' Vlaanderen. Uitgave 2024. Instituut voor Natuur- en Bosonderzoek.
#' \doi{10.21436/inbor.114075267}.
#' }
#'
#' @examples
Expand Down Expand Up @@ -566,8 +570,7 @@ read_watersurfaces_hab <-
#' across
#' arrange
#' mutate
#' mutate_at
#' mutate_if
#' na_if
#' rename
#' select
#' left_join
Expand All @@ -582,7 +585,8 @@ read_watersurfaces <-
function(file = NULL,
extended = FALSE,
fix_geom = FALSE,
version = c("watersurfaces_v1.2",
version = c("watersurfaces_v2024",
"watersurfaces_v1.2",
"watersurfaces_v1.1",
"watersurfaces_v1.0")) {
version <- match.arg(version)
Expand Down Expand Up @@ -631,11 +635,9 @@ read_watersurfaces <-
)

wfd_typetransl <- read_sf(file, layer = "LktKRWTYPE") %>%
mutate_if(., is.character,
.funs = function(x) {
return(`Encoding<-`(x, "UTF-8"))
}
) %>%
mutate(across(where(is.character),
~ return(`Encoding<-`(.x, "UTF-8"))
)) %>%
mutate(across(c(.data$Code), as.factor)) %>%
rename(
wfd_type = .data$Code,
Expand Down Expand Up @@ -664,6 +666,7 @@ read_watersurfaces <-
"C", "circumneutraal",
"Cb", "circumneutraal, sterk gebufferd",
"CbFe", "circumneutraal, sterk gebufferd, ijzerrijk",
"CFe", "circumneutraal, ijzerrijk",
"Czb", "circumneutraal, zwak gebufferd",
"Z", "zuur",
"Zm", "zwak zuur",
Expand All @@ -676,6 +679,21 @@ read_watersurfaces <-
)
}

if (version == "watersurfaces_v2024") {
wfd_type_alttransl <- data.frame(wfd_type = "-", wfd_type_name = "geen ander watertype") %>%
bind_rows(wfd_typetransl) %>%
bind_rows(wfd_typetransl %>%
mutate(wfd_type = paste0("(",wfd_type,")"),
wfd_type_name = paste(wfd_type_name, "(weinig waarschijnlijk)"))) %>%
rename(wfd_type_alt_name = wfd_type_name,
wfd_type_alternative = wfd_type) %>%
mutate(
wfd_type_alternative = factor(.data$wfd_type_alternative,
levels = .$wfd_type_alternative
)
)
}

if (fix_geom) {
validities <- st_is_valid(watersurfaces)
n_invalid <- sum(!validities | is.na(validities))
Expand All @@ -691,18 +709,25 @@ read_watersurfaces <-
watersurfaces %>%
{
if (version == "watersurfaces_v1.2") {
rename(., water_level_management = .data$PEILBEHEER)
rename(., water_level_management = .data$PEILBEHEER,
hyla_code = .data$HYLAC)
} else if (version == "watersurfaces_v2024") {
rename(.,
wfd_type_alternative = .data$KRWTYPEA,
water_level_management = .data$PEILBEHEER) %>%
mutate(across(where(is.character), ~na_if(., "")))
} else {
.
rename(., hyla_code = .data$HYLAC)
}
} %>%
select(
polygon_id = .data$WVLC,
wfd_code = .data$WTRLICHC,
hyla_code = .data$HYLAC,
matches("^hyla_code$"),
name = .data$NAAM,
area_name = .data$GEBIED,
wfd_type = .data$KRWTYPE,
matches("^wfd_type_alternative$"),
wfd_type_certain = .data$KRWTYPES,
depth_class = .data$DIEPKL,
connectivity = .data$CONNECT,
Expand All @@ -729,23 +754,29 @@ read_watersurfaces <-
factor(
levels =
levels(wfd_typetransl$wfd_type)
),
hyla_code = ifelse(.data$hyla_code == 0,
NA,
.data$hyla_code
)
)
) %>%
mutate(across(
matches("^wfd_type_alternative$"),
~ factor(.,
levels =
levels(wfd_type_alttransl$wfd_type_alternative)
)
)) %>%
mutate(across(
matches("^hyla_code$"),
~ ifelse(.data$hyla_code == 0,
NA,
.data$hyla_code)
)) %>%
arrange(.data$polygon_id)

if (version == "watersurfaces_v1.0") {
watersurfaces <-
watersurfaces %>%
mutate_at(
.vars = c("wfd_code", "name"),
.funs = function(x) {
ifelse(x == "<Null>", NA, x)
}
) %>%
mutate(across(c("wfd_code", "name"),
~ ifelse(.x == "<Null>", NA, .x)
)) %>%
mutate(wfd_type_certain = ifelse(is.na(.data$wfd_type_certain),
na_lgl,
.data$wfd_type_certain %in%
Expand Down Expand Up @@ -777,11 +808,9 @@ read_watersurfaces <-
if (extended) {
if (version == "watersurfaces_v1.1") {
connectivitytransl <- read_sf(file, layer = "LktCONNECT") %>%
mutate_if(., is.character,
.funs = function(x) {
return(`Encoding<-`(x, "UTF-8"))
}
) %>%
mutate(across(where(is.character),
~ return(`Encoding<-`(.x, "UTF-8"))
)) %>%
mutate(across(c(.data$Code), as.factor)) %>%
rename(
connectivity = .data$Code,
Expand Down Expand Up @@ -823,8 +852,23 @@ read_watersurfaces <-
to = wfd_typetransl$wfd_type_name
)
) %>%
# following match is only partial in case of v1.2
left_join(connectivitytransl, by = "connectivity") %>%
{
if (version == "watersurfaces_v2024") {
left_join(., wfd_type_alttransl, by = "wfd_type_alternative") %>%
mutate(
wfd_type_alt_name =
.data$wfd_type_alternative %>%
mapvalues(
from = wfd_type_alttransl$wfd_type_alternative,
to = wfd_type_alttransl$wfd_type_alt_name
)
)
} else {
.
}
} %>%
#following match is only partial in case of v1.2
left_join(., connectivitytransl, by = "connectivity") %>%
mutate(
connectivity_name =
.data$connectivity %>%
Expand All @@ -834,10 +878,19 @@ read_watersurfaces <-
)
) %>%
select(
1:6,
.data$wfd_type_name,
7:9,
.data$connectivity_name,
polygon_id,
wfd_code,
matches("^hyla_code$"),
name,
area_name,
wfd_type,
wfd_type_name,
matches("^wfd_type_alternative$"),
matches("^wfd_type_alt_name$"),
wfd_type_certain,
depth_class,
connectivity,
connectivity_name,
everything()
)
}
Expand Down
27 changes: 16 additions & 11 deletions man/read_watersurfaces.Rd
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