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Commit 63ab3cda authored by Fabian Stenzel's avatar Fabian Stenzel
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ecorisk updated

parent dd7ad27c
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2 merge requests!6Merge reviewed package into main,!5Merge review_paper version to master
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with 19 additions and 81 deletions
R/ecorisk.R
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− 81
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......@@ -2220,9 +2220,9 @@ calculate_within_biome_diffs <- function(biome_classes, # nolint
plotting = FALSE,
plot_folder,
time_span_reference,
vars_ecorisk) {
vars_ecorisk,
ecorisk_components = 13) {
biomes_abbrv <- get_biome_names(1)
ecorisk_components <- 11
# nbiomes, nEcoRiskvars, nHISTclasses
intra_biome_distrib <- array(
0,
......@@ -2352,7 +2352,6 @@ calculate_within_biome_diffs <- function(biome_classes, # nolint
)
} # end if plotting
}
ecorisk_dimensions <- names(ecorisk)
dim(intra_biome_distrib) <- c(biome = length(biome_classes$biome_names), variable = ecorisk_components, bin = 1 / res)
......@@ -2619,7 +2618,7 @@ plot_ecorisk_map <- function(
#' Function to plot an aggregated radial status of EcoRisk values [0-1]
#' for the different sub-categories to screen
#'
#' @param data EcoRisk data array c(4/19[biomes],[nEcoRiskcomponents],
#' @param data EcoRisk data array c([nEcoRiskcomponents],
#' 3[min,mean,max])
#' @param title character string title for plot, default empty
#' @param zoom scaling factor for circle plot. defaults to 1
......@@ -2640,71 +2639,27 @@ plot_ecorisk_radial_to_screen <- function(data, # nolint
use_quantile = TRUE) {
ecorisk_dims <- length(data[, 1])
if (ecorisk_dims == 11) {
names <- c(
ecorisk = "ecorisk",
deltav = "vegetation\nstructure", local = "local\nchange",
global = "global\nimportance", balance = "ecosystem\nbalance",
cstocks = "carbon\nstocks", cfluxes = "carbon\nfluxes",
wstocks = "water stocks", wfluxes = "water fluxes",
nstocks = "nitrogen\nstocks", nfluxes = "nitrogen\nfluxes"
)
# c(blue-green, yellow, violet, red, blue, orange, green, pink, grey,
# purple, green-blue, yellow-orange)
set <- RColorBrewer::brewer.pal(12, "Set3")
colz <- set[c(4, 7, 8, 11, 2, 3, 10, 5, 1, 12, 6)] # missing 2,9
# ecorisk vs lc gi eb cs cf ws wf ns nf
angles <- matrix(
c(90, 270, 216, 252, 180, 216, 144, 180, 108, 144, 0, 30, -30, 0, -60,
-30, -90, -60, 60, 90, 30, 60),
byrow = TRUE,
nrow = length(colz)
)
} else if (ecorisk_dims == 10) {
names <- c(
ecorisk = "ecorisk", deltav = "vegetation\nstructure",
local = "local\nchange", global = "global\nimportance",
balance = "ecosystem\nbalance", cstocks = "carbon stocks",
cfluxes = "carbon fluxes", wfluxes = "water fluxes",
nstocks = "nitrogen\nstocks", nfluxes = "nitrogen fluxes"
)
if (ecorisk_dims == 8) {
#names <- c(
# ecorisk = "ecorisk", deltav = "vegetation\nstructure",
# local = "local\nchange", global = "global\nimportance",
# balance = "ecosystem\nbalance", cstocks = "carbon\nstocks",
# cfluxes = "carbon fluxes", wfluxes = "water fluxes"
#)
# take the names of the ecorisk list dimensions, removing "_total"
names <- gsub("_", "\n",gsub("_total","", dimnames(data)[[1]]))
# c(blue-green, yellow, violet, red, blue, orange, green, pink, grey,
# purple, green-blue, yellow-orange)
set <- RColorBrewer::brewer.pal(12, "Set3")
colz <- set[c(4, 7, 8, 11, 1, 3, 10, 5, 12, 6)]
# ecorisk vs lc gi eb cs cf wf ns nf
colz <- set[c(4, 7, 8, 11, 1, 10, 5, 6)]
# ecorisk vs lc gi eb ct wt nt
angles <- matrix(
c(90, 270, 216, 252, 180, 216, 144, 180, 108, 144, -18, 18, -54, -18, -90,
-54, 54, 90, 18, 54),
c(90, 270, 216, 252, 180, 216, 144, 180, 108, 144, -18, 18, -54, -18, 18, 54),
byrow = TRUE,
nrow = length(colz)
)
} else if (ecorisk_dims == 8) {
names <- c(
ecorisk = "ecorisk", deltav = "vegetation\nstructure",
local = "local\nchange", global = "global\nimportance",
balance = "ecosystem\nbalance", cstocks = "carbon\nstocks",
cfluxes = "carbon fluxes", wfluxes = "water fluxes"
)
colz <- c(
"darkgoldenrod", RColorBrewer::brewer.pal(5, "Greens")[5],
RColorBrewer::brewer.pal(6, "Set1")[seq(2, 6, by = 2)],
rev(RColorBrewer::brewer.pal(6, "Oranges")[c(4, 5)]),
RColorBrewer::brewer.pal(6, "PuBu")[6]
)
angles <- matrix(
c(234, 270, 198, 234, 162, 198, 126, 162, 90, 126, 18, 54, -18, 18, -54,
-18),
byrow = TRUE,
nrow = length(colz)
)
} else {
stop("Unknown number of dimensions for ecorisk data:", ecorisk_dims)
}
......@@ -2730,28 +2685,12 @@ plot_ecorisk_radial_to_screen <- function(data, # nolint
)
}
if (ecorisk_dims == 11) {
graphics::text(names,
# er vs lc gi eb cs cf ws wf ns nf
x = c(1.1, 1.0, 0.2, -0.8, -1.6, -0.6, 0.1, 0.8, 1.05, -1.7, -1.4),
y = c(-0.15, -0.9, -1.3, -1.3, -0.9, 1.2, 1.2, 0.85, 0.25, 0.3, 0.85),
adj = 0
)
} else if (ecorisk_dims == 10) {
if (ecorisk_dims == 8) {
graphics::text(names,
x = c(1.1, 1.0, 0.2, -0.8, -1.6, -0.4, 0.7, 1.05, -1.7, -1.5),
y = c(-0.15, -0.9, -1.3, -1.3, -0.9, 1.2, 1, 0.25, 0.3, 1), adj = 0
)
} else if (ecorisk_dims == 8) {
graphics::text(
names,
x = c(1.1, 0.6, -0.2, -1.2, -1.7, -1.5, -0.4, 0.7),
y = c(-0.3, -1.1, -1.3, -1, -0.5, 1, 1.2, 1),
x = c( 1.1, 1.0, 0.2, -0.8, -1.6,-0.25, 0.7, -1.3),
y = c(-0.15, -0.9, -1.3, -1.3, -0.9, 1.2, 1, 1),
adj = 0
)
} else {
stop("Unknown number of dimensions for ecorisk data:", ecorisk_dims)
}
......@@ -2857,7 +2796,6 @@ plot_ecorisk_radial_to_screen <- function(data, # nolint
}
} else if (type == "regular") {
circlize::draw.sector(180, 360, rou1 = 1, col = "gray80")
for (i in seq_along(angles[, 1])) {
......
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