R/POST_FATE.graphic_evolutionPixels.R
In leca-dev/RFate: FATE with R
Defines functions
POST_FATE.graphic_evolutionPixels
Documented in
POST_FATE.graphic_evolutionPixels
### HEADER #####################################################################
##' @title Create a graphical representation of the evolution of PFG abundance
##' through time for 5 (or more) pixels of a \code{FATE} simulation
##'
##' @name POST_FATE.graphic_evolutionPixels
##'
##' @author Maya Guéguen
##'
##' @description This script is designed to produce one graphical representation
##' for a \code{FATE} simulation : the evolution through time of the
##' abundance of each PFG for 5 (or more) randomly selected cells of the studied
##' area.
##'
##' @param name.simulation a \code{string} corresponding to the main directory
##' or simulation name of the \code{FATE} simulation
##' @param file.simulParam default \code{NULL}. \cr A \code{string}
##' corresponding to the name of a parameter file that will be contained into
##' the \code{PARAM_SIMUL} folder of the \code{FATE} simulation
##' @param opt.cells_ID (\emph{optional}) default \code{NULL}. \cr The cells ID
##' of the studied area for which PFG abundances will be extracted
##' @param opt.doPlot (\emph{optional}) default \code{TRUE}. \cr If \code{TRUE},
##' plot(s) will be processed, otherwise only the calculation and reorganization
##' of outputs will occur, be saved and returned
##'
##'
##'
##' @details
##'
##' This function allows to obtain, for a specific \code{FATE} simulation and
##' a specific parameter file within this simulation, one preanalytical graphic :
##'
##' \itemize{
##' \item{the evolution of \strong{abundance} of each Plant Functional Group
##' through simulation time, within 5 (or more) randomly selected pixels of
##' the studied area (\code{FATE} \emph{arbitrary unit})
##' }
##' \item{\strong{if light was activated} (see
##' \code{\link{PRE_FATE.params_globalParameters}}), \cr evolution of
##' \strong{light resources} within the selected pixels is also represented
##' (\emph{\code{1}: Low, \code{2}: Medium, \code{3}: High})
##' }
##' \item{\strong{if soil was activated} (see
##' \code{\link{PRE_FATE.params_globalParameters}}), \cr evolution of
##' \strong{soil resources} within the selected pixels is also represented
##' (user-defined scale) \cr \cr
##' }
##' }
##'
##' \strong{It requires} that the \code{\link{POST_FATE.temporalEvolution}}
##' function has been run and that the file
##' \code{POST_FATE_TABLE_PIXEL_evolution_abundance.csv} exists (as well as the
##' \code{POST_FATE_TABLE_PIXEL_evolution_light.csv} and
##' \code{POST_FATE_TABLE_PIXEL_evolution_soil.csv} files if those modules were
##' activated).
##'
##'
##' @return A \code{list} containing one \code{data.frame} object with the
##' following columns, and one \code{ggplot2} object :
##'
##' \describe{
##' \item{tab}{
##' \describe{
##' \item{\code{TYPE}}{concerned information (either '\code{light}',
##' '\code{abundance}' or '\code{soil}')}
##' \item{\code{GROUP}}{concerned entity (either
##' '\code{STRATUM_[...]}', PFG name or '\code{soil}')}
##' \item{\code{ID.pixel}}{number of the concerned pixel}
##' \item{\code{HAB}}{habitat of the concerned pixel}
##' \item{\code{YEAR}}{concerned simulation year}
##' \item{\code{value}}{concerned value extracted from \code{.csv} files
##' produced by \code{\link{POST_FATE.temporalEvolution}}}
##' }
##' }
##' \item{plot}{\code{ggplot2} object, representing the evolution of each PFG
##' abundance, \emph{and light and soil resources if those modules were
##' activated} \cr \cr}
##' }
##'
##'
##' One \code{POST_FATE_TABLE_PIXEL_evolution_pixels_[...].csv} file is created :
##' \describe{
##' \item{\emph{pixels ids}}{always, containing the \code{data.frame} detailed
##' above}
##' }
##'
##'
##' One \code{POST_FATE_[...].pdf} file is created :
##' \describe{
##' \item{\file{GRAPHIC_A \cr pixels}}{to visualize for each PFG the evolution
##' of its abundance within each selected pixel through simulation time}
##' }
##'
##'
##' @keywords FATE, outputs, abundance through time
##'
##' @seealso \code{\link{POST_FATE.temporalEvolution}}
##'
##' @export
##'
##' @importFrom utils write.csv
##' @importFrom grDevices colorRampPalette
##' @importFrom reshape2 melt
##' @importFrom foreach foreach %do%
##'
##' @importFrom ggplot2 ggplot ggsave aes_string
##' geom_line geom_point
##' scale_color_manual
##' facet_grid labs theme element_text element_blank
##' @importFrom ggthemes theme_fivethirtyeight
## @importFrom ggnewscale new_scale_color
##'
## END OF HEADER ###############################################################
POST_FATE.graphic_evolutionPixels = function(
name.simulation
, file.simulParam = NULL
, opt.cells_ID = NULL
, opt.doPlot = TRUE
){
#############################################################################
if (!isNamespaceLoaded("ggnewscale")) {
if (!requireNamespace('ggnewscale', quietly = TRUE)) stop("Package 'ggnewscale' not found")
}
## CHECK parameter name.simulation
.testParam_existFolder(name.simulation, "PARAM_SIMUL/")
.testParam_existFolder(name.simulation, "RESULTS/")
.testParam_existFolder(name.simulation, "DATA/")
name.simulation = sub("/", "", name.simulation)
## CHECK parameter file.simulParam
abs.simulParams = .getParam_abs.simulParams(file.simulParam, name.simulation)
cat("\n\n #------------------------------------------------------------#")
cat("\n # POST_FATE.graphic_evolutionPixels")
cat("\n #------------------------------------------------------------# \n")
#############################################################################
res = foreach (abs.simulParam = abs.simulParams) %do%
{
cat("\n+++++++\n")
cat("\n Simulation name : ", name.simulation)
cat("\n Simulation file : ", abs.simulParam)
cat("\n")
## Get results directories ------------------------------------------------
GLOB_DIR = .getGraphics_results(name.simulation = name.simulation
, abs.simulParam = abs.simulParam)
## Get number of PFGs -----------------------------------------------------
## Get PFG names ----------------------------------------------------------
GLOB_SIM = .getGraphics_PFG(name.simulation = name.simulation
, abs.simulParam = abs.simulParam)
## Get raster mask --------------------------------------------------------
GLOB_MASK = .getGraphics_mask(name.simulation = name.simulation
, abs.simulParam = abs.simulParam)
## Get the abundance table ------------------------------------------------
file.abundance = paste0(name.simulation
, "/RESULTS/POST_FATE_TABLE_PIXEL_evolution_abundance_"
, basename(GLOB_DIR$dir.save)
, ".csv")
.testParam_existFile(file.abundance)
tab.abundance = fread(file.abundance)
tab.abundance = as.data.frame(tab.abundance, stringsAsFactors = FALSE)
tab.abundance$TYPE = "abundance"
colnames(tab.abundance)[which(colnames(tab.abundance) == "PFG")] = "GROUP"
years = colnames(tab.abundance)
years = years[which(!(years %in% c("TYPE", "GROUP", "ID.pixel", "X", "Y", "HAB")))]
years = as.numeric(years)
strata = paste0("Stratum ", 0:(GLOB_SIM$no_STRATA - 1))
## Get resources tables ---------------------------------------------------
if (GLOB_SIM$doLight)
{
file.light = paste0(name.simulation
, "/RESULTS/POST_FATE_TABLE_PIXEL_evolution_light_"
, basename(GLOB_DIR$dir.save)
, ".csv")
.testParam_existFile(file.light)
tab.light = fread(file.light)
tab.light = as.data.frame(tab.light, stringsAsFactors = FALSE)
tab.light$STRATUM = paste0("Stratum ", tab.light$STRATUM)
tab.light$TYPE = "light"
colnames(tab.light)[which(colnames(tab.light) == "STRATUM")] = "GROUP"
tab.abundance = rbind(tab.abundance, tab.light)
}
if (GLOB_SIM$doSoil)
{
file.soil = paste0(name.simulation
, "/RESULTS/POST_FATE_TABLE_PIXEL_evolution_soil_"
, basename(GLOB_DIR$dir.save)
, ".csv")
.testParam_existFile(file.soil)
tab.soil = fread(file.soil)
tab.soil = as.data.frame(tab.soil, stringsAsFactors = FALSE)
tab.soil$GROUP = "soil"
tab.soil$TYPE = "soil"
tab.abundance = rbind(tab.abundance, tab.soil)
}
## Get concerned cells id -------------------------------------------------
IDS = sort(sample(unique(tab.abundance$ID.pixel), 5))
if (!is.null(opt.cells_ID))
{
if (sum(opt.cells_ID %in% GLOB_MASK$ind_1_mask) == length(opt.cells_ID))
{
IDS = sort(opt.cells_ID)
} else
{
warning(paste0("The values given in `opt.cells_ID` do not match "
, "with any cells of the studied area \n"
, "(obtained from the raster file `"
, GLOB_MASK$file.mask
, "`)\n"
, "They will be replaced by randomly selected cells."))
}
}
cat("\n Number of years : ", length(years))
cat("\n Selected years : ", years)
cat("\n Selected cells : ", IDS)
cat("\n")
## Transform the data inside the table ------------------------------------
distriAbund = tab.abundance[which(tab.abundance$ID.pixel %in% IDS), , drop = FALSE]
distriAbund = distriAbund[, c("TYPE", "GROUP", "ID.pixel", "HAB", as.character(years))]
distriAbund = melt(distriAbund, id.vars = c("TYPE", "GROUP", "ID.pixel", "HAB"))
colnames(distriAbund) = c("TYPE", "GROUP", "ID.pixel", "HAB", "YEAR", "value")
distriAbund$YEAR = as.numeric(as.character(distriAbund$YEAR))
distriAbund$TYPE = factor(distriAbund$TYPE, c("light", "abundance", "soil"))
distriAbund$GROUP = factor(distriAbund$GROUP, c(strata, GLOB_SIM$PFG, "soil"))
write.csv(distriAbund
, file = paste0(name.simulation
, "/RESULTS/POST_FATE_TABLE_PIXEL_evolution_pixels_"
, ifelse(length(IDS) <= 5
, paste0(IDS, collapse = "_")
, length(IDS))
, "_"
, basename(GLOB_DIR$dir.save)
, ".csv")
, row.names = FALSE)
message(paste0("\n The output file \n"
, " > POST_FATE_TABLE_PIXEL_evolution_pixels_"
, ifelse(length(IDS) <= 5
, paste0(IDS, collapse = "_")
, length(IDS))
, "_"
, basename(GLOB_DIR$dir.save)
, ".csv \n"
, "has been successfully created !\n"))
## produce the plot -------------------------------------------------------
if (opt.doPlot)
{
cat("\n ---------- PRODUCING PLOT \n")
vec_col1 = c('#a6cee3','#1f78b4','#b2df8a','#33a02c','#fb9a99','#e31a1c','#fdbf6f','#ff7f00','#cab2d6')
val_col1 = c(rep(rgb(1,1,1,1), GLOB_SIM$no_STRATA)
, colorRampPalette(vec_col1)(GLOB_SIM$no_PFG)
, "grey30")
names(val_col1) = c(strata, GLOB_SIM$PFG, "soil")
vec_col2 = c('#FEC44F', '#FB9A29', '#EC7014', '#CC4C02', '#993404', '#662506')
val_col2 = rev(colorRampPalette(vec_col2)(3))
names(val_col2) = 1:3
pp = ggplot(distriAbund, aes_string(x = "YEAR", y = "value")) +
geom_line(data = distriAbund[which(distriAbund$TYPE == "soil"),]
, color = "grey30"
, lwd = 0.7) +
geom_line(data = distriAbund[which(distriAbund$TYPE == "abundance"),]
, aes_string(color = "GROUP")
, lwd = 0.7) +
scale_color_manual("", values = val_col1) +
ggnewscale::new_scale_color() +
geom_point(data = distriAbund[which(distriAbund$TYPE == "light"), ]
, aes_string(x = "YEAR", y = "as.numeric(GROUP)-1", color = "factor(value)")
, alpha = 0.4, pch = 15, size = 15
, inherit.aes = FALSE) +
scale_color_manual("", values = val_col2, labels = c("Low", "Medium", "High")) +
facet_grid("TYPE ~ ID.pixel", scales = "free_y") +
labs(x = "", y = ""
, title = paste0("GRAPH A : evolution of species' abundance")
, subtitle = paste0("For each PFG, the line represents the "
, "evolution through time of its abundance\n"
, "(as well as the light and soil resources if available)"
, "for the selected pixels within the studied area.\n")) +
.getGraphics_theme()
ggsave(filename = paste0(name.simulation
, "/RESULTS/POST_FATE_GRAPHIC_A_evolution_pixels_"
, ifelse(length(IDS) <= 5
, paste0(IDS, collapse = "_")
, length(IDS))
, "_"
, basename(GLOB_DIR$dir.save)
, ".pdf")
, plot = pp, width = 10, height = 8)
} else
{
pp = NULL
} ## END opt.doPlot
## ------------------------------------------------------------------------
cat("\n> Done!\n")
return(list(tab = distriAbund, plot = pp))
} ## END loop on abs.simulParams
names(res) = abs.simulParams
return(res)
}
leca-dev/RFate documentation built on Sept. 19, 2024, 6:09 a.m.
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Defines functions POST_FATE.graphic_evolutionPixels
Documented in POST_FATE.graphic_evolutionPixels
### HEADER #####################################################################
##' @title Create a graphical representation of the evolution of PFG abundance
##' through time for 5 (or more) pixels of a \code{FATE} simulation
##'
##' @name POST_FATE.graphic_evolutionPixels
##'
##' @author Maya Guéguen
##'
##' @description This script is designed to produce one graphical representation
##' for a \code{FATE} simulation : the evolution through time of the
##' abundance of each PFG for 5 (or more) randomly selected cells of the studied
##' area.
##'
##' @param name.simulation a \code{string} corresponding to the main directory
##' or simulation name of the \code{FATE} simulation
##' @param file.simulParam default \code{NULL}. \cr A \code{string}
##' corresponding to the name of a parameter file that will be contained into
##' the \code{PARAM_SIMUL} folder of the \code{FATE} simulation
##' @param opt.cells_ID (\emph{optional}) default \code{NULL}. \cr The cells ID
##' of the studied area for which PFG abundances will be extracted
##' @param opt.doPlot (\emph{optional}) default \code{TRUE}. \cr If \code{TRUE},
##' plot(s) will be processed, otherwise only the calculation and reorganization
##' of outputs will occur, be saved and returned
##'
##'
##'
##' @details
##'
##' This function allows to obtain, for a specific \code{FATE} simulation and
##' a specific parameter file within this simulation, one preanalytical graphic :
##'
##' \itemize{
##' \item{the evolution of \strong{abundance} of each Plant Functional Group
##' through simulation time, within 5 (or more) randomly selected pixels of
##' the studied area (\code{FATE} \emph{arbitrary unit})
##' }
##' \item{\strong{if light was activated} (see
##' \code{\link{PRE_FATE.params_globalParameters}}), \cr evolution of
##' \strong{light resources} within the selected pixels is also represented
##' (\emph{\code{1}: Low, \code{2}: Medium, \code{3}: High})
##' }
##' \item{\strong{if soil was activated} (see
##' \code{\link{PRE_FATE.params_globalParameters}}), \cr evolution of
##' \strong{soil resources} within the selected pixels is also represented
##' (user-defined scale) \cr \cr
##' }
##' }
##'
##' \strong{It requires} that the \code{\link{POST_FATE.temporalEvolution}}
##' function has been run and that the file
##' \code{POST_FATE_TABLE_PIXEL_evolution_abundance.csv} exists (as well as the
##' \code{POST_FATE_TABLE_PIXEL_evolution_light.csv} and
##' \code{POST_FATE_TABLE_PIXEL_evolution_soil.csv} files if those modules were
##' activated).
##'
##'
##' @return A \code{list} containing one \code{data.frame} object with the
##' following columns, and one \code{ggplot2} object :
##'
##' \describe{
##' \item{tab}{
##' \describe{
##' \item{\code{TYPE}}{concerned information (either '\code{light}',
##' '\code{abundance}' or '\code{soil}')}
##' \item{\code{GROUP}}{concerned entity (either
##' '\code{STRATUM_[...]}', PFG name or '\code{soil}')}
##' \item{\code{ID.pixel}}{number of the concerned pixel}
##' \item{\code{HAB}}{habitat of the concerned pixel}
##' \item{\code{YEAR}}{concerned simulation year}
##' \item{\code{value}}{concerned value extracted from \code{.csv} files
##' produced by \code{\link{POST_FATE.temporalEvolution}}}
##' }
##' }
##' \item{plot}{\code{ggplot2} object, representing the evolution of each PFG
##' abundance, \emph{and light and soil resources if those modules were
##' activated} \cr \cr}
##' }
##'
##'
##' One \code{POST_FATE_TABLE_PIXEL_evolution_pixels_[...].csv} file is created :
##' \describe{
##' \item{\emph{pixels ids}}{always, containing the \code{data.frame} detailed
##' above}
##' }
##'
##'
##' One \code{POST_FATE_[...].pdf} file is created :
##' \describe{
##' \item{\file{GRAPHIC_A \cr pixels}}{to visualize for each PFG the evolution
##' of its abundance within each selected pixel through simulation time}
##' }
##'
##'
##' @keywords FATE, outputs, abundance through time
##'
##' @seealso \code{\link{POST_FATE.temporalEvolution}}
##'
##' @export
##'
##' @importFrom utils write.csv
##' @importFrom grDevices colorRampPalette
##' @importFrom reshape2 melt
##' @importFrom foreach foreach %do%
##'
##' @importFrom ggplot2 ggplot ggsave aes_string
##' geom_line geom_point
##' scale_color_manual
##' facet_grid labs theme element_text element_blank
##' @importFrom ggthemes theme_fivethirtyeight
## @importFrom ggnewscale new_scale_color
##'
## END OF HEADER ###############################################################
POST_FATE.graphic_evolutionPixels = function(
name.simulation
, file.simulParam = NULL
, opt.cells_ID = NULL
, opt.doPlot = TRUE
){
#############################################################################
if (!isNamespaceLoaded("ggnewscale")) {
if (!requireNamespace('ggnewscale', quietly = TRUE)) stop("Package 'ggnewscale' not found")
}
## CHECK parameter name.simulation
.testParam_existFolder(name.simulation, "PARAM_SIMUL/")
.testParam_existFolder(name.simulation, "RESULTS/")
.testParam_existFolder(name.simulation, "DATA/")
name.simulation = sub("/", "", name.simulation)
## CHECK parameter file.simulParam
abs.simulParams = .getParam_abs.simulParams(file.simulParam, name.simulation)
cat("\n\n #------------------------------------------------------------#")
cat("\n # POST_FATE.graphic_evolutionPixels")
cat("\n #------------------------------------------------------------# \n")
#############################################################################
res = foreach (abs.simulParam = abs.simulParams) %do%
{
cat("\n+++++++\n")
cat("\n Simulation name : ", name.simulation)
cat("\n Simulation file : ", abs.simulParam)
cat("\n")
## Get results directories ------------------------------------------------
GLOB_DIR = .getGraphics_results(name.simulation = name.simulation
, abs.simulParam = abs.simulParam)
## Get number of PFGs -----------------------------------------------------
## Get PFG names ----------------------------------------------------------
GLOB_SIM = .getGraphics_PFG(name.simulation = name.simulation
, abs.simulParam = abs.simulParam)
## Get raster mask --------------------------------------------------------
GLOB_MASK = .getGraphics_mask(name.simulation = name.simulation
, abs.simulParam = abs.simulParam)
## Get the abundance table ------------------------------------------------
file.abundance = paste0(name.simulation
, "/RESULTS/POST_FATE_TABLE_PIXEL_evolution_abundance_"
, basename(GLOB_DIR$dir.save)
, ".csv")
.testParam_existFile(file.abundance)
tab.abundance = fread(file.abundance)
tab.abundance = as.data.frame(tab.abundance, stringsAsFactors = FALSE)
tab.abundance$TYPE = "abundance"
colnames(tab.abundance)[which(colnames(tab.abundance) == "PFG")] = "GROUP"
years = colnames(tab.abundance)
years = years[which(!(years %in% c("TYPE", "GROUP", "ID.pixel", "X", "Y", "HAB")))]
years = as.numeric(years)
strata = paste0("Stratum ", 0:(GLOB_SIM$no_STRATA - 1))
## Get resources tables ---------------------------------------------------
if (GLOB_SIM$doLight)
{
file.light = paste0(name.simulation
, "/RESULTS/POST_FATE_TABLE_PIXEL_evolution_light_"
, basename(GLOB_DIR$dir.save)
, ".csv")
.testParam_existFile(file.light)
tab.light = fread(file.light)
tab.light = as.data.frame(tab.light, stringsAsFactors = FALSE)
tab.light$STRATUM = paste0("Stratum ", tab.light$STRATUM)
tab.light$TYPE = "light"
colnames(tab.light)[which(colnames(tab.light) == "STRATUM")] = "GROUP"
tab.abundance = rbind(tab.abundance, tab.light)
}
if (GLOB_SIM$doSoil)
{
file.soil = paste0(name.simulation
, "/RESULTS/POST_FATE_TABLE_PIXEL_evolution_soil_"
, basename(GLOB_DIR$dir.save)
, ".csv")
.testParam_existFile(file.soil)
tab.soil = fread(file.soil)
tab.soil = as.data.frame(tab.soil, stringsAsFactors = FALSE)
tab.soil$GROUP = "soil"
tab.soil$TYPE = "soil"
tab.abundance = rbind(tab.abundance, tab.soil)
}
## Get concerned cells id -------------------------------------------------
IDS = sort(sample(unique(tab.abundance$ID.pixel), 5))
if (!is.null(opt.cells_ID))
{
if (sum(opt.cells_ID %in% GLOB_MASK$ind_1_mask) == length(opt.cells_ID))
{
IDS = sort(opt.cells_ID)
} else
{
warning(paste0("The values given in `opt.cells_ID` do not match "
, "with any cells of the studied area \n"
, "(obtained from the raster file `"
, GLOB_MASK$file.mask
, "`)\n"
, "They will be replaced by randomly selected cells."))
}
}
cat("\n Number of years : ", length(years))
cat("\n Selected years : ", years)
cat("\n Selected cells : ", IDS)
cat("\n")
## Transform the data inside the table ------------------------------------
distriAbund = tab.abundance[which(tab.abundance$ID.pixel %in% IDS), , drop = FALSE]
distriAbund = distriAbund[, c("TYPE", "GROUP", "ID.pixel", "HAB", as.character(years))]
distriAbund = melt(distriAbund, id.vars = c("TYPE", "GROUP", "ID.pixel", "HAB"))
colnames(distriAbund) = c("TYPE", "GROUP", "ID.pixel", "HAB", "YEAR", "value")
distriAbund$YEAR = as.numeric(as.character(distriAbund$YEAR))
distriAbund$TYPE = factor(distriAbund$TYPE, c("light", "abundance", "soil"))
distriAbund$GROUP = factor(distriAbund$GROUP, c(strata, GLOB_SIM$PFG, "soil"))
write.csv(distriAbund
, file = paste0(name.simulation
, "/RESULTS/POST_FATE_TABLE_PIXEL_evolution_pixels_"
, ifelse(length(IDS) <= 5
, paste0(IDS, collapse = "_")
, length(IDS))
, "_"
, basename(GLOB_DIR$dir.save)
, ".csv")
, row.names = FALSE)
message(paste0("\n The output file \n"
, " > POST_FATE_TABLE_PIXEL_evolution_pixels_"
, ifelse(length(IDS) <= 5
, paste0(IDS, collapse = "_")
, length(IDS))
, "_"
, basename(GLOB_DIR$dir.save)
, ".csv \n"
, "has been successfully created !\n"))
## produce the plot -------------------------------------------------------
if (opt.doPlot)
{
cat("\n ---------- PRODUCING PLOT \n")
vec_col1 = c('#a6cee3','#1f78b4','#b2df8a','#33a02c','#fb9a99','#e31a1c','#fdbf6f','#ff7f00','#cab2d6')
val_col1 = c(rep(rgb(1,1,1,1), GLOB_SIM$no_STRATA)
, colorRampPalette(vec_col1)(GLOB_SIM$no_PFG)
, "grey30")
names(val_col1) = c(strata, GLOB_SIM$PFG, "soil")
vec_col2 = c('#FEC44F', '#FB9A29', '#EC7014', '#CC4C02', '#993404', '#662506')
val_col2 = rev(colorRampPalette(vec_col2)(3))
names(val_col2) = 1:3
pp = ggplot(distriAbund, aes_string(x = "YEAR", y = "value")) +
geom_line(data = distriAbund[which(distriAbund$TYPE == "soil"),]
, color = "grey30"
, lwd = 0.7) +
geom_line(data = distriAbund[which(distriAbund$TYPE == "abundance"),]
, aes_string(color = "GROUP")
, lwd = 0.7) +
scale_color_manual("", values = val_col1) +
ggnewscale::new_scale_color() +
geom_point(data = distriAbund[which(distriAbund$TYPE == "light"), ]
, aes_string(x = "YEAR", y = "as.numeric(GROUP)-1", color = "factor(value)")
, alpha = 0.4, pch = 15, size = 15
, inherit.aes = FALSE) +
scale_color_manual("", values = val_col2, labels = c("Low", "Medium", "High")) +
facet_grid("TYPE ~ ID.pixel", scales = "free_y") +
labs(x = "", y = ""
, title = paste0("GRAPH A : evolution of species' abundance")
, subtitle = paste0("For each PFG, the line represents the "
, "evolution through time of its abundance\n"
, "(as well as the light and soil resources if available)"
, "for the selected pixels within the studied area.\n")) +
.getGraphics_theme()
ggsave(filename = paste0(name.simulation
, "/RESULTS/POST_FATE_GRAPHIC_A_evolution_pixels_"
, ifelse(length(IDS) <= 5
, paste0(IDS, collapse = "_")
, length(IDS))
, "_"
, basename(GLOB_DIR$dir.save)
, ".pdf")
, plot = pp, width = 10, height = 8)
} else
{
pp = NULL
} ## END opt.doPlot
## ------------------------------------------------------------------------
cat("\n> Done!\n")
return(list(tab = distriAbund, plot = pp))
} ## END loop on abs.simulParams
names(res) = abs.simulParams
return(res)
}
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