POST_FATE.graphic_evolutionPixels: Create a graphical representation of the evolution of PFG...
In MayaGueguen/RFate: Vegetation modelling with the FATE model

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/POST_FATE.graphic_evolutionPixels.R

This script is designed to produce one graphical representation for a FATE simulation : the evolution through time of the abundance of each PFG for 5 (or more) randomly selected cells of the studied area.

POST_FATE.graphic_evolutionPixels(
  name.simulation,
  file.simulParam = NULL,
  opt.cells_ID = NULL,
  opt.fixedScale = TRUE,
  opt.doPlot = TRUE
)

`name.simulation`	a `string` corresponding to the main directory or simulation name of the `FATE` simulation
`file.simulParam`	default `NULL`. A `string` corresponding to the name of a parameter file that will be contained into the `PARAM_SIMUL` folder of the `FATE` simulation
`opt.cells_ID`	(optional) default `NULL`. The cells ID of the studied area for which PFG abundances will be extracted
`opt.fixedScale`	(optional) default `TRUE`. If `FALSE`, the ordinate scale will be adapted for each PFG for the graphical representation of the evolution of abundances through time
`opt.doPlot`	(optional) default `TRUE`. If `TRUE`, plot(s) will be processed, otherwise only the calculation and reorganization of outputs will occur, be saved and returned

This function allows to obtain, for a specific FATE simulation and a specific parameter file within this simulation, one preanalytical graphic :

the evolution of abundance of each Plant Functional Group through simulation time, within 5 (or more) randomly selected pixels of the studied area (FATE arbitrary unit)
if light was activated (see PRE_FATE.params_globalParameters),
evolution of light resources within the selected pixels is also represented (1: Low, 2: Medium, 3: High)
if soil was activated (see PRE_FATE.params_globalParameters),
evolution of soil resources within the selected pixels is also represented (user-defined scale)

It requires that the POST_FATE.temporalEvolution function has been run and that the file POST_FATE_TABLE_PIXEL_evolution_abundance.csv exists (as well as the POST_FATE_TABLE_PIXEL_evolution_light.csv and POST_FATE_TABLE_PIXEL_evolution_soil.csv files if those modules were activated).

A list containing one data.frame object with the following columns, and one ggplot2 object :

tab

TYPE: concerned information (either 'light', 'abundance' or 'soil')
GROUP: concerned entity (either 'STRATUM_[...]', PFG name or 'soil')
ID.pixel: number of the concerned pixel
HAB: habitat of the concerned pixel
YEAR: concerned simulation year
value: concerned value extracted from .csv files produced by POST_FATE.temporalEvolution

plot

ggplot2 object, representing the evolution of each PFG abundance, and light and soil resources if those modules were activated

One POST_FATE_TABLE_PIXEL_evolution_pixels_[...].csv file is created :

pixels ids: always, containing the data.frame detailed above

One POST_FATE_[...].pdf file is created :

‘GRAPHIC_A pixels’: to visualize for each PFG the evolution of its abundance within each selected pixel through simulation time

Maya Guéguen

POST_FATE.temporalEvolution

## Not run:                       
POST_FATE.graphic_evolutionPixels(name.simulation = "FATE_simulation"
                                  , file.simulParam = "Simul_parameters_V1.txt")
                                    
POST_FATE.graphic_evolutionPixels(name.simulation = "FATE_simulation"
                                  , file.simulParam = "Simul_parameters_V1.txt"
                                  , opt.fixedScale = FALSE)

## End(Not run)
                                    


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## Load example data