POST_FATE.graphic_evolutionStability: Create a graphical representation of the evolution of habitat...
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_evolutionStability.R

This script is designed to produce one graphical representation for a FATE simulation : the evolution through time of the total abundance and evenness of each habitat.

POST_FATE.graphic_evolutionStability(
  name.simulation,
  file.simulParam = NULL,
  movingWindow_size = 3,
  movingWindow_step = 1,
  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
`movingWindow_size`	default `3`. An `integer` corresponding to the size (in years) of the moving window that will be used to calculate metrics of habitat stability
`movingWindow_step`	default `1`. An `integer` corresponding to the step (in years) between the years of the moving window
`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 total abundance (FATE arbitrary unit) and evenness (between 0 and 1) of each habitat through simulation time, with evenness representing the uniformity of the species composition of the habitat (similar to Shannon entropy) :

\text{evenness} = - \frac{Σ(\text{proportion}_{\text{ PFG}_i} * log(\text{proportion}_{\text{ PFG}_i}))}{log(\text{no.PFG})}

with

\text{proportion}_{\text{ PFG}_i} = \frac{abund_{\text{ PFG}_i \text{, }\text{Habitat}_j}}{abund_{\text{ PFG}_{all}\text{, } \text{Habitat}_j}}

If the information has been provided (see POST_FATE.temporalEvolution), the graphics will be also done per habitat.

It requires that the POST_FATE.temporalEvolution function has been run and that the file POST_FATE_TABLE_PIXEL_evolution_abundance.csv exists.

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

tab.hab

HAB: concerned habitat
year: concerned simulation year
totalAbundance: total abundance over all the pixels within the concerned habitat
no.PFG: number of PFG over all the pixels within the concerned habitat
evenness: evenness over all the pixels within the concerned habitat

tab.stab

HAB: concerned habitat
no.years: number of simulation years used (moving window size)
yearStep: step between each simulation year of the moving window
yearStart: first simulation year of the moving window
yearEnd: last simulation year of the moving window
metric: concerned metric (either totalAbundance or evenness)
mean: mean value of the concerned metric over the years of the concerned moving window
sd: value of standard deviation of the concerned metric over the years of the concerned moving window
cv: value of coefficient of variation of the concerned metric over the years of the concerned moving window

plot.stab

ggplot2 object, representing the evolution of total abundance and evenness of each habitat

Two POST_FATE_TABLE_HAB_evolution_[...].csv files are created :

‘stability1’: always, containing tab.hab
‘stability2’: if successive years available, containing tab.stab

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

‘GRAPHIC_A stability’: to visualize for each habitat the evolution of its total abundance and its evenness through simulation time

Maya Guéguen

POST_FATE.temporalEvolution

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

## End(Not run)



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## Load example data