CreateProjMatrix: Creating a dataframe compiling the wanted projections
In BIOMOD: Ensemble platform for species distribution modeling

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

Creating a dataframe for the convinience of using it within the ProDensFunc() function.

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CreateProjMatrix(ANN=TRUE, CTA=TRUE, GLM=TRUE, GBM=TRUE, GAM=TRUE, SRE=TRUE, FDA=TRUE,
                 MARS=TRUE, RF=TRUE, Sp, Probs=TRUE, Bin=FALSE, Filt=FALSE, which.proj)

`ANN`	if TRUE, the model will be used to render projections
`CTA`	if TRUE, the model will be used to render projections
`GLM`	if TRUE, the model will be used to render projections
`GBM`	if TRUE, the model will be used to render projections
`GAM`	if TRUE, the model will be used to render projections
`SRE`	if TRUE, the model will be used to render projections
`FDA`	if TRUE, the model will be used to render projections
`MARS`	if TRUE, the model will be used to render projections
`RF`	if TRUE, the model will be used to render projections
`Sp`	the name of the species for which you wish to compile the projections
`Probs`	set it to TRUE if you want the projections in probabilities to be compiled
`Bin`	set it to TRUE if you want the projections in binary to be compiled
`Filt`	set it to TRUE if you want the projections in filtered values to be compiled
`which.proj`	a collection of projection names that have been run by BIOMOD with the Projection() function

Note that the models set to TRUE need to have been run in the Models function to be able to run with Projection(). Else, they simply won't be taken into account.

No values are returned but 2 types of objects are produced in Rs memory. The names under which the objects are created follow the same logic : "SpName_ProjMat" for the probabilities with an extension for bianry and/or filtered. This one contains the collection of projections. And "SpName_ProjMat_Groups" is a matrix containing various indexes for each line to keep track of where the projections come from.

Wilfried Thuiller, Bruno Lafourcade

Projection, ProbDensFunc

## Not run: 
data(Sp.Env)
data(CoorXY)

#This command is necessary for the run of BIOMOD as a new dataframe is produced for the Models function
Initial.State(Response=Sp.Env$Sp281, Explanatory=Sp.Env[,4:10], sp.name='Sp281',
IndependentResponse=NULL, IndependentExplanatory=NULL)

#Here are done 1 PA runs and 1 repetitions for each run. This will hence take several minutes.
Models(RF=TRUE, SRE=TRUE, GLM = FALSE, TypeGLM = "quad", Test = "AIC", CTA = FALSE, CV.tree = 50, ANN = FALSE, CV.ann = 2,
   NbRunEval = 1, DataSplit = 80, Roc=TRUE, Optimized.Threshold.Roc=TRUE, Kappa=TRUE, TSS=TRUE, VarImport=5,
   NbRepPA=1, strategy="circles", coor=CoorXY, distance=2, nb.absences=1000)


#Render Future projections under climate change scenario
data(Future1)
head(Future1) #the head() function enables to visualise the 5 firts lines of a dataframe
Projection(Proj = Future1[,4:10], Proj.name="Future1", RF=TRUE, SRE=TRUE, BinKappa=TRUE, FiltKappa=TRUE)


#view the results produced, example with the projections in probabilities :
load("proj.Future1/Proj_Future1_Sp281")
Proj_Future1_Sp281[100:150,,1,1]

#crate projection matrix
CreateProjMatrix(ANN=TRUE, CTA=TRUE, GLM=TRUE, GBM=TRUE, GAM=TRUE, SRE=TRUE,
    FDA=TRUE, MARS=TRUE, RF=TRUE, Sp="Sp281", Probs=TRUE, Bin=FALSE, Filt=FALSE, which.proj="Future1")

#objects created
head(Sp281_ProjMat)
Sp281_ProjMat_Groups

## End(Not run)