createParameters: Format input parameters
In CIAT-DAPA/analogues: Identification of Climate Analogues

Description Usage Arguments See Also Examples

Loads required packages and formats input parameters.

1 2	createParameters(x, y, vars, weights, ndivisions, env.data.ref, env.data.targ, growing.season, rotation, threshold, outfile, fname, writefile)

`x`	numeric: latitude (decimal degrees)
`y`	numeric: longitude (decimal degrees)
`vars`	character vector: a vector with the name of the climatic variable(s) to use, e.g. c("prec","tmean"), or bioclimatic variable e.g. "bio_1"
`weights`	numeric vector: vector of length equal to the number of variables. Each value in the vector gives the weight given to each variable in the range 0-1. The sum of the weights must equal 1.
`ndivisions`	numeric vector: the number of divisions (usually months) for each variable. ndivisions=12 for climatic variables and ndivisions=1 for bioclimatic (or other types of variables) variables.
`env.data.ref`	list: a list of length equal to the number of variables that specifies the reference climatic conditions. Each element in the list is either a RasterLayer or a RasterStack object. RasterLayer applies to bioclimatic variables, whereas RasterStack applies for monthly data.
`env.data.targ`	list: a list of length equal to the number of variables that specifies the target climatic conditions. Each element in the list is either a RasterLayer or a RasterStack object. RasterLayer applies to bioclimatic variables, whereas RasterStack applies for monthly data.
`growing.season`	numeric vector: growing season (months) of interest in the analysis. Specified as a vector of length 2, where the first value specifies the start and the second value specifies the end of growing season. Not relevant for bioclimatic variables
`rotation`	character: should a rotation be applied. i.e. "tmean", "prec", "both" or "none". Rotation will allow comparisons between sites with different seasonality (e.g. northern vs. southern hemisphere)
`threshold`	numeric: value between 0-1. Only sites with a climatic similarity above this threshold will be saved and displayed.
`outfile`	character: directory where the resultant similarity map will be saved
`fname`	character: name of output file
`writefile`	logical: if the output file is to be written on disk. Otherwise only an object will be returned.

calc_similarity

data(climstack) #contains 2 RasterStack objects: prec and tavg

#create params, give equal weights to both variables
params <- createParameters(x=-75.5, y=3.2, vars=c("prec","tmean"),weights=c(0.5,0.5),
                        ndivisions=c(12,12),growing.season=c(1,12),rotation="tmean",threshold=1,
                        env.data.ref=list(prec,tavg), env.data.targ=list(prec,tavg),
                        outfile="~/.",fname='similarity',writefile=FALSE)