EcotoneFinder (version 0.2.3)

DistEco: Tools for internal data structure exploration

Description

Tools for internal data structure exploration

Usage

DistEco(data, distance.method = "inner_product", transpose = TRUE,
  symm = FALSE, plot = c("heatmap", "network"),
  palette = "colorblind", spinglass = TRUE, run = 10,
  spinglass.groups = c("rounded", "raw"), manual.groups = NULL,
  return.network = TRUE, ...)

Arguments

data

A community or environmental matrix, containing species or variables as columns and sites as rows.

distance.method

The distance method to be used for the calculation of the distance matrix. Must be one of philentropy::distance

transpose

Logical. If TRUE, the distance matrix is calculated between species. If FALSE, it is calculated between sites.

symm

Logical indicating if x should be treated symmetrically; can only be true when x is a square matrix. See stats::heatmap.

plot

The kind of plot produced by the function. Can be <U+201C>heatmap<U+201D> or <U+201C>network<U+201D>.

palette

The colour palette for the network, if spinglass = TRUE. Must be one of the palettes supported by qgraph. Default to <U+201C>colorblind<U+201D>.

spinglass

Logical. Whether or not to run a spinglass algorithm to produce statistical groups for the network. The spinglass algorithm is performed with the CommunityNetwork function.

run

Number of runs for the spinglass algorithm. Higher numbers produce more trustable results but rapidly increase computation time. Default to 10.

spinglass.groups

If spinglass = TRUE, the type of grouping to use from the results of the spinglass algorithm. See Details.

manual.groups

If spinglass = FALSE, an object that indicates which nodes belong together. Can be a list in which each element is a vector of integers identifying the numbers of the nodes that belong together, or a factor.

return.network

Logical. If TRUE, the qgraph object is returned as output of the function.

...

Additionnal parameters for heatmap or qgraph.

Value

A plot corresponding to the plot argument.

Examples

# NOT RUN {
 ### Artificial data:
 SyntheticTrial <- SyntheticData(SpeciesNum = 21, CommunityNum = 3,
                                 SpCo = NULL, Length = 500,
                                 Parameters = list(a=rep(60, 3),
                                                 b=c(0,250,500),
                                                 c=rep(0.01,3)),
                                 pal = c("#008585", "#FBF2C4", "#C7522B"))

 ## Network of species, with raw spinglass groups:
 DistEco(SyntheticTrial[,2:ncol(SyntheticTrial)], transpose = TRUE,
         plot = c("network"), spinglass = TRUE, run = 10,
         spinglass.groups = c("raw"))

 ## Heatmap of species:
 DistEco(SyntheticTrial[,2:ncol(SyntheticTrial)], transpose = TRUE,
         symm = FALSE, plot = c("heatmap"))


# }