EcotoneFinderSeries {EcotoneFinder}

Extension of EcotoneFinder for space/time series

Description

Extension of EcotoneFinder for space/time series

Usage

EcotoneFinderSeries(data, dist, series = NULL, method = c("dca",
  "fanny", "vegclust", "diversity", "cmeans", "all"), groups = NULL,
  m.exp = 2, standardize = NULL, diversity = c("shannon", "richness",
  "expShannon", "pielou", "all"), na.rm = FALSE)

Arguments

data

A list of dataframes corresponding to the series or a single dataframe with a series factor. Species must appear as columns.

dist

A vector or column containing the gradient along which the analysis will be done. Must be of the same lenght as data.

series

If data is a single dataframe, must be the name or the number of the factor column identifying the series.

method

One of c("dca", "fanny", "vegclust", "diversity", "cmeans", "all"). Tell the function which analysis to perform. See details.

groups

Interger. The desired number of clusters if any of the clustering method is selected.

m.exp

Integer. The membership exponent for any of the clustering method.

standardize

Standardize method to apply to the data before further analysis (for fanny and cmeans). Must be one of decostand methods (see decostand).

diversity

diversity indice to be calculated. See details.

na.rm

Logical. Should NAs be removed.

Details

EcotoneFinderSeries is a generalisation of the EcotoneFinder function to handle space/time series of data. If a dataframe is provided, it will convert it internally to a named list according to the factor provided by the series argument. The methods of analysis and standardizations, as well as the diversity indices are the same as those of the EcotoneFinder function.

Value

A list of lists containing the outcomes of the EcotoneFinder function for each series.

Examples

 ############# Synthetic time series data:
 SyntheticTrialSeries <- SyntheticDataSeries(CommunityPool = 40,
                                             CommunityNum = 4, SpCo = NULL,
                                             Length = 500, SeriesNum = 5,
                                             Parameters = list(a=rep(60, 4),
                                                               b=c(0,200,350,500),
                                                               c=rep(0.03,4)),
                                             dev.c = .015,
                                             pal = c("#008585", "#B8CDAE", "#E6C186", "#C7522B"),
                                             replacement = FALSE,
                                             Parameters.repl = TRUE)

 EcoTimeSeriesTrial <- EcotoneFinderSeries(data = SyntheticTrialSeries,
                                           dist = "Distance", method = "cmeans",
                                           series = "Time", groups = 4,
                                           standardize = "hellinger", na.rm = TRUE)