PAM_indices: Biodiversity indices derived from PAM
In biosurvey: Tools for Biological Survey Planning

Description Usage Arguments Details Value See Also Examples

Calculates a set of biodiversity indices using values contained in a presence-absence matrix.

1	PAM_indices(PAM, indices = "all", exclude_column = NULL)

`PAM`	matrix, data.frame, or base_PAM object containing information on species presence and absence for a set of sites. Sites are organized in the rows and species in the columns. See details.
`indices`	(character) code for indices to be calculated. Basic indices are calculated all the time; other indices need to be specified. Options are: "all", "basic, "AB", "BW", "BL", "SCSC", "SCSR", "DF", "CC", "WRN", "SRC", "CMSC", "CMSR", "MCC", and "MRC". Default = "all". See details.
`exclude_column`	(optional) name or numeric index of columns to be excluded. Default = NULL.

Descriptions of the codes of all indices to be calculated are presented in the table below. If indices = "basic", only basic indices are calculated. However, basic indices are calculated in all cases not matter the code(s) defined in indices. Some indices require previous calculations of other indices, in such cases, all indices required are added to the final list. For further details on the way calculations are performed and the meaning of the indices see Soberón and Cavner (2015) doi: 10.17161/bi.v10i0.4801.

Code	Index	Calculation
RI	Richness	Basic
RA	Range	Basic
RIN	Richness normalized	Basic
RAN	Range normalized	Basic
AB	Additive Beta	Needs to be defined
BW	Beta Whittaker	Needs to be defined
BL	Beta Legendre	Needs to be defined and DF
SCSC	Schluter covariance sites-composition	Needs to be defined and CMSC
SCSR	Schluter covariance species-ranges	Needs to be defined and CMSR
DF	Dispersion field	Needs to be defined
SCC	Shared community composition	Needs to be defined
WRN	Wright-Reeves nestedness	Needs to be defined, BW, and DF
SRC	Stone-Roberts C-score	Needs to be defined and DF
CMSC	Covariance matrix sites-composition	Needs to be defined, DF, and BW
CMSR	Covariance matrix species-ranges	Needs to be defined, SCC, and BW
MCC	Mean composition covariance	Calculated with CMSC
MRC	Mean range covariance	Calculated with CMSR

If PAM is a matrix or data.frame, the result is a list with the results described below (depending on indices). If PAM is a base_PAM object, a base_PAM object will be returned and the list described above will be appended to the element PAM_indices in such an element.

prepare_base_PAM

# Data
data("sp_data", package = "biosurvey")

# PAM
pam <- PAM_from_table(data = sp_data, ID_column = "ID",
                      species_column = "Species")

pam_ind <- PAM_indices(pam, exclude_column = 1)
pam_ind[1:3]