PAM_indices {biosurvey}R Documentation

Biodiversity indices derived from PAM


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


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



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.


(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.


(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 SoberĂ³n 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.

See Also



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

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

pam_ind <- PAM_indices(pam, exclude_column = 1)

[Package biosurvey version 0.1.1 Index]