mobify: Make a mob_in object from long data.frame

Description Usage Arguments Value

Description

This is a wrapper for make_mob_in() that accepts a long format data frame as input and converts it to a community matrix comm and a plot attribute table plot_attr. Both are then passed on to make_mob_in(). Furthermore, it has an option to exclude samples with low numbers of individuals and their respective gammas.

Usage

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mobify(dat, taxon = "verbatim_scientific_name", alpha_id = "alpha_id",
  gamma_id = NULL, count = "individual_count",
  coord_names = c("Longitude", "Latitude"), min_n = 5,
  exclude_gamma = T, ...)

Arguments

dat

A single long format data.frame with species observations as rows. Species name (i.e taxon), individual counts (i.e count), and corresponding sample level information (i.e alpha_id,gamma_id,coord_names) must be in columns. Additional colmns may be present, but must be consitent within samples (i.e. alpha_id's).

taxon

name of taxon column

alpha_id

name of alpha_id column. This assigns the observation to a sample at the alpha scale.

gamma_id

name of gamma_id column. This assigns the observation to a group at the gamma scale

count

name of the column containing the individual counts (i.e. abundances) of the observation.

coord_names

character vector with the names of the x and y coordinates.

min_n

numeric. minimal number of indiviual required for a sample to be considered.

exclude_gamma

boolean. If samples are excluded due to low sample size (see min_n), shall the entire group (i.e. gamma_id) be excluded?

...

arguments passed on to make_mob_in.

Value

a mob_in object.


T-Engel/hammeRs documentation built on May 22, 2019, 2:16 p.m.