summary.partition: Summarizing Partitioned Diversity

In partitionr/PARTITIONR: Heirarchical Partitioning of Diversity

Description

summary method for class "partition"

Usage

## S3 method for class 'partition'
summary(object, p.value = "one-sided", ...)

## S3 method for class 'summary_partition'
print(x, ...)

Arguments

object	an object of class "partition", a result of a call to partition
p.value	a character; if "one-sided", the p-values are interpreted at < observed and significance at p = 0.05. if "two-sided", the p-values are interpreted at both > and < observed and significance at p = 0.025.
...	additional arguments affecting the summary produced
x	an obect of class "summary_parition", a result of a call to summary.partition

Details

summary.partition tries to be smart about formating the observed and expected diversity values and significance.

P-values are calculated as 1 - ((# expected values < observed values)/# Simulations).

Errors will be thrown if p.value is not equal to either "one-sided" or "two-sided".

Value

The observed and mean expected values of alpha and beta diversity, as well as the the p-values (number of randomizations < observed diversity) of each diversity level and interpretations of these. Values are rounded to number of places given by 1/# Simulations

Test	"INDIVIDUAL" or "SAMPLE" randomization as specified in partition function
P-value	"one-sided" or "two-sided" interpretation of results
Randomizations	number of randomizations run as specified in partition function
q	Hill number as specified in partition function
Gamma	observed gammma (regional) diversity
Observed	observed lowest level alpha and additive and multiplicative beta diversities from the species matrix supplied to partition.
Expected	mean lowest level alpha and addtive and multiplicative beta diversities from randomizations of partition.
P(<Obs)	probability of an expected value being lower than the observed value based on number of randomizations

Significance interpretations depend on p.value: if "one-sided", the p-values are interpreted at < observed and significance at p = 0.05. If "two-sided", the p-values are interpreted at > and < observed and significance at p = 0.025; with 0.975 being significant probability of observed being less than expected.

See Also

The diversiting partitioning function partition.

Examples

## Not run: 
## One-tailed p-values
summary(partition.obj)

## Two-tailed p-values
summary(partition.obj, p.value = "two-sided")

## End(Not run)

partitionr/PARTITIONR documentation built on Dec. 3, 2019, 11:11 p.m.