boot_networklevel_once: Bootstrap network level metric once.

In valentinitnelav/bootstrapnet: Bootstrap Network Metrics

Bootstrap network level metric once.

Description

You will rarely use this function alone. It was designed to be executed in parallel by boot_networklevel_n. See more details there.

Usage

boot_networklevel_once(
  data,
  col_lower,
  col_higher,
  index,
  level,
  start,
  step,
  seed,
  ...
)

Arguments

data	See boot_networklevel_n.
col_lower	See boot_networklevel_n.
col_higher	See boot_networklevel_n.
index	See boot_networklevel_n.
level	See boot_networklevel_n.
start	See boot_networklevel_n.
step	See boot_networklevel_n.
seed	Set seed to get reproducible random results. Passed to set.seed().
...	See boot_networklevel_n.

Value

Returns a data frame of one or two columns depending on the provided index metric and level value. For example if index='nestedness' and level='both', then it returns a one column data frame. But in case of index='niche overlap', it returns a two columns data frame, first column ('niche.overlap.HL') corresponding to the higher level (e.g. insects), and the second column ('niche.overlap.LL') for the lower level (e.g. plants). The number of rows in the returned data frame corresponds to the number of splits given by bootstrapnet:::sample_indices (is the length/number of elements of the list returned by this function). The last value(s) in the data frame correspond to the results of networklevel on the entire network - see in examples.

References

This function is a wrapper of networklevel.

Examples

library(bootstrapnet)
library(bipartite)
library(data.table)

data(Safariland)

df <- web_matrix_to_df(Safariland)
setDT(df) # df must be a data.table and not data.frame

# Example with "nestedness":

boot_networklevel_once(data = df,
                       col_lower = "lower", # column name for plants
                       col_higher = "higher", # column name for insects
                       index = "nestedness",
                       level = "both",
                       start = 100,
                       step = 100,
                       seed = 2020-11-5)
# Returns a one column data frame. The last value must equal the result of:
set.seed(42) # this is the same seed used in the boot_networklevel_once() function
bipartite::networklevel(table(df$lower, df$higher),
                       index = "nestedness")
# which is also the equivalent of:
Safariland_sorted <- Safariland[order(rownames(Safariland)), order(colnames(Safariland))]
set.seed(42)
bipartite::networklevel(Safariland_sorted, index = "nestedness")


# Example with "niche overlap":

boot_networklevel_once(data = df,
                       col_lower = "lower", # column name for plants
                       col_higher = "higher", # column name for insects
                       index = "niche overlap",
                       level = "both",
                       start = 100,
                       step = 100,
                       seed = 2020-11-5)
# Returns a two column data frame

valentinitnelav/bootstrapnet documentation built on June 5, 2024, 3:21 p.m.