sampling.robustness {ANTs}R Documentation

Metric robustness

Description

Performs a matrix boostrapping approach to estimate the confidence intervals surrounding each pairwise association.

Usage

sampling.robustness(
  df,
  subsampling = c(5, 10, 20, 30, 40, 50),
  metric = "met.strength",
  assoc.indices = FALSE,
  actor,
  receiver,
  scan,
  id,
  index = "sri",
  progress = TRUE,
  ...
)

Arguments

df

a data frame of individual associations

subsampling

a vector of integers indicating the percentage of data to remove

metric

the network metric to compute

assoc.indices

a bolean indicating if association indices must be used

actor

If argument assoc.indices is FALSE, fill this argument, an integer or a string indicating the column of the individuals performing the behaviour.

receiver

If argument assoc.indices is FALSE, fill this argument, an integer or a string indicating the column of the individuals receiving the behaviour.

scan

If argument assoc.indices is TRUE, fill this argument, a numeric or character vector representing one or more columns used as scan factors.

id

If argument assoc.indices is TRUE, fill this argument, a numeric or character vector indicating the column holding ids of individuals.

index

a string indicating the association index to compute:

progress

a boolean indicating if function should print progress.

...

additional argument related to the computation of the metric declared.

  • 'sri' for Simple ratio index: x/x+yAB+yA+yB

  • 'hw' for Half-weight index: x/x+yAB+1/2(yA+yB)

  • 'sr' for Square root index:x/sqr((x+yAB+yA)(x+yAB+yB))

Details

This process evaluates network metrics robustness by performing a bootstrap process to remove a certain percent of the data collected and recomputing the network metric of interest. This has been used in Balasubramaniam et al. 2018 to assess sensitivty of sampling effort of global network metrics in primate networks.

Value

3 elements:

Author(s)

Sebastian Sosa

References

Balasubramaniam, K. N., Beisner, B. A., Berman, C. M., De Marco, A., Duboscq, J., Koirala, S., ... & Ogawa, H. (2018). The influence of phylogeny, social style, and sociodemographic factors on macaque social network structure. American journal of primatology, 80(1), e22727.

Examples

#Example for node measures
test <- sampling.robustness(sim.focal.directed, actor = "actor", 
receiver = "receiver", metric = "met.strength")

# objects returned by the function
test$metrics
test$summary
test$plot

# Examples with metric extra arguments
sampling.robustness(sim.focal.directed, actor = "actor", 
                   receiver = "receiver", metric = "met.affinity")
sampling.robustness(sim.focal.directed, actor = "actor", 
                   receiver = "receiver", metric = "met.affinity", binary = FALSE)

# Examples with association data
test2 <- sampling.robustness(df = sim.grp, assoc.indices = TRUE,
                             scan = c("time", "location"), id = "ID", metric = "met.strength")

# Example of how to test global network metric robustness 
#by removing 10% of the observations simulated 100 times
test <- sampling.robustness(sim.focal.directed, subsampling = rep(10, 100),
                            actor = "actor", receiver = "receiver", metric = "met.diameter")

[Package ANTs version 0.0.16 Index]