Description Usage Arguments Value References Examples
View source: R/informed_matreorder.R
Implements the Informed MatReorder method described in Strauss & Holekamp (in revision) to infer a dominance hierarchy over multiple study periods. For each study period, ranks are inferred as modifications of the ranks from the previous study period. First, new contestants are added according to the convention specified by the user, and emigrated/dead contestants are removed. Then, matrix reordering is used to change the position of contestants for whom data from the current study period are inconsistent with this ordering. The optimal order is selected as the order that is most consistent with the data from the current period and is minimally changed from the previous study period.
1 2 3 4 5 6 7 8 9 | informed_matreorder(
contestants,
convention,
n = 50,
shuffles = 10,
require.corroboration = FALSE,
initial.ranks = NULL,
interactions
)
|
contestants |
A dataframe with the identities of the contestants for each study period along with the relevant data for adding them to the hierarchy. There should be one row per contestant per study period. Periods should appear in chronological order. The dataframe should contain the following columns:
|
convention |
A flag determining how new individuals are added to the hierarchy. The value of this flag influences how the convention1 and convention2 columns of the contestants argument are interpreted. Currently this function supports four options:
|
n |
Number of separate reordering attempts per study period. Recommended 100. |
shuffles |
Number of reshuffling steps per reordering attempt. Recommended at least 10. |
require.corroboration |
A logical indicating whether to require corroborating evidence from multiple study periods before changing a contestant's position in the order. Useful for reducing the sensitivity of the method to aberrant observations that don't reflect a lasting change in the true latent hierarchy. If true, evidence indicating a change in status must be corroborated by an additional observation in the following periods. See Strauss & Holekamp (in revision) for full details. |
initial.ranks |
The initial ordering of individuals for the first study period. Required if using maternal rank inheritance as the convention. For other conventions, if initial.ranks is not specified, the order determined by convention1 is used to create the initial order. |
interactions |
A dataframe of interaction data with the following columns:
|
Produces a dataframe with the following columns:
Study period.
Identity of contestant.
Ordinal rank of contestant in study period. Lower numbers equal higher rank.
Rank of contestant standardized for group size. Values range from 1 (highest rank) to -1 (lowest rank).
Identity of contestants arranged in the previous order (the order they were in before updating the order based on observations from current study period).
Strauss ED & Holekamp KE (in revision). Journal of Animal Ecology.
1 2 3 4 5 | conts <- C.crocuta.female$contestants[C.crocuta.female$contestants$period <= 1990,]
female.ranks <- informed_matreorder(contestants = conts,
convention = 'mri', n =1, shuffles = 10, require.corroboration = TRUE,
initial.ranks = C.crocuta.female$initial.ranks,
interactions = C.crocuta.female$interactions)
|
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