Calculate one of a variety of measures of mating synchrony.
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a matingScene object that includes the flowering schedule for the scene of interest.
character, partial matching allowed, describing what type
of synchrony will be calculated. "augspurger" is based on the method
described in Augspurger (1983). "kempenaers" is based on the method
described in Kempenaers (1993). "sync_prop" will calculate individual
synchrony based on the proportion of the sum of all individuals' days
available to mate that coincided with the individual's days available for mating.
"overlap" is based on the method described in Ison et al. (2014) and will
calculate a synchrony value based on the number of days both
individuals were flowering divided by the number of days either individual
was available for mating. "sync_nn" gives the average of the kth nearest
neighbor, or rather the kth most synchronous individual. "peak-n" will
calculate the number of individuals receptive on the peak day
(day with highest mating receptivity) divided by the number of individuals
in the population. "peak-observations" will calculate the number of individuals
receptive on the peak day divided by the total number of observations -
this method is useful for comparing to data that has no information on
individuals. "average-peak" calculates the average (determined by argument
one of "population", "pairwise", "individual", or "all" - see Value for more details.
character. Identifies whether to take the mean or median when calculating averages
integer between 1 and n-1 (inclusive) or numeric between 0 and 1 (exclusive). The kth nearest neighbor to be averaged when calculating population synchrony. If k is in (0,1) then the k*nth nearest neighbor will be found
logical. Whether or not to include self comparisons when calculation synchrony. Defaults to FALSE.
the timeframe that synchrony is to be calculated over; options are 'within,' for synchrony within a season, or 'between,' for synchrony across multiple seasons. Defaults to 'within'.
Measures of synchrony are based on methods described in Augspurger (1983), Kempenaers (1983), and from Ison et al. (2014), as well as variations on different factors of those measures.
A potentials object containing one more more of the following, depending the
subject is "population"
synchrony will return a numeric
value that has a range depending on the
subject is "pairwise"
synchrony will return a matrix
with all pairwise synchrony comparisons. It is important to note two things:
method is set to "sync_nn" then the pairwise comparisons will
be in descending order and cannot be indexed by ID order.  if
compareToSelf is set to FALSE, the matrix will have dimensions 100
rows by 99 columns. Similar to
overlap, indexing will be
subject is "individual"
returns a data frame with a row for id and a row for individual synchrony.
subject is "all"
synchrony will return a list
containing the values described above for population, pairwise, and
Augspurger, C.K. (1983) Phenology, flowering synchrony, and fruit set of
six neotropical shrubs. Biotropica 15, 257-267.
Ison, J.L., S. Wagenius, D. Reitz., M.V. Ashley. (2014) Mating between Echinacea angustifolia (Asteraceae) individuals increases with their flowering synchrony and spatial proximity. American Journal of Botany 101, 180-189
Kempenaers, B. (1993) The use of a breeding synchrony index. Ornis Scandinavica, 24, 1.
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