Description Usage Arguments Details Value Author(s) References Examples
Calculate one of a variety of measures of mating synchrony.
1 2 3 
scene 
a matingScene object that includes the flowering schedule for the scene of interest. 
method 
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. "peakn" 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. "peakobservations" 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. "averagepeak" calculates the average (determined by argument

subject 
one of "population", "pairwise", "individual", or "all"  see Value for more details. 
averageType 
character. Identifies whether to take the mean or median when calculating averages 
syncNN 
integer between 1 and n1 (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 
compareToSelf 
logical. Whether or not to include self comparisons when calculation synchrony. Defaults to FALSE. 
frame 
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'. 
resolution 
if 
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
input for subject
:
If subject
is "population" synchrony
will return a numeric
value that has a range depending on the method
. If
subject
is "pairwise" synchrony
will return a matrix
with all pairwise synchrony comparisons. It is important to note two things:
[1] if method
is set to "sync_nn" then the pairwise comparisons will
be in descending order and cannot be indexed by ID order. [2] if
compareToSelf
is set to FALSE, the matrix will have dimensions 100
rows by 99 columns. Similar to overlap
, indexing will be
affected. If subject
is "individual" synchrony
will
returns a data frame with a row for id and a row for individual synchrony.
If subject
is "all" synchrony
will return a list
containing the values described above for population, pairwise, and
individual synchrony.
Danny Hanson
Augspurger, C.K. (1983) Phenology, flowering synchrony, and fruit set of
six neotropical shrubs. Biotropica 15, 257267.
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, 180189
Kempenaers, B. (1993) The use of a breeding synchrony index.
Ornis Scandinavica, 24, 1.
1 2 3 4 5  pop < simulateScene(size = 150)
synchrony(pop, "augs")
pop2 < simulateScene(size = 1234, sdDur = 5, sk = 1)
syncVals < synchrony(pop2, "sync_nn", "all", "median", 123)

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