Description Usage Arguments Details Value See Also Examples
epp
combines a SpatialPointsBreeding
, a
SpatialPolygons*
as obtained from DirichletPolygons
and a
eppMatrix
to create the spatial context for every potential and
realized extra-pair male-female combination.
1 2 3 4 5 6 7 8 9 10 |
breedingDat |
A SpatialPointsBreeding object, created by the
|
polygonsDat |
A SpatialPolygons* object as obtained by calling
|
eppDat |
An object of class |
maxlag |
A numeric value indicating the maximum breeding distance for which male-female combinations should be calculated. When plotting it defines the outermost row of neighbors plotted around a focal id set by zoom |
x, height |
an |
zoom |
a |
zoom.col |
background color of the id (and hence the polygon) set by
|
... |
further arguments to pass to |
relativeValues |
Defines the unit of the y-axis. TRUE plots proportions, FALSE absolute numbers. |
'plot' plots the territories, the identity of males ('m...') and females
('f...') at breeding sites (numbers), and the extra-pair events (dashed red
arrows). Individuals that had extra-pair offspring are marked red. The
parameter 'zoom' can be used to make a detailed visual check of a specific
location (nestbox) and its surroundings.
'barplot' displays the
distribution of extra-pair events over different breeding distances between
the partners (in the number of territories) as vertical bars. Note that the
distribution of all potential extra-pair partners is displayed as a dashed
line only if the argument 'relativeValues' is TRUE.
Returns an S4-class epp-object with 5 slots:
breedingDat |
Input breeding data-set. |
polygonsDat |
Either polygons are estimated automatically using Thiessen Polygons, or input breeding polygons. |
eppDat |
Input data.frame with all male-female combinations that had EPP together. |
maxlag |
Input rank. Defaults to 3. |
EPP |
|
vignette(expp)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 | ### Simple example with three breeding pairs
require(expp)
# create raw data
set.seed(1310)
b = data.frame(id = as.integer(10:12), x = rnorm(3), y = rnorm(3),
male = paste0("m",1:3), female = paste0("f",1:3), xx = rnorm(3), stringsAsFactors=FALSE )
eppPairs = data.frame(male = c("m1", "m2", "m1"), female=c("f3", "f1", "f2") )
# prepare data
breedingDat = SpatialPointsBreeding(b, id = 'id', coords = ~ x + y, breeding = ~ male + female)
polygonsDat = DirichletPolygons(breedingDat)
eppDat = eppMatrix(eppPairs, pairs = ~ male + female)
plot(breedingDat, eppDat)
# convert to epp class
x = epp(breedingDat, polygonsDat, eppDat, maxlag = 3)
as.data.frame(x)
#plot
plot(x)
### Example on a random data set with n breeding pairs and n/2 extra-pair paternity rate
# create raw data
set.seed(123)
n = 20
b = data.frame(id = 1:n, x = rnorm(n), y = rnorm(n),
male = paste0("m",1:n), female = paste0("f",1:n), xx = rnorm(n), stringsAsFactors=FALSE )
eppPairs = data.frame(male = sample(b$male, round(n/2) ), female = sample(b$female, round(n/2) ) )
# prepare data
breedingDat = SpatialPointsBreeding(b, id = 'id', coords = ~ x + y, breeding = ~ male + female)
polygonsDat = DirichletPolygons(breedingDat)
eppDat = eppMatrix(eppPairs, pairs = ~ male + female)
# convert to epp class
x = epp(breedingDat, polygonsDat, eppDat, maxlag = 10)
# plot
plot(x)
barplot(x)
barplot(x, relativeValues = TRUE)
### Real data example
# Raw datasets
data(bluetit_breeding)
data(bluetit_epp)
# select one year
year = 2010
b = bluetit_breeding[bluetit_breeding$year_ == year, ]
eppPairs = bluetit_epp[bluetit_epp$year_ == year, ]
# prepare data
breedingDat = SpatialPointsBreeding(b, id = 'id', coords = ~ x + y, breeding = ~ male + female)
polygonsDat = DirichletPolygons(breedingDat)
eppDat = eppMatrix(eppPairs, pairs = ~ male + female)
# convert to epp class
x = epp(breedingDat, polygonsDat, eppDat, maxlag = 2)
# plot
plot(x)
barplot(x)
# plot zoom
plot(x, zoom = 120, maxlag = 3)
# run model on epp probability
dat = as.data.frame(x)
nrow(dat[dat$epp == 1, c('male', 'female')] )
nrow(unique(eppPairs))
if(require(lme4))
(summary(glmer(epp ~ rank + male_age_MALE + (1|male) + (1|female),
data = dat, family = binomial)))
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