Overall goodness-of-fit test for the Cormack-Jolly-Seber model

This function performs the overall goodness-of-fit test for the Cormack-Jolly-Seber model. It is obtained as the sum of the 4 components Test3.SR, Test3.SM, Test2.CT and Test2.CL.

overall_CJS(X, freq, rounding = 3)

Arguments

X	is a matrix of encounter histories
freq	is a vector of the number of individuals with the corresponding encounter history
rounding	is the level of rounding for outputs; default is 3

Value

This function returns a data.frame with the value of the test statistic, the degrees of freedom and the p-value of the test.

Author

Olivier Gimenez <olivier.gimenez@cefe.cnrs.fr>,Jean-Dominique Lebreton, Rémi Choquet, Roger Pradel

Examples

# read in the classical dipper dataset
dipper = system.file("extdata", "ed.inp", package = "R2ucare")
dipper = read_inp(dipper,group.df=data.frame(sex=c('Male','Female')))

# Get encounter histories, counts and groups:
dip.hist = dipper$encounter_histories
dip.freq = dipper$sample_size
dip.group = dipper$groups

# split the dataset in males/females
mask = (dip.group == 'Female')
dip.fem.hist = dip.hist[mask,]
dip.fem.freq = dip.freq[mask]
mask = (dip.group == 'Male')
dip.mal.hist = dip.hist[mask,]
dip.mal.freq = dip.freq[mask]

# for females
overall_CJS(dip.fem.hist, dip.fem.freq)
#>                           chi2 degree_of_freedom p_value
#> Gof test for CJS model: 10.276                12   0.592