Summarizing lmf fits

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Description

summary method for class "lmf".

Usage

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  ## S3 method for class 'lmf'
summary(object, what.level = c("age", "year", "total"), ...)
  ## S3 method for class 'summary.lmf'
print(x, digits = max(3, getOption("digits") - 3),
  signif.stars = getOption("show.signif.stars"), ...)

Arguments

object

an object of class "lmf".

what.level

the lowest level of organisation at which parameters should be summarized. Options are "age" to summarize from the level of specific age classes, "year" to summarize from the level of years and "total" (default) to summarize the temporal parameters.

x

an object of class "summary.lmf".

digits

the number of significant digits to use when printing.

signif.stars

logical. If TRUE, 'significance stars' are printed for each coefficient.

...

further arguments passed to or from other methods.

Details

print.summary.lmf formats the coefficients, standard errors and variance-covariance matrices into easily read tables. The tests of significance of the coefficients of selection should be considered as suggestive and should be interpreted with caution. For tests of signifcanse a robust approach is provided through the function boot.lmf.

Value

The function summary.lmf computes and returns a list of summary statistics of the fitted lmf model given in object.

An object of class "summary.lmf" is a list containing at most the following components:

call

the matched call.

what.level

the lowest level of organisation at which parameters should be summarized.

uage

the unique age classes in the data set.

nage

the number of unique age classes in the data set.

uyear

the unique years in the data set.

nyear

the number of unique years in the data set.

l

the estimated projection matrix.

lambda

the deterministic multiplicative growth rate of the population.

u

the stable age distribution.

v

the vector of reproductive values for each age class.

sigma2.e

the environmental variance of the population.

sigma2.dj

a list containing the demographic variance for each age class. Sorted by age class.

sigma2.dj.dof

a list containing the degrees of freedom (dof) for the demographic variance for each age class. Sorted by age class.

sigma2.dj.sd

a list containing the standard deviation (sd) for the demographic variance for each age class. Sorted by age class.

sigma2.d

the total demographic variance of the population.

sigma2.d.dof

the degrees of freedom (dof) for the total demographic variance of the population.

sigma2.d.sd

the standard deviation (sd) for the total demographic variance of the population.

coefficients.ajt

the estimated selection coefficients for each age class within each year, with standard errors, t values and p-values.

Ajt

a list containing the named variance-covariance matrix for each age class within each year. Sorted by age class and year.

coefficients.at

the estimated selection coefficients within each year, with standard errors, t values and p-values.

At

a list containing the named variance-covariance matrix for each year. Sorted by year.

coefficients.atC

the estimated selection coefficients within each year corrected for sampling error, with standard errors, t values and p-values.

coefficients.aM

the estimated temporal mean selection coefficients, with standard errors, t values and p-values.

M

the estimated temporal covariance matrix (fluctuating selection).

coefficients.anf

the estimated temporal mean selection coefficients under the assumtion of no fluctuating selection, with standard errors, t values and p-values.

Anf

the estimated temporal covariance matrix assuming no fluctuating selection.

Author(s)

Thomas Kvalnes

See Also

lmf, summary, boot.lmf

Examples

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#Data set from Engen et al. 2012
data(sparrowdata)
#Fit model
lmf.1 <- lmf(formula = cbind(recruits, survival) ~ weight + tars,
               age = age, year = year, data = sparrowdata)
#Summary
summary(lmf.1)
#Summary from within years
summary(lmf.1, what.level = "year")
#Summary from within age classes
summary(lmf.1, what.level = "age")