EstimateBreed (version 1.0.2)

tamef: Effective Population Size

Description

Estimates the effective population size (\(N_e\)) adapted from Morais (1997). The function provides two different calculation methods: 'classic' and 'alternative'.

The classic method follows the equation:

$$N_e = \frac{\left(\sum SI\right)^2}{\sum \left(\frac{SI^2}{NE}\right)}$$

The alternative method is calculated as:

$$N_e = \frac{4 \sum SI}{2 + \sum \left(\frac{SI}{NE}\right)}$$

Usage

tamef(GEN, SI, NE, remove_na = TRUE, method = "classic", verbose = TRUE)

Value

The result is the effective population size for any variable, based on the number of individuals conducted and selected.

Arguments

GEN

The column with the name of the genotype (progeny).

SI

The column with the number of individuals selected.

NE

Number of individuals conducted during the selection period.

remove_na

Logical argument. If 'TRUE', missing values will be removed.

method

Character string specifying the calculation method. Options are classic' (default) or 'alternative'. 'classic' uses the variance-based method, while 'alternative' uses an adjusted method that accounts for reproductive variation.

verbose

Logical argument. Runs the code silently if FALSE.

Author

Willyan Junior Adorian Bandeira

Ivan Ricardo Carvalho

Murilo Vieira Loro

Leonardo Cesar Pradebon

Jose Antonio Gonzalez da Silva

References

Morais, R. P. (1997). Effective population size and genetic diversity in improved populations of self-pollinated plants (Doctoral dissertation, University of Campinas).

Examples

library(EstimateBreed)

GEN <- c("Genotype1", "Genotype2", "Genotype3", "Genotype4", "Genotype5")
SI <- c(10, 15, 12, 18, 14)
NE <- c(100, 150, 120, 180, 140)
data <- data.frame(GEN,SI,NE)

with(data, tamef(GEN, SI, NE, method = "classic"))