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PSIMEX (version 1.1)

SIMEX Algorithm on Pedigree Structures

Description

Generalization of the SIMEX algorithm from Cook & Stefanski (1994) for the calculation of inbreeding depression or heritability on pedigree structures affected by missing or misassigned paternities. It simulates errors and tracks the behavior of the estimate as a function of the error proportion. It extrapolates back a true value corresponding to the null error rate.

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Version

Install

install.packages('PSIMEX')

Monthly Downloads

16

Version

1.1

License

GPL (>= 2)

Maintainer

Erica Ponzi

Last Published

August 28th, 2017

Functions in PSIMEX (1.1)

PSIMEX-package

PSIMEX
Psimex

Pedigree SIMEX
data

Trait data
extrapolation

Extrapolation phase for the SIMEX algorithm on pedigrees
fit.nls

Fitting a non linear function on the data
initial

Calculation of the initial error prone value for inbreeding depression
plot.Psimex

A plot illustrating the extrapolation phase of the P-SIMEX algorithm
plot.simul.Psimex

A plot illustrating the simulation phase of the P-SIMEX algorithm
simul.na.top.herit

Simulation phase for P-SIMEX on heritability with missing paternities and errors in the first generations of the pedigree.
simul.na.uni

Simulation phase for P-SIMEX on inbreeding depression with missing paternities and uniform errors.
simul.na.bottom.herit

Simulation phase for P-SIMEX on heritability with missing paternities and errors in the last generations of the pedigree.
simul.na.top

Simulation phase for P-SIMEX on inbreeding depression with missing paternities and errors in the first generations of the pedigree.
initial_herit

Calculation of the initial error prone value for heritability
pedigree

Pedigree data
simul.replace.similar

Simulation phase for P-SIMEX on inbreeding depression with misassignment error and replacement with similar individuals.
simul.replace.similar.herit

Simulation phase for P-SIMEX on heritability with misassignment error and replacement with similar individuals.
simul.replace.uni

Simulation phase for P-SIMEX on inbreeding depression with misassignment error and uniform replacement.
simul.replace.uni.herit

Simulation phase for P-SIMEX on heritability with misassignment error and uniform replacement.
simul.na.uni.herit

Simulation phase for P-SIMEX on heritability with missing paternities and uniform errors.
simul.replace

Simulation phase for the P-SIMEX with misassignment error.
simul.na

Simulation phase for the P-SIMEX with missing paternities.
simul.na.bottom

Simulation phase for P-SIMEX on inbreeding depression with missing paternities and errors in the last generations of the pedigree.