gfitpca: Goodness of fit with principal component analysis

Description Usage Arguments Details Author(s) See Also Examples

Description

Perform a priori goodness of fit using the two first components obtained with PCA.

Usage

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gfitpca(target, sumstat, index, cprob=0.1, xlim=NULL, ylim=NULL, ...)

Arguments

target

a data frame or vector of the observed summary statistic.

sumstat

a matrix or data frame of the simulated summary statistics.

index

a vector of models names. It must be character and have the same length as the number of row in sumstat to indicate which row belong to which model.

cprob

cprob is the proportion of points outside the displayed envelope. Default to 0.1 which corresponds to a 90% envelope.

xlim, ylim

optional, numeric vectors of length 2, giving the x and y coordinates ranges.

...

other parameters passed to plot.

Details

The function performs PCA using the a priori simulated summary statistics. It displays envelopes containing 1-hprob percent of the simulations. The projection of the observed summary statistics is displayed in order to check if they are contained or not in the envelopes. If the projection lies outside the envelope of a given model, it is an indication of poor fit.

Author(s)

Louisiane Lemaire and Michael Blum

See Also

abc, plot.gfit, summary.gfit, gfit

Examples

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## human demographic history
require(abc.data)
data(human)
## five R objects are loaded. See ?human and vignette("abc") for details.

## Perform a priori goodness of fit for 3 different demographic models
## The envelopes containing 90% of the simulations are displayed.
## For the European data, a reasonable fit is only provided by the 
## bottleneck model.
## The number of simulations is reduced to improve speed (do not do that
## with your own data)
index<-c(1:5000,50001:55000,100001:105000)
gfitpca(target=stat.voight["italian",], sumstat=stat.3pops.sim[index,],
index=models[index], cprob=0.1)

Example output

Loading required package: abc.data
Loading required package: nnet
Loading required package: quantreg
Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve

Loading required package: MASS
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22

abc documentation built on May 2, 2019, 3:32 p.m.

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