Nothing
## ----echo = FALSE-------------------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
## -----------------------------------------------------------------------------
library(conStruct)
data(conStruct.data)
## ----eval=FALSE---------------------------------------------------------------
# # load the example dataset
# data(conStruct.data)
#
# # run a conStruct analysis
#
# # you have to specify:
# # the number of layers (K)
# # the allele frequency data (freqs)
# # the geographic distance matrix (geoDist)
# # the sampling coordinates (coords)
#
# my.run <- conStruct(spatial = TRUE,
# K = 3,
# freqs = conStruct.data$allele.frequencies,
# geoDist = conStruct.data$geoDist,
# coords = conStruct.data$coords,
# prefix = "spK3")
## ----eval=FALSE---------------------------------------------------------------
# # load the example dataset
# data(conStruct.data)
#
# # run a conStruct analysis
#
# # you have to specify:
# # the number of layers (K)
# # the allele frequency data (freqs)
# # the sampling coordinates (coords)
# #
# # if you're running the nonspatial model,
# # you do not have to specify
# # the geographic distance matrix (geoDist)
#
# my.run <- conStruct(spatial = FALSE,
# K = 2,
# freqs = conStruct.data$allele.frequencies,
# geoDist = NULL,
# coords = conStruct.data$coords,
# prefix = "nspK2")
## ----eval=FALSE---------------------------------------------------------------
# my.run <- conStruct(spatial = TRUE,
# K = 3,
# freqs = conStruct.data$allele.frequencies,
# geoDist = conStruct.data$geoDist,
# coords = conStruct.data$coords,
# prefix = "spK3",
# n.chains = 1,
# n.iter = 1000,
# make.figs = TRUE,
# save.files = TRUE)
## ----echo=FALSE,fig.width=7,fig.height=2.7------------------------------------
par(mfrow=c(1,3),mar=c(4,3,1.5,1))
plot(c(0,rnorm(500,1,0.2)),type='l',
xlab="",yaxt='n',ylab="")
mtext(side=2,text="parameter estimate",padj=-1)
mtext(side=3,text="(a) looks good",padj=-0.1)
plot(c(0,rnorm(500,c(log(seq(0,1,length.out=500))),0.2)),type='l',
xlab="",yaxt='n',ylab="")
mtext(side=1,text="mcmc iterations",padj=2.6)
mtext(side=3,text="(b) hasn't converged",padj=-0.1)
plot(c(0,rnorm(150,1,0.2),rnorm(200,3,0.2),rnorm(150,1,0.2)),type='l',
xlab="",yaxt='n',ylab="")
mtext(side=3,text="(c) multi-modal",padj=-0.1)
## ----echo=FALSE,fig.width=7,fig.height=3--------------------------------------
w <- matrix(rnorm(40,sample(2:10,40,replace=TRUE),1),
nrow=20,ncol=2)
w <- w/rowSums(w)
w <- cbind(pmax(rnorm(20,0.15,0.005),0),w)
w <- w/rowSums(w)
conStruct::make.structure.plot(w)
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