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# Claas Heuer, July 2015

# first get svn
sudo apt-get install subversion

# get the r-forge project:
mkdir project
cd project

svn checkout svn+ssh://cheuer@r-forge.r-project.org/svnroot/cgen/

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# Claas Heuer, July 2015
# adopted from: http://www.r-bloggers.com/setup-up-the-inverse-of-additive-relationship-matrix-in-r/


ped <- data.frame( id=c(  1,   2,   3,   4,   5,   6,   7,   8,   9,  10),
                  fid=c( NA,  NA,   2,   2,   4,   2,   5,   5,  NA,   8),
                  mid=c( NA,  NA,   1,  NA,   3,   3,   6,   6,  NA,   9))

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# Claas Heuer, 2015

library(cpgen)
library(pedigreemm)
library(MCMCglmm)


setwd("/home/claas/kaki/Analysedaten")
X<-cscanx("Xa")

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# Claas Heuer, 2015

library(rjags)

# some data
n = 1296
p_success <- 0.94
x <- as.integer(p_success*n)
y <- c(rep(1,x),rep(0,n-x))

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# Claas Heuer, 2015

# plotting distributions (or any function) 
# is straightforward using the 'curve' function

# lets plot the pdf of a normal distribution with mean=0 and sd=1

curve(dnorm(x,0,1),from = -10, to = 10, n = 100)

# 'curve' evaluates the function given as first argument with one unknown over

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# Claas Heuer, 2015
# 
# Generating 2 random vectors 
# that have some given correlation
#

# actually, this is a covariance
cor = 0.98

# sample size

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library(MCMCglmm)

n = 10000

x <- rnorm(n)
y <- rnorm(n)

dat <- data.frame(x=x,y=y)
model <- MCMCglmm(cbind(y,x)~ -1 + trait,rcov= ~us(trait):units, data=dat, family=c("gaussian","gaussian"))

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# modified from Marvin Gertz, 2015
#
# Custom BLUP ############
    blupLHS <- function (formula, ped, data, alpha, trim = FALSE)
    {
        colnames(ped)[1:3] <- c("ID", "SIRE", "DAM")
        if (any(!all.vars(formula) %in% colnames(ped)))
            stop("Formula has variables which are not present in the data.")
        ww <- match(all.vars(formula)[-1], colnames(ped))
        ped$b <- apply(ped, 1, function(x) !any(is.na(x[ww])))

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# get dependencies

# X11 stuff
sudo yum install libXt-devel
sudo yum install libX11-devel

# readline
sudo yum install readline-devel

# get R

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# Centos 6.5 comes with very old packages
# first we need to get git

sudo yum install git

# then update binutils to build OpenBLAS 

# this is also needed 

sudo yum install texinfo