cheuerde

file_journals <- ReadBib("journals.bib")
dates <- unlist(unique(file_journals$year))[order(unlist(unique(file_journals$year)),decreasing = TRUE)]

#Prints recerences
for (date in dates) {
  cat(paste0("##",date),"\n")
  print(file_journals[list(year=date)],.opts = list(style="markdown",bib.style ="authoryear" ,max.names =10,dashed=FALSE))
  cat("\n")
}

cheuerde

name: "Alex_Singleton"
navbar:
  title: "Alex Singleton"
  left:
    - text: "Publications"
      icon: fa-book  fa-2x
      href: publications.html
    - text: "CV"
      icon: fa-file  fa-2x
      href: cv.html

cheuerde

// Claas Heuer, February 2016
//
// Note: This is copied and modified form the sources of the 
// cran package: 'pedigreemm'
#include <R.h>
#include <Rdefines.h>
#include "Rcpp.h"


/**

cheuerde

# Claas Heuer, August 2016
#
# Wrapper for standalone software "GEMMA"
# http://www.xzlab.org/software.html
# NOTE: the binary executable "gemma" must be
# in $PATH (e.g.: sudo cp gemma /usr/bin/)

# Y is a matrix of phenotypes (each column one trait).
# Z is the matrix of marker covariates.
# G is a genomic relationship matrix, may be NULL (then GEMMA will compute it).

cheuerde

# Claas Heuer, July 2016
#
# Stan model for multivariate mixed model with two
# random effects that can be specified by
# their according design matrices
# Help for the LKJ prior from here: http://stla.github.io/stlapblog/posts/StanLKJprior.html

library(pacman)
pacman::p_load(rstan, BGLR, shinystan)

cheuerde

# Claas Heuer, July 2016
#
# Stan model for bivariate mixed model with two
# random effects that can be specified by
# their according design matrices

library(pacman)
pacman::p_load(rstan, BGLR, shinystan)

mvntest <- "

cheuerde

# Claas Heuer, July 2016
#
# Vifm is a midnight commander like two-pane file
# manager for the terminal.
# Very intuitive to use for vim users
#
# https://github.com/vifm/vifm
# https://github.com/vifm/vifm-colors
# http://vifm.info/colorschemes.shtml
# http://vifm.info/manual.shtml#Pane manipulation

cheuerde

# Claas Heuer, July 2016
#
# Run Dropbox on a linux server

# from here: https://www.dropbox.com/install?os=lnx

# get and extract dropbox
cd ~ && wget -O - "https://www.dropbox.com/download?plat=lnx.x86_64" | tar xzf -

# run for first time ussing x-forwarding and setup sync

cheuerde

# Claas Heuer, February 2016
#
# Maximum Likelihood Estimation of parameters of bivariate normal distribution.
# We attempt to estimate the correlation between the two random vectors
# (as well as means and variances). A prior on the correlation coefficient 
# is put that forces that estimate between -1 and 1.
# We do something similar for the variance components to force
# those to be positive.

library(mvtnorm)

cheuerde

# from here: http://doingbayesiandataanalysis.blogspot.com/2012/06/mixture-of-normal-distributions.html

library(rjags)

modelstring <- "
model {
    # Likelihood:
    for( i in 1 : N ) {
      y[i] ~ dnorm( mu[i] , tau[i] ) 
      mu[i] <- muOfClust[ clust[i] ]