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# A species list, which ecologies often have, but may not know the family names, or if they do, 
# they (meaning me) may spell the names wrong from time to time
> splist <- c("annona_cherimola", 'annona_muricata', "quercus_robur", 
  "shorea_robusta", "pandanus_patina", "oryza_sativa", "durio_zibethinus",
  "rubus_ulmifolius", "asclepias_curassavica", "pistacia_lentiscus")

# Get the Taxonomic Serial Number for each species, which are unique (note that there could be many TSN's within a species 
# for each subspecies for example. So you may want to query for you species using get_itis_xml in the demos on the github
# site and then make sure you get the TSN for the right subspecies or species
> tsns <- laply(splist, get_tsn, searchtype = "sciname", by_ = "name", 

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> berkey98
          trial pubyear npat   PD    AL var_PD cov_PD_AL var_AL
1 Pihlstrom1983    1983   14 0.47 -0.32 0.0075    0.0030 0.0077
2    Lindhe1982    1982   15 0.20 -0.60 0.0057    0.0009 0.0008
3   Knowles1979    1979   78 0.40 -0.12 0.0021    0.0007 0.0014
4  Ramfjord1987    1987   89 0.26 -0.31 0.0029    0.0009 0.0015
5    Becker1988    1988   16 0.56 -0.39 0.0148    0.0072 0.0304

> model <- mvmeta(cbind(PD,AL),S=berkey98[6:8],data=berkey98,lab=list(mlab=trial))

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# Intro Tutorial to R
# Scott Chamberlain <myrmecocystus@gmail.com>
# w/ code edited from Nathan Kraft and Dan Bunker

##########    HELP     ##########
# Getting Help with R on listserves online, etc.
# Go here for correct way to make reproducible examples to submit to help lists:
#   https://github.com/hadley/devtools/wiki/Reproducibility

# Code writing style:

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ezLev=function(x,new_order){
  for(i in rev(new_order)){
		x=relevel(x,ref=i)
	}
	return(x)
}

ggcorplot = function(data,var_text_size,cor_text_limits){
	# normalize data
	for(i in 1:length(data)){

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####################################################### 
#### Created by Rolf Lohaus, EEB Dept., Rice University
####
#### Part of the code modified and extended from 
####    Robert I. Kabacoff's Quick-R website 
####    (http://www.statmethods.net)
#######################################################

###############  HIGH-LEVEL PLOTTING FUNCTIONS  ###############

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######################################
## Function that organizes the data so that PGLMM can be fit
## Created by Matthew Helmus
######################################

PGLMM.data<-function(modelflag=1,sim.dat=NULL,samp=NULL,tree=NULL,traits=NULL,env=NULL,Vcomp=NULL)
{ 
  if (!require(ape))
    {
      stop("The 'ape' package is required")

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######################################
## Function calls a PGLMM for logistic regression
## Created by Matthew Helmus
######################################

PGLMM.fit<-function(dat=NULL,Y=NULL,X=NULL,VV=NULL,sp.init=0.5,maxit=25,exitcountermax=50) # [B,B0,s,S95int,LL,flag]=PGLMM_nosparse_funct(Y,X,VV,s)
{
    if (!require(corpcor))
    {
      stop("The 'corpcor' package is required")

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######################################
## Created by Matthew Helmus
######################################


PGLMM.reml<-function(sp)
{
  #global tH tinvW tVV tX

  sp<-abs(Re(sp))

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# library(plotrix)
# library(ape)


# PGLMM_model_simulations.m

# Simulates models used to test the PGLMM models
# 23 June 2010 MATLAB CODE
# 6 September 2011 R CODE TRANSLATION - HELMUS

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# Example Code
# Load functions 
source("/path/where/you/have/this/file/PGLMM.data.R")
source("/path/where/you/have/this/file/PGLMM.fit.R")
source("/path/where/you/have/this/file/PGLMM.reml.R")
source("/path/where/you/have/this/file/PGLMM.sim.R")


# Simulate a dataset for the example
modelflag <- 1