David Bapst dwbapst

## count words in PDFs.R

library(pdftools)
# finds files in current directory
pdfs <- list.files(pattern = "pdf",  full.names = TRUE)

# uses pdftools to convert pdfs to plain-text, replaces line breaks with spaces
  # and then counts the words, ignoring non-word symbols
readCleanCount<-function(pdf){
	txt<-pdf_text(pdf)
	txt<-paste(gsub(txt,pattern="\r\n",replace=" "),collapse=" ")

## stepAIC forward example.R
#So here's an example of that


x<-rnorm(100)
y<-rnorm(100)
z<-rnorm(100)
xy<-x+2*y+rnorm(100)

# everything needs to be in a dataframe
data<-data.frame(xy,x,y,z)

## myBiPlot.R
# x is the score for the horizontal axis, xx is the loading for that axis
# y is the score for the vertical axis, yy is the loading for that axis
# and the labels for each can also be set

myBiPlot<-function(x,y,xx,yy
		,xlab="",ylab=""
		,xxlab="",yylab=""){
	oldPar<-par(no.readonly=TRUE)
	par(mar=c(5,5,5,5))
	#

## nest migration script 03-28-18
# for nest migrations - source functions, modify vectors of lists of nesting species, then run
# use kable to produce markdown table for pasting to Silph Road

#approximate ranges for each species in the nesting lists
getRangesForNestingSpecies<-function(nestingSpecies, arbMax=256){
	nNesting<-length(nestingSpecies)
	intLength<-arbMax/nNesting
	lowBound<-((1:nNesting)-1)*intLength
	upperBound<-lowBound+intLength
	res<-cbind(lowBound,upperBound)

## Forced Nest Migration Script 09-14-18.R
# for nest migrations - source functions, modify vectors of lists of nesting species, then run
# use kable to produce markdown table for pasting to Silph Road

#approximate ranges for each species in the nesting lists
getRangesForNestingSpecies<-function(nestingSpecies, arbMax=256){
	nNesting<-length(nestingSpecies)
	intLength<-arbMax/nNesting
	lowBound<-((1:nNesting)-1)*intLength
	upperBound<-lowBound+intLength
	res<-cbind(lowBound,upperBound)

## calculating_league_CPs_stats_01-08-18.R

setwd("D:\\dave\\fun\\Pokemon\\analyses of pokemon stuff\\PvP Analysis")

# CP_multiplier
CP_multiplier<-c(0.094, 0.135137432, 0.16639787, 0.192650919, 0.21573247, 0.236572661,
	 0.25572005, 0.273530381, 0.29024988, 0.306057377, 0.3210876, 0.335445036, 0.34921268,
	 0.362457751, 0.37523559, 0.387592406, 0.39956728, 0.411193551, 0.42250001, 0.432926419,
	 0.44310755, 0.453059958, 0.46279839, 0.472336083, 0.48168495, 0.4908558, 0.49985844,
	 0.508701765, 0.51739395, 0.525942511, 0.53435433, 0.542635767, 0.55079269, 0.558830576,
	 0.56675452, 0.574569153, 0.58227891, 0.589887917, 0.59740001, 0.604818814, 0.61215729,

## cutting_early_divergences_from_trees_03-12-19.html
<!DOCTYPE html>

<html xmlns="http://www.w3.org/1999/xhtml">

<head>

<meta charset="utf-8" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />

## make_78taxon_phylopic_tree.R

devtools::install_github("dwbapst/paleotree", ref="dev_refinedphylopicfun")
library(paleotree)

taxaSeventyEight <- c(
	"Archaeopteryx", "Pinus", "Procoptodon", "Olenellus", "Eldredgeops",
	"Quetzalcoatlus", "Homo", "Tyrannosaurus", "Triceratops", "Giraffa",
	"Bolivina", "Cancer", "Dicellograptus", "Dunkleosteus", "Solanum",
	"Anomalocaris", "Climacograptus", "Halysites", "Cyrtograptus",
	"Procoptodon", "Megacerops", "Moropus", "Dimetrodon", "Lingula",

## Cal3_minMax_problem.R
library(paleotree)


#Simulate some fossil ranges with simFossilRecord
set.seed(444)
record<-simFossilRecord(p=0.1, q=0.1, nruns=1,
                        nTotalTaxa=c(30,40), nExtant=0)
taxa<-fossilRecord2fossilTaxa(record)
#simulate a fossil record with imperfect sampling with sampleRanges
rangesCont <- sampleRanges(taxa,r=0.5)

## remove_pika_aipom_05-06-19.R

filename <- "remove_pika_aipom"

# remove taxa
removeTaxa <- c("Pikachu", "Aipom")


####################################
###################################

	library(pdftools)
	# finds files in current directory
	pdfs <- list.files(pattern = "pdf", full.names = TRUE)

	# uses pdftools to convert pdfs to plain-text, replaces line breaks with spaces
	# and then counts the words, ignoring non-word symbols
	readCleanCount<-function(pdf){
	txt<-pdf_text(pdf)
	txt<-paste(gsub(txt,pattern="\r\n",replace=" "),collapse=" ")
	#So here's an example of that


	x<-rnorm(100)
	y<-rnorm(100)
	z<-rnorm(100)
	xy<-x+2*y+rnorm(100)

	# everything needs to be in a dataframe
	data<-data.frame(xy,x,y,z)
	# x is the score for the horizontal axis, xx is the loading for that axis
	# y is the score for the vertical axis, yy is the loading for that axis
	# and the labels for each can also be set

	myBiPlot<-function(x,y,xx,yy
	,xlab="",ylab=""
	,xxlab="",yylab=""){
	oldPar<-par(no.readonly=TRUE)
	par(mar=c(5,5,5,5))
	#
	# for nest migrations - source functions, modify vectors of lists of nesting species, then run
	# use kable to produce markdown table for pasting to Silph Road

	#approximate ranges for each species in the nesting lists
	getRangesForNestingSpecies<-function(nestingSpecies, arbMax=256){
	nNesting<-length(nestingSpecies)
	intLength<-arbMax/nNesting
	lowBound<-((1:nNesting)-1)*intLength
	upperBound<-lowBound+intLength
	res<-cbind(lowBound,upperBound)

	setwd("D:\\dave\\fun\\Pokemon\\analyses of pokemon stuff\\PvP Analysis")

	# CP_multiplier
	CP_multiplier<-c(0.094, 0.135137432, 0.16639787, 0.192650919, 0.21573247, 0.236572661,
	0.25572005, 0.273530381, 0.29024988, 0.306057377, 0.3210876, 0.335445036, 0.34921268,
	0.362457751, 0.37523559, 0.387592406, 0.39956728, 0.411193551, 0.42250001, 0.432926419,
	0.44310755, 0.453059958, 0.46279839, 0.472336083, 0.48168495, 0.4908558, 0.49985844,
	0.508701765, 0.51739395, 0.525942511, 0.53435433, 0.542635767, 0.55079269, 0.558830576,
	0.56675452, 0.574569153, 0.58227891, 0.589887917, 0.59740001, 0.604818814, 0.61215729,
	<!DOCTYPE html>

	<html xmlns="http://www.w3.org/1999/xhtml">

	<head>

	<meta charset="utf-8" />
	<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
	<meta name="generator" content="pandoc" />

	devtools::install_github("dwbapst/paleotree", ref="dev_refinedphylopicfun")
	library(paleotree)

	taxaSeventyEight <- c(
	"Archaeopteryx", "Pinus", "Procoptodon", "Olenellus", "Eldredgeops",
	"Quetzalcoatlus", "Homo", "Tyrannosaurus", "Triceratops", "Giraffa",
	"Bolivina", "Cancer", "Dicellograptus", "Dunkleosteus", "Solanum",
	"Anomalocaris", "Climacograptus", "Halysites", "Cyrtograptus",
	"Procoptodon", "Megacerops", "Moropus", "Dimetrodon", "Lingula",
	library(paleotree)


	#Simulate some fossil ranges with simFossilRecord
	set.seed(444)
	record<-simFossilRecord(p=0.1, q=0.1, nruns=1,
	nTotalTaxa=c(30,40), nExtant=0)
	taxa<-fossilRecord2fossilTaxa(record)
	#simulate a fossil record with imperfect sampling with sampleRanges
	rangesCont <- sampleRanges(taxa,r=0.5)

	filename <- "remove_pika_aipom"

	# remove taxa
	removeTaxa <- c("Pikachu", "Aipom")



	####################################
	###################################