Oreotrephes

require(rvest)
output_file_name<-'output.txt'
for(i in 6174:45000){  #or 1, or whatever
  url <- paste0("http://naeb.brit.org/uses/",i) #
  message("Scraping ", url)
  use_page_i <- read_html(paste0("http://naeb.brit.org/uses/",i))
  links_i <- use_page_i %>% html_elements("a")
  species_i <- links_i[8] %>% html_text2()
  write(species_i,file=output_file_name,append=TRUE)
}

Oreotrephes

require(dplyr)

#Goal - collapse information from duplicate rows

name<-c("John","John","Frank","Frank","Sue","Sue","Bob")
rank<-c("","sergeant",""," ","lieutenant","major","")
force<-c("army","","navy","navy","army","army","navy")
testdf<-data.frame(name,rank,force)

testdf

Oreotrephes

#okay this seems to work fine:
#out of 816 rows to start with
#extracts corolla lengths for 611
#capsule lengths for 436
#both for 432

#I've checked the first 15 rows or so and spot check othres and this seems to be working.

#However, I'm don't know why the first function (capsule) seems to want greedy (ie. "capsule.*)
#while the second function (corolla) seems to want nongreedy (ie. "corolla.*?)

Oreotrephes

market.compare<-function(market.name,df,uses){
  this.market.uses<-df[df$Market==market.name,uses]
  other.market.uses<-df[df$Market!=market.name,uses]
  this.market.unique<-setdiff(this.market.uses,other.market.uses)
  this.market.total<-unique(this.market.uses)
  percent.unique<-length(this.market.unique)/length(this.market.total)
  percent.unique
  }

market.compare("Calle Santa Cruz",sample,"Medicinal.Use.categories")

Oreotrephes

#looks familiar
summaryfunction2<-function(x,y){
  signs<-substr(as.character(sign(x)),1,1)
  signs[signs=="1"]<-"+"
  significance<-cut(abs(y), c(0, 0.001, 0.01, 0.05, Inf), labels=c("***", "**", "*", ""), right=FALSE)
  paste(signs, significance)
}

#use that function in a function
process<-function(lm){

Oreotrephes

  summaryfunction2<-function(x,y){
  signs<-substr(as.character(sign(x)),1,1)
  signs[signs=="1"]<-"+"
  significance<-cut(abs(y), c(0, 0.001, 0.01, 0.05, Inf), labels=c("***", "**", "*", ""), right=FALSE)
  paste(signs, significance)
}
  
process<-function(lm){
 coef<-data.frame(summary(lm)$coefficients)[-1,-c(2,3)]
 coef$comb<-summaryfunction2(coef$Estimate,coef$Pr...t..)

Oreotrephes

  summaryfunction2<-function(x,y){
  signs<-substr(as.character(sign(x)),1,1)
  signs[signs=="1"]<-"+"
  significance<-cut(abs(y), c(0, 0.001, 0.01, 0.05, Inf), labels=c("***", "**", "*", ""), right=FALSE)
  paste(signs, significance)
}
  
process<-function(lm){
 coef<-data.frame(summary(lm)$coefficients)[-1,-c(2,3)]
 coef$comb<-summaryfunction2(coef$Estimate,coef$Pr...t..)

Oreotrephes

summaryfunction<-function(x){
  a<-if(is.na(x)){"NA"} else if(x<0){"-"} else {"+"}
  b<-if(is.na(x)){"NA"} else if(abs(x)<0.001){"***"} else if(abs(x)<0.01){"**"} else if(abs(x)<0.05){"*"} else{" "}
paste(a,b)
  }
  
#individually are fine
summaryfunction(listy[1])
summaryfunction(listy[2])

Oreotrephes

#It aint pretty but it works

###################################################################################################################################
classify <- function(dendrogram,height){

#this little function will return tip lables
 members <- function(n) {
    labels<-c()
    if (is.leaf(n)) {
        a <- attributes(n)

Oreotrephes

#ALL THIS IS IN TERMINAL

#First, install gpsbabel through some means. I have homebrew, so I did
$ brew install gpsbabel
#Navigated to wherever the gpx files are
$ cd ~/Downloads/activities
#and converted them
$ for i in *.gpx; do gpsbabel -t -i gpx -f $i -o unicsv -F $i.csv; done
#runs enormously fast!
#okay, so how long are all those put together?