map_dois.R

############################################################################################
### Get the DOIs and full citations for peer reviewed litterature                        ###
### by the SNAPP working Group Evidence Based - https://www.nceas.ucsb.edu/portal/12696  ###
### Author: Julien Brun (ORCID: 0000-0002-7751-6238) and Ian McCullough                  ###
### Contributors:  Justin Kroes and Kendall Miller                                       ###
### Contact: scicomp@nceas.ucsb.edu                                                      ###
############################################################################################

# Clear environment
rm(list = ls())

# Source the created function to ping the Crossref API and match a title with a doi
source("get_dois.R")

#Set the working directory
setwd("/Users/brun/GitHubnceas/SNAPP/evidence-based-heatmap")

# Load the data
data_review <- "Sam_data/evidence_based_5_13_16.RData"


####### MAIN #######

#load the data to get the titles
load(data_review)

#get the unqiue titles
titles = unique(data.biblio$Title)
nb.titles <- length(titles)

#initilaize the dataframe to store the results
dois <- data.frame(Dois = character(),
                   Title.formatted = character(),
                   Fullcitation = character(),
                   Title.reviewer = character(),
                   Title.identical = logical(),
                   stringsAsFactors=FALSE)

# loop throught the titles
for (i in 1:nb.titles ){
  title = titles[i]
  #year = data.biblio[data.biblio$Titl3==title,data.biblio$]
  print(title)
  #Query the API
  gotback <- getdoi(title)
  #Store the results
  newRow <- c(gotback,title,identical(gotback[2],title))
  #print(newRow)
  dois[i,] <- newRow
  print(dois)
}


# write a csv
write.table(dois, file = "dois_last_newgetdois.csv", sep=";",col.names = TRUE, row.names =F)

#### END ####