Look up citation counts with rcrossref

getCiteCounts.R

getCiteCounts <- function(citekeys, bibtex){
  ## This function takes a list of citation keys, for ex. from lit review notes
  ## and a master bibtex file with citekeys and DOIs
  ## Returns a vector of number of times each article was cited from CrossRef
  
  
  # Check for and load/install required packages
  # --> stringr, rcrossref
  if (!'stringr' %in% installed.packages()) install.packages('stringr')
  require(stringr, quietly=TRUE)
  if (!'rcrossref' %in% installed.packages()){
    if(!'devtools' %in% installed.packages()) install.packages('devtools')
    devtools::install_github('ropensci/rcrossref')
  }
  require(rcrossref)
  
  # Load and parse bibtex file pulling out citation keys and DOIs only
  keys <- c()
  dois <- c()
  pass <- FALSE
  lib <- file(bibtex, open='r')
  for(line in readLines(lib, warn=F)){
    if(str_sub(str_trim(tolower(line)), 1, 9) == '@preamble'){
      pass <- TRUE
    } else if (str_trim(line) == '"}'){
      pass <- FALSE
    }
    if(pass) next
    if(str_sub(line, 1, 1) == '@'){
      key <- str_match(line, "@\\w+[\\{]([^\\,]+)[\\,]")[1,2]
      doi <- ''
    }
    if(str_sub(str_trim(line), 1,3) == 'doi'){
      doi <- str_split(line, '\\{|\\}')[[1]][2]
    }
    if(line == '}'){
      keys <- c(keys, key)
      dois <- c(dois, doi)
    }
  }
  close(lib)
  biblib <- dois
  names(biblib) <- keys
  
  getCites <- function(key){
    # Helper function to look up citation key on CrossRef
    # Does its best to handle blank keys and missing DOIs
    if(key == ''){
      return(NA)
    }
    doi <- biblib[key]
    if(is.na(doi)){
      print(paste('Citekey not found in bibfile:', key))
      return(NA)
    } else if (doi == ''){
      return(NA)
    }
    cites <- cr_citation_count(doi)
    if(!is.numeric(cites)){
      return(NA)
    } else {
      return(cites)
    }
  }
  
  cites <- rep(NA, length(citekeys))
  
  for(i in 1:length(citekeys)){
    cites[i] <- getCites(citekeys[i])
  }
  
  return(cites)
}

####---- How To Use ----####
## Load a csv with your research notes (indexed by citekey)
# litdata <- read.csv('path/to/your/file', stringsAsFactors = FALSE)

## Point R at your Master BibTeX file
# MasterBibtex <- 'path/to/bibtex.lib'

## Use getCiteCounts to add citation counts as a new column
# litdata$Citations <- getCiteCounts(litdata$Citekey, MasterBibtex)

## Win!


####---- Demo ----####
extable <- read.csv('test.csv', stringsAsFactors = FALSE)
MasterBibtex <- 'test.bib'
extable$Citations <- getCiteCounts(extable$Citekey, MasterBibtex)

test.bib

@article{Ripamonti2009,
    author = {Ripamonti, Carla Ida and Farina, Gabriella and Garassino, Marina Chiara},
    doi = {10.1002/cncr.24351},
    journal = {Cancer},
    number = {S13},
    pages = {3128--3134},
    title = {{Predictive models in palliative care}},
    url = {http://dx.doi.org/10.1002/cncr.24351},
    volume = {115},
    year = {2009}
}

@article{Kaizhu2006,
    author = {Kaizhu, Huang and Haiqin, Yang and Irwin, King and Lyu, M R},
    doi = {10.1109/tbme.2006.872819},
    journal = {Biomedical Engineering, IEEE Transactions on},
    number = {5},
    pages = {821--831},
    title = {{Maximizing sensitivity in medical diagnosis using biased minimax probability Machine}},
    volume = {53},
    year = {2006}
}

@article{Own2012,
    author = {Own, Hala S. and Abraham, Ajith},
    doi = {10.1016/j.asoc.2011.11.025},
    journal = {Applied Soft Computing},
    month = mar,
    number = {3},
    pages = {999--1005},
    publisher = {Elsevier B.V.},
    title = {{A new weighted rough set framework based classification for Egyptian NeoNatal Jaundice}},
    url = {http://linkinghub.elsevier.com/retrieve/pii/S1568494611004674},
    volume = {12},
    year = {2012}
}

@article{Dick2009,
    author = {Dick, Thomas E and Baekey, David M and Paton, Julian F R and Lindsey, Bruce G and Morris, Kendall F},
    doi = {10.1016/j.resp.2009.07.009},
    journal = {Respiratory physiology \& neurobiology},
    month = aug,
    number = {1-2},
    pages = {76--85},
    title = {{Cardio-respiratory coupling depends on the pons.}},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/19643216},
    volume = {168},
    year = {2009}
}

@article{Allahviranloo2014,
    author = {Allahviranloo, Mahdieh and Chow, Joseph Y.J. and Recker, Will W.},
    doi = {10.1016/j.tre.2013.12.004},
    journal = {Transportation Research Part E: Logistics and Transportation Review},
    pages = {68--88},
    title = {{Selective vehicle routing problems under uncertainty without recourse}},
    url = {http://www.sciencedirect.com/science/article/pii/S1366554513001981},
    volume = {62},
    year = {2014}
}

@article{Yue2006,
    author = {Yue, Dongxia and Xu, Xiaofeng and Li, Zizhen and Hui, Cang and Li, Wenlong and Yang, Hequn and Ge, Jianping},
    doi = {10.1016/j.ecolecon.2005.07.029},
    journal = {Ecological Economics},
    month = jun,
    number = {2},
    pages = {393--406},
    title = {{Spatiotemporal analysis of ecological footprint and biological capacity of Gansu, China 1991–2015: Down from the environmental cliff}},
    url = {http://linkinghub.elsevier.com/retrieve/pii/S0921800905003290},
    volume = {58},
    year = {2006}
}


@article{Odum2000,
    author = {Odum, Howard T. and Odum, Eugene P.},
    doi = {10.1007/s100210000005},
    journal = {Ecosystems},
    month = jan,
    number = {1},
    pages = {21--23},
    title = {{The Energetic Basis for Valuation of Ecosystem Services}},
    url = {http://www.springerlink.com/openurl.asp?genre=article\&id=doi:10.1007/s100210000005},
    volume = {3},
    year = {2000}
}

@article{Huh2013,
    author = {Huh, Jina and Le, Thai and Reeder, Blaine and Thompson, Hilaire J and Demiris, George},
    doi = {10.1016/j.ijmedinf.2013.08.009},
    journal = {International journal of medical informatics},
    month = nov,
    number = {11},
    pages = {1092--103},
    publisher = {Elsevier Ireland Ltd},
    title = {{Perspectives on wellness self-monitoring tools for older adults.}},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/24041452},
    volume = {82},
    year = {2013}
}


@article{Hug2004,
    author = {Hug, Florian and Bader, Hans-Peter and Scheidegger, Ruth and Baccini, Peter},
    doi = {10.1007/s10098-003-0230-y},
    journal = {Clean Technologies and Environmental Policy},
    month = apr,
    number = {2},
    pages = {138--148},
    title = {{A dynamic model to illustrate the development of an interregional energy household to a sustainable status}},
    url = {http://www.springerlink.com/openurl.asp?genre=article\&id=doi:10.1007/s10098-003-0230-y},
    volume = {6},
    year = {2004}
}

@article{Feng2006,
    author = {Feng, Li and Liu, Ziyan},
    doi = {10.1109/PES.2006.1709073},
    journal = {2006 IEEE Power Engineering Society General Meeting},
    pages = {6 pp.},
    publisher = {Ieee},
    title = {{Genetic algorithms and rough fuzzy neural network-based hybrid approach for short-term load forecasting}},
    url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=1709073},
    year = {2006}
}

@article{Calabrese2011,
    author = {Calabrese, Francesco and Colonna, Massimo and Lovisolo, Piero and Parata, Dario and Ratti, Carlo},
    doi = {10.1109/TITS.2010.2074196},
    journal = {IEEE Transactions on Intelligent Transportation Systems},
    month = mar,
    number = {1},
    pages = {141--151},
    title = {{Real-Time Urban Monitoring Using Cell Phones: A Case Study in Rome}},
    url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=5594641},
    volume = {12},
    year = {2011}
}

@article{Vielma2012,
    author = {Vielma, J.P. and Ahmed, S. and Nemhauser, G.L.},
    doi = {10.1016/j.orl.2012.01.007},
    journal = {Operations Research Letters},
    month = may,
    number = {3},
    pages = {153--158},
    title = {{Mixed integer linear programming formulations for probabilistic constraints}},
    url = {http://www.sciencedirect.com/science/article/pii/S0167637712000168},
    volume = {40},
    year = {2012}
}


@article{Dietterich2000,
    author = {Dietterich, Thomas G.},
    journal = {Multiple classifier systems},
    title = {{Ensemble methods in machine learning}},
    url = {http://www.springerlink.com/index/LG5742LR8810612K.pdf},
    year = {2000}
}


@article{Nitzsche2014,
    author = {Nitzsche, T and Thiele, S and H\"{a}ber, a and Winter, a},
    doi = {10.3414/ME13-02-0010},
    journal = {Methods of information in medicine},
    month = jan,
    number = {3},
    pages = {167--72},
    title = {{Communication architecture for AAL. Supporting patient care by health care providers in AAL-enhanced living quarters.}},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/24728125},
    volume = {53},
    year = {2014}
}

@article{Lucas1999,
    author = {Lucas, PJF Peter J F and Abu-Hanna, Ameen},
    doi = {10.1016/s0933-3657(98)00047-5},
    journal = {Artificial Intelligence in Medicine},
    number = {2},
    pages = {105--119},
    title = {{Prognostic methods in medicine}},
    url = {http://igitur-archive.library.uu.nl/math/2007-0104-200831/abu-hanna\_97\_prosnostic.pdf http://www.sciencedirect.com/science/article/pii/S0933365798000475},
    volume = {15},
    year = {1999}
}

@article{Dawson1991,
    author = {Dawson, Norma Jean},
    doi = {10.1016/0277-9536(91)90131-u},
    journal = {Social Science \& Medicine},
    number = {1},
    pages = {83--87},
    title = {{Need satisfaction in terminal care settings}},
    url = {http://www.sciencedirect.com/science/article/pii/027795369190131U},
    volume = {32},
    year = {1991}
}

@article{Ludwig2012,
    author = {Ludwig, Wolfram and Wolf, Klaus-Hendrik and Duwenkamp, Christopher and Gusew, Nathalie and Hellrung, Nils and Marschollek, Michael and Wagner, Markus and Haux, Reinhold},
    doi = {10.1016/j.cmpb.2011.11.001},
    journal = {Computer methods and programs in biomedicine},
    month = may,
    number = {2},
    pages = {70--8},
    publisher = {Elsevier Ireland Ltd},
    title = {{Health-enabling technologies for the elderly--an overview of services based on a literature review.}},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/22115611},
    volume = {106},
    year = {2012}
}

test.csv