vignettes/vignette_2_extract.md

In kamclean/impactr:

Extract Publication Data

Keeping accurate and up-to-date information regarding the output from an author / research group can be a time-consuming task, however remains essential in order to evaluate the research impact. There are multiple repositories on-line such as PubMed or CrossRef which store this information, and can already be accessed using an API in R in order to extract this data on an automatic basis.

There are excellent packages that already exist to access this data - RISmed for PubMed and rcrossref for CrossRef. While these provide a vast quantity of useful information, this is often outwith a dataframe/tibble format and so requires a significant quantity of post-processing to otherwise achieve an easily usable output.

1. Extract Data

The functions extract_pmid() (PubMed) and extract_doi() (CrossRef) use unique identifiers to extract important information regarding publications. This can be used for the purposes of citation, cataloguing publications, or for further evaluation of impact (see ImpactR: Citations).

However, it should be noted that the information extracted is dependent on the accuracy and completeness of the information within these repositories. Therefore, some additional editing may be required to remove heterogeneity / make corrections / supply missing data.

a). extract_pmid()

The extract_pmid() function only requires a vector/list of PubMed identification numbers to extract publication information.

The function will automatically extract the authors (auth_group, auth_n, authors), and the associated altmetric score (altmetric). However, this functionality has been made optional as it can extend the run time of the function (particularly in the case of a large number of authors).

out_pubmed <- impactr::extract_pmid(pmid = c(26769786, 26195471, 30513129),
                                    get_altmetric = FALSE, get_impact = FALSE)

## [1] "Chunk 1"
## [1] 1
## [1] 2
## [1] 3

pmid doi pmc title journal\_nlm journal\_issn journal\_full journal\_abbr journal\_vol journal\_issue journal\_pages author\_n author\_list author\_group collab\_n collab\_list type status date\_publish year author 26769786 10.1136/bmjopen-2015-009812 PMC4735315 Outcomes After Kidney injury in Surgery (OAKS): protocol for a multicentre, observational cohort study of acute kidney injury following major gastrointestinal and liver surgery. 101552874 2044-6055, 2044-6055 BMJ open BMJ Open 6 1 e009812 0 NA STARSurg Collaborative 40 Bath M; Glasbey J; Claireaux H; Drake T; Gundogan B; Khatri C; Kong N; McNamee L; Mohan M; Amin H; Barai I; Bhanderi S; Brown FS; Chapman SJ; Corbridge O; Cumber E; Deekonda P; Dennis Y; Gokani V; Ibrahim I; Kamarajah SK; Logan AE; Mills A; Phan PN; Robinson C; Sethi R; Shaw A; Suresh R; Suresh S; Wigley C; Wilson H; Arulkumaran N; Richards T; Duthie F; Thomas M; Prowle J; Harrison E; Fitzgerald JE; Bhangu A; Nepogodiev D Journal Article, Multicenter Study, Observational Study, Research Support, Non-U.S. Gov’t epublish 2016-01-14 2016 NA… 26195471 10.1136/bmjopen-2015-008811 PMC4513439 Determining Surgical Complications in the Overweight (DISCOVER): a multicentre observational cohort study to evaluate the role of obesity as a risk factor for postoperative complications in general surgery. 101552874 2044-6055, 2044-6055 BMJ open BMJ Open 5 7 e008811 11 Nepogodiev D; Chapman SJ; Glasbey J; Kelly M; Khatri C; Drake TM; Kong CY; Mitchell H; Harrison EM; Fitzgerald JE; Bhangu A STARSurg Collaborative 0 NA Journal Article, Multicenter Study, Observational Study, Research Support, Non-U.S. Gov’t epublish 2015-07-20 2015 Nepogodiev D; Chapman SJ; Glasbey J; Kelly M; Khat… 30513129 10.1002/bjs5.86 PMC6254006 Prognostic model to predict postoperative acute kidney injury in patients undergoing major gastrointestinal surgery based on a national prospective observational cohort study. 101722685 2474-9842, 2474-9842 BJS open BJS Open 2 6 400-410 0 NA STARSurg Collaborative 1784 Nepogodiev D; Walker K; Glasbey JC; Drake TM; Borakati A; Kamarajah S; McLean K; Khatri C; Arulkumaran N; Harrison EM; Fitzgerald JE; Cromwell D; Prowle J; Bhangu A; Walker K; Drake TM; Cromwell D; Glasbey JC; Borakati A; Drake TM; Kamarajah S; McLean K; Bath MF; Claireaux HA; Gundogan B; Mohan M; Deekonda P; Kong C; Joyce H; Mcnamee L; Woin E; Burke J; Khatri C; Fitzgerald JE; Harrison EM; Bhangu A; Nepogodiev D; Arulkumaran N; Bell S; Duthie F; Hughes J; Pinkney TD; Prowle J; Richards T; Thomas M; Dynes K; Patel P; Wigley C; Suresh R; Shaw A; Klimach S; Jull P; Evans D; Preece R; Ibrahim I; Manikavasagar V; Brown FS; Deekonda P; Teo R; Sim DPY; Borakati A; Logan AE; Barai I; Amin H; Suresh S; Sethi R; Bolton W; Corbridge O; Horne L; Attalla M; Morley R; Hoskins T; McAllister R; Lee S; Dennis Y; Nixon G; Heywood E; Wilson H; Ng L; Samaraweera S; Mill A; Doherty C; Woin E; Belchos J; Phan V; Chouari T; Gardner T; Goergen N; Hayes JDB; MacLeod CS; McCormack R; McKinley A; McKinstry S; Milligan W; Ooi L; Rafiq NM; Sammut T; Sinclair E; Smith M; Baker C; Boulton APR; Collins J; Copley HC; Fearnhead N; Fox H; Mah T; McKenna J; Naruka V; Nigam N; Nourallah B; Perera S; Qureshi A; Saggar S; Sun L; Wang X; Yang DD; Caroll P; Doyle C; Elangovan S; Falamarzi A; Gascon Perai K; Greenan E; Jain D; Lang-Orsini M; Lim S; O’Byrne L; Ridgway P; Van der Laan S; Wong J; Arthur J; Barclay J; Bradley P; Edwin C; Finch E; Hayashi E; Hopkins M; Kelly D; Kelly M; McCartan N; Ormrod A; Pakenham A; Hayward J; Hitchen C; Kishore A; Martins T; Philomen J; Rao R; Rickards C; Burns N; Copeland M; Durand C; Dyal A; Ghaffar A; Gidwani A; Grant M; Gribbon C; Gruhn A; Leer M; Ahmad K; Beattie G; Beatty M; Campbell G; Donaldson G; Graham S; Holmes D; Kanabar S; Liu H; McCann C; Stewart R; Vara S; Ajibola-Taylor O; Andah EJE; Ani C; Cabdi NMO; Ito G; Jones M; Komoriyama A; Patel P; Titu L; Basra M; Gallogly P; Harinath G; Leong SH; Pradhan A; Siddiqui I; Zaat S; Ali A; Galea M; Looi WL; Ng JCK; Atkin G; Azizi A; Cargill Z; China Z; Elliot J; Jebakumar R; Lam J; Mudalige G; Onyerindu C; Renju M; Shankar Babu V; Hussain M; Joji N; Lovett B; Mownah H; Ali B; Cresswell B; Dhillon AK; Dupaguntla YS; Hungwe C; Lowe-Zinola JD; Tsang JCH; Bevan K; Cardus C; Duggal A; Hossain S; McHugh M; Scott M; Chan F; Evans R; Gurung E; Haughey B; Jacob-Ramsdale B; Kerr M; Lee J; McCann E; O’Boyle K; Reid N; Hayat F; Hodgson S; Johnston R; Jones W; Khan M; Linn T; Long S; Seetharam P; Shaman S; Smart B; Anilkumar A; Davies J; Griffith J; Hughes B; Islam Y; Kidanu D; Mushaini N; Qamar I; Robinson H; Schramm M; Yan Tan C; Apperley H; Billyard C; Blazeby JM; Cannon SP; Carse S; Göpfert A; Loizidou A; Parkin J; Sanders E; Sharma S; Slade G; Telfer R; Whybrow Huppatz I; Worley E; Chandramoorthy L; Friend C; Harris L; Jain P; Karim MJ; Killington K; McGillicuddy J; Rafferty C; Rahunathan N; Rayne T; Varathan Y; Verma N; Zanichelli D; Arneill M; Brown F; Campbell B; Crozier L; Henry J; McCusker C; Prabakaran P; Wilson R; Asif U; Connor M; Dindyal S; Math N; Pagarkar A; Saleem H; Seth I; Sharma S; Standfield N; Swartbol T; Adamson R; Choi JE; El Tokhy O; Ho W; Javaid NR; Kelly M; Mehdi AS; Menon D; Plumptre I; Sturrock S; Turner J; Warren O; Crane E; Ferris B; Gadsby C; Smallwood J; Vipond M; Wilson V; Amarnath T; Doshi A; Gregory C; Kandiah K; Powell B; Spoor H; Toh C; Vizor R; Common M; Dunleavy K; Harris S; Luo C; Mesbah Z; Prem Kumar A; Redmond A; Skulsky S; Walsh T; Daly D; Deery L; Epanomeritakis E; Harty M; Kane D; Khan K; Mackey R; McConville J; McGinnity K; Nixon G; Ang A; Kee JY; Leung E; Norman S; Palaniappan SV; Partha Sarathy P; Yeoh T; Frost J; Hazeldine P; Jones L; Karbowiak M; Macdonald C; Mutarambirwa A; Omotade A; Runkel M; Ryan G; Sawers N; Searle C; Suresh S; Vig S; Ahmad A; McGartland R; Sim R; Song A; Wayman J; Brown R; Chang LH; Concannon K; Crilly C; Arnold TJ; Burgin A; Cadden F; Choy CH; Coleman M; Lim D; Luk J; Mahankali-Rao P; Prudence-Taylor AJ; Ramakrishnan D; Russell J; Fawole A; Gohil J; Green B; Hussain A; McMenamin L; McMenamin L; Tang M; Azmi F; Benchetrit S; Cope T; Haque A; Harlinska A; Holdsworth R; Ivo T; Martin J; Nisar T; Patel A; Sasapu K; Trevett J; Vernet G; Aamir A; Bird C; Durham-Hall A; Gibson W; Hartley J; May N; Maynard V; Johnson S; McDonald Wood C; O’Brien M; Orbell J; Stringfellow TD; Tenters F; Tresidder S; Cheung W; Grant A; Tod N; Bews-Hair M; Lim ZH; Lim SW; Vella-Baldacchino M; Auckburally S; Chopada A; Easdon S; Goodson R; McCurdie F; Narouz M; Radford A; Rea E; Taylor O; Yu T; Alfa-Wali M; Amani L; Auluck I; Bruce P; Emberton J; Kumar R; Lagzouli N; Mehta A; Murtaza A; Raja M; Dennahy IS; Frew K; Given A; He YY; Karim MA; MacDonald E; McDonald E; McVinnie D; Ng SK; Pettit A; Sim DPY; Berthaume-Hawkins SD; Charnley R; Fenton K; Jones D; Murphy C; Ng JQ; Reehal R; Robinson H; Seraj SS; Shang E; Tonks A; White P; Yeo A; Chong P; Gabriel R; Patel N; Richardson E; Symons L; Aubrey-Jones D; Dawood S; Dobrzynska M; Faulkner S; Griffiths H; Mahmood F; Patel P; Perry M; Power A; Simpson R; Ali A; Brobbey P; Burrows A; Elder P; Ganyani R; Horseman C; Hurst P; Mann H; Marimuthu K; McBride S; Pilsworth E; Powers N; Stanier P; Innes R; Kersey T; Kopczynska M; Langasco N; Patel N; Rajagopal R; Atkins B; Beasley W; Cheng Lim Z; Gill A; Li Ang H; Williams H; Yogeswara T; Carter R; Fam M; Fong J; Latter J; Long M; Mackinnon S; McKenzie C; Osmanska J; Raghuvir V; Shafi A; Tsang K; Walker L; Bountra K; Coldicutt O; Fletcher D; Hudson S; Iqbal S; Lopez Bernal T; Martin JWB; Moss-Lawton F; Smallwood J; Vipond M; Cardwell A; Edgerton K; Laws J; Rai A; Robinson K; Waite K; Ward J; Youssef H; Knight C; Koo PY; Lazarou A; Stanger S; Thorn C; Triniman MC; Botha A; Boyles L; Cumming S; Deepak S; Ezzat A; Fowler AJ; Gwozdz AM; Hussain SF; Khan S; Li H; Lu Morrell B; Neville J; Nitiahpapand R; Pickering O; Sagoo H; Sharma E; Welsh K; Denley S; Khan S; Agarwal M; Al-Saadi N; Bhambra R; Gupta A; Jawad ZAR; Jiao LR; Khan K; Mahir G; Singagireson S; Thoms BL; Tseu B; Wei R; Yang N; Britton N; Leinhardt D; Mahfooz M; Palkhi A; Price M; Sheikh S; Barker M; Bowley D; Cant M; Datta U; Farooqi M; Lee A; Morley G; Naushad Amin M; Parry A; Patel S; Strang S; Yoganayagam N; Adlan A; Chandramoorthy S; Choudhary Y; Das K; Feldman M; France B; Grace R; Puddy H; Soor P; Ali M; Dhillon P; Faraj A; Gerard L; Glover M; Imran H; Kim S; Patrick Y; Peto J; Prabhudesai A; Smith R; Tang A; Vadgama N; Dhaliwal R; Ecclestone T; Harris A; Ong D; Patel D; Philp C; Stewart E; Wang L; Wong E; Xu Y; Ashaye T; Fozard T; Galloway F; Kaptanis S; Mistry P; Nguyen T; Olagbaiye F; Osman M; Philip Z; Rembacken R; Tayeh S; Theodoropoulou K; Herman A; Lau J; Saha A; Trotter M; Adeleye O; Cave D; Gunwa T; Magalhães J; Makwana S; Mason R; Parish M; Regan H; Renwick P; Roberts G; Salekin D; Sivakumar C; Tariq A; Liew I; McDade A; Stewart D; Hague M; Hudson-Peacock N; Jackson CES; James F; Pitt J; Walker EY; Aftab R; Ang JJ; Anwar S; Battle J; Budd E; Chui J; Crook H; Davies P; Easby S; Hackney E; Ho B; Imam SZ; Rammell J; Andrews H; Perry C; Schinle P; Ahmed P; Aquilina T; Balai E; Church M; Cumber E; Curtis A; Davies G; Dennis Y; Dumann E; Greenhalgh S; Kim P; King S; Metcalfe KHM; Passby L; Redgrave N; Soonawalla Z; Waters S; Zornoza A; Gulzar I; Hole J; Hull K; Ishaq H; Karaj J; Kelkar A; Love E; Patel S; Thakrar D; Vine M; Waterman A; Dib NP; Francis N; 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Wright S; Bruce C; Francois V; Hamdan K; Limb C; Lunt AJ; Manley L; Marks M; Phillips CFE; Agnew CJF; Barr CJ; Benons N; Hart SJ; Kandage D; Krysztopik R; Mahalingam P; Mock J; Rajendran S; Stoddart MT; Clements B; Gillespie H; Lee S; McDougall R; Murray C; O’Loane R; Periketi S; Tan S; Amoah R; Bhudia R; Dudley B; Gilbert A; Griffiths B; Khan H; McKigney N; Roberts B; Samuel R; Seelarbokus A; Stubbing-Moore A; Thompson G; Williams P; Ahmed N; Akhtar R; Chandler E; Chappelow I; Gil H; Gower T; Kale A; Lingam G; Rutler L; Sellahewa C; Sheikh A; Stringer H; Taylor R; Aglan H; Ashraf MR; Choo S; Das E; Epstein J; Gentry R; Mills D; Poolovadoo Y; Ward N; Bull K; Cole A; Hack J; Khawari S; Lake C; Mandishona T; Perry R; Sleight S; Sultan S; Thornton T; Williams S; Arif T; Castle A; Chauhan P; Chesner R; Eilon T; Kamarajah S; Kambasha C; Lock L; Loka T; Mohammad F; Motahariasl S; Roper L; Sadhra SS; Sheikh A; Toma T; Wadood Q; Yip J; Ainger E; Busti S; Cunliffe L; Flamini T; Gaffing S; Moorcroft C; Peter M; Simpson L; Stokes E; Stott G; Wilson J; York J; Yousaf A; Borakati A; Brown M; Goaman A; Hodgson B; Ijeomah A; Iroegbu U; Kaur G; Lowe C; Mahmood S; Sattar Z; Sen P; Szuman A; Abbas N; Al-Ausi M; Anto N; Bhome R; Eccles L; Elliott J; Hughes EJ; Jones A; Karunatilleke AS; Knight JS; Manson CCF; Mekhail I; Michaels L; Noton TM; Okenyi E; Reeves T; Yasin IH; Banfield DA; Harris R; Lim D; Mason-Apps C; Roe T; Sandhu J; Shafiq N; Stickler E; Tam JP; Williams LM; Ainsworth P; Boualbanat Y; Doull C; Egan E; Evans L; Hassanin K; Ninkovic-Hall G; Odunlami W; Shergill M; Traish M; Cummings D; Kershaw S; Ong J; Reid F; Toellner H; Alwandi A; Amer M; George D; Haynes K; Hughes K; Peakall L; Premakumar Y; Punjabi N; Ramwell A; Sawkins H; Ashwood J; Baker A; Baron C; Bhide I; Blake E; De Cates C; Esmail R; Hosamuddin H; Kapp J; Nguru N; Raja M; Thomson F; Ahmed H; Aishwarya G; Al-Huneidi R; Ali S; Aziz R; Burke D; Clarke B; Kausar A; Maskill D; Mecia L; Myers L; Smith ACD; Walker G; Wroe N; Donohoe C; Gibbons D; Jordan P; Keogh C; Kiely A; Lalor P; McCrohan M; Powell C; Power Foley M; Reynolds J; Silke E; Thorpe O; Tseun Han Kong J; White C; Ali Q; Dalrymple J; Ge Y; Khan H; Luo RS; Paine H; Paraskeva B; Parker L; Pillai K; Salciccioli J; Selvadurai S; Sonagara V; Springford LR; Tan L; Appleton S; Leadholm N; Zhang Y; Ahern D; Cotter M; Cremen S; Durrigan T; Flack V; Hrvacic N; Jones H; Jong B; Keane K; O’Connell PR; O’Sullivan J; Pek G; Shirazi S; Barker C; Brown A; Carr W; Chen Y; Guillotte C; Harte J; Kokayi A; Lau K; McFarlane S; Morrison S; Broad J; Kenefick N; Makanji D; Printz V; Saito R; Thomas O; Breen H; Kirk S; Kong CH; O’Kane A; Eddama M; Engledow A; Freeman SK; Frost A; Goh C; Lee G; Poonawala R; Suri A; Taribagil P; Brown H; Christie S; Dean S; Gravell R; Haywood E; Holt F; Pilsworth E; Rabiu R; Roscoe HW; Shergill S; Sriram A; Sureshkumar A; Tan LC; Tanna A; Vakharia A; Bhullar S; Brannick S; Dunne E; Frere M; Kerin M; Muthu Kumar K; Pratumsuwan T; Quek R; Salman M; Van Den Berg N; Wong C; Ahluwalia J; Bagga R; Borg CM; Calabria C; Draper A; Farwana M; Joyce H; Khan A; Mazza M; Pankin G; Sait MS; Sandhu N; Virani N; Wong J; Woodhams K; Croghan N; Ghag S; Hogg G; Ismail O; John N; Nadeem K; Naqi M; Noe SM; Sharma A; Tan S; Begum F; Best R; Collishaw A; Glasbey J; Golding D; Gwilym B; Harrison P; Jackman T; Lewis N; Luk YL; Porter T; Potluri S; Stechman M; Tate S; Thomas D; Walford B; Auld F; Bleakley A; Johnston S; Jones C; Khaw J; Milne S; O’Neill S; Singh KKR; Smith R; Swan A; Thorley N; Yalamarthi S; Yin ZD; Ali A; Balian V; Bana R; Clark K; Livesey C; McLachlan G; Mohammad M; Pranesh N; Richards C; Ross F; Sajid M; Brooke M; Francombe J; Gresly J; Hutchinson S; Kerrigan K; Matthews E; Nur S; Parsons L; Sandhu A; Vyas M; White F; Zulkifli A; Zuzarte L; Al-Mousawi A; Arya J; Azam S; Azri Yahaya A; Gill K; Hallan R; Hathaway C; Leptidis I; McDonagh L; Mitrasinovic S; Mushtaq N; Pang N; Peiris GB; Rinkoff S; Chan L; Christopher E; Farhan-Alanie MMH; Gonzalez-Ciscar A; Graham CJ; Lim H; McLean KA; Paterson HM; Rogers A; Roy C; Rutherford D; Smith F; Zubikarai G; Al-Khudairi R; Bamford M; Chang M; Cheng J; Hedley C; Joseph R; Mitchell B; Perera S; Rothwell L; Siddiqui A; Smith J; Taylor K; Wroe Wright O; Baryan HK; Boyd G; Conchie H; Cox L; Davies J; Gardner S; Hill N; Krishna K; Lakin F; Scotcher S; Alberts J; Asad M; Barraclough J; Campbell A; Marshall D; Wakeford W; Cronbach P; D’Souza F; Gammeri E; Houlton J; Hall M; Kethees A; Patel R; Perera M; Prowle J; Shaid M; Webb E; Beattie S; Chadwick M; El-Taji O; Haddad S; Mann M; Patel M; Popat K; Rimmer L; Riyat H; Smith H; Anandarajah C; Cipparrone M; Desai K; Gao C; Goh ET; Howlader M; Jeffreys N; Karmarkar A; Mathew G; Mukhtar H; Ozcan E; Renukanthan A; Sarens N; Sinha C; Woolley A; Bogle R; Komolafe O; Loo F; Waugh D; Zeng R; Crewe A; Mathias J; Mills A; Owen A; Prior A; Saunders I; Baker A; Crilly L; McKeon J; Ubhi HK; Adeogun A; Carr R; Davison C; Devalia S; Hayat A; Karsan RB; Osborne C; Scott K; Weegenaar C; Wijeyaratne M; Babatunde F; Barnor-Ahiaku E; Beattie G; Chitsabesan P; Dixon O; Hall N; Ilenkovan N; Mackrell T; Nithianandasivam N; Orr J; Palazzo F; Saad M; Sandland-Taylor L; Sherlock J; Ashdown T; Chandler S; Garsaa T; Lloyd J; Loh SY; Ng S; Perkins C; Powell-Chandler A; Smith F; Underhill R Journal Article epublish 2018-07-27 2018 NA…

In general, it appears that the information on PubMed tends to be the most accurate/up-to-date, however the Digital Object Identifier (DOI) occasionally is not updated to reflect the final DOI for the paper (this can either be amended or the publisher contacted to correct).

b). extract_doi()

The extract_doi() function only requires a vector/list of Digital Object Identifiers (DOI), and uses the rcrossref package to extract publication information.

The function will automatically extract the authors (auth_group, auth_n, authors), and the associated altmetric score (altmetric). However, this functionality has been made optional as it can extend the run time of the function (particularly in the case of a large number of authors). It should be also noted that crossref tends to record authorship less well (compared to PubMed).

# Example output from user_roles_n()
out_doi <- impactr::extract_doi(doi = out_pubmed$doi,
                       get_authors = TRUE, get_altmetric = FALSE, get_impact = FALSE)

doi author\_group title year journal\_abbr volume issue pages cite\_cr auth\_n author journal\_full journal\_issn 10.1136/bmjopen-2015-009812 NA Outcomes After Kidney injury in Surgery (OAKS): protocol for a multicentre, observational cohort study of acute kidney injury following major gastrointestinal and liver surgery 2016 BMJ Open 6 1 e009812 16 NA NA BMJ Open 2044-6055 10.1136/bmjopen-2015-008811 NA Determining Surgical Complications in the Overweight (DISCOVER): a multicentre observational cohort study to evaluate the role of obesity as a risk factor for postoperative complications in general surgery 2015 BMJ Open 5 7 e008811 13 11 Nepogodiev D, Chapman SJ, Glasbey J, Kelly M, Khat… BMJ Open 2044-6055 10.1002/bjs5.86 STARSurg Collaborative Prognostic model to predict postoperative acute kidney injury in patients undergoing major gastrointestinal surgery based on a national prospective observational cohort study 2018 BJS Open 2 6 400-410 3 NA NA BJS Open 2474-9842

kamclean/impactr documentation built on Jan. 11, 2023, 2:51 p.m.