划重点:利用R语言几行代码,快速从pubmed根据keywords搜索数据(不会爬虫也没关系),查看下载数据,整理数据格式,一步到位。
meta分析大家都知道,数据收集和整理是整个过程中非常熬人
上菜!
输入1:包的安装及调用
install.packages('pubmedR') # 首次使用先安装library(pubmedR) # 调用
第一步:确定检索关键词和其他信息
如下,[Title/Abstract ]中是关键词,示例中是“bibliometric”,如果有多个关键,遵循的是pubmed检索规则,如用&符号隔开。[LA]是目标语言,此处是英文。[PT]文献类型,发表的期刊。[DP]是时间间隔。
query <- "bibliometric*[Title/Abstract] AND english[LA] AND Journal Article[PT] AND 2000:2020[DP]"
第二步:检索文献,可以看看文献总数
如下,需要注意的是api_key这个参数,不指定的话每秒请求3次数据,如果指定的话每秒请求10次数据,如果瓜客们的数据量大,建议指定。那么如何指定呢,需要在NCBI注册一个账号,然后进入账号设置里设置,会自动给出一长串字符串,即该账号的api,然后粘贴在R代码中就好了。
res <- pmQueryTotalCount(query = query, api_key = NULL)# res <- pmQueryTotalCount(query = query, api_key = api_key) res$total_count
第三步:下载数据,并将XML格式转换
如下,如果pmApiRequest这行操作失败,是由于Rstudio的语言环境不是英文导致的,需要运行Sys.setlocale(category = "LC_ALL", locale = "C")这行修改当前的语言环境。
D <- pmApiRequest(query = query, limit = res$total_count, api_key = api_key)D$query_translation# Sys.setlocale(category = "LC_ALL", locale = "C")M <- pmApi2df(D,format = "bibliometrix")
第四步:整理成常规表格,并查看汇总的数据
# install.packages("bibliometrix") 初次使用请先安装library(bibliometrix)M <- convert2df(M, dbsource = "pubmed", format = "api")results <- biblioAnalysis(M)summary(results)
结果如下:
包括文献类型、作者列表、发表年份分布、被引用排名、文献数据库来源、相关的关键词等等
MAIN INFORMATION ABOUT DATA
Timespan 2000 : 2020
Sources (Journals, Books, etc) 1312
Documents 3054
Average years from publication 4.85
Average citations per documents 0
Average citations per year per doc 0
References 1
DOCUMENT TYPES
biography 4
case reports 3
comment 8
comparative study 102
editorial 3
evaluation study 19
historical article 84
introductory journal article 3
journal article 2821
letter 3
review 4
DOCUMENT CONTENTS
Keywords Plus (ID) 2306
Author's Keywords (DE) 4422
AUTHORS
Authors 9262
Author Appearances 13651
Authors of single-authored documents 234
Authors of multi-authored documents 9028
AUTHORS COLLABORATION
Single-authored documents 313
Documents per Author 0.33
Authors per Document 3.03
Co-Authors per Documents 4.47
Collaboration Index 3.3
Annual Scientific Production
Year Articles
2000 7
2001 17
2002 10
2003 13
2004 23
2005 38
2006 36
2007 40
2008 58
2009 67
2010 83
2011 114
2012 148
2013 190
2014 193
2015 270
2016 301
2017 340
2018 464
2019 531
2020 111
Annual Percentage Growth Rate 14.81834
Most Productive Authors
Authors Articles Authors Articles Fractionalized
1 SWEILEH WM 63 SWEILEH WM 26.40
2 ZYOUD SH 59 ZYOUD SH 18.74
3 AL-JABI SW 48 HO YS 15.05
4 HO YS 37 AL-JABI SW 13.00
5 WANG Y 28 HUH S 9.33
6 YOON DY 28 BORNMANN L 9.29
7 SAWALHA AF 26 SMITH DR 9.00
8 ZHANG Y 26 E\036ENEL E 8.20
9 GRONEBERG DA 23 YEUNG AWK 6.72
10 BORNMANN L 22 SHAMIM T 6.00
Top manuscripts per citations
Paper TC TCperYear
1 TAO Z, 2020, ANN TRANSL MED 0 0
2 SALMERC3N-MANZANO E, 2020, INT J ENVIRON RES PUBLIC HEALTH 0 0
3 C\026ZEN C\aD1NAR D0, 2019, INT J NURS PRACT 0 0
4 KAMBHAMPATI SBS, 2020, J CLIN ORTHOP TRAUMA 0 0
5 BLAE>UN VOE!NER H, 2020, COMPUT INFORM NURS 0 0
6 SEVERIN A, 2018, F1000RES 0 0
7 JUSUE-TORRES I, 2020, CUREUS 0 0
8 CHARFI R, 2020, TUNIS MED 0 0
9 JACOB RR, 2020, IMPLEMENT SCI 0 0
10 GOERLANDT F, 2020, INT J ENVIRON RES PUBLIC HEALTH 0 0
Corresponding Author's Countries
Country Articles Freq SCP MCP MCP_Ratio
1 NA 3054 1 3054 0 0
SCP: Single Country Publications
MCP: Multiple Country Publications
Total Citations per Country
Country Total Citations Average Article Citations
1 NA 0 0
Most Relevant Sources
Sources Articles
1 PLOS ONE 110
2 SCIENTOMETRICS 70
3 WORLD NEUROSURGERY 57
4 INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 44
5 ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 42
6 MEDICINE 33
7 NEURAL REGENERATION RESEARCH 29
8 JOURNAL OF THE MEDICAL LIBRARY ASSOCIATION : JMLA 27
9 BMJ OPEN 26
10 PEERJ 26
Most Relevant Keywords
Author Keywords (DE) Articles Keywords-Plus (ID) Articles
1 BIBLIOMETRICS 701 BIBLIOMETRICS 1614
2 BIBLIOMETRIC ANALYSIS 359 HUMANS 1590
3 BIBLIOMETRIC 189 PERIODICALS AS TOPIC 621
4 CITATION ANALYSIS 129 BIOMEDICAL RESEARCH 499
5 H INDEX 100 PUBLISHING 433
6 CITATIONS 86 JOURNAL IMPACT FACTOR 329
7 PUBLICATIONS 86 PUBLICATIONS 266
8 SCIENTOMETRICS 75 RESEARCH 259
9 CITATION 73 UNITED STATES 227
10 WEB OF SCIENCE 69 FEMALE 184
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