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pacman::p_load(bibliometrix,pubmedR)#加载包
file = 'E:/精鼎统计/pubmed-bibliometr-set.txt'
M <- convert2df(file, dbsource = "pubmed", format = "pubmed")
names(M)
# [1] "AU" "AF" "DE" "AID" "OT" "PHST" "DT" "AB"
# [9] "C1" "OI" "CI" "CIN" "CN" "COIS" "CON" "CRDT"
# [17] "DCOM" "DEP" "PY" "EDAT" "EFR" "EIN" "FIR" "FPS"
# [25] "GN" "GR" "IS" "IR" "SN" "JID" "SO" "LA"
# [33] "LID" "LR" "MHDA" "MID" "OAB" "OABL" "OID" "ORI"
# [41] "OTO" "OWN" "PP" "PL" "PMC" "PMCR" "PMID" "PS"
# [49] "PST" "RF" "RIN" "RN" "RPI" "SB" "SI" "SO2"
# [57] "STAT" "J9" "TI" "TT" "UIN" "UOF" "VL" "DI"
# [65] "DB" "ID" "RP" "TC" "CR" "AU_UN" "AU1_UN" "AU_UN_NR"
# [73] "SR_FULL" "SR"
head(M$SO2)
# [1] "EUR J PHYS REHABIL MED. 2018 OCT;54(5):792-796. DOI: 10.23736/S1973-9087.18.05462-X. EPUB 2018 AUG 29."
# [2] "IR J MED SCI. 2019 AUG;188(3):939-951. DOI: 10.1007/S11845-018-1936-5. EPUB 2018 DEC 3."
# [3] "FEMS MICROBIOL LETT. 2018 APR 1;365(8). DOI: 10.1093/FEMSLE/FNY059."
# [4] "SHENG WU GONG CHENG XUE BAO. 2020 FEB 25;36(2):241-249. DOI: 10.13345/J.CJB.190223."
# [5] "NURS OUTLOOK. 2019 NOV-DEC;67(6):680-695. DOI: 10.1016/J.OUTLOOK.2019.04.009. EPUB 2019 MAY 2."
# [6] "NEUROL INDIA. 2018 JAN-FEB;66(1):96-104. DOI: 10.4103/0028-3886.222880."
M$Time <- str_extract(M$SO2,'\\d{4} [A-Z]{3}')#提取第一个时间;若没有第一个时间,则提取第二个时间;若2个时间都没有则返回缺失值NA;格式如“2018 JAN-FEB”,则返回“2018 JAN”。
M$PD <- str_extract(M$PD,'[A-Z]+')#提取月份
M$PD[1:10]
# [1] "OCT" "AUG" "APR" "FEB" "NOV" "JAN" "JUL" "JUL" "JUL" "OCT"
Mon2Num <- function(x) match(tolower(x), tolower(month.abb))#月份英文缩写转数字函数
M$PD_number <- Mon2Num(M$PD)
M$PD_number[1:10]
# [1] 10 8 4 2 11 1 7 7 7 10
query <- 'bibliometrics [MeSH] AND english[LA] AND 2009/01:2019/12[DP]'#数据检索规则
pmQueryTotalCount(query)#验证规则有效性
# $total_count
# [1] 7048
#
# $query_translation
# [1] "\"bibliometrics\"[MeSH Terms] AND english[LA] AND 2009/01[PDAT] : 2019/12[PDAT]"
#
# $web_history
# Web history object (QueryKey = 1, WebEnv = MCID_5f4ef38...)
Bp <- pmApiRequest(query, limit = 100)#下载xml格式的题录数据
Sys.setlocale('LC_ALL','C')#设置本地标准格式
M1 <- convert2df(Bp, dbsource = "pubmed", format = "api")#xml格式换成数据框格式
names(M1)
# [1] "AU" "AF" "TI" "SO" "SO_CO" "LA" "DT" "DE" "ID" "MESH"
# [11] "AB" "C1" "CR" "TC" "SN" "J9" "JI" "PY" "PY_IS" "VL"
# [21] "DI" "PG" "GRANT_ID" "GRANT_ORG" "UT" "PMID" "DB" "AU_UN" "AU_CO" "AU1_CO"
# [31] "SR_FULL" "SR"
source('E:/精鼎统计/bibliometrics analysis base.R') #导入视频课程自定义函数集
M1 <- pmApi2df_new(Bp)
names(M2)
# [1] "AU" "AF" "TI" "SO" "SO_CO" "LA" "DT" "DE" "ID" "MESH"
# [11] "AB" "C1" "CR" "TC" "SN" "J9" "JI" "PY" "PY_IS" "PD"
# [21] "VL" "DI" "PG" "GRANT_ID" "GRANT_ORG" "UT" "PMID" "DB" "AU_UN" "AU_CO"
# [31] "AU1_CO"
M1$PD[1:10]
# [1] 4 2 3 2 2 1 1 1 1
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