+
+
@@ -2893,9 +2899,9 @@
@@ -2910,7 +2916,7 @@ Bibliographic Studies
-Reproducible Bibliometric Analysis of Pathology Articles Using PubMed, E-direct, WoS, Google Scholar
-Serdar Balcı, MD, Pathologist
-2019-01-13
+Reproducible Bibliometric Analysis of Pathology Articles Using PubMed, E-direct, WoS, Google Scholar
+Serdar Balcı, MD, Pathologist
+2019-03-30
1 Introduction
If you want to see the code used in the analysis please click the code button on the right upper corner or throughout the page.
I would like to hear your feedback: https://goo.gl/forms/YjGZ5DHgtPlR1RnB3
-This document will be continiously updated and the last update was on 2019-01-13.
+This document will be continiously updated and the last update was on 2019-03-30.
@@ -2929,6 +2935,8 @@ 2.2 Articles per Journals per Cou
+ +
@@ -2952,6 +2960,8 @@2.3 Most Common MeSH Terms and Ke
2.2 Articles per Journals per Cou
2.3 Most Common MeSH Terms and Keywords used in Pathology Articles from Turkey
In this analysis we aimed to identify the common research topics Turkish pathologists are interested. We extracted most common MeSH terms and keywords from PubMed articles using EDirect: MeSH Terms Pathology Articles From Turkey
+ +
@@ -2952,6 +2960,8 @@
2.3 Most Common MeSH Terms and Ke
+
+
@@ -2999,7 +3009,7 @@ 3 Sources Used For Analysis
4 Feedback
Serdar Balcı, MD, Pathologist would like to hear your feedback: https://goo.gl/forms/YjGZ5DHgtPlR1RnB3
-This document will be continiously updated and the last update was on 2019-01-13.
+This document will be continiously updated and the last update was on 2019-03-30.
+
+
+```{r global_options, include=FALSE}
+knitr::opts_chunk$set(fig.width = 12, fig.height = 8,
+ # fig.path = 'figures/',
+ echo = FALSE, warning = FALSE, message = FALSE, error = FALSE, eval = TRUE, tidy = TRUE, comment = NA)
+```
+
+```{r library, include=FALSE}
+library(tidyverse)
+```
+
+
+
+
+# Introduction
+
+- Selected Pathology Journals are used for the query^[[Selected Pathology Journals](PancreasStudies/data/journal_list_from_my_collections)]
+
+
+
+
+# PubMed
+
+## Data Download from PubMed via EDirect
+
+- Data is downloaded from PubMed via Edirect^[https://dataguide.nlm.nih.gov/edirect/overview.html]
+
+-
+
+
+## rentrez
+
+# europepmc
+
+
+
+# WOS
+
+[WOS.Rmd](WOS.Rmd)
+
+```{r}
+PMID_List_for_WOS_pancreas <- paste0("PMID=(", pmid_only_path_journals$PMID, ") OR")
+
+write(PMID_List_for_WOS_pancreas,
+ here::here("PancreasStudies/data/PMID_List_for_WOS_pancreas.txt")
+)
+
+```
+
+
+
+
+
+
+
+# Scopus
+
+[scopus.Rmd](scopus.Rmd)
+
+
+# Vosviewer
+
+Author Thesaurus is used.^[[Author Thesaurus](data/thesaurus_authors.txt)]
+
+Code for interactive graph.^[[Interactive Graph Code](data/VOSviewer_interactive_graphcode.txt)]
+
+
+
+
+
+
+# Cite Space
+
+# CitNetExplorer
+
+# Lens
+
+```
+(citation_id_type: "pmid" AND citation_id: 28984336) OR (citation_id_type: "pmid" AND citation_id: 21682559)
+```
+
+```{r}
+pmid_only_path_journals <-
+read_delim("PancreasStudies/data/pmid_only_path_journals.txt", "\n", col_names = "PMID", col_types = "c")
+
+pmid_only_path_journals2 <- paste0("(citation_id_type: 'pmid' AND citation_id:",pmid_only_path_journals$PMID, ") OR ", collapse = "")
+
+write(pmid_only_path_journals2,
+"PancreasStudies/data/lensSearch.txt"
+)
+```
+
+
+
+
+# openknowledgemaps
+
+Open Knowledge Maps (2019). Overview of research on intraductal tubulopapillary neoplasm. Retrieved from https://openknowledgemaps.org/map/cc04c53301920a93d451aa2ce3010243/ [30 Mar 2019].
+
+
+# bibliometrix
+
+# ORCID
+
+# Semantic Scholar
+
+[SemanticScholar.Rmd](SemanticScholar.Rmd)
+
+
+# Microsoft Academic
+
+# Scopus
+
+# Altmetrics
+
+
+
+# Grid
+
+https://grid.ac/
+
+
+# ROR
+
+https://ror.org/search?page=1&query=turkey
+
+
+# Cobalmetrics
+
+https://cobaltmetrics.com/
+
+- Toward privacy-preserving altmetrics exploration with Cobaltmetrics and ORCID
+
+https://medium.com/thunken/toward-privacy-preserving-altmetrics-exploration-with-cobaltmetrics-and-orcid-f5ab6fa7898a
+
+
+# OpenCitations
+
+http://opencitations.net
+
+http://opencitations.net/download
+
+http://opencitations.net/corpus
+
+https://github.com/opencitations
+
+- The OpenCitations Data Model
+https://figshare.com/articles/Metadata_for_the_OpenCitations_Corpus/3443876
+
+- Creating Open Citation Data with BCite
+https://semsci.github.io/SemSci2018/papers/1/bcite-semsci2018.html
+
+https://github.com/opencitations/bcite
+
+
+# Open Knowledge Maps
+
+Open Knowledge Maps (2019). Overview of research on (pathology[affiliation] or patoloji[affiliation]) and (turkey[affiliation] or türkiye[affiliation]). Retrieved from https://openknowledgemaps.org/map/e4dbf6c89015e402d6d7d560ab79e17a/ [30 Mar 2019].
+
+
+https://openknowledgemaps.org/index
+
+
+
+# iris.ai
+
+https://the.iris.ai/map/02f89d24-0415-43ab-878a-853ec17c5a59
+
+# lens.org
+
+https://www.lens.org/lens/scholar/search/results?dateFilterField=year_published&filterMap=%7B%7D&orcids=0000-0002-7852-3851&orderBy=%2Bpublished&preview=true&previewType=SCHOLAR_ANALYSIS®exEnabled=false
+
+https://www.lens.org/lens/scholar/search/results?q=(author.affiliation.name:%20%22pathology%22%20%20OR%20author.affiliation.name:%20%22patoloji%22)%20%20AND%20(author.affiliation.name:%20%22Turkey%22%20%20OR%20author.affiliation.name:%20%22T%C3%BCrkiye%22)
+
+https://www.lens.org/lens/scholar/search/analysis?q=(author.affiliation.name:%20%22neurosurgery%22%20%20OR%20author.affiliation.name:%20%22sport%22%20)%20AND%20(abstract:%20%22sport%22%20%20OR%20title:%20%22sport%22)&page=0&limit=10&orderBy=%2Bscore&dateFilterField=year_published&preview=false®exEnabled=false
+
+
+# To Do
+
+- find a way to auto import journal names
+- remove last OR
+- Auto run posiible analysis via cron
+- Find a way to auto copy into googledrive
+- push to blog, netlify ...
+- Add from
+-- [Sources.Rmd](Sources.Rmd)
+-- [Bibliyometri.Rmd](Bibliyometri.Rmd)
+
+
+
+
+# About & Feedback
+
+
+[Serdar Balcı, MD, Pathologist](https://github.com/sbalci) would like to hear your feedback: https://goo.gl/forms/YjGZ5DHgtPlR1RnB3
+
+This document will be continiously updated and the last update was on `r Sys.Date()`.
+
+---
+
+
+
+
+
+
+
+---
+
+# References
+
+
+
+
diff --git a/PancreasStudies.nb.html b/PancreasStudies.nb.html
new file mode 100644
index 0000000..9d04fc5
--- /dev/null
+++ b/PancreasStudies.nb.html
@@ -0,0 +1,3267 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Pancreas Studies in Various Bibliometric Tools
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Pancreas Studies in Various Bibliometric Tools
+Pancreas Studies in Pathology Journals
+Serdar Balcı, MD, Pathologist
+2019-03-31
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+1 Introduction
+
+- Selected Pathology Journals are used for the query1
+
+
+
+2 PubMed
+
+2.1 Data Download from PubMed via EDirect
+
+Data is downloaded from PubMed via Edirect2
+
+
+2.2 rentrez
+
+
+
+3 europepmc
+
+
+4 WOS
+
+
+
+
+
+
+
+
+
+
+5 Scopus
+
+
+
+
+7 Cite Space
+
+
+8 CitNetExplorer
+
+
+9 Lens
+(citation_id_type: "pmid" AND citation_id: 28984336) OR (citation_id_type: "pmid" AND citation_id: 21682559)
+
+
+
+pmid_only_path_journals <-
+read_delim("PancreasStudies/data/pmid_only_path_journals.txt", "\n", col_names = "PMID", col_types = "c")
+
+pmid_only_path_journals2 <- paste0("(citation_id_type: 'pmid' AND citation_id:",pmid_only_path_journals$PMID, ") OR ", collapse = "")
+
+write(pmid_only_path_journals2,
+"PancreasStudies/data/lensSearch.txt"
+)
+
+
+
+
+
+10 openknowledgemaps
+Open Knowledge Maps (2019). Overview of research on intraductal tubulopapillary neoplasm. Retrieved from https://openknowledgemaps.org/map/cc04c53301920a93d451aa2ce3010243/ [30 Mar 2019].
+
+
+11 bibliometrix
+
+
+12 ORCID
+
+
+13 Semantic Scholar
+
+
+
+14 Microsoft Academic
+
+
+15 Scopus
+
+
+16 Altmetrics
+
+
+17 Grid
+
+
+
+18 ROR
+
+
+
+19 Cobalmetrics
+
+
+- Toward privacy-preserving altmetrics exploration with Cobaltmetrics and ORCID
+
+
+
+
+20 OpenCitations
+
+http://opencitations.net/download
+http://opencitations.net/corpus
+https://github.com/opencitations
+
+The OpenCitations Data Model
+https://figshare.com/articles/Metadata_for_the_OpenCitations_Corpus/3443876
Creating Open Citation Data with BCite
+https://semsci.github.io/SemSci2018/papers/1/bcite-semsci2018.html
+
+
+
+21 Open Knowledge Maps
+Open Knowledge Maps (2019). Overview of research on (pathology[affiliation] or patoloji[affiliation]) and (turkey[affiliation] or türkiye[affiliation]). Retrieved from https://openknowledgemaps.org/map/e4dbf6c89015e402d6d7d560ab79e17a/ [30 Mar 2019].
+
+
+
+22 iris.ai
+https://the.iris.ai/map/02f89d24-0415-43ab-878a-853ec17c5a59
+
+
+23 lens.org
+
+
+
+
+
+24 To Do
+
+- find a way to auto import journal names
+- remove last OR
+- Auto run posiible analysis via cron
+- Find a way to auto copy into googledrive
+- push to blog, netlify …
+- Add from – Sources.Rmd
+– Bibliyometri.Rmd
+
+
+
+25 About & Feedback
+Serdar Balcı, MD, Pathologist would like to hear your feedback: https://goo.gl/forms/YjGZ5DHgtPlR1RnB3
+This document will be continiously updated and the last update was on 2019-03-31.
+
+
+
+
+
+
+
+
+
+
+26 References
+
+
+
+
+
+
+
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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.Rmd b/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.Rmd
index b9e2285..5d993d3 100644
--- a/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.Rmd
+++ b/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.Rmd
@@ -139,6 +139,221 @@ Indexes=SCI-EXPANDED, SSCI, A&HCI, CPCI-S, CPCI-SSH, BKCI-S, BKCI-SSH, ESCI Time
```
+# Hacettepe[Affiliation] AND Pathology[Affiliation]
+```{r Search PubMed download all articles uid, eval=FALSE, include=FALSE}
+myTerm <- rstudioapi::terminalCreate(show = FALSE)
+rstudioapi::terminalSend(
+ myTerm,
+ "esearch -db pubmed -query \"hacettepe[Affiliation] AND (pathology[Affiliation] OR patoloji[Affiliation])\" -datetype PDAT -mindate 1800 -maxdate 3000 | \ efetch -format uid > data/pubmed_result_hacettepe_pathology_uid.txt \n"
+)
+Sys.sleep(1)
+repeat {
+ Sys.sleep(0.1)
+ if (rstudioapi::terminalBusy(myTerm) == FALSE) {
+ print("Code Executed")
+ break
+ }
+}
+
+file.info(here::here("data/pubmed_result_hacettepe_pathology_uid.txt"))$ctime
+```
+
+
+```{r Search PubMed download all articles xml, eval=FALSE, include=FALSE}
+myTerm <- rstudioapi::terminalCreate(show = FALSE)
+rstudioapi::terminalSend(
+ myTerm,
+ "esearch -db pubmed -query \"hacettepe[Affiliation] AND (pathology[Affiliation] OR patoloji[Affiliation])\" -datetype PDAT -mindate 1800 -maxdate 3000 | \ efetch -format xml > data/pubmed_result_hacettepe_pathology_uid.xml \n"
+)
+Sys.sleep(1)
+repeat {
+ Sys.sleep(0.1)
+ if (rstudioapi::terminalBusy(myTerm) == FALSE) {
+ print("Code Executed")
+ break
+ }
+}
+
+file.info(here::here("data/pubmed_result_hacettepe_pathology_uid.xml"))$ctime
+```
+
+
+
+
+```{r extract if pathology and hacettepe in same affiliation, eval=FALSE, include=FALSE}
+
+myTerm <- rstudioapi::terminalCreate(show = FALSE)
+rstudioapi::terminalSend(
+myTerm,
+"xtract -input data/pubmed_result_hacettepe_pathology_uid.xml -pattern PubmedArticle -tab \"|\" -sep \";\" -def \"NA\" -element MedlineCitation/PMID ArticleTitle Journal/ISSN ISOAbbreviation PubDate/Year Affiliation> data/data_hacettepepathology.csv \n"
+)
+Sys.sleep(1)
+repeat {
+Sys.sleep(0.1)
+if (rstudioapi::terminalBusy(myTerm) == FALSE) {
+print("Code Executed")
+break
+}
+}
+
+```
+
+
+## read extracted data
+
+
+```{r read data}
+library(readr)
+data_hacettepePathology <- read_delim(here::here("data/data_hacettepepathology.csv"),
+ "|",
+ escape_double = FALSE,
+ col_names = FALSE,
+ trim_ws = TRUE)
+# View(data_hacettepePathology)
+
+names(data_hacettepePathology) <- c("PMID", "ArticleTitle", "ISSN", "ISOAbbreviation", "PubDate", "Affiliation")
+
+```
+
+
+```{r separate affiliations}
+library(tidyverse)
+library(stringr)
+str_count(string = data_hacettepePathology$Affiliation, pattern = ";") %>%
+ max()
+
+```
+
+
+```{r plain affiliation characters, include=FALSE}
+
+# to.plain <- function(s) {
+# # 1 character substitutions
+# old1 <- "çğşıüöÇĞŞİÖÜ"
+# new1 <- "cgsiuocgsiou"
+# s1 <- chartr(old1, new1, s)
+# # 2 character substitutions
+# old2 <- c("œ", "ß", "æ", "ø")
+# new2 <- c("oe", "ss", "ae", "oe")
+# s2 <- s1
+# for(i in seq_along(old2)) s2 <- gsub(old2[i], new2[i], s2, fixed = TRUE)
+# s2
+# }
+
+data_hacettepePathology2 <- data_hacettepePathology %>%
+ select(PMID, Affiliation)
+
+
+# [[:alpha:]]
+
+
+
+# data_hacettepePathology2$Affiliation <- data_hacettepePathology2$Affiliation %>%
+# tolower() %>%
+# to.plain()
+
+
+data_hacettepePathology2 <- data_hacettepePathology2 %>%
+ separate(col = "Affiliation", sep = ";", into = paste0("Affiliation", 1:6925))
+
+
+```
+
+
+
+
+```{r}
+library(tidyverse)
+library(reshape2)
+
+DT.m1 <- melt(data_hacettepePathology2,
+ id.vars = c("PMID"),
+ measure.vars = paste0("Affiliation", 1:6925))
+
+DT.m2 <- DT.m1 %>%
+ filter(!is.na(value))
+
+DT.m2$count <- 1
+
+```
+
+
+```{r}
+DT.m2$hacettepe <-
+ grepl(
+ pattern = ("[Hh]acettepe"),
+ x =
+ DT.m2$value
+ )
+
+DT.m2$pathology <-
+ grepl(
+ pattern = ("[Pp]athology|[Pp]atoloji"),
+ x =
+ DT.m2$value
+ )
+
+DT.m2$speach <-
+ grepl(
+ pattern = ("[Ss]peach|[Ss]peech"),
+ x =
+ DT.m2$value
+ )
+
+
+```
+
+```{r}
+DT.m3 <- DT.m2 %>%
+ filter(hacettepe == TRUE & pathology == TRUE) %>%
+ filter(speach==FALSE)
+
+```
+
+```{r}
+final_hacettepePathology <- data_hacettepePathology %>%
+ filter(PMID %in% DT.m3$PMID) %>%
+ select(-c("Affiliation")) %>%
+ left_join(DT.m3, by="PMID") %>%
+ select(c("PMID", "ArticleTitle", "ISSN", "ISOAbbreviation", "PubDate"), Affiliation = value) %>%
+ unique() %>%
+ mutate(PMIDLink = paste0("https://www.ncbi.nlm.nih.gov/pubmed/", PMID, ""))
+
+writexl::write_xlsx(final_hacettepePathology, here::here("data/final_hacettepePathology.xlsx"))
+
+```
+
+
+```{r}
+cat(paste0(final_hacettepePathology$PMID, " OR ")
+)
+```
+
+
+```
+(hacettepe[Affiliation] AND (pathology[Affiliation] OR patoloji[Affiliation])) NOT (speach[Affiliation] OR speech[Affiliation])
+```
+
+```
+(Turkey[Affiliation] OR Turkiye[Affiliation]) AND ((pathology[Affiliation] OR patoloji[Affiliation]) NOT (speach[Affiliation] OR speech[Affiliation]))
+```
+
+
+```{r}
+library(tidyverse)
+library(tidylog)
+library(mmpipe)
+final_hacettepePathology <- data_hacettepePathology %V>%
+ filter(PMID %in% DT.m3$PMID) %V>%
+ select(-c("Affiliation")) %V>%
+ left_join(DT.m3, by="PMID") %V>%
+ select(c("PMID", "ArticleTitle", "ISSN", "ISOAbbreviation", "PubDate"), Affiliation = value) %V>%
+ unique() %V>%
+ mutate(PMIDLink = paste0("https://www.ncbi.nlm.nih.gov/pubmed/", PMID, ""))
+
+
+```
+
diff --git a/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.nb.html b/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.nb.html
index b9165c2..a1e5325 100644
--- a/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.nb.html
+++ b/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.nb.html
@@ -1801,7 +1801,7 @@ europepmc
ylab("Proportion of Pathology articles \n from Turkey in Europe PMC")
-
+
@@ -1874,10 +1874,164 @@ Data retriveal from PubMed using EDirect
WOS data for VOSviewer
(AD=Turkey AND SU=Pathology) OR (CU=Turkey AND SU=Pathology)
Indexes=SCI-EXPANDED, SSCI, A&HCI, CPCI-S, CPCI-SSH, BKCI-S, BKCI-SSH, ESCI Timespan=All years
+
+
+Hacettepe[Affiliation] AND Pathology[Affiliation]
+
+
+
+
+
+
+
+read extracted data
+
+
+
+library(readr)
+data_hacettepePathology <- read_delim(here::here("data/data_hacettepepathology.csv"),
+ "|",
+ escape_double = FALSE,
+ col_names = FALSE,
+ trim_ws = TRUE)
+
+
+Parsed with column specification:
+cols(
+ X1 = [32mcol_double()[39m,
+ X2 = [31mcol_character()[39m,
+ X3 = [31mcol_character()[39m,
+ X4 = [31mcol_character()[39m,
+ X5 = [32mcol_double()[39m,
+ X6 = [31mcol_character()[39m
+)
+4 parsing failures.
+row col expected actual file
+210 -- 6 columns 8 columns '/Users/serdarbalciold/RepTemplates/pubmed/data/data_hacettepepathology.csv'
+242 -- 6 columns 8 columns '/Users/serdarbalciold/RepTemplates/pubmed/data/data_hacettepepathology.csv'
+243 -- 6 columns 8 columns '/Users/serdarbalciold/RepTemplates/pubmed/data/data_hacettepepathology.csv'
+281 -- 6 columns 8 columns '/Users/serdarbalciold/RepTemplates/pubmed/data/data_hacettepepathology.csv'
+
+
+# View(data_hacettepePathology)
+
+names(data_hacettepePathology) <- c("PMID", "ArticleTitle", "ISSN", "ISOAbbreviation", "PubDate", "Affiliation")
+
+
+
+
+
+
+
+library(tidyverse)
+library(stringr)
+str_count(string = data_hacettepePathology$Affiliation, pattern = ";") %>%
+ max()
+
+
+[1] 6924
+
+
+
+
+
+
+
+
+library(tidyverse)
+library(reshape2)
+
+DT.m1 <- melt(data_hacettepePathology2,
+ id.vars = c("PMID"),
+ measure.vars = paste0("Affiliation", 1:6925))
+
+DT.m2 <- DT.m1 %>%
+ filter(!is.na(value))
+
+DT.m2$count <- 1
+
+
+
+
+
+
+
+DT.m2$hacettepe <-
+ grepl(
+ pattern = ("[Hh]acettepe"),
+ x =
+ DT.m2$value
+ )
+
+
+
+
+
+
+DT.m3 <- DT.m2 %>%
+ filter(hacettepe == TRUE & pathology == TRUE) %>%
+ filter(speach==FALSE)
+
+
+
+
+
+
+final_hacettepePathology <- data_hacettepePathology %>%
+ filter(PMID %in% DT.m3$PMID) %>%
+ select(-c("Affiliation")) %>%
+ left_join(DT.m3, by="PMID") %>%
+ select(c("PMID", "ArticleTitle", "ISSN", "ISOAbbreviation", "PubDate")), Affiliation = value)
+
+
+
+Error: unexpected ',' in:
+" left_join(DT.m3, by="PMID") %>%
+ select(c("PMID", "ArticleTitle", "ISSN", "ISOAbbreviation", "PubDate")),"
+
+
+
+
+
+
+cat(paste0(final_hacettepePathology$PMID, " OR ")
+)
+
+
+
+30711942 OR 30711942 OR 30711942 OR 30614391 OR 30607566 OR 30553274 OR 30543088 OR 30420050 OR 30420050 OR 30378176 OR 30361868 OR 30356178 OR 30342481 OR 30337132 OR 30326153 OR 30264475 OR 30258736 OR 30222718 OR 30215711 OR 30213486 OR 30194012 OR 30177831 OR 30177831 OR 30177831 OR 30177831 OR 30151600 OR 30121298 OR 30066674 OR 30061063 OR 30039725 OR 29963264 OR 29933323 OR 29843558 OR 29758192 OR 29744787 OR 29737941 OR 29729229 OR 29631339 OR 29610498 OR 29565209 OR 29564756 OR 29557778 OR 29521057 OR 29481086 OR 29455242 OR 29433873 OR 29391599 OR 29391317 OR 29386221 OR 29368083 OR 29368083 OR 29342030 OR 29333888 OR 29307770 OR 29286564 OR 29278522 OR 29276876 OR 29221145 OR 29217050 OR 29183666 OR 29147924 OR 29147924 OR 29113255 OR 29107076 OR 29101765 OR 29071270 OR 28988523 OR 28957973 OR 28938499 OR 28885322 OR 28877062 OR 28872973 OR 28871709 OR 28843712 OR 28832323 OR 28832077 OR 28832074 OR 28786167 OR 28754454 OR 28705285 OR 28684169 OR 28645584 OR 28627959 OR 28616233 OR 28601298 OR 28597078 OR 28593113 OR 28576480 OR 28575990 OR 28566877 OR 28554554 OR 28549792 OR 28549792 OR 28488171 OR 28471040 OR 28452074 OR 28443589 OR 28333838 OR 28263489 OR 28263489 OR 28219585 OR 28216139 OR 28216139 OR 28203472 OR 28155970 OR 28155970 OR 28109637 OR 28083971 OR 29745124 OR 28028337 OR 27974811 OR 27932539 OR 27922519 OR 27909626 OR 27906844 OR 27896834 OR 27864098 OR 27857123 OR 27853495 OR 27810370 OR 27807490 OR 27561188 OR 27603550 OR 27513982 OR 27703380 OR 27699733 OR 27640103 OR 27640103 OR 27606145 OR 27575604 OR 27547915 OR 27520411 OR 27476657 OR 27448951 OR 27416885 OR 27409664 OR 27390585 OR 27366187 OR 27347166 OR 27303936 OR 27259049 OR 27216000 OR 27206703 OR 27180062 OR 27132540 OR 27129763 OR 27067808 OR 27062662 OR 27042238 OR 27026777 OR 27003050 OR 26997452 OR 26980028 OR 26970763 OR 26965579 OR 26945448 OR 26943384 OR 26872278 OR 26854080 OR 26848216 OR 26797858 OR 26797858 OR 26743593 OR 29090887 OR 29090884 OR 29090871 OR 28276221 OR 26681974 OR 26662466 OR 26584874 OR 26584697 OR 26578207 OR 26578207 OR 26575115 OR 26563115 OR 26550397 OR 26527231 OR 26519197 OR 26456966 OR 26449317 OR 26449317 OR 26449317 OR 26407049 OR 26397478 OR 26346511 OR 26341890 OR 26339344 OR 26332388 OR 26293571 OR 26242854 OR 26207004 OR 26100969 OR 26095595 OR 26090243 OR 26081979 OR 26081979 OR 26067811 OR 26064727 OR 26052757 OR 26045846 OR 25994764 OR 25906124 OR 25883712 OR 25842994 OR 25821721 OR 25811726 OR 25810266 OR 25769540 OR 25759781 OR 25755968 OR 25743721 OR 27708922 OR 25692090 OR 25667467 OR 25560609 OR 27047934 OR 25529806 OR 25498489 OR 25457509 OR 25378828 OR 25223322 OR 25218282 OR 25171023 OR 25110239 OR 25087613 OR 24977003 OR 24947701 OR 24913330 OR 24856141 OR 24840535 OR 24794787 OR 24794787 OR 24782301 OR 24777267 OR 24731921 OR 24718000 OR 24667046 OR 24585772 OR 24523789 OR 24505496 OR 24430434 OR 24385732 OR 24326152 OR 24285274 OR 24080633 OR 24022314 OR 24018817 OR 23998291 OR 23653827 OR 28509218 OR 23588333 OR 23551548 OR 23419599 OR 24592101 OR 23219110 OR 23153936 OR 23030256 OR 23011824 OR 23011823 OR 23011821 OR 22961375 OR 22316516 OR 22301705 OR 22158496 OR 21810125 OR 21665002 OR 21630194 OR 21496526 OR 21492232 OR 21469428 OR 21437995 OR 21074692 OR 21074691 OR 21069451 OR 20952300 OR 20952295 OR 20719821 OR 20674190 OR 20465615 OR 20418233 OR 20173504 OR 20060354 OR 19851201 OR 19468034 OR 19462235 OR 19403544 OR 19363472 OR 19232840 OR 19178738 OR 19130459 OR 19065380 OR 19024599 OR 19014058 OR 18844937 OR 18773281 OR 18446633 OR 18379707 OR 18374497 OR 18365589 OR 18246753 OR 18085395 OR 18066567 OR 17947476 OR 17926107 OR 17922596 OR 17619723 OR 17587245 OR 17573765 OR 17543474 OR 17451888 OR 17291234 OR 17130035 OR 17007443 OR 16912900 OR 16752009 OR 16489441 OR 16343208 OR 16328667 OR 16320561 OR 16194892 OR 16175081 OR 16021510 OR 16014115 OR 15998374 OR 15913445 OR 15802396 OR 15762048 OR 15670313 OR 15658132 OR 15623491 OR 15622249 OR 15456418 OR 15334737 OR 15249720 OR 15204955 OR 15073846 OR 15032077 OR 14692804 OR 14521262 OR 12911737 OR 12488986 OR 12464212 OR 12049830 OR 12007023 OR 11926913 OR 11925832 OR 11793117 OR 11699420 OR 11585325 OR 11568381 OR 11564220 OR 11462912 OR 11409483 OR 11263931 OR 11057782 OR 11053680 OR 10997737 OR 10985626 OR 10885604 OR 10828801 OR 10819111 OR 10699830 OR 10679036 OR 10671893 OR 10636586 OR 10508882 OR 10192575 OR 9863925 OR 9849847 OR 9821039 OR 9744734 OR 9732936 OR 9646237 OR 9641241 OR 9625858 OR 9181320 OR 9085813 OR 9152975 OR 8899473 OR 7768662 OR 11578422 OR 8191601 OR 8368909 OR 8372026 OR 8516224 OR 8444560 OR 8096638 OR 8419633 OR 17588038 OR 1813402 OR 2287298 OR 2283976 OR 2626097 OR
+
+
+
+(hacettepe[Affiliation] AND (pathology[Affiliation] OR patoloji[Affiliation])) NOT (speach[Affiliation] OR speech[Affiliation])
+(Turkey[Affiliation] OR Turkiye[Affiliation]) AND ((pathology[Affiliation] OR patoloji[Affiliation]) NOT (speach[Affiliation] OR speech[Affiliation]))
+
+
+
+final_hacettepePathology <- data_hacettepePathology %V>%
+ filter(PMID %in% DT.m3$PMID) %V>%
+ select(-c("Affiliation")) %V>%
+ left_join(DT.m3, by="PMID") %V>%
+ select(c("PMID", "ArticleTitle", "ISSN", "ISOAbbreviation", "PubDate"), Affiliation = value) %V>%
+ unique() %V>%
+ mutate(PMIDLink = paste0("https://www.ncbi.nlm.nih.gov/pubmed/", PMID, ""))
+
+
+
+filter: removed 241 rows (39%)
+select: dropped one variable (Affiliation)
+left_join: added 98 rows and added 6 columns (variable, value, count, hacettepe, pathology, …)
+select: dropped 6 variables (variable, value, count, hacettepe, pathology, …)
+mutate: new variable 'PMIDLink' with 374 unique values and 0% NA
+
+
+
+
+
-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
diff --git a/Sources.Rmd b/Sources.Rmd
index 6563058..532d77f 100644
--- a/Sources.Rmd
+++ b/Sources.Rmd
@@ -200,6 +200,8 @@ caffeinate
https://labs.cognitive.microsoft.com/en-us/project-academic-knowledge
+https://academic.microsoft.com/author/2608586067/publication/search?q=Serdar%20Balci
+
## Scopus
https://www.scopus.com/sources
@@ -249,6 +251,28 @@ https://semsci.github.io/SemSci2018/papers/1/bcite-semsci2018.html
https://github.com/opencitations/bcite
+## Open Knowledge Maps
+
+Open Knowledge Maps (2019). Overview of research on (pathology[affiliation] or patoloji[affiliation]) and (turkey[affiliation] or türkiye[affiliation]). Retrieved from https://openknowledgemaps.org/map/e4dbf6c89015e402d6d7d560ab79e17a/ [30 Mar 2019].
+
+
+https://openknowledgemaps.org/index
+
+
+
+## iris.ai
+
+https://the.iris.ai/map/02f89d24-0415-43ab-878a-853ec17c5a59
+
+## lens.org
+
+https://www.lens.org/lens/scholar/search/results?dateFilterField=year_published&filterMap=%7B%7D&orcids=0000-0002-7852-3851&orderBy=%2Bpublished&preview=true&previewType=SCHOLAR_ANALYSIS®exEnabled=false
+
+https://www.lens.org/lens/scholar/search/results?q=(author.affiliation.name:%20%22pathology%22%20%20OR%20author.affiliation.name:%20%22patoloji%22)%20%20AND%20(author.affiliation.name:%20%22Turkey%22%20%20OR%20author.affiliation.name:%20%22T%C3%BCrkiye%22)
+
+https://www.lens.org/lens/scholar/search/analysis?q=(author.affiliation.name:%20%22neurosurgery%22%20%20OR%20author.affiliation.name:%20%22sport%22%20)%20AND%20(abstract:%20%22sport%22%20%20OR%20title:%20%22sport%22)&page=0&limit=10&orderBy=%2Bscore&dateFilterField=year_published&preview=false®exEnabled=false
+
+
---
# Feedback
diff --git a/Sources.nb.html b/Sources.nb.html
index 118ac55..7b96d53 100644
--- a/Sources.nb.html
+++ b/Sources.nb.html
@@ -11,7 +11,7 @@
-
+
Bibliographic Studies
@@ -2551,7 +2551,7 @@
var currentIndex = 1;
// select all R code blocks
- var rCodeBlocks = $('pre.r, pre.python, pre.bash, pre.sql, pre.cpp, pre.stan');
+ var rCodeBlocks = $('pre.r, pre.python, pre.bash, pre.sql, pre.cpp, pre.stan, pre.julia');
rCodeBlocks.each(function() {
// create a collapsable div to wrap the code in
@@ -2640,9 +2640,7 @@
-
-
-
-
+
+
+
+
+
+
+
+
+
+
@@ -2893,9 +2899,9 @@
Bibliographic Studies
-Sources Used For Analysis
-Serdar Balcı, MD, Pathologist
-2019-01-23
+Sources Used For Analysis
+Serdar Balcı, MD, Pathologist
+2019-03-30
@@ -3006,6 +3012,7 @@ 2.3 Semantic Scholar
2.4 Microsoft Academic
https://labs.cognitive.microsoft.com/en-us/project-academic-knowledge
+https://academic.microsoft.com/author/2608586067/publication/search?q=Serdar%20Balci
2.5 Scopus
@@ -3044,13 +3051,28 @@ 2.10 OpenCitations
https://semsci.github.io/SemSci2018/papers/1/bcite-semsci2018.html
+
+
+2.11 Open Knowledge Maps
+Open Knowledge Maps (2019). Overview of research on (pathology[affiliation] or patoloji[affiliation]) and (turkey[affiliation] or türkiye[affiliation]). Retrieved from https://openknowledgemaps.org/map/e4dbf6c89015e402d6d7d560ab79e17a/ [30 Mar 2019].
+
+
+
+2.12 iris.ai
+https://the.iris.ai/map/02f89d24-0415-43ab-878a-853ec17c5a59
+
+
+2.13 lens.org
+
+
+
3 Feedback
Serdar Balcı, MD, Pathologist would like to hear your feedback: https://goo.gl/forms/YjGZ5DHgtPlR1RnB3
-This document will be continiously updated and the last update was on 2019-01-23.
+This document will be continiously updated and the last update was on 2019-03-30.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+USCAP Abstracts vs Published Articles
+
+
+
+
+
+Search methods:
+Journal:
+Modern Pathology
+Laboratory Investigation
+Conference:
+USCAP
+Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology
+From pdf ??
+
+
+
+
+
+
+install.packages("pdftools")
+
+
+Installing package into ‘/Users/serdarbalciold/Library/R/3.5/library’
+(as ‘lib’ is unspecified)
+also installing the dependency ‘qpdf’
+
+trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/qpdf_1.1.tgz'
+Content type 'application/x-gzip' length 3730250 bytes (3.6 MB)
+==================================================
+downloaded 3.6 MB
+
+trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/pdftools_2.2.tgz'
+Content type 'application/x-gzip' length 6580512 bytes (6.3 MB)
+==================================================
+downloaded 6.3 MB
+
+
+
+The downloaded binary packages are in
+ /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFaS0NC/downloaded_packages
+
+
+
+
+
+
+# download.file("https://github.com/Huitziii/crispy-pdf/raw/master/71_PV.62.pdf",
+ # "./71_PV.62.pdf")
+text <- pdf_text("data/eurospine/2014/eurospine-2014-2014qf.pdf")
+
+
+
+Error in pdf_text("data/eurospine/2014/eurospine-2014-2014qf.pdf") :
+ could not find function "pdf_text"
+
+
+
+
+
+
+
+
+
+
+
+library(tidyverse)
+library(officer)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+lyon2014$content_type
+
+
+
+<content_type>
+ Public:
+ add_ext: function (extension, type)
+ add_override: function (value)
+ add_slide: function (partname)
+ clone: function (deep = FALSE)
+ initialize: function (package_dir)
+ remove_slide: function (partname)
+ save: function ()
+ Private:
+ default: application/vnd.openxmlformats-package.relationships+xml ...
+ filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ override: application/vnd.openxmlformats-officedocument.wordproces ...
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+glimpse(lyon2014)
+
+
+
+List of 1308
+ $ package_dir : chr "/var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFaS0NC/file138a4c66125c"
+ $ doc_properties:Classes 'core_properties', 'R6' <core_properties>
+ Public:
+ clone: function (deep = FALSE)
+ get_data: function ()
+ initialize: function (package_dir)
+ save: function ()
+ set_created: function (value)
+ set_creator: function (value)
+ set_description: function (value)
+ set_keywords: function (value)
+ set_last_modified: function (value)
+ set_modified_by: function (value)
+ set_subject: function (value)
+ set_title: function (value)
+ Private:
+ doc: xml_document, xml_node
+ filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ set_core_property: function (tag, ns, value, attrs = NULL)
+ $ content_type :Classes 'content_type', 'R6' <content_type>
+ Public:
+ add_ext: function (extension, type)
+ add_override: function (value)
+ add_slide: function (partname)
+ clone: function (deep = FALSE)
+ initialize: function (package_dir)
+ remove_slide: function (partname)
+ save: function ()
+ Private:
+ default: application/vnd.openxmlformats-package.relationships+xml ...
+ filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ override: application/vnd.openxmlformats-officedocument.wordproces ...
+ $ doc_obj :Classes 'docx_part', 'openxml_document', 'R6' <docx_part>
+ Inherits from: <openxml_document>
+ Public:
+ clone: function (deep = FALSE)
+ cursor_backward: function ()
+ cursor_begin: function ()
+ cursor_bookmark: function (id)
+ cursor_end: function ()
+ cursor_forward: function ()
+ cursor_reach: function (keyword)
+ cursor_replace_first_img: function (id, src, width, height)
+ cursor_replace_first_text: function (id, text)
+ dir_name: function ()
+ docx_show_chunk: function ()
+ feed: function (file)
+ file_name: function ()
+ get: function ()
+ get_at_cursor: function ()
+ has_bookmark: function (id)
+ initialize: function (path, main_file, cursor, body_xpath)
+ length: function ()
+ name: function ()
+ rel_df: function ()
+ relationship: function ()
+ remove: function ()
+ replace_all_text: function (oldValue, newValue, onlyAtCursor = TRUE, warn = TRUE,
+ save: function ()
+ set_cursor: function (cursor)
+ Private:
+ body_xpath: /w:document/w:body
+ cursor: /w:document/w:body/*[1307]
+ doc: xml_document, xml_node
+ filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ package_dir: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ reldir: word
+ rels_doc: relationship, R6
+ rels_filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ $ styles :'data.frame': 4 obs. of 5 variables:
+ ..$ style_type: chr [1:4] "paragraph" "character" "table" "numbering"
+ ..$ style_id : chr [1:4] "Normal" "DefaultParagraphFont" "TableNormal" "NoList"
+ ..$ style_name: chr [1:4] "Normal" "Default Paragraph Font" "Normal Table" "No List"
+ ..$ is_custom : logi [1:4] FALSE FALSE FALSE FALSE
+ ..$ is_default: logi [1:4] TRUE TRUE TRUE TRUE
+ $ headers :List of 2
+ ..$ header1.xml:Classes 'docx_part', 'openxml_document', 'R6' <docx_part>
+ Inherits from: <openxml_document>
+ Public:
+ clone: function (deep = FALSE)
+ cursor_backward: function ()
+ cursor_begin: function ()
+ cursor_bookmark: function (id)
+ cursor_end: function ()
+ cursor_forward: function ()
+ cursor_reach: function (keyword)
+ cursor_replace_first_img: function (id, src, width, height)
+ cursor_replace_first_text: function (id, text)
+ dir_name: function ()
+ docx_show_chunk: function ()
+ feed: function (file)
+ file_name: function ()
+ get: function ()
+ get_at_cursor: function ()
+ has_bookmark: function (id)
+ initialize: function (path, main_file, cursor, body_xpath)
+ length: function ()
+ name: function ()
+ rel_df: function ()
+ relationship: function ()
+ remove: function ()
+ replace_all_text: function (oldValue, newValue, onlyAtCursor = TRUE, warn = TRUE,
+ save: function ()
+ set_cursor: function (cursor)
+ Private:
+ body_xpath: /w:hdr
+ cursor: /w:hdr/*[1]
+ doc: xml_document, xml_node
+ filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ package_dir: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ reldir: word
+ rels_doc: relationship, R6
+ rels_filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ ..$ header2.xml:Classes 'docx_part', 'openxml_document', 'R6' <docx_part>
+ Inherits from: <openxml_document>
+ Public:
+ clone: function (deep = FALSE)
+ cursor_backward: function ()
+ cursor_begin: function ()
+ cursor_bookmark: function (id)
+ cursor_end: function ()
+ cursor_forward: function ()
+ cursor_reach: function (keyword)
+ cursor_replace_first_img: function (id, src, width, height)
+ cursor_replace_first_text: function (id, text)
+ dir_name: function ()
+ docx_show_chunk: function ()
+ feed: function (file)
+ file_name: function ()
+ get: function ()
+ get_at_cursor: function ()
+ has_bookmark: function (id)
+ initialize: function (path, main_file, cursor, body_xpath)
+ length: function ()
+ name: function ()
+ rel_df: function ()
+ relationship: function ()
+ remove: function ()
+ replace_all_text: function (oldValue, newValue, onlyAtCursor = TRUE, warn = TRUE,
+ save: function ()
+ set_cursor: function (cursor)
+ Private:
+ body_xpath: /w:hdr
+ cursor: /w:hdr/*[1]
+ doc: xml_document, xml_node
+ filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ package_dir: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ reldir: word
+ rels_doc: relationship, R6
+ rels_filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ $ footers :List of 2
+ ..$ footer1.xml:Classes 'docx_part', 'openxml_document', 'R6' <docx_part>
+ Inherits from: <openxml_document>
+ Public:
+ clone: function (deep = FALSE)
+ cursor_backward: function ()
+ cursor_begin: function ()
+ cursor_bookmark: function (id)
+ cursor_end: function ()
+ cursor_forward: function ()
+ cursor_reach: function (keyword)
+ cursor_replace_first_img: function (id, src, width, height)
+ cursor_replace_first_text: function (id, text)
+ dir_name: function ()
+ docx_show_chunk: function ()
+ feed: function (file)
+ file_name: function ()
+ get: function ()
+ get_at_cursor: function ()
+ has_bookmark: function (id)
+ initialize: function (path, main_file, cursor, body_xpath)
+ length: function ()
+ name: function ()
+ rel_df: function ()
+ relationship: function ()
+ remove: function ()
+ replace_all_text: function (oldValue, newValue, onlyAtCursor = TRUE, warn = TRUE,
+ save: function ()
+ set_cursor: function (cursor)
+ Private:
+ body_xpath: /w:ftr
+ cursor: /w:ftr/*[1]
+ doc: xml_document, xml_node
+ filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ package_dir: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ reldir: word
+ rels_doc: relationship, R6
+ rels_filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ ..$ footer2.xml:Classes 'docx_part', 'openxml_document', 'R6' <docx_part>
+ Inherits from: <openxml_document>
+ Public:
+ clone: function (deep = FALSE)
+ cursor_backward: function ()
+ cursor_begin: function ()
+ cursor_bookmark: function (id)
+ cursor_end: function ()
+ cursor_forward: function ()
+ cursor_reach: function (keyword)
+ cursor_replace_first_img: function (id, src, width, height)
+ cursor_replace_first_text: function (id, text)
+ dir_name: function ()
+ docx_show_chunk: function ()
+ feed: function (file)
+ file_name: function ()
+ get: function ()
+ get_at_cursor: function ()
+ has_bookmark: function (id)
+ initialize: function (path, main_file, cursor, body_xpath)
+ length: function ()
+ name: function ()
+ rel_df: function ()
+ relationship: function ()
+ remove: function ()
+ replace_all_text: function (oldValue, newValue, onlyAtCursor = TRUE, warn = TRUE,
+ save: function ()
+ set_cursor: function (cursor)
+ Private:
+ body_xpath: /w:ftr
+ cursor: /w:ftr/*[1]
+ doc: xml_document, xml_node
+ filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ package_dir: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ reldir: word
+ rels_doc: relationship, R6
+ rels_filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ $ footnotes :Classes 'docx_part', 'openxml_document', 'R6' <docx_part>
+ Inherits from: <openxml_document>
+ Public:
+ clone: function (deep = FALSE)
+ cursor_backward: function ()
+ cursor_begin: function ()
+ cursor_bookmark: function (id)
+ cursor_end: function ()
+ cursor_forward: function ()
+ cursor_reach: function (keyword)
+ cursor_replace_first_img: function (id, src, width, height)
+ cursor_replace_first_text: function (id, text)
+ dir_name: function ()
+ docx_show_chunk: function ()
+ feed: function (file)
+ file_name: function ()
+ get: function ()
+ get_at_cursor: function ()
+ has_bookmark: function (id)
+ initialize: function (path, main_file, cursor, body_xpath)
+ length: function ()
+ name: function ()
+ rel_df: function ()
+ relationship: function ()
+ remove: function ()
+ replace_all_text: function (oldValue, newValue, onlyAtCursor = TRUE, warn = TRUE,
+ save: function ()
+ set_cursor: function (cursor)
+ Private:
+ body_xpath: /w:footnotes
+ cursor: /w:footnotes/*[last()]
+ doc: xml_document, xml_node
+ filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ package_dir: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ reldir: word
+ rels_doc: relationship, R6
+ rels_filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ $ default_styles:List of 4
+ ..$ paragraph: chr "Normal"
+ ..$ character: chr "Default Paragraph Font"
+ ..$ table : chr "Normal Table"
+ ..$ numbering: chr "No List"
+ $ sect_dim :List of 3
+ ..$ page : Named int [1:2] 11920 15820
+ .. ..- attr(*, "names")= chr [1:2] "width" "height"
+ ..$ landscape: logi FALSE
+ ..$ margins : Named int [1:4] 540 1080 900 900
+ .. ..- attr(*, "names")= chr [1:4] "top" "bottom" "left" "right"
+ $ NA:
+
+
+Error in object[[i]] : subscript out of bounds
+
+
+
+
+
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
+
+
+
+
+
+
+
+
+
+
+
+
4 Feedback
Serdar Balcı, MD, Pathologist would like to hear your feedback: https://goo.gl/forms/YjGZ5DHgtPlR1RnB3
-This document will be continiously updated and the last update was on 2019-01-13.
+This document will be continiously updated and the last update was on 2019-03-30.
+ + +```{r global_options, include=FALSE} +knitr::opts_chunk$set(fig.width = 12, fig.height = 8, + # fig.path = 'figures/', + echo = FALSE, warning = FALSE, message = FALSE, error = FALSE, eval = TRUE, tidy = TRUE, comment = NA) +``` + +```{r library, include=FALSE} +library(tidyverse) +``` + + + + +# Introduction + +- Selected Pathology Journals are used for the query^[[Selected Pathology Journals](PancreasStudies/data/journal_list_from_my_collections)] + + + + +# PubMed + +## Data Download from PubMed via EDirect + +- Data is downloaded from PubMed via Edirect^[https://dataguide.nlm.nih.gov/edirect/overview.html] + +- + + +## rentrez + +# europepmc + + + +# WOS + +[WOS.Rmd](WOS.Rmd) + +```{r} +PMID_List_for_WOS_pancreas <- paste0("PMID=(", pmid_only_path_journals$PMID, ") OR") + +write(PMID_List_for_WOS_pancreas, + here::here("PancreasStudies/data/PMID_List_for_WOS_pancreas.txt") +) + +``` + + + + + + + +# Scopus + +[scopus.Rmd](scopus.Rmd) + + +# Vosviewer + +Author Thesaurus is used.^[[Author Thesaurus](data/thesaurus_authors.txt)] + +Code for interactive graph.^[[Interactive Graph Code](data/VOSviewer_interactive_graphcode.txt)] + + + + + + +# Cite Space + +# CitNetExplorer + +# Lens + +``` +(citation_id_type: "pmid" AND citation_id: 28984336) OR (citation_id_type: "pmid" AND citation_id: 21682559) +``` + +```{r} +pmid_only_path_journals <- +read_delim("PancreasStudies/data/pmid_only_path_journals.txt", "\n", col_names = "PMID", col_types = "c") + +pmid_only_path_journals2 <- paste0("(citation_id_type: 'pmid' AND citation_id:",pmid_only_path_journals$PMID, ") OR ", collapse = "") + +write(pmid_only_path_journals2, +"PancreasStudies/data/lensSearch.txt" +) +``` + + + + +# openknowledgemaps + +Open Knowledge Maps (2019). Overview of research on intraductal tubulopapillary neoplasm. Retrieved from https://openknowledgemaps.org/map/cc04c53301920a93d451aa2ce3010243/ [30 Mar 2019]. + + +# bibliometrix + +# ORCID + +# Semantic Scholar + +[SemanticScholar.Rmd](SemanticScholar.Rmd) + + +# Microsoft Academic + +# Scopus + +# Altmetrics + + + +# Grid + +https://grid.ac/ + + +# ROR + +https://ror.org/search?page=1&query=turkey + + +# Cobalmetrics + +https://cobaltmetrics.com/ + +- Toward privacy-preserving altmetrics exploration with Cobaltmetrics and ORCID + +https://medium.com/thunken/toward-privacy-preserving-altmetrics-exploration-with-cobaltmetrics-and-orcid-f5ab6fa7898a + + +# OpenCitations + +http://opencitations.net + +http://opencitations.net/download + +http://opencitations.net/corpus + +https://github.com/opencitations + +- The OpenCitations Data Model +https://figshare.com/articles/Metadata_for_the_OpenCitations_Corpus/3443876 + +- Creating Open Citation Data with BCite +https://semsci.github.io/SemSci2018/papers/1/bcite-semsci2018.html + +https://github.com/opencitations/bcite + + +# Open Knowledge Maps + +Open Knowledge Maps (2019). Overview of research on (pathology[affiliation] or patoloji[affiliation]) and (turkey[affiliation] or türkiye[affiliation]). Retrieved from https://openknowledgemaps.org/map/e4dbf6c89015e402d6d7d560ab79e17a/ [30 Mar 2019]. + + +https://openknowledgemaps.org/index + + + +# iris.ai + +https://the.iris.ai/map/02f89d24-0415-43ab-878a-853ec17c5a59 + +# lens.org + +https://www.lens.org/lens/scholar/search/results?dateFilterField=year_published&filterMap=%7B%7D&orcids=0000-0002-7852-3851&orderBy=%2Bpublished&preview=true&previewType=SCHOLAR_ANALYSIS®exEnabled=false + +https://www.lens.org/lens/scholar/search/results?q=(author.affiliation.name:%20%22pathology%22%20%20OR%20author.affiliation.name:%20%22patoloji%22)%20%20AND%20(author.affiliation.name:%20%22Turkey%22%20%20OR%20author.affiliation.name:%20%22T%C3%BCrkiye%22) + +https://www.lens.org/lens/scholar/search/analysis?q=(author.affiliation.name:%20%22neurosurgery%22%20%20OR%20author.affiliation.name:%20%22sport%22%20)%20AND%20(abstract:%20%22sport%22%20%20OR%20title:%20%22sport%22)&page=0&limit=10&orderBy=%2Bscore&dateFilterField=year_published&preview=false®exEnabled=false + + +# To Do + +- find a way to auto import journal names +- remove last OR +- Auto run posiible analysis via cron +- Find a way to auto copy into googledrive +- push to blog, netlify ... +- Add from +-- [Sources.Rmd](Sources.Rmd) +-- [Bibliyometri.Rmd](Bibliyometri.Rmd) + + + + +# About & Feedback + + +[Serdar Balcı, MD, Pathologist](https://github.com/sbalci) would like to hear your feedback: https://goo.gl/forms/YjGZ5DHgtPlR1RnB3 + +This document will be continiously updated and the last update was on `r Sys.Date()`. + +--- + + + + + + + +--- + +# References + + + + diff --git a/PancreasStudies.nb.html b/PancreasStudies.nb.html new file mode 100644 index 0000000..9d04fc5 --- /dev/null +++ b/PancreasStudies.nb.html @@ -0,0 +1,3267 @@ + + + + + + + + + + + + + + + +
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.Rmd b/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.Rmd
index b9e2285..5d993d3 100644
--- a/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.Rmd
+++ b/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.Rmd
@@ -139,6 +139,221 @@ Indexes=SCI-EXPANDED, SSCI, A&HCI, CPCI-S, CPCI-SSH, BKCI-S, BKCI-SSH, ESCI Time
```
+# Hacettepe[Affiliation] AND Pathology[Affiliation]
+```{r Search PubMed download all articles uid, eval=FALSE, include=FALSE}
+myTerm <- rstudioapi::terminalCreate(show = FALSE)
+rstudioapi::terminalSend(
+ myTerm,
+ "esearch -db pubmed -query \"hacettepe[Affiliation] AND (pathology[Affiliation] OR patoloji[Affiliation])\" -datetype PDAT -mindate 1800 -maxdate 3000 | \ efetch -format uid > data/pubmed_result_hacettepe_pathology_uid.txt \n"
+)
+Sys.sleep(1)
+repeat {
+ Sys.sleep(0.1)
+ if (rstudioapi::terminalBusy(myTerm) == FALSE) {
+ print("Code Executed")
+ break
+ }
+}
+
+file.info(here::here("data/pubmed_result_hacettepe_pathology_uid.txt"))$ctime
+```
+
+
+```{r Search PubMed download all articles xml, eval=FALSE, include=FALSE}
+myTerm <- rstudioapi::terminalCreate(show = FALSE)
+rstudioapi::terminalSend(
+ myTerm,
+ "esearch -db pubmed -query \"hacettepe[Affiliation] AND (pathology[Affiliation] OR patoloji[Affiliation])\" -datetype PDAT -mindate 1800 -maxdate 3000 | \ efetch -format xml > data/pubmed_result_hacettepe_pathology_uid.xml \n"
+)
+Sys.sleep(1)
+repeat {
+ Sys.sleep(0.1)
+ if (rstudioapi::terminalBusy(myTerm) == FALSE) {
+ print("Code Executed")
+ break
+ }
+}
+
+file.info(here::here("data/pubmed_result_hacettepe_pathology_uid.xml"))$ctime
+```
+
+
+
+
+```{r extract if pathology and hacettepe in same affiliation, eval=FALSE, include=FALSE}
+
+myTerm <- rstudioapi::terminalCreate(show = FALSE)
+rstudioapi::terminalSend(
+myTerm,
+"xtract -input data/pubmed_result_hacettepe_pathology_uid.xml -pattern PubmedArticle -tab \"|\" -sep \";\" -def \"NA\" -element MedlineCitation/PMID ArticleTitle Journal/ISSN ISOAbbreviation PubDate/Year Affiliation> data/data_hacettepepathology.csv \n"
+)
+Sys.sleep(1)
+repeat {
+Sys.sleep(0.1)
+if (rstudioapi::terminalBusy(myTerm) == FALSE) {
+print("Code Executed")
+break
+}
+}
+
+```
+
+
+## read extracted data
+
+
+```{r read data}
+library(readr)
+data_hacettepePathology <- read_delim(here::here("data/data_hacettepepathology.csv"),
+ "|",
+ escape_double = FALSE,
+ col_names = FALSE,
+ trim_ws = TRUE)
+# View(data_hacettepePathology)
+
+names(data_hacettepePathology) <- c("PMID", "ArticleTitle", "ISSN", "ISOAbbreviation", "PubDate", "Affiliation")
+
+```
+
+
+```{r separate affiliations}
+library(tidyverse)
+library(stringr)
+str_count(string = data_hacettepePathology$Affiliation, pattern = ";") %>%
+ max()
+
+```
+
+
+```{r plain affiliation characters, include=FALSE}
+
+# to.plain <- function(s) {
+# # 1 character substitutions
+# old1 <- "çğşıüöÇĞŞİÖÜ"
+# new1 <- "cgsiuocgsiou"
+# s1 <- chartr(old1, new1, s)
+# # 2 character substitutions
+# old2 <- c("œ", "ß", "æ", "ø")
+# new2 <- c("oe", "ss", "ae", "oe")
+# s2 <- s1
+# for(i in seq_along(old2)) s2 <- gsub(old2[i], new2[i], s2, fixed = TRUE)
+# s2
+# }
+
+data_hacettepePathology2 <- data_hacettepePathology %>%
+ select(PMID, Affiliation)
+
+
+# [[:alpha:]]
+
+
+
+# data_hacettepePathology2$Affiliation <- data_hacettepePathology2$Affiliation %>%
+# tolower() %>%
+# to.plain()
+
+
+data_hacettepePathology2 <- data_hacettepePathology2 %>%
+ separate(col = "Affiliation", sep = ";", into = paste0("Affiliation", 1:6925))
+
+
+```
+
+
+
+
+```{r}
+library(tidyverse)
+library(reshape2)
+
+DT.m1 <- melt(data_hacettepePathology2,
+ id.vars = c("PMID"),
+ measure.vars = paste0("Affiliation", 1:6925))
+
+DT.m2 <- DT.m1 %>%
+ filter(!is.na(value))
+
+DT.m2$count <- 1
+
+```
+
+
+```{r}
+DT.m2$hacettepe <-
+ grepl(
+ pattern = ("[Hh]acettepe"),
+ x =
+ DT.m2$value
+ )
+
+DT.m2$pathology <-
+ grepl(
+ pattern = ("[Pp]athology|[Pp]atoloji"),
+ x =
+ DT.m2$value
+ )
+
+DT.m2$speach <-
+ grepl(
+ pattern = ("[Ss]peach|[Ss]peech"),
+ x =
+ DT.m2$value
+ )
+
+
+```
+
+```{r}
+DT.m3 <- DT.m2 %>%
+ filter(hacettepe == TRUE & pathology == TRUE) %>%
+ filter(speach==FALSE)
+
+```
+
+```{r}
+final_hacettepePathology <- data_hacettepePathology %>%
+ filter(PMID %in% DT.m3$PMID) %>%
+ select(-c("Affiliation")) %>%
+ left_join(DT.m3, by="PMID") %>%
+ select(c("PMID", "ArticleTitle", "ISSN", "ISOAbbreviation", "PubDate"), Affiliation = value) %>%
+ unique() %>%
+ mutate(PMIDLink = paste0("https://www.ncbi.nlm.nih.gov/pubmed/", PMID, ""))
+
+writexl::write_xlsx(final_hacettepePathology, here::here("data/final_hacettepePathology.xlsx"))
+
+```
+
+
+```{r}
+cat(paste0(final_hacettepePathology$PMID, " OR ")
+)
+```
+
+
+```
+(hacettepe[Affiliation] AND (pathology[Affiliation] OR patoloji[Affiliation])) NOT (speach[Affiliation] OR speech[Affiliation])
+```
+
+```
+(Turkey[Affiliation] OR Turkiye[Affiliation]) AND ((pathology[Affiliation] OR patoloji[Affiliation]) NOT (speach[Affiliation] OR speech[Affiliation]))
+```
+
+
+```{r}
+library(tidyverse)
+library(tidylog)
+library(mmpipe)
+final_hacettepePathology <- data_hacettepePathology %V>%
+ filter(PMID %in% DT.m3$PMID) %V>%
+ select(-c("Affiliation")) %V>%
+ left_join(DT.m3, by="PMID") %V>%
+ select(c("PMID", "ArticleTitle", "ISSN", "ISOAbbreviation", "PubDate"), Affiliation = value) %V>%
+ unique() %V>%
+ mutate(PMIDLink = paste0("https://www.ncbi.nlm.nih.gov/pubmed/", PMID, ""))
+
+
+```
+
diff --git a/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.nb.html b/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.nb.html
index b9165c2..a1e5325 100644
--- a/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.nb.html
+++ b/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.nb.html
@@ -1801,7 +1801,7 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Pancreas Studies in Various Bibliometric Tools
+Pancreas Studies in Pathology Journals
+Serdar Balcı, MD, Pathologist
+2019-03-31
+ +
+
+1 Introduction
+-
+
- Selected Pathology Journals are used for the query1 +
+
+2 PubMed
+
+
+2.1 Data Download from PubMed via EDirect
+-
+
Data is downloaded from PubMed via Edirect2
+
+
+
+2.2 rentrez
+
+
+3 europepmc
+
+
+4 WOS
+ + + + + + + + +
+
+
+5 Scopus
+ +
+
+7 Cite Space
+
+
+8 CitNetExplorer
+
+
+
+
+
+
+9 Lens
+(citation_id_type: "pmid" AND citation_id: 28984336) OR (citation_id_type: "pmid" AND citation_id: 21682559)pmid_only_path_journals <-
+read_delim("PancreasStudies/data/pmid_only_path_journals.txt", "\n", col_names = "PMID", col_types = "c")
+
+pmid_only_path_journals2 <- paste0("(citation_id_type: 'pmid' AND citation_id:",pmid_only_path_journals$PMID, ") OR ", collapse = "")
+
+write(pmid_only_path_journals2,
+"PancreasStudies/data/lensSearch.txt"
+)
+
+10 openknowledgemaps
+Open Knowledge Maps (2019). Overview of research on intraductal tubulopapillary neoplasm. Retrieved from https://openknowledgemaps.org/map/cc04c53301920a93d451aa2ce3010243/ [30 Mar 2019].
+
+
+11 bibliometrix
+
+
+12 ORCID
+
+
+13 Semantic Scholar
+ +
+
+14 Microsoft Academic
+
+
+15 Scopus
+
+
+16 Altmetrics
+
+
+17 Grid
+ +
+
+18 ROR
+ +
+
+19 Cobalmetrics
+ +-
+
- Toward privacy-preserving altmetrics exploration with Cobaltmetrics and ORCID +
+
+20 OpenCitations
+ +http://opencitations.net/download
+http://opencitations.net/corpus
+https://github.com/opencitations
+-
+
The OpenCitations Data Model
+https://figshare.com/articles/Metadata_for_the_OpenCitations_Corpus/3443876
+Creating Open Citation Data with BCite
+https://semsci.github.io/SemSci2018/papers/1/bcite-semsci2018.html
+
+
+21 Open Knowledge Maps
+Open Knowledge Maps (2019). Overview of research on (pathology[affiliation] or patoloji[affiliation]) and (turkey[affiliation] or türkiye[affiliation]). Retrieved from https://openknowledgemaps.org/map/e4dbf6c89015e402d6d7d560ab79e17a/ [30 Mar 2019].
+ +
+
+22 iris.ai
+https://the.iris.ai/map/02f89d24-0415-43ab-878a-853ec17c5a59
+
+
+23 lens.org
+ + + +
+
+24 To Do
+-
+
- find a way to auto import journal names +
- remove last OR +
- Auto run posiible analysis via cron +
- Find a way to auto copy into googledrive +
- push to blog, netlify … +
- Add from – Sources.Rmd
+– Bibliyometri.Rmd
+
+
+ +
+
+25 About & Feedback
+Serdar Balcı, MD, Pathologist would like to hear your feedback: https://goo.gl/forms/YjGZ5DHgtPlR1RnB3
+This document will be continiously updated and the last update was on 2019-03-31.
++ +
+
+
+
+
++
+
+26 References
+ +
+
+ +
+
++ +
---
title: "Pancreas Studies in Various Bibliometric Tools"
subtitle: "Pancreas Studies in Pathology Journals"
author: "Serdar Balcı, MD, Pathologist"
date: '`r format(Sys.Date())`'
output: 
  html_notebook: 
    code_folding: hide
    fig_caption: yes
    highlight: monochrome
    number_sections: yes
    theme: paper
    toc: yes
    toc_depth: 5
    toc_float: yes
---

<!-- Open all links in new tab-->  
<!-- <base target="_blank"/>    -->


<!-- Go to www.addthis.com/dashboard to customize your tools --> <script type="text/javascript" src="//s7.addthis.com/js/300/addthis_widget.js#pubid=ra-5bc36900a405090b">  
</script> 


```{r global_options, include=FALSE}
knitr::opts_chunk$set(fig.width = 12, fig.height = 8, 
                      # fig.path = 'figures/',
                      echo = FALSE, warning = FALSE, message = FALSE, error = FALSE, eval = TRUE, tidy = TRUE, comment = NA)
```

```{r library, include=FALSE}
library(tidyverse)
```




# Introduction

- Selected Pathology Journals are used for the query^[[Selected Pathology Journals](PancreasStudies/data/journal_list_from_my_collections)]




# PubMed

## Data Download from PubMed via EDirect

- Data is downloaded from PubMed via Edirect^[https://dataguide.nlm.nih.gov/edirect/overview.html]

- 


## rentrez

# europepmc



# WOS

[WOS.Rmd](WOS.Rmd)

```{r}
PMID_List_for_WOS_pancreas <- paste0("PMID=(", pmid_only_path_journals$PMID, ") OR")

write(PMID_List_for_WOS_pancreas,
      here::here("PancreasStudies/data/PMID_List_for_WOS_pancreas.txt")
)

```







# Scopus

[scopus.Rmd](scopus.Rmd)


# Vosviewer

Author Thesaurus is used.^[[Author Thesaurus](data/thesaurus_authors.txt)]

Code for interactive graph.^[[Interactive Graph Code](data/VOSviewer_interactive_graphcode.txt)]






# Cite Space

# CitNetExplorer

# Lens

```
(citation_id_type: "pmid"  AND citation_id: 28984336)  OR (citation_id_type: "pmid"  AND citation_id: 21682559)
```

```{r}
pmid_only_path_journals <- 
read_delim("PancreasStudies/data/pmid_only_path_journals.txt", "\n", col_names = "PMID", col_types = "c")

pmid_only_path_journals2 <- paste0("(citation_id_type: 'pmid'  AND citation_id:",pmid_only_path_journals$PMID, ") OR ", collapse = "")

write(pmid_only_path_journals2,
"PancreasStudies/data/lensSearch.txt"
)
```




# openknowledgemaps

Open Knowledge Maps (2019). Overview of research on intraductal tubulopapillary neoplasm. Retrieved from https://openknowledgemaps.org/map/cc04c53301920a93d451aa2ce3010243/ [30 Mar 2019]. 


# bibliometrix

# ORCID

# Semantic Scholar

[SemanticScholar.Rmd](SemanticScholar.Rmd)


# Microsoft Academic

# Scopus

# Altmetrics



# Grid

https://grid.ac/


# ROR

https://ror.org/search?page=1&query=turkey


# Cobalmetrics

https://cobaltmetrics.com/

- Toward privacy-preserving altmetrics exploration with Cobaltmetrics and ORCID

https://medium.com/thunken/toward-privacy-preserving-altmetrics-exploration-with-cobaltmetrics-and-orcid-f5ab6fa7898a


# OpenCitations

http://opencitations.net

http://opencitations.net/download

http://opencitations.net/corpus

https://github.com/opencitations

- The OpenCitations Data Model  
https://figshare.com/articles/Metadata_for_the_OpenCitations_Corpus/3443876

- Creating Open Citation Data with BCite  
https://semsci.github.io/SemSci2018/papers/1/bcite-semsci2018.html

https://github.com/opencitations/bcite


# Open Knowledge Maps

Open Knowledge Maps (2019). Overview of research on (pathology[affiliation] or patoloji[affiliation]) and (turkey[affiliation] or türkiye[affiliation]). Retrieved from https://openknowledgemaps.org/map/e4dbf6c89015e402d6d7d560ab79e17a/ [30 Mar 2019]. 


https://openknowledgemaps.org/index



# iris.ai

https://the.iris.ai/map/02f89d24-0415-43ab-878a-853ec17c5a59

# lens.org

https://www.lens.org/lens/scholar/search/results?dateFilterField=year_published&filterMap=%7B%7D&orcids=0000-0002-7852-3851&orderBy=%2Bpublished&preview=true&previewType=SCHOLAR_ANALYSIS&regexEnabled=false

https://www.lens.org/lens/scholar/search/results?q=(author.affiliation.name:%20%22pathology%22%20%20OR%20author.affiliation.name:%20%22patoloji%22)%20%20AND%20(author.affiliation.name:%20%22Turkey%22%20%20OR%20author.affiliation.name:%20%22T%C3%BCrkiye%22)

https://www.lens.org/lens/scholar/search/analysis?q=(author.affiliation.name:%20%22neurosurgery%22%20%20OR%20author.affiliation.name:%20%22sport%22%20)%20AND%20(abstract:%20%22sport%22%20%20OR%20title:%20%22sport%22)&page=0&limit=10&orderBy=%2Bscore&dateFilterField=year_published&preview=false&regexEnabled=false


# To Do

- find a way to auto import journal names
- remove last OR
- Auto run posiible analysis via cron
- Find a way to auto copy into googledrive
- push to blog, netlify ...
- Add from
-- [Sources.Rmd](Sources.Rmd)  
-- [Bibliyometri.Rmd](Bibliyometri.Rmd)  




# About & Feedback


[Serdar Balcı, MD, Pathologist](https://github.com/sbalci) would like to hear your feedback: https://goo.gl/forms/YjGZ5DHgtPlR1RnB3

This document will be continiously updated and the last update was on `r Sys.Date()`.

---

<script id="dsq-count-scr" src="//https-sbalci-github-io.disqus.com/count.js" async></script>

<div id="disqus_thread"></div>
<script>

/**
*  RECOMMENDED CONFIGURATION VARIABLES: EDIT AND UNCOMMENT THE SECTION BELOW TO INSERT DYNAMIC VALUES FROM YOUR PLATFORM OR CMS.
*  LEARN WHY DEFINING THESE VARIABLES IS IMPORTANT: https://disqus.com/admin/universalcode/#configuration-variables*/
/*
var disqus_config = function () {
this.page.url = PAGE_URL;  // Replace PAGE_URL with your page's canonical URL variable
this.page.identifier = PAGE_IDENTIFIER; // Replace PAGE_IDENTIFIER with your page's unique identifier variable
};
*/
(function() { // DON'T EDIT BELOW THIS LINE
var d = document, s = d.createElement('script');
s.src = 'https://https-sbalci-github-io.disqus.com/embed.js';
s.setAttribute('data-timestamp', +new Date());
(d.head || d.body).appendChild(s);
})();
</script>
<noscript>Please enable JavaScript to view the <a href="https://disqus.com/?ref_noscript">comments powered by Disqus.</a></noscript>

---

# References





+
+
+europepmc
ylab("Proportion of Pathology articles \n from Turkey in Europe PMC") -
Data retriveal from PubMed using EDirect
WOS data for VOSviewer
(AD=Turkey AND SU=Pathology) OR (CU=Turkey AND SU=Pathology)
Indexes=SCI-EXPANDED, SSCI, A&HCI, CPCI-S, CPCI-SSH, BKCI-S, BKCI-SSH, ESCI Timespan=All yearsHacettepe[Affiliation] AND Pathology[Affiliation]
+ + + + + + +
+
read extracted data
+ + + +library(readr)
+data_hacettepePathology <- read_delim(here::here("data/data_hacettepepathology.csv"),
+ "|",
+ escape_double = FALSE,
+ col_names = FALSE,
+ trim_ws = TRUE)Parsed with column specification:
+cols(
+ X1 = [32mcol_double()[39m,
+ X2 = [31mcol_character()[39m,
+ X3 = [31mcol_character()[39m,
+ X4 = [31mcol_character()[39m,
+ X5 = [32mcol_double()[39m,
+ X6 = [31mcol_character()[39m
+)
+4 parsing failures.
+row col expected actual file
+210 -- 6 columns 8 columns '/Users/serdarbalciold/RepTemplates/pubmed/data/data_hacettepepathology.csv'
+242 -- 6 columns 8 columns '/Users/serdarbalciold/RepTemplates/pubmed/data/data_hacettepepathology.csv'
+243 -- 6 columns 8 columns '/Users/serdarbalciold/RepTemplates/pubmed/data/data_hacettepepathology.csv'
+281 -- 6 columns 8 columns '/Users/serdarbalciold/RepTemplates/pubmed/data/data_hacettepepathology.csv'# View(data_hacettepePathology)
+
+names(data_hacettepePathology) <- c("PMID", "ArticleTitle", "ISSN", "ISOAbbreviation", "PubDate", "Affiliation")
+library(tidyverse)
+library(stringr)
+str_count(string = data_hacettepePathology$Affiliation, pattern = ";") %>%
+ max()[1] 6924library(tidyverse)
+library(reshape2)
+
+DT.m1 <- melt(data_hacettepePathology2,
+ id.vars = c("PMID"),
+ measure.vars = paste0("Affiliation", 1:6925))
+
+DT.m2 <- DT.m1 %>%
+ filter(!is.na(value))
+
+DT.m2$count <- 1
+DT.m2$hacettepe <-
+ grepl(
+ pattern = ("[Hh]acettepe"),
+ x =
+ DT.m2$value
+ )DT.m3 <- DT.m2 %>%
+ filter(hacettepe == TRUE & pathology == TRUE) %>%
+ filter(speach==FALSE)
+final_hacettepePathology <- data_hacettepePathology %>%
+ filter(PMID %in% DT.m3$PMID) %>%
+ select(-c("Affiliation")) %>%
+ left_join(DT.m3, by="PMID") %>%
+ select(c("PMID", "ArticleTitle", "ISSN", "ISOAbbreviation", "PubDate")), Affiliation = value)
+Error: unexpected ',' in:
+" left_join(DT.m3, by="PMID") %>%
+ select(c("PMID", "ArticleTitle", "ISSN", "ISOAbbreviation", "PubDate")),"cat(paste0(final_hacettepePathology$PMID, " OR ")
+)
+30711942 OR 30711942 OR 30711942 OR 30614391 OR 30607566 OR 30553274 OR 30543088 OR 30420050 OR 30420050 OR 30378176 OR 30361868 OR 30356178 OR 30342481 OR 30337132 OR 30326153 OR 30264475 OR 30258736 OR 30222718 OR 30215711 OR 30213486 OR 30194012 OR 30177831 OR 30177831 OR 30177831 OR 30177831 OR 30151600 OR 30121298 OR 30066674 OR 30061063 OR 30039725 OR 29963264 OR 29933323 OR 29843558 OR 29758192 OR 29744787 OR 29737941 OR 29729229 OR 29631339 OR 29610498 OR 29565209 OR 29564756 OR 29557778 OR 29521057 OR 29481086 OR 29455242 OR 29433873 OR 29391599 OR 29391317 OR 29386221 OR 29368083 OR 29368083 OR 29342030 OR 29333888 OR 29307770 OR 29286564 OR 29278522 OR 29276876 OR 29221145 OR 29217050 OR 29183666 OR 29147924 OR 29147924 OR 29113255 OR 29107076 OR 29101765 OR 29071270 OR 28988523 OR 28957973 OR 28938499 OR 28885322 OR 28877062 OR 28872973 OR 28871709 OR 28843712 OR 28832323 OR 28832077 OR 28832074 OR 28786167 OR 28754454 OR 28705285 OR 28684169 OR 28645584 OR 28627959 OR 28616233 OR 28601298 OR 28597078 OR 28593113 OR 28576480 OR 28575990 OR 28566877 OR 28554554 OR 28549792 OR 28549792 OR 28488171 OR 28471040 OR 28452074 OR 28443589 OR 28333838 OR 28263489 OR 28263489 OR 28219585 OR 28216139 OR 28216139 OR 28203472 OR 28155970 OR 28155970 OR 28109637 OR 28083971 OR 29745124 OR 28028337 OR 27974811 OR 27932539 OR 27922519 OR 27909626 OR 27906844 OR 27896834 OR 27864098 OR 27857123 OR 27853495 OR 27810370 OR 27807490 OR 27561188 OR 27603550 OR 27513982 OR 27703380 OR 27699733 OR 27640103 OR 27640103 OR 27606145 OR 27575604 OR 27547915 OR 27520411 OR 27476657 OR 27448951 OR 27416885 OR 27409664 OR 27390585 OR 27366187 OR 27347166 OR 27303936 OR 27259049 OR 27216000 OR 27206703 OR 27180062 OR 27132540 OR 27129763 OR 27067808 OR 27062662 OR 27042238 OR 27026777 OR 27003050 OR 26997452 OR 26980028 OR 26970763 OR 26965579 OR 26945448 OR 26943384 OR 26872278 OR 26854080 OR 26848216 OR 26797858 OR 26797858 OR 26743593 OR 29090887 OR 29090884 OR 29090871 OR 28276221 OR 26681974 OR 26662466 OR 26584874 OR 26584697 OR 26578207 OR 26578207 OR 26575115 OR 26563115 OR 26550397 OR 26527231 OR 26519197 OR 26456966 OR 26449317 OR 26449317 OR 26449317 OR 26407049 OR 26397478 OR 26346511 OR 26341890 OR 26339344 OR 26332388 OR 26293571 OR 26242854 OR 26207004 OR 26100969 OR 26095595 OR 26090243 OR 26081979 OR 26081979 OR 26067811 OR 26064727 OR 26052757 OR 26045846 OR 25994764 OR 25906124 OR 25883712 OR 25842994 OR 25821721 OR 25811726 OR 25810266 OR 25769540 OR 25759781 OR 25755968 OR 25743721 OR 27708922 OR 25692090 OR 25667467 OR 25560609 OR 27047934 OR 25529806 OR 25498489 OR 25457509 OR 25378828 OR 25223322 OR 25218282 OR 25171023 OR 25110239 OR 25087613 OR 24977003 OR 24947701 OR 24913330 OR 24856141 OR 24840535 OR 24794787 OR 24794787 OR 24782301 OR 24777267 OR 24731921 OR 24718000 OR 24667046 OR 24585772 OR 24523789 OR 24505496 OR 24430434 OR 24385732 OR 24326152 OR 24285274 OR 24080633 OR 24022314 OR 24018817 OR 23998291 OR 23653827 OR 28509218 OR 23588333 OR 23551548 OR 23419599 OR 24592101 OR 23219110 OR 23153936 OR 23030256 OR 23011824 OR 23011823 OR 23011821 OR 22961375 OR 22316516 OR 22301705 OR 22158496 OR 21810125 OR 21665002 OR 21630194 OR 21496526 OR 21492232 OR 21469428 OR 21437995 OR 21074692 OR 21074691 OR 21069451 OR 20952300 OR 20952295 OR 20719821 OR 20674190 OR 20465615 OR 20418233 OR 20173504 OR 20060354 OR 19851201 OR 19468034 OR 19462235 OR 19403544 OR 19363472 OR 19232840 OR 19178738 OR 19130459 OR 19065380 OR 19024599 OR 19014058 OR 18844937 OR 18773281 OR 18446633 OR 18379707 OR 18374497 OR 18365589 OR 18246753 OR 18085395 OR 18066567 OR 17947476 OR 17926107 OR 17922596 OR 17619723 OR 17587245 OR 17573765 OR 17543474 OR 17451888 OR 17291234 OR 17130035 OR 17007443 OR 16912900 OR 16752009 OR 16489441 OR 16343208 OR 16328667 OR 16320561 OR 16194892 OR 16175081 OR 16021510 OR 16014115 OR 15998374 OR 15913445 OR 15802396 OR 15762048 OR 15670313 OR 15658132 OR 15623491 OR 15622249 OR 15456418 OR 15334737 OR 15249720 OR 15204955 OR 15073846 OR 15032077 OR 14692804 OR 14521262 OR 12911737 OR 12488986 OR 12464212 OR 12049830 OR 12007023 OR 11926913 OR 11925832 OR 11793117 OR 11699420 OR 11585325 OR 11568381 OR 11564220 OR 11462912 OR 11409483 OR 11263931 OR 11057782 OR 11053680 OR 10997737 OR 10985626 OR 10885604 OR 10828801 OR 10819111 OR 10699830 OR 10679036 OR 10671893 OR 10636586 OR 10508882 OR 10192575 OR 9863925 OR 9849847 OR 9821039 OR 9744734 OR 9732936 OR 9646237 OR 9641241 OR 9625858 OR 9181320 OR 9085813 OR 9152975 OR 8899473 OR 7768662 OR 11578422 OR 8191601 OR 8368909 OR 8372026 OR 8516224 OR 8444560 OR 8096638 OR 8419633 OR 17588038 OR 1813402 OR 2287298 OR 2283976 OR 2626097 OR (hacettepe[Affiliation] AND (pathology[Affiliation] OR patoloji[Affiliation])) NOT (speach[Affiliation] OR speech[Affiliation]) (Turkey[Affiliation] OR Turkiye[Affiliation]) AND ((pathology[Affiliation] OR patoloji[Affiliation]) NOT (speach[Affiliation] OR speech[Affiliation]))final_hacettepePathology <- data_hacettepePathology %V>%
+ filter(PMID %in% DT.m3$PMID) %V>%
+ select(-c("Affiliation")) %V>%
+ left_join(DT.m3, by="PMID") %V>%
+ select(c("PMID", "ArticleTitle", "ISSN", "ISOAbbreviation", "PubDate"), Affiliation = value) %V>%
+ unique() %V>%
+ mutate(PMIDLink = paste0("https://www.ncbi.nlm.nih.gov/pubmed/", PMID, ""))
+filter: removed 241 rows (39%)
+select: dropped one variable (Affiliation)
+left_join: added 98 rows and added 6 columns (variable, value, count, hacettepe, pathology, …)
+select: dropped 6 variables (variable, value, count, hacettepe, pathology, …)
+mutate: new variable 'PMIDLink' with 374 unique values and 0% NA
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
@@ -2893,9 +2899,9 @@
@@ -3006,6 +3012,7 @@ Bibliographic Studies
-Sources Used For Analysis
-Serdar Balcı, MD, Pathologist
-2019-01-23
+Sources Used For Analysis
+Serdar Balcı, MD, Pathologist
+2019-03-30
2.3 Semantic Scholar
2.4 Microsoft Academic
https://labs.cognitive.microsoft.com/en-us/project-academic-knowledge
+https://academic.microsoft.com/author/2608586067/publication/search?q=Serdar%20Balci
2.5 Scopus
@@ -3044,13 +3051,28 @@2.10 OpenCitations
https://semsci.github.io/SemSci2018/papers/1/bcite-semsci2018.html +
+
+2.11 Open Knowledge Maps
+Open Knowledge Maps (2019). Overview of research on (pathology[affiliation] or patoloji[affiliation]) and (turkey[affiliation] or türkiye[affiliation]). Retrieved from https://openknowledgemaps.org/map/e4dbf6c89015e402d6d7d560ab79e17a/ [30 Mar 2019].
+ +
+
+2.12 iris.ai
+https://the.iris.ai/map/02f89d24-0415-43ab-878a-853ec17c5a59
+
+
2.13 lens.org
+ + +3 Feedback
Serdar Balcı, MD, Pathologist would like to hear your feedback: https://goo.gl/forms/YjGZ5DHgtPlR1RnB3
-This document will be continiously updated and the last update was on 2019-01-23.
+This document will be continiously updated and the last update was on 2019-03-30.
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+
+
+
+
+ + + +
+ + + +
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+USCAP Abstracts vs Published Articles
+ +Search methods:
+Journal:
+Modern Pathology
+Laboratory Investigation
Conference:
+USCAP
+Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology
From pdf ??
+
+ + + +
install.packages("pdftools")Installing package into ‘/Users/serdarbalciold/Library/R/3.5/library’
+(as ‘lib’ is unspecified)
+also installing the dependency ‘qpdf’
+
+trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/qpdf_1.1.tgz'
+Content type 'application/x-gzip' length 3730250 bytes (3.6 MB)
+==================================================
+downloaded 3.6 MB
+
+trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/pdftools_2.2.tgz'
+Content type 'application/x-gzip' length 6580512 bytes (6.3 MB)
+==================================================
+downloaded 6.3 MB
+The downloaded binary packages are in
+ /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFaS0NC/downloaded_packages# download.file("https://github.com/Huitziii/crispy-pdf/raw/master/71_PV.62.pdf",
+ # "./71_PV.62.pdf")
+text <- pdf_text("data/eurospine/2014/eurospine-2014-2014qf.pdf")
+Error in pdf_text("data/eurospine/2014/eurospine-2014-2014qf.pdf") :
+ could not find function "pdf_text"+ + + +
library(tidyverse)
+library(officer)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+lyon2014$content_type
+<content_type>
+ Public:
+ add_ext: function (extension, type)
+ add_override: function (value)
+ add_slide: function (partname)
+ clone: function (deep = FALSE)
+ initialize: function (package_dir)
+ remove_slide: function (partname)
+ save: function ()
+ Private:
+ default: application/vnd.openxmlformats-package.relationships+xml ...
+ filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ override: application/vnd.openxmlformats-officedocument.wordproces ...
+
+
+
+
+
+
+
+
+glimpse(lyon2014)
+List of 1308
+ $ package_dir : chr "/var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFaS0NC/file138a4c66125c"
+ $ doc_properties:Classes 'core_properties', 'R6' <core_properties>
+ Public:
+ clone: function (deep = FALSE)
+ get_data: function ()
+ initialize: function (package_dir)
+ save: function ()
+ set_created: function (value)
+ set_creator: function (value)
+ set_description: function (value)
+ set_keywords: function (value)
+ set_last_modified: function (value)
+ set_modified_by: function (value)
+ set_subject: function (value)
+ set_title: function (value)
+ Private:
+ doc: xml_document, xml_node
+ filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ set_core_property: function (tag, ns, value, attrs = NULL)
+ $ content_type :Classes 'content_type', 'R6' <content_type>
+ Public:
+ add_ext: function (extension, type)
+ add_override: function (value)
+ add_slide: function (partname)
+ clone: function (deep = FALSE)
+ initialize: function (package_dir)
+ remove_slide: function (partname)
+ save: function ()
+ Private:
+ default: application/vnd.openxmlformats-package.relationships+xml ...
+ filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ override: application/vnd.openxmlformats-officedocument.wordproces ...
+ $ doc_obj :Classes 'docx_part', 'openxml_document', 'R6' <docx_part>
+ Inherits from: <openxml_document>
+ Public:
+ clone: function (deep = FALSE)
+ cursor_backward: function ()
+ cursor_begin: function ()
+ cursor_bookmark: function (id)
+ cursor_end: function ()
+ cursor_forward: function ()
+ cursor_reach: function (keyword)
+ cursor_replace_first_img: function (id, src, width, height)
+ cursor_replace_first_text: function (id, text)
+ dir_name: function ()
+ docx_show_chunk: function ()
+ feed: function (file)
+ file_name: function ()
+ get: function ()
+ get_at_cursor: function ()
+ has_bookmark: function (id)
+ initialize: function (path, main_file, cursor, body_xpath)
+ length: function ()
+ name: function ()
+ rel_df: function ()
+ relationship: function ()
+ remove: function ()
+ replace_all_text: function (oldValue, newValue, onlyAtCursor = TRUE, warn = TRUE,
+ save: function ()
+ set_cursor: function (cursor)
+ Private:
+ body_xpath: /w:document/w:body
+ cursor: /w:document/w:body/*[1307]
+ doc: xml_document, xml_node
+ filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ package_dir: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ reldir: word
+ rels_doc: relationship, R6
+ rels_filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ $ styles :'data.frame': 4 obs. of 5 variables:
+ ..$ style_type: chr [1:4] "paragraph" "character" "table" "numbering"
+ ..$ style_id : chr [1:4] "Normal" "DefaultParagraphFont" "TableNormal" "NoList"
+ ..$ style_name: chr [1:4] "Normal" "Default Paragraph Font" "Normal Table" "No List"
+ ..$ is_custom : logi [1:4] FALSE FALSE FALSE FALSE
+ ..$ is_default: logi [1:4] TRUE TRUE TRUE TRUE
+ $ headers :List of 2
+ ..$ header1.xml:Classes 'docx_part', 'openxml_document', 'R6' <docx_part>
+ Inherits from: <openxml_document>
+ Public:
+ clone: function (deep = FALSE)
+ cursor_backward: function ()
+ cursor_begin: function ()
+ cursor_bookmark: function (id)
+ cursor_end: function ()
+ cursor_forward: function ()
+ cursor_reach: function (keyword)
+ cursor_replace_first_img: function (id, src, width, height)
+ cursor_replace_first_text: function (id, text)
+ dir_name: function ()
+ docx_show_chunk: function ()
+ feed: function (file)
+ file_name: function ()
+ get: function ()
+ get_at_cursor: function ()
+ has_bookmark: function (id)
+ initialize: function (path, main_file, cursor, body_xpath)
+ length: function ()
+ name: function ()
+ rel_df: function ()
+ relationship: function ()
+ remove: function ()
+ replace_all_text: function (oldValue, newValue, onlyAtCursor = TRUE, warn = TRUE,
+ save: function ()
+ set_cursor: function (cursor)
+ Private:
+ body_xpath: /w:hdr
+ cursor: /w:hdr/*[1]
+ doc: xml_document, xml_node
+ filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ package_dir: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ reldir: word
+ rels_doc: relationship, R6
+ rels_filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ ..$ header2.xml:Classes 'docx_part', 'openxml_document', 'R6' <docx_part>
+ Inherits from: <openxml_document>
+ Public:
+ clone: function (deep = FALSE)
+ cursor_backward: function ()
+ cursor_begin: function ()
+ cursor_bookmark: function (id)
+ cursor_end: function ()
+ cursor_forward: function ()
+ cursor_reach: function (keyword)
+ cursor_replace_first_img: function (id, src, width, height)
+ cursor_replace_first_text: function (id, text)
+ dir_name: function ()
+ docx_show_chunk: function ()
+ feed: function (file)
+ file_name: function ()
+ get: function ()
+ get_at_cursor: function ()
+ has_bookmark: function (id)
+ initialize: function (path, main_file, cursor, body_xpath)
+ length: function ()
+ name: function ()
+ rel_df: function ()
+ relationship: function ()
+ remove: function ()
+ replace_all_text: function (oldValue, newValue, onlyAtCursor = TRUE, warn = TRUE,
+ save: function ()
+ set_cursor: function (cursor)
+ Private:
+ body_xpath: /w:hdr
+ cursor: /w:hdr/*[1]
+ doc: xml_document, xml_node
+ filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ package_dir: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ reldir: word
+ rels_doc: relationship, R6
+ rels_filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ $ footers :List of 2
+ ..$ footer1.xml:Classes 'docx_part', 'openxml_document', 'R6' <docx_part>
+ Inherits from: <openxml_document>
+ Public:
+ clone: function (deep = FALSE)
+ cursor_backward: function ()
+ cursor_begin: function ()
+ cursor_bookmark: function (id)
+ cursor_end: function ()
+ cursor_forward: function ()
+ cursor_reach: function (keyword)
+ cursor_replace_first_img: function (id, src, width, height)
+ cursor_replace_first_text: function (id, text)
+ dir_name: function ()
+ docx_show_chunk: function ()
+ feed: function (file)
+ file_name: function ()
+ get: function ()
+ get_at_cursor: function ()
+ has_bookmark: function (id)
+ initialize: function (path, main_file, cursor, body_xpath)
+ length: function ()
+ name: function ()
+ rel_df: function ()
+ relationship: function ()
+ remove: function ()
+ replace_all_text: function (oldValue, newValue, onlyAtCursor = TRUE, warn = TRUE,
+ save: function ()
+ set_cursor: function (cursor)
+ Private:
+ body_xpath: /w:ftr
+ cursor: /w:ftr/*[1]
+ doc: xml_document, xml_node
+ filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ package_dir: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ reldir: word
+ rels_doc: relationship, R6
+ rels_filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ ..$ footer2.xml:Classes 'docx_part', 'openxml_document', 'R6' <docx_part>
+ Inherits from: <openxml_document>
+ Public:
+ clone: function (deep = FALSE)
+ cursor_backward: function ()
+ cursor_begin: function ()
+ cursor_bookmark: function (id)
+ cursor_end: function ()
+ cursor_forward: function ()
+ cursor_reach: function (keyword)
+ cursor_replace_first_img: function (id, src, width, height)
+ cursor_replace_first_text: function (id, text)
+ dir_name: function ()
+ docx_show_chunk: function ()
+ feed: function (file)
+ file_name: function ()
+ get: function ()
+ get_at_cursor: function ()
+ has_bookmark: function (id)
+ initialize: function (path, main_file, cursor, body_xpath)
+ length: function ()
+ name: function ()
+ rel_df: function ()
+ relationship: function ()
+ remove: function ()
+ replace_all_text: function (oldValue, newValue, onlyAtCursor = TRUE, warn = TRUE,
+ save: function ()
+ set_cursor: function (cursor)
+ Private:
+ body_xpath: /w:ftr
+ cursor: /w:ftr/*[1]
+ doc: xml_document, xml_node
+ filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ package_dir: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ reldir: word
+ rels_doc: relationship, R6
+ rels_filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ $ footnotes :Classes 'docx_part', 'openxml_document', 'R6' <docx_part>
+ Inherits from: <openxml_document>
+ Public:
+ clone: function (deep = FALSE)
+ cursor_backward: function ()
+ cursor_begin: function ()
+ cursor_bookmark: function (id)
+ cursor_end: function ()
+ cursor_forward: function ()
+ cursor_reach: function (keyword)
+ cursor_replace_first_img: function (id, src, width, height)
+ cursor_replace_first_text: function (id, text)
+ dir_name: function ()
+ docx_show_chunk: function ()
+ feed: function (file)
+ file_name: function ()
+ get: function ()
+ get_at_cursor: function ()
+ has_bookmark: function (id)
+ initialize: function (path, main_file, cursor, body_xpath)
+ length: function ()
+ name: function ()
+ rel_df: function ()
+ relationship: function ()
+ remove: function ()
+ replace_all_text: function (oldValue, newValue, onlyAtCursor = TRUE, warn = TRUE,
+ save: function ()
+ set_cursor: function (cursor)
+ Private:
+ body_xpath: /w:footnotes
+ cursor: /w:footnotes/*[last()]
+ doc: xml_document, xml_node
+ filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ package_dir: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ reldir: word
+ rels_doc: relationship, R6
+ rels_filename: /var/folders/76/rq_s_23s7fd5r8hqrbg8rmnc0000gp/T//RtmpFa ...
+ $ default_styles:List of 4
+ ..$ paragraph: chr "Normal"
+ ..$ character: chr "Default Paragraph Font"
+ ..$ table : chr "Normal Table"
+ ..$ numbering: chr "No List"
+ $ sect_dim :List of 3
+ ..$ page : Named int [1:2] 11920 15820
+ .. ..- attr(*, "names")= chr [1:2] "width" "height"
+ ..$ landscape: logi FALSE
+ ..$ margins : Named int [1:4] 540 1080 900 900
+ .. ..- attr(*, "names")= chr [1:4] "top" "bottom" "left" "right"
+ $ NA:Error in object[[i]] : subscript out of 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
+
+
+
+