diff --git a/.DS_Store b/.DS_Store
index 1709ca6..40a046c 100644
Binary files a/.DS_Store and b/.DS_Store differ
diff --git a/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.Rmd b/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.Rmd
index 8c96d75..5cc7469 100644
--- a/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.Rmd
+++ b/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.Rmd
@@ -91,7 +91,7 @@ repeat {
myTerm <- rstudioapi::terminalCreate(show = FALSE)
rstudioapi::terminalSend(
myTerm,
-"xtract -input data/pubmed_result_TurkPath.xml -pattern PubmedArticle -element MedlineCitation/PMID -block ArticleId -if ArticleId@IdType -equals doi -element ArticleId > data/pubmed_result_TurkPath.txt \n"
+"xtract -input data/pubmed_result_TurkPath.xml -pattern PubmedArticle -block ArticleId -if ArticleId@IdType -equals doi -element ArticleId > data/pubmed_result_TurkPath_doi.txt \n"
)
Sys.sleep(1)
repeat {
@@ -106,12 +106,24 @@ break
```{r}
library(tidyverse)
-pubmed_result_TurkPath <- read_csv(file = "data/pubmed_result_TurkPath.csv")
-pubmed_result_TurkPath_doi <- pubmed_result_TurkPath_doi$V2
+pubmed_result_TurkPath_doi <- read.delim("data/pubmed_result_TurkPath_doi.txt", header = FALSE)
```
```{r}
-write(pubmed_result_TurkPath_doi, "data/pubmed_result_TurkPath_doi.txt")
+pubmed_result_TurkPath_doi$V1[grep("^10.", pubmed_result_TurkPath_doi$V1)]
+
+pubmed_result_TurkPath_doi$V2 <- grepl(
+ pattern = "^10.",
+ x = pubmed_result_TurkPath_doi$V1
+)
+
+pubmed_result_TurkPath_doi2 <- pubmed_result_TurkPath_doi %>%
+ filter(pubmed_result_TurkPath_doi$V2 == TRUE) %>%
+ select(V1)
+
+write_csv(pubmed_result_TurkPath_doi2, "data/pubmed_result_TurkPath_doi2.txt", col_names = FALSE)
+
+
```
diff --git a/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.nb.html b/PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.nb.html
index 0889a0e..edfdd2c 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")
-
+
@@ -1820,11 +1820,11 @@ Data retriveal from PubMed using EDirect
-
+
myTerm <- rstudioapi::terminalCreate(show = FALSE)
rstudioapi::terminalSend(
myTerm,
-"xtract -input data/pubmed_result_TurkPath.xml -pattern PubmedArticle -element MedlineCitation/PMID -block ArticleId -if ArticleId@IdType -equals doi -element ArticleId > data/pubmed_result_TurkPath.txt \n"
+"xtract -input data/pubmed_result_TurkPath.xml -pattern PubmedArticle -block ArticleId -if ArticleId@IdType -equals doi -element ArticleId > data/pubmed_result_TurkPath_doi.txt \n"
)
Sys.sleep(1)
repeat {
@@ -1835,34 +1835,36 @@ Data retriveal from PubMed using EDirect
}
}
+
+[1] "Code Executed"
+
-
-pubmed_result_TurkPath <- read_csv(file = "data/pubmed_result_TurkPath.csv")
-
+
+library(tidyverse)
+pubmed_result_TurkPath_doi <- read.delim("data/pubmed_result_TurkPath_doi.txt", header = FALSE)
-
-Parsed with column specification:
-cols(
- `30632530 10.5606/ArchRheumatol.2018.6652` = [31mcol_character()[39m
-)
-
-
-write(pubmed_result_TurkPath_doi, "data/pubmed_result_TurkPath_doi.txt")
+
+write(pubmed_result_TurkPath_doi2, "data/pubmed_result_TurkPath_doi2.txt")
+
+
+Error in cat(x, file = file, sep = c(rep.int(sep, ncolumns - 1), "\n"), :
+ argument 1 (type 'list') cannot be handled by 'cat'
+
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