updated on 2018-07-02 16:51:44

sbalci · Jul 2, 2018 · 0875c71 · 0875c71
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commit 0875c71
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diff --git a/SchedulePubMedAnalysis-old.log b/SchedulePubMedAnalysis-old.log
diff --git a/SchedulePubMedAnalysis.R b/SchedulePubMedAnalysis.R
@@ -1,6 +1,6 @@
-library(rmarkdown)
-library(pander)
-library(rstudioapi)
+require(rmarkdown)
+# require(pander)
+require(rstudioapi)
 #
 # rmarkdown::render(input = "SchedulePubMedAnalysis.Rmd", output_format = "html_notebook", output_file = "docs/SchedulePubMedAnalysis.html"
 #                    , quiet = TRUE

diff --git a/SchedulePubMedAnalysis.log b/SchedulePubMedAnalysis.log
diff --git a/SchedulePubMedAnalysis2.Rmd b/SchedulePubMedAnalysis2.Rmd
@@ -111,37 +111,37 @@ Articles are downloaded as `xml`.
 MeSH terms are extracted from xml. [Common terms](https://www.nlm.nih.gov/bsd/indexing/training/CHK_010.html) are excluded and [major topics](https://www.nlm.nih.gov/bsd/disted/meshtutorial/principlesofmedlinesubjectindexing/majortopics/) are selected.
 
 ```{r extract major MeSH topics -excluding common tags- from xml, message=FALSE, warning=FALSE}
-myTerm <- rstudioapi::terminalCreate(show = FALSE)
-rstudioapi::terminalSend(
-myTerm,
-"xtract -input /Users/serdarbalciold/RepTemplates/pubmed/data/PathologyTurkey.xml -pattern MeshHeading -if DescriptorName@MajorTopicYN -equals Y -or QualifierName@MajorTopicYN -equals Y -element DescriptorName| grep -vxf /Users/serdarbalciold/RepTemplates/pubmed/data/checktags.txt | sort-uniq-count-rank > /Users/serdarbalciold/RepTemplates/pubmed/data/PathologyTurkeyMeSH.csv \n"
-)
-Sys.sleep(1)
-repeat {
-Sys.sleep(0.1)
-if (rstudioapi::terminalBusy(myTerm) == FALSE) {
-print("Code Executed")
-break
-}
-}
+# myTerm <- rstudioapi::terminalCreate(show = FALSE)
+# rstudioapi::terminalSend(
+# myTerm,
+# "xtract -input /Users/serdarbalciold/RepTemplates/pubmed/data/PathologyTurkey.xml -pattern MeshHeading -if DescriptorName@MajorTopicYN -equals Y -or QualifierName@MajorTopicYN -equals Y -element DescriptorName| grep -vxf /Users/serdarbalciold/RepTemplates/pubmed/data/checktags.txt | sort-uniq-count-rank > /Users/serdarbalciold/RepTemplates/pubmed/data/PathologyTurkeyMeSH.csv \n"
+# )
+# Sys.sleep(1)
+# repeat {
+# Sys.sleep(0.1)
+# if (rstudioapi::terminalBusy(myTerm) == FALSE) {
+# print("Code Executed")
+# break
+# }
+# }
 ```
 
 Keywords are extracted from `xml`.
 
 ```{r extract author keywords from xml, message=FALSE, warning=FALSE, results='asis'}
-myTerm <- rstudioapi::terminalCreate(show = FALSE)
-rstudioapi::terminalSend(
-myTerm,
-"xtract -input /Users/serdarbalciold/RepTemplates/pubmed/data/PathologyTurkey.xml -pattern Keyword -element Keyword | sort-uniq-count-rank > /Users/serdarbalciold/RepTemplates/pubmed/data/authorkeywords.csv \n"
-)
-Sys.sleep(1)
-repeat {
-Sys.sleep(0.1)
-if (rstudioapi::terminalBusy(myTerm) == FALSE) {
-print("Code Executed")
-break
-}
-}
+# myTerm <- rstudioapi::terminalCreate(show = FALSE)
+# rstudioapi::terminalSend(
+# myTerm,
+# "xtract -input /Users/serdarbalciold/RepTemplates/pubmed/data/PathologyTurkey.xml -pattern Keyword -element Keyword | sort-uniq-count-rank > /Users/serdarbalciold/RepTemplates/pubmed/data/authorkeywords.csv \n"
+# )
+# Sys.sleep(1)
+# repeat {
+# Sys.sleep(0.1)
+# if (rstudioapi::terminalBusy(myTerm) == FALSE) {
+# print("Code Executed")
+# break
+# }
+# }
 ```
 
 

diff --git a/SchedulePubMedAnalysis2.nb.html b/SchedulePubMedAnalysis2.nb.html
diff --git a/docs/SchedulePubMedAnalysis.nb.html b/docs/SchedulePubMedAnalysis.nb.html