Papers Page Code - Revision history

Public at 17:02, 16 September 2019

2019-09-16T17:02:04Z

← Older revision		Revision as of 17:02, 16 September 2019
Line 1:		Line 1:
	==Word Cloud==		==Word Cloud==
	[[~~File:time series.jpg]~~]
	~~[http://files.gersteinlab.org/public-docs/2019/02.13/wordcloud_time_series.jpg Original Image File~~]		Link to [[Word Cloud]]

	== (Lab Member) Papers Page Rebuild and Further Info (Private)==		== (Lab Member) Papers Page Rebuild and Further Info (Private)==

Public: /* Word Cloud */

2019-03-08T15:25:40Z

Word Cloud

← Older revision		Revision as of 15:25, 8 March 2019
Line 1:		Line 1:
	==Word Cloud==		==Word Cloud==
	[[File:~~Wordcloud~~ time series.jpg]]		[[File:time series.jpg]]
	[http://files.gersteinlab.org/public-docs/2019/02.13/wordcloud_time_series.jpg Original Image File]		[http://files.gersteinlab.org/public-docs/2019/02.13/wordcloud_time_series.jpg Original Image File]

Public at 21:54, 13 February 2019

2019-02-13T21:54:11Z

← Older revision		Revision as of 21:54, 13 February 2019
Line 1:		Line 1:
			==Word Cloud==
			[[File:Wordcloud time series.jpg]]
			[http://files.gersteinlab.org/public-docs/2019/02.13/wordcloud_time_series.jpg Original Image File]

	== (Lab Member) Papers Page Rebuild and Further Info (Private)==		== (Lab Member) Papers Page Rebuild and Further Info (Private)==
	*Private Wiki includes instructions about how to update papers page and further info, click here [http://wiki.gersteinlab.org/labinfo/Papers_Page_Documentation Private Wiki]		*Private Wiki includes instructions about how to update papers page and further info, click here [http://wiki.gersteinlab.org/labinfo/Papers_Page_Documentation Private Wiki]

Public: /* Old Papers Server ... and also R code for NSF colab */

2017-11-20T13:27:41Z

Old Papers Server ... and also R code for NSF colab

← Older revision		Revision as of 13:27, 20 November 2017
Line 127:		Line 127:
	pmquery.dataframe$Initials <- getInitials(pmquery.dataframe$firstname)		pmquery.dataframe$Initials <- getInitials(pmquery.dataframe$firstname)
	pmquery.dataframe$ColabType <- 'Co-Author'		pmquery.dataframe$ColabType <- 'Co-Author'
	pmquery.dataframe <- pmquery.dataframe[!duplicated(paste(pmquery.dataframe$lastname,pmquery.dataframe$Initials)),]		pmquery.dataframe <- pmquery.dataframe[!duplicated(paste(pmquery.dataframe$lastname,pmquery.dataframe$Initials)),]
	pmquery.dataframe <- pmquery.dataframe[order(pmquery.dataframe$lastname,pmquery.dataframe$Initials),]		pmquery.dataframe <- pmquery.dataframe[order(pmquery.dataframe$lastname,pmquery.dataframe$Initials),]

Public: /* Old Papers Server ... and also R code for NSF colab */

2017-11-20T13:27:12Z

Old Papers Server ... and also R code for NSF colab

Public: /* Old Papers Server ... and also R code for NSF colab */

2017-11-20T13:24:56Z

Old Papers Server ... and also R code for NSF colab

← Older revision		Revision as of 13:24, 20 November 2017
Line 108:		Line 108:

	R Code for compiling list of NSF co-authors:		R Code for compiling list of NSF co-authors:
			This is buggy and approximate, but a good place to start

	https://github.com/ejfertig/NSFBiosketch/blob/master/CollaboratorList.Rmd		https://github.com/ejfertig/NSFBiosketch/blob/master/CollaboratorList.Rmd

Public: /* Old Papers Server ... and also R code for NSF colab */

2017-11-20T02:36:37Z

Old Papers Server ... and also R code for NSF colab

← Older revision		Revision as of 02:36, 20 November 2017
Line 120:		Line 120:
	pmquery <- sapply(articles_to_list(fetch_pubmed_data(get_pubmed_ids(paste0(author,'[Author]')))),article_to_df)		pmquery <- sapply(articles_to_list(fetch_pubmed_data(get_pubmed_ids(paste0(author,'[Author]')))),article_to_df)
	names(pmquery) <- NULL		names(pmquery) <- NULL
	~~# filter out oddly formatted references~~
	pmquery <- pmquery[sapply(pmquery,function(x){any(colnames(x)=='year')})]		pmquery <- pmquery[sapply(pmquery,function(x){any(colnames(x)=='year')})]
	datePMID <- as.Date(sapply(pmquery,function(x){paste(x[1,'year'],		datePMID <- as.Date(sapply(pmquery,function(x){paste(x[1,'year'], x[1,'month'], x[1,'day'],sep="-")}))
	x[1,'month'],
	x[1,'day'],sep="-")}))
	pmquery <- pmquery[datePMID >= queryDate]		pmquery <- pmquery[datePMID >= queryDate]
	pmquery.dataframe <- ldply(pmquery,data.frame)		pmquery.dataframe <- ldply(pmquery,data.frame)
	~~# format author names~~
	pmquery.dataframe$Initials <- getInitials(pmquery.dataframe$firstname)		pmquery.dataframe$Initials <- getInitials(pmquery.dataframe$firstname)
	pmquery.dataframe$ColabType <- 'Co-Author'		pmquery.dataframe$ColabType <- 'Co-Author'
	~~# find unique co-authors~~
	pmquery.dataframe <- pmquery.dataframe[!duplicated(paste(pmquery.dataframe$lastname,pmquery.dataframe$Initials)),]		pmquery.dataframe <- pmquery.dataframe[!duplicated(paste(pmquery.dataframe$lastname,pmquery.dataframe$Initials)),]
	~~# alphabetize the list~~
	pmquery.dataframe <- pmquery.dataframe[order(pmquery.dataframe$lastname,pmquery.dataframe$Initials),]		pmquery.dataframe <- pmquery.dataframe[order(pmquery.dataframe$lastname,pmquery.dataframe$Initials),]

Public: /* Old Papers Server */

2017-11-20T02:07:05Z

Old Papers Server

@@ Line 102: / Line 102: @@
 *[[Papers_Page_Code_Old]]
-==Old Papers Server==
+==Old Papers Server ... and also R code for NSF colab ==
 *Old version of pagers website  [http://oldpapers.gersteinlab.org Old Papers]
 *Other info of papers [[Paper_search]]

Public: /* Papers GitHub */

2016-02-10T15:25:26Z

Papers GitHub

← Older revision		Revision as of 15:25, 10 February 2016
Line 4:		Line 4:
	==Papers GitHub==		==Papers GitHub==
	Papers 2.0 is now version controlled under GitHub: https://github.com/gersteinlab/papers.gersteinlab.org		Papers 2.0 is now version controlled under GitHub: https://github.com/gersteinlab/papers.gersteinlab.org


	==SpreadSheet Structure==		==SpreadSheet Structure==

Public: /* SpreadSheet Structure */

2016-02-10T15:24:23Z

SpreadSheet Structure

← Older revision		Revision as of 15:24, 10 February 2016
Line 1:		Line 1:
	== (Lab Member) Papers Page Rebuild and Further Info (Private)==		== (Lab Member) Papers Page Rebuild and Further Info (Private)==
	*Private Wiki includes instructions about how to update papers page and further info, click here [http://wiki.gersteinlab.org/labinfo/Papers_Page_Documentation Private Wiki]		*Private Wiki includes instructions about how to update papers page and further info, click here [http://wiki.gersteinlab.org/labinfo/Papers_Page_Documentation Private Wiki]

			==Papers GitHub==
			Papers 2.0 is now version controlled under GitHub: https://github.com/gersteinlab/papers.gersteinlab.org


	==SpreadSheet Structure==		==SpreadSheet Structure==

← Older revision		Revision as of 13:27, 20 November 2017
Line 112:		Line 112:
	https://github.com/ejfertig/NSFBiosketch/blob/master/CollaboratorList.Rmd		https://github.com/ejfertig/NSFBiosketch/blob/master/CollaboratorList.Rmd

	library('easyPubMed')		library('easyPubMed')
	library('plyr')		library('plyr')
	library('xlsx')		library('xlsx')
	author <- 'Gerstein M'		author <- 'Gerstein M'
	authorFilter <- 'Gerstein Maya'		authorFilter <- 'Gerstein Maya'
	currentDate <- Sys.Date()		currentDate <- Sys.Date()
	queryDate <- seq(Sys.Date(), length = 2, by = "-48 months")[2]		queryDate <- seq(Sys.Date(), length = 2, by = "-48 months")[2]
	pmquery <- sapply(articles_to_list(fetch_pubmed_data(get_pubmed_ids(paste0(author,'[Author]')))),article_to_df)		pmquery <- sapply(articles_to_list(fetch_pubmed_data(get_pubmed_ids(paste0(author,'[Author]')))),article_to_df)
	names(pmquery) <- NULL		names(pmquery) <- NULL
	pmquery <- pmquery[sapply(pmquery,function(x){any(colnames(x)=='year')})]		pmquery <- pmquery[sapply(pmquery,function(x){any(colnames(x)=='year')})]
	datePMID <- as.Date(sapply(pmquery,function(x){paste(x[1,'year'], x[1,'month'], x[1,'day'],sep="-")}))		datePMID <- as.Date(sapply(pmquery,function(x){paste(x[1,'year'], x[1,'month'], x[1,'day'],sep="-")}))
	pmquery <- pmquery[datePMID >= queryDate]		pmquery <- pmquery[datePMID >= queryDate]
	pmquery.dataframe <- ldply(pmquery,data.frame)		pmquery.dataframe <- ldply(pmquery,data.frame)
	pmquery.dataframe$Initials <- getInitials(pmquery.dataframe$firstname)		pmquery.dataframe$Initials <- getInitials(pmquery.dataframe$firstname)
	pmquery.dataframe$ColabType <- 'Co-Author'		pmquery.dataframe$ColabType <- 'Co-Author'
	pmquery.dataframe <- pmquery.dataframe[!duplicated(paste(pmquery.dataframe$lastname,pmquery.dataframe$Initials)),]		pmquery.dataframe <- pmquery.dataframe[!duplicated(paste(pmquery.dataframe$lastname,pmquery.dataframe$Initials)),]
	pmquery.dataframe <- pmquery.dataframe[order(pmquery.dataframe$lastname,pmquery.dataframe$Initials),]		pmquery.dataframe <- pmquery.dataframe[order(pmquery.dataframe$lastname,pmquery.dataframe$Initials),]