| Title: | 'Pubmed' Word Clouds |
| Description: | Create a word cloud using the abstract of publications from 'Pubmed'. |
| Version: | 0.3.6 |
| Date: | 2019-02-28 |
| Author: | Felix Yanhui Fan <nolanfyh@gmail.com> |
| Imports: | XML, stringr, RCurl, wordcloud, tm, RColorBrewer |
| Maintainer: | Felix Yanhui Fan <nolanfyh@gmail.com> |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: | http://felixfan.github.io/PubMedWordcloud/ |
| RoxygenNote: | 6.0.1 |
| NeedsCompilation: | no |
| Packaged: | 2019-03-01 02:04:15 UTC; alicefelix |
| Repository: | CRAN |
| Date/Publication: | 2019-03-01 05:30:07 UTC |
clean data
Description
remove Punctuations, remove Numbers, Translate characters to lower or upper case, remove stopwords, remove user specified words, Stemming words.
Usage
cleanAbstracts(abstracts, rmNum = TRUE, tolw = TRUE, toup = FALSE,
rmWords = TRUE, yrWords = NULL, stemDoc = FALSE)
Arguments
abstracts |
output of getAbstracts, or just a paragraph of text |
rmNum |
Remove the text document with any numbers in it or not |
tolw |
Translate characters in character vectors to lower case or not |
toup |
Translate characters in character vectors to upper case or not |
rmWords |
Remove a set of English stopwords (e.g., 'the') or not |
yrWords |
A character vector listing the words to be removed. |
stemDoc |
Stem words in a text document using Porter's stemming algorithm. |
See Also
Examples
# Abs=getAbstracts(c("22693232", "22564732"))
# cleanAbs=cleanAbstracts(Abs)
# text="Jobs received a number of honors and public recognition."
# cleanD=cleanAbstracts(text)
plot colors
Description
plot colors.
Usage
colSets(type)
Arguments
type |
palette names from the lists: Accent, Dark2, Pastel1, Pastel2, Paired, Set1, Set2, Set3. |
Examples
# colors= colSets(type="Accent")
# colors= colSets(type="Paired")
# colors= colSets(type="Set3")
edit PMIDs
Description
add two sets of PMIDs together, or exclude one set PMIDs from another set of PMIDs.
Usage
editPMIDs(x, y, method = c("add", "exclude"))
Arguments
x |
output of getPMIDs, or a set of PMIDs |
y |
output of getPMIDs, or a set of PMIDs |
method |
can be 'add' (default) or 'exclude'. see details. |
Details
when method is 'add', PMIDs in 'x' and 'y' will be combined. when method is 'exclude', PMIDs in 'y' will be excluded from 'x'.
See Also
Examples
# pmid1=getPMIDs(author="Yan-Hui Fan",dFrom=2007,dTo=2013,n=10)
# rm1="22698742"
# pmids1=editPMIDs(x=pmid1,y=rm1,method="exclude")
# pmid2=getPMIDs(author="Yanhui Fan",dFrom=2007,dTo=2013,n=10)
# rm2="20576513"
# pmids2=editPMIDs(x=pmid2,y=rm2,method="exclude")
# pmids=editPMIDs(x=pmids1,y=pmids2,method="add")
get Abstracts
Description
retrieve abstracts of the specified PMIDs from PubMed.
Usage
getAbstracts(pmid, https = TRUE, s = 100)
Arguments
pmid |
a set of PMIDs |
https |
use https instead of http |
s |
download how many PMIDs each time |
See Also
Examples
# pmids=c("22693232", "22564732", "22301463", "22015308", "21283797", "19412437")
# abstracts=getAbstracts(pmids)
# pmid="22693232"
# abstract=getAbstracts(pmid)
# pmids=getPMIDs(author="Yan-Hui Fan",dFrom=2007,dTo=2013,n=10)
# abstracts=getAbstracts(pmids)
get PMIDs using author names
Description
retrieve PMIDs (each PMID is 8 digits long) from PubMed for author and the specified date.
Usage
getPMIDs(author, dFrom, dTo, n = 500, https = TRUE)
Arguments
author |
author's name |
dFrom |
start year |
dTo |
end year |
n |
max number of retrieved articles |
https |
use https instead of http |
See Also
Examples
# getPMIDs(author="Yan-Hui Fan",dFrom=2007,dTo=2013,n=10)
# getPMIDs(author="Yanhui Fan",dFrom=2007,dTo=2013,n=10)
get PMIDs using Journal names and Keywords
Description
retrieve PMIDs (each PMID is 8 digits long) from PubMed for Specific Journal, Keywords and date.
Usage
getPMIDsByKeyWords(keys = NULL, journal = NULL, dFrom = NULL,
dTo = NULL, n = 10000, https = TRUE)
Arguments
keys |
keywords |
journal |
journal name |
dFrom |
start year |
dTo |
end year |
n |
max number of retrieved articles |
https |
use https instead of http |
See Also
Examples
# getPMIDsByKeyWords(keys="breast cancer", journal="science",dTo=2013)
# getPMIDsByKeyWords(keys="breast cancer", journal="science")
# getPMIDsByKeyWords(keys="breast cancer",dFrom=2012,dTo=2013)
# getPMIDsByKeyWords(journal="science",dFrom=2012,dTo=2013)
PubMed wordcloud using function 'wordcloud' of package wordcloud
Description
PubMed wordcloud.
Usage
plotWordCloud(abs, scale = c(3, 0.3), min.freq = 1, max.words = 100,
random.order = FALSE, rot.per = 0.35, use.r.layout = FALSE,
colors = brewer.pal(8, "Dark2"))
Arguments
abs |
output of cleanAbstracts, or a data frame with one colume of 'word' and one colume of 'freq'. |
scale |
A vector of length 2 indicating the range of the size of the words. |
min.freq |
words with frequency below min.freq will not be plotted |
max.words |
Maximum number of words to be plotted. least frequent terms dropped |
random.order |
plot words in random order. If false, they will be plotted in decreasing frequency |
rot.per |
proportion words with 90 degree rotation |
use.r.layout |
if false, then c++ code is used for collision detection, otherwise R is used |
colors |
color words from least to most frequent |
Details
This function just call 'wordcloud' from package wordcloud. See package wordcloud for more details about the parameters.
Examples
# text="Jobs received a number of honors and public recognition."
# cleanD=cleanAbstracts(text)
# plotWordCloud(cleanD,min.freq=1,scale=c(2,1))