Best regards,

Matt Bascom

I don’t have much experience on the Windows OS — *maybe* RJSONIO is not compiled for 2.10 yet?? But this is really just a wild guess.

See here for difference between rjson and RJSONIO.

If you want to play with the tick marks layout you could take look at axis.

Claudia

Thank you for the interesting code. I tried unpacked the RJSONIO file folder into ..\R\win-library\2.10 but I get the following error:

Loading required package: RJSONIO
Error in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
‘RJSONIO’ is not a valid installed packag

Any thought on why it’s not working? The code works using the rjson package. What functionality is lost by not using RJSONIO? Also, how can we change the chart axis tick marks to highlight the dates returned by the API?

Thank you!!

Matt

Pubmed has an API, provided by NCBI. Details are here. So all we’d need to do is concatenate the appropriate URL string then parse the results in R. Results are in xml, so we’d need the XML library.

To map keywords by publication date (like in the NYT example) we need to submit two different queries:

1. For the first query we use the esearch utility to retrieve two important variables, WebEnv and QueryKey.
For the search term “h1n1″ the URL needs to look like:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmax=0&term=h1n1&usehistory=y

#Read in:
raw.data < - readLines("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmax=0&term=h1n1&usehistory=y")

# Parse the result for WebEnv and QueryKey:
library(XML)
parsed.data < - xmlTreeParse(raw.data)
xmlValue(xmlChildren(xmlRoot(parsed.data))$QueryKey)
xmlValue(xmlChildren(xmlRoot(parsed.data))$WebEnv)


2. For the second query we use the esummary utility to retrieve the actual records. So the URL, using WebEnv and QueryKey, from the previous query looks in my example looks like:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=xml&query_key=1&WebEnv=NCID_1_51824642_130.14.18.46_9001_1255542890

Now parse the result for PubDate.

For an example in php see here

I will make this a separate post once I get time to write out the details. Or maybe someone else will.

thanks for the tutorial! It solved some issues I had with running a model on Xgrid with external input files.

Nice site btw. hope to see some more code snippets soon.

Cheers,
Koen

Right now the way it works is not very intuitive, but if you switch to PLAIN TEXT (top of the box where the code is displayed) you get the original code without the line numbers. (Yes, I need to find some time to get a better plugin for displaying code and fix up a few other things also.)

I am afraid I don’t know any details about their request throttling.

To get your example to run, I had to remove “amp;” from line 23. That wasn’t present on line 15.

Is request throttling handled automatically by NYT? I ask because I thought I read somewhere that NYT submissions are limited to 2/sec.