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ejfertig / NSFBiosketch

R markdown file to extract list of collaborators and affiliations from pubmed for NSF biosketch
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Question regarding new NSF xls(x) format #1

Open idoerg opened 7 years ago

idoerg commented 7 years ago

Thanks so much for putting this out there. So useful.

Quick question: NSF requires the COI document to be entered in a specific .xls(x) document that NSF provides and which should be uploaded as an xls(x) file. Does your script output in that format?

New rules: (4/2017): https://www.nsf.gov/bfa/dias/policy/coa.jsp

Excel sheet which NSF requires as input: https://www.nsf.gov/bfa/dias/policy/coa/coa_template.xlsx

Thanks again! Iddo

ejfertig commented 7 years ago

I'm glad it helps. My tech is working on a shiny version which should be better.

So you can input an xlsx with current collaborators who aren't co authors for sorting. The script would need to be edited for trainees. It then will create both the word file and csv in the required format. I found that my word file was too long and a lot of the affiliations were sloppy. So I wrote a second script that if you hand edited the affiliations in the csv it would input that file and recreate the word doc.

Hopefully this is spelled out which is which in the readme.

Let me know if you have other questions.

E

Sent from my iPhone

On Aug 20, 2017, at 5:01 PM, Iddo Friedberg notifications@github.com<mailto:notifications@github.com> wrote:

Thanks so much for putting this out there. So useful.

Quick question: NSF requires the COI document to be entered in a specific .xls(x) document that NSF provides and which should be uploaded as an xls(x) file. Does your script output in that format?

New rules: (4/2017): https://www.nsf.gov/bfa/dias/policy/coa.jsp

Excel sheet: https://www.nsf.gov/bfa/dias/policy/coa/coa_template.xlsx

Thanks again! Iddo

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idoerg commented 7 years ago

Great, thanks.

I had some issues installing due to my R illiteracy, but I managed to get through.

However, now I am hitting a runtime error. Running this with the following changes:

author <- 'Friedberg I' authorFilter <- 'Friedberg I' affiliationFilter <- 'Iowa State University'

And hitting an issue here:

93: pmquery.dataframe$Initials <- getInitials(pmquery.dataframe$firstname)

Error in strsplit(s, split = " ") : non-character argument 4. strsplit(s, split = " ") 3. lapply(X = X, FUN = FUN, ...) 2. sapply(strsplit(s, split = " "), function(x) { toupper(paste(substring(x, 1, 1), collapse = "")) }) 1. getInitials(pmquery.dataframe$firstname)

Let me know what other info I can provide to help. Like I said, R is not really one of my languages.

Best,

Iddo

ejfertig commented 7 years ago

You’re going to run into a problem there because you are filtering yourself out as well as searching for yourself. authorFilter is meant to be for someone else who has a similar name (but ideally different pair of first initiations or affiliation).

Can you please save your R workspace up to the step where it crashes and sends and I can try to debug?

E

Elana J. Fertig, PhD Assistant Professor of Oncology Division of Biostatistics and Bioinformatics Johns Hopkins University 550 N Broadway, 1101 E Baltimore, MD 21205 office: 410 955 4268 mobile: 301 801 0138 email: ejfertig@jhmi.edumailto:ejfertig@jhmi.edu http://www.fertiglab.com @FertigLab

On Aug 20, 2017, at 9:28 PM, Iddo Friedberg notifications@github.com<mailto:notifications@github.com> wrote:

Great, thanks.

I had some issues installing due to my R illiteracy, but I managed to get through.

However, now I am hitting a runtime error. Running this with the following changes:

author <- 'Friedberg I' authorFilter <- 'Friedberg I' affiliationFilter <- 'Iowa State University'

Anf hitting an issue here:

96: pmquery.dataframe$Initials <- getInitials(pmquery.dataframe$firstname)

Error in strsplit(s, split = " ") : non-character argument 4. strsplit(s, split = " ") 3. lapply(X = X, FUN = FUN, ...) 2. sapply(strsplit(s, split = " "), function(x) { toupper(paste(substring(x, 1, 1), collapse = "")) }) 1. getInitials(pmquery.dataframe$firstname)

Let me know what other info I can provide to help.

Best,

Iddo

On Sun, Aug 20, 2017 at 5:17 PM, Elana J Fertig notifications@github.com<mailto:notifications@github.com> wrote:

I'm glad it helps. My tech is working on a shiny version which should be better.

So you can input an xlsx with current collaborators who aren't co authors for sorting. The script would need to be edited for trainees. It then will create both the word file and csv in the required format. I found that my word file was too long and a lot of the affiliations were sloppy. So I wrote a second script that if you hand edited the affiliations in the csv it would input that file and recreate the word doc.

Hopefully this is spelled out which is which in the readme.

Let me know if you have other questions.

E

Sent from my iPhone

On Aug 20, 2017, at 5:01 PM, Iddo Friedberg notifications@github.com<mailto:notifications@github.com< mailto:notifications@github.com>> wrote:

Thanks so much for putting this out there. So useful.

Quick question: NSF requires the COI document to be entered in a specific .xls(x) document that NSF provides and which should be uploaded as an xls(x) file. Does your script output in that format?

New rules: (4/2017): https://www.nsf.gov/bfa/dias/policy/coa.jsp

Excel sheet: https://www.nsf.gov/bfa/dias/policy/coa/coa_template.xlsx

Thanks again! Iddo

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