Hello, I was wondering if anyone knows of a way to automate in R (or any software) the process of importing correlation values from PDF to usable data in a table format that can be used in meta-analysis? My process has been to copy the correlations manually one-by-one from the PDF to excel (which takes a lifetime!), and then import the excel data into R. I'm sure there must be a better, faster, and less error-prone way to do this. Thank you, Kiet ---- Kiet D. Huynh, Ph.D. Pronouns: he/him CLEAR Goldblum-Carr Postdoctoral Fellow Palo Alto University 1791 Arastradero Rd. Palo Alto, CA 94304
[R-meta] Importing Correlations from PDF to table format
4 messages · Kiet Huynh, James Pustejovsky, Wolfgang Viechtbauer
The pdftools package might be helpful: https://github.com/ropensci/pdftools It has very low-level utilities for extracting text from pdf. You'd still have to do some data clean-up to get the correlations into the form needed for analysis. The tabulizer package is meant to provide tools customized for working with pdf tables: https://github.com/ropensci/tabulizer But it requires Java and it appears to be archived on CRAN. I'm not sure what its development status is. Caveat emptor, I guess. James
On Fri, Feb 25, 2022 at 12:20 PM Kiet Huynh <kietduchuynh at gmail.com> wrote:
Hello,
I was wondering if anyone knows of a way to automate in R (or any
software) the process of importing correlation values from PDF to usable
data in a table format that can be used in meta-analysis? My process has
been to copy the correlations manually one-by-one from the PDF to excel
(which takes a lifetime!), and then import the excel data into R. I'm sure
there must be a better, faster, and less error-prone way to do this.
Thank you,
Kiet
----
Kiet D. Huynh, Ph.D.
Pronouns: he/him
CLEAR Goldblum-Carr Postdoctoral Fellow
Palo Alto University
1791 Arastradero Rd.
Palo Alto, CA 94304
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2 days later
Hi James, Thank you for recommending these helpful packages. I was able to import the pdf correlation table into a dataframe format in R. Are you aware of any R code that could convert that correlation matrix dataframe into a meta-analysis type dataframe (i.e., a column for variable 1, a column for variable 2, and a column for correlation effect size)? Best, Kiet
On Feb 25, 2022, at 10:58 AM, James Pustejovsky <jepusto at gmail.com> wrote: The pdftools package might be helpful: https://github.com/ropensci/pdftools <https://github.com/ropensci/pdftools> It has very low-level utilities for extracting text from pdf. You'd still have to do some data clean-up to get the correlations into the form needed for analysis. The tabulizer package is meant to provide tools customized for working with pdf tables: https://github.com/ropensci/tabulizer <https://github.com/ropensci/tabulizer> But it requires Java and it appears to be archived on CRAN. I'm not sure what its development status is. Caveat emptor, I guess. James On Fri, Feb 25, 2022 at 12:20 PM Kiet Huynh <kietduchuynh at gmail.com <mailto:kietduchuynh at gmail.com>> wrote: Hello, I was wondering if anyone knows of a way to automate in R (or any software) the process of importing correlation values from PDF to usable data in a table format that can be used in meta-analysis? My process has been to copy the correlations manually one-by-one from the PDF to excel (which takes a lifetime!), and then import the excel data into R. I'm sure there must be a better, faster, and less error-prone way to do this. Thank you, Kiet ---- Kiet D. Huynh, Ph.D. Pronouns: he/him CLEAR Goldblum-Carr Postdoctoral Fellow Palo Alto University 1791 Arastradero Rd. Palo Alto, CA 94304 [[alternative HTML version deleted]]
_______________________________________________ R-sig-meta-analysis mailing list R-sig-meta-analysis at r-project.org <mailto:R-sig-meta-analysis at r-project.org> https://stat.ethz.ch/mailman/listinfo/r-sig-meta-analysis <https://stat.ethz.ch/mailman/listinfo/r-sig-meta-analysis>
Hi Kiet, The rcalc() function from metafor could be used for this. It even computes the var-cov matrix of the elements in the correlation matrix for you: library(metafor) R <- matrix(c(1, .3, .5, .3, 1, .6, .5, .4, 1), 3, 3) R rcalc(R, ni=50) Best, Wolfgang
-----Original Message----- From: R-sig-meta-analysis [mailto:r-sig-meta-analysis-bounces at r-project.org] On Behalf Of Kiet Huynh Sent: Monday, 28 February, 2022 19:45 To: James Pustejovsky Cc: R meta Subject: Re: [R-meta] Importing Correlations from PDF to table format Hi James, Thank you for recommending these helpful packages. I was able to import the pdf correlation table into a dataframe format in R. Are you aware of any R code that could convert that correlation matrix dataframe into a meta-analysis type dataframe (i.e., a column for variable 1, a column for variable 2, and a column for correlation effect size)? Best, Kiet
On Feb 25, 2022, at 10:58 AM, James Pustejovsky <jepusto at gmail.com> wrote: The pdftools package might be helpful: https://github.com/ropensci/pdftools <https://github.com/ropensci/pdftools> It has very low-level utilities for extracting text from pdf. You'd still have
to do some data clean-up to get the correlations into the form needed for analysis.
The tabulizer package is meant to provide tools customized for working with pdf
tables:
https://github.com/ropensci/tabulizer <https://github.com/ropensci/tabulizer> But it requires Java and it appears to be archived on CRAN. I'm not sure what
its development status is. Caveat emptor, I guess.
James On Fri, Feb 25, 2022 at 12:20 PM Kiet Huynh <kietduchuynh at gmail.com
<mailto:kietduchuynh at gmail.com>> wrote:
Hello, I was wondering if anyone knows of a way to automate in R (or any software) the
process of importing correlation values from PDF to usable data in a table format that can be used in meta-analysis? My process has been to copy the correlations manually one-by-one from the PDF to excel (which takes a lifetime!), and then import the excel data into R. I'm sure there must be a better, faster, and less error-prone way to do this.
Thank you, Kiet ---- Kiet D. Huynh, Ph.D. Pronouns: he/him CLEAR Goldblum-Carr Postdoctoral Fellow Palo Alto University 1791 Arastradero Rd. Palo Alto, CA 94304