Publication ready tables

[kristyrobledo]

I'd like to put together some functions to manipulate outputs into publication ready tables.

eg. "table 1"

• mean (SD) by group
• median (Q1-Q3) option to have median (min-max) instead
• n (%) (with the option to have a p-value as well)

also thinking 'logistic regression' table (n/N for each group, OR 95% CI, pvalue) survival analysis table (event rates by group, Hazard ratio 95% CI, pvalue) etc .....

Hopefully they will all be ready to go straight into a kable(). also thinking of a way to toggle these last two tables into create nice forestplots instead of a table.

[jenrichmond]

Hi Kristy A bit like the tableone package?

https://cran.r-project.org/web/packages/tableone/vignettes/introduction.html

Jen

On Sun, 17 Nov 2019 at 7:07 pm, kristyrobledo notifications@github.com wrote:

I'd like to put together some functions to manipulate outputs into publication ready tables.

eg. "table 1"

• mean (SD) by group
• median (Q1-Q3) option to have median (min-max) instead
• n (%) (with the option to have a p-value as well)

also thinking 'logistic regression' table (n/N for each group, OR 95% CI, pvalue) survival analysis table (event rates by group, Hazard ratio 95% CI, pvalue) etc .....

Hopefully they will all be ready to go straight into a kable(). also thinking of a way to toggle these last two tables into create nice forestplots instead of a table.

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[kristyrobledo]

hahah yes - exactly! (seriously sometimes I just need to spend more time googling to find what I want before recreating the wheel)

OK so build on that I guess, with the other analysis tables.

[jenrichmond]

:) I only learned about this one a week ago! And not from googling !!

[kristyrobledo]

thinking out loud.... is there anyway to search all the R packages easily to find packages to do certain things?? eg each package has key words attached to it, and then you search to (easily) find what you want...

[ekothe]

I think you might also want to have a look at papaja for the tables https://github.com/crsh/papaja

[jenrichmond]

emily is the table queen! thanks for telling me about tableone!

On Mon, Nov 18, 2019 at 10:41 AM Emily Kothe notifications@github.com wrote:

I think you might also want to have a look at papaja for the tables https://github.com/crsh/papaja

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[orchid00]

hi @kristyrobledo to your question

is the anyway to search all the R packages

• the answer is yes!

One option is METACRAN https://www.r-pkg.org/ it has a very specific search, the only drawback might be only searching on CRAN. The other option is R Package Documentation https://rdrr.io/ - but it didn't return the packages that metacran found Third option: https://www.rdocumentation.org

there might be many other options

[kristyrobledo]

seriously, sometimes its just about finding the right R package!!! Maybe we need an R package to help us find the right R package...... maybe pulling together the information from the above 3 sources?

[kristyrobledo]

I think you might also want to have a look at papaja for the tables https://github.com/crsh/papaja

this is fantastic - thanks so much @ekothe! the wrapper apa_table() seems to be exactly what I was thinking :)

[njtierney]

This is indeed an interesting topic! There was a bit of a discussion around searching through R packages at a past unconf in the USA: https://github.com/ropensci/unconf17/issues/78

Which resulted in the package metrics package - https://github.com/ropenscilabs/packagemetrics

Which resulted in a table of packages that make tables :tada: : https://github.com/ropenscilabs/packagemetrics#creating-a-pretty-metrics_table

Perhaps that can provide a good starting place for some discussion on creating tables?

In addition to what has been discussed, there is also the janitor package, by @sfirke, which contains loads of really nice data cleaning shortcuts, and a really nice flexible approach to creating tables - atabyl. You can read more in this tabyl vignette, which has these really nice adorn_ functions for adding extra columns.

[robjhyndman]

Very useful @njtierney! It is also worth looking at the Reproducible Research task view which lists some table-making packages including some not on the "table of tables" you link to.

[orchid00]

@kristyrobledo what about this https://www.littlemissdata.com/blog/prettytables

[kristyrobledo]

We have burned this to the ground....

ApaTables and papaja kind of answered this question.