Add supp table 4 for survival results

[jharenza]

Purpose/implementation Section

What scientific question is your analysis addressing?

Add survival results for those results described in the manuscript

What was your approach?

tidy sweeping

What GitHub issue does your pull request address?

1359

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

lr_subtypes_df <- broom::tidy(lr_subtypes$model) %>%
  mutate(HR = exp(estimate),
         conf.low = exp(conf.low),
         conf.high = exp(conf.high)
  )

does not give the expected result

Is there anything that you want to discuss further?

I think I might also want to recode the NAs to not have numbers and Inf to not be undefined excel values

Update - I recoded Inf to character, but left the NA because I guess #NA is an excel NA, which is fine.

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

yes

Results

What types of results are included (e.g., table, figure)?

supp table S4 and moved KR to S5

What is your summary of the results?

Reproducibility Checklist

• [x] The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• [x] This analysis has been added to continuous integration.

Documentation Checklist

• [x] This analysis module has a README and it is up to date.
• [x] This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• [x] The analytical code is documented and contains comments.

[jharenza]

@sjspielman - made some updates- let me know what you think

[jharenza]

Hmm, I was thinking it was a supplement since it doesn't fit into the table, but that is a good point that the guidelines generally count put KR toward supplements. I'll have to look at that again, but maybe we can do in another PR, and I'd have to update the manuscript ref as well.

[jharenza]

@sjspielman to note on here - according to this, we do need to use one of our supp tables for this info, so we are good as is.

To maximize readability, we encourage you to provide the list of a specific reagent or resource (e.g., oligonucleotides, RNA sequences) as a supplemental table if there are more than 10 items under the subheading (for example, “See Table S1 for a list of oligonucleotides.”).