USEPA / CompTox-ToxCast-tcplFit2

Performs basic concentration response curve fitting
https://cran.r-project.org/package=tcplfit2
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Create unit tests for HTPP global data fit with tcplfit2 #63

Open sedavid01 opened 8 months ago

sedavid01 commented 8 months ago

Goal: The goal of this issue is to create unit tests for high-phenotypic profiling (HTPP) data such that we ensure that as the codebase of tcplfit2 is updated that the updates do not break/alter the results previously obtained in previous analyses with tcplfit2.

Needs for finishing this ticket:

sedavid01 commented 8 months ago

Mostly a note so I do not forget the data subset creation steps discussed in 1:1 meeting:

  1. Move the data from Derik to the data-raw sub-dir of tcplfit2 R package. (DO NOT add or commit to Git history.)
  2. Add the sub-directory & RData files with data from Derik to the '.gitignore' file in the repo so the datasets do not get tracked with Git and pushed up to the remote repo.
  3. Create an R Script to generate the sub-set of data for testing. (Make sure to add the use_data and sessionInfo call to the end of this script but comment out for now until review and green light. The use_data will want to be internal - a sys type data saved under the data sub-directory with use_data.)

Once we have the sub-set together we will want to check back with the HTPP team that it meets their criteria before we create/save the sub-set and develop the tests.

@brown-jason, please review this plan and let me know if you have any comments, questions, and/or concerns.

sedavid01 commented 8 months ago

@gracezhihuizhao, next steps on the subsets:

Apply these to #62 and #38 as well.

sedavid01 commented 7 months ago

Update on dropped doses for HTPP data: