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itchyshin / mice_sex_diff

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Code clean up #3

Closed dfalster closed 4 years ago

dfalster commented 4 years ago

Hi folks, I pushed up some initial efforts towards reformatting analysis, including

The above are all included in commits up to b4b1ab9e6054cccffc36615f5d41f832eb60680e

Besides renaming and styling, i haven't looked beyond line 440.

As far as I can tell, the code incorporating these changes is producing same results,. But please check!

Things to do from here

Shall we meet to talk through some of these?

Regarding the exclusions, at this point we have 

has_problems <- c(84, 144, 158, 160, 161, 162, 163, 165, 166, 167, 168, 221, 222, 231)
meta_clean <- results_alltraits_grouping2 %>% filter(!id %in% has_problems)
meta_problem <- results_alltraits_grouping2 %>% filter(id %in% has_problems)

It's dangerous to use numbers, because if variable processing changes at all the numbers point to wrong rows.

itchyshin commented 4 years ago

Hi, Daniel

This is great - Susi is away from Friday. Probably we can meet next Monday all of us? Susi, Felix, you and me?

Best

Shinichi

On Thu, Dec 5, 2019 at 8:45 AM Daniel Falster notifications@github.com wrote:

Hi folks, I pushed up some initial efforts towards reformatting analysis, including

  • use styler to style all code
  • using here so that files load reliably
  • some renaming of variables and function to be a bit more consistent
  • move some data fiels from export to data
  • cleanup dataset construction to use fewer intermediates
  • started cleaning up headers and section markers
  • update "cleaned" data object to include all cleaning

The above are all included in commits up to b4b1ab9 https://github.com/itchyshin/mice_sex_diff/commit/b4b1ab9e6054cccffc36615f5d41f832eb60680e

Besides renaming and styling, i haven't looked beyond line 440 https://github.com/itchyshin/mice_sex_diff/blob/master/scripts/2019_Nov1-FiguresRearranged_IMPC_variance_and_sex_difference.Rmd#L444 .

As far as I can tell, the code incorporating these changes is producing same results,. But please check!

Things to do from here

  • Is it ok to move main script to project root and rename `analysis.Rmd"?
  • Look at all the points in the code marked with "Review"
  • clean up headers (we have lots of header pages which make menu structure really strange)
  • better encoding of exclusions (e.g. at
  • clean up figure code, perhaps put in operate file?
  • Add docker file for persistent running
  • Felix was against it but I still prefer to push all these functions off into another file. Makes it so much more readable. What do others think?

Shall we meet to talk through some of these?

Regarding the exclusions, at this point https://github.com/itchyshin/mice_sex_diff/blob/master/scripts/2019_Nov1-FiguresRearranged_IMPC_variance_and_sex_difference.Rmd#L429 we have

has_problems <- c(84, 144, 158, 160, 161, 162, 163, 165, 166, 167, 168, 221, 222, 231) meta_clean <- results_alltraits_grouping2 %>% filter(!id %in% has_problems) meta_problem <- results_alltraits_grouping2 %>% filter(id %in% has_problems)

It's dangerous to use numbers, because if variable processing changes at all the numbers point to wrong rows.

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dfalster commented 4 years ago

I can do that