Dev #45
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Dev #45
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jkamins7
commented
Oct 26, 2021
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General things to do :
- make sure formatR is run on each file
- go through and remove functions which are unused
- document config options
- write some global documentation on how to use the pipeline with docker
I think if we do these, plus address the individual points, then we should be ok to master
| @@ -119,17 +119,7 @@ make_initial_values_filename <- function(cholera_directory, | |||
| covariate_name_part, | |||
| config, | |||
| config_dict) { | |||
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| if ("file_names" %in% names(config)) { | |||
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Why did this get removed? was it broken, or did we have a merge issue?
| @@ -139,18 +129,19 @@ make_initial_values_filename <- function(cholera_directory, | |||
| return(paste(filename, config[["file_names"]][["stan_output_filename"]], sep = "/")) | |||
| } | |||
| } | |||
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This should be fixed by formatr, so seems like we need someone to install
| @@ -0,0 +1,92 @@ | |||
| testthat::skip_on_ci() | |||
| source("~/cholera-mapping-pipeline/packages/taxdat/R/database_api_key.R") | |||
| testthat::skip_on_ci() | |||
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You should only skip on ci once
| time_overlap <- function(tl, tr, res_time, tl_vec, tr_vec){ | ||
| # TODO | ||
| warning("This function is not written") | ||
| time_overlap <- function(tl, tr, res_time, tl_vec, tr_vec) { |
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Should we delete this?
| @@ -1,64 +1,201 @@ | |||
| #' @export | |||
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We should make sure that all of these functions are still used somewhere before merging.
jkamins7
requested review from
eclee25 and
javierps
and removed request for
eclee25
Clean all temporary tables
Fix aggregation
Update postprocessing
Sfrac upper limit to exactly 1
Dev drop low pop lps fix
Revert setting Mainland and ZNZ as ADM0 level
Updated natural scale for manuscript figure 5c
…lera-mapping-pipeline into dev_update_postprocessing
Added stats for targeting strategy
…lera-mapping-pipeline into dev_update_postprocessing
new updates about manuscript figures and functions
…lera-mapping-pipeline into dev_update_postprocessing
removed some unnecessary code
…lera-mapping-pipeline into dev_update_postprocessing
updated figure code
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master is no longer the default branch on this repo |
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