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Upkeep for ManyEcoEvo (2024) #97

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11 of 32 tasks
egouldo opened this issue Aug 10, 2024 · 0 comments
Open
11 of 32 tasks

Upkeep for ManyEcoEvo (2024) #97

egouldo opened this issue Aug 10, 2024 · 0 comments
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upkeep maintenance, infrastructure, and similar

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egouldo commented Aug 10, 2024

To begin

  • pr_init("upkeep-2024-08")

Pre-history

  • usethis::use_readme_rmd()
  • usethis::use_roxygen_md()
  • usethis::use_github_links()
  • usethis::use_pkgdown_github_pages()
  • usethis::use_tidy_github_labels()
  • usethis::use_tidy_style()
  • urlchecker::url_check()
  • Defensive programming / argument checks #116
  • generalise all fns so dataset checks aren't hard-coded for ManyAnalysts datasets c("eucalyptus", "blue tit").

2020

  • usethis::use_package_doc()
  • usethis::use_testthat(3)
  • Align the names of R/ files and test/ files

2021

  • Remove check environments section from cran-comments.md
  • Use lifecycle instead of artisanal deprecation messages

2022

  • Handle and close any still-open master --> main issues
  • usethis:::use_codecov_badge("egouldo/ManyEcoEvo")
  • Update pkgdown site using instructions at https://tidytemplate.tidyverse.org
  • Update lifecycle badges with more accessible SVGs: usethis::use_lifecycle()

2023

  • usethis::use_tidy_logo(); pkgdown::build_favicons(overwrite = TRUE)
  • usethis::use_tidy_coc()
  • Modernize citation files; see updated use_citation()
  • Use pak::pak("egouldo/ManyEcoEvo") in README
  • Consider running usethis::use_tidy_dependencies() and/or replace compat files with use_standalone()
  • Use cli errors or file an issue if you don't have time to do it now
  • usethis::use_standalone("r-lib/rlang", "types-check") instead of home grown argument checkers;
    or file an issue if you don't have time to do it now
  • Add alt-text to pictures, plots, etc; see https://posit.co/blog/knitr-fig-alt/ for examples

To finish

  • usethis::use_package("R", "Depends", "4.0")
  • usethis::use_tidy_description()
  • usethis::use_tidy_github_actions()
  • devtools::build_readme()
  • Re-publish released site if needed

Created on 2024-08-10 with usethis::use_tidy_upkeep_issue(), using usethis v2.2.3, edited by hand in issue

@egouldo egouldo added the upkeep maintenance, infrastructure, and similar label Aug 10, 2024
@egouldo egouldo self-assigned this Aug 10, 2024
@egouldo egouldo added this to the Software Manuscript Submit milestone Aug 10, 2024
egouldo added a commit that referenced this issue Aug 12, 2024
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egouldo added a commit that referenced this issue Aug 14, 2024
- correctly apply `fns` in list-col using `pmap()` approach on entire dataframe, with support of wrapper / parser fun that parses the required variables to either `standardise_response()` or `process_response()`
- #97 delete comment
egouldo added a commit that referenced this issue Aug 14, 2024
#97 delete comment
#97 lint
egouldo added a commit that referenced this issue Aug 14, 2024
egouldo added a commit that referenced this issue Aug 14, 2024
egouldo added a commit that referenced this issue Aug 14, 2024
egouldo added a commit that referenced this issue Aug 14, 2024
egouldo added a commit that referenced this issue Aug 14, 2024
egouldo added a commit that referenced this issue Aug 14, 2024
egouldo added a commit that referenced this issue Aug 14, 2024
egouldo added a commit that referenced this issue Aug 14, 2024
egouldo added a commit that referenced this issue Aug 14, 2024
egouldo added a commit that referenced this issue Aug 26, 2024
style: remove todo comments #97, shutup noisy joins by supplying `by` arg in join call.
egouldo added a commit that referenced this issue Aug 26, 2024
style: linespacing / and indentation #97
egouldo added a commit that referenced this issue Aug 26, 2024
- switch arg to `data` from `ManyEcoEvo`
- expose argument to user `n_min` and `n_max`
- explicit join by argument in join
- ensure filter diversity_indices for each reduced subset
- ensure filter diversity_data on effects_analysis and NOT data

---

This step filters datasets into a `'effects_analysis'` column, and therefore any filtering of the `diversity_*` data must be based on `effects_analysis`

refs: #102 #97
egouldo added a commit that referenced this issue Aug 27, 2024
- expose filtering of subsets to user argument: ignore outlier generation for some subsets
- Expose `n_min` and `n_max` args to user
- Add argument checks #116, inc. checking filter expressions for existance of col names in `data`
- Conditionally slice depending on whether `n_*` args supplied in call
- Define internal helper fns to reduce duplicate code
- Permit multiple logical expressions in argument ignore_subsets
- Allow different values of `n_min` and `n_max` for different `dataset`s

bug!: properly evaluate whether arg `ignore_subsets` is null and parse to `filter_vars`, see `dplyr::dplyr_data_masking`

docs!: Update docs #118

- include functional updates in roxygen docs #102
- rm targets pipeline family tag

style: tidy lint #97

- linespacing / whitespace
- rm TODO comments
- Add section header comments
egouldo added a commit that referenced this issue Aug 27, 2024
egouldo added a commit that referenced this issue Aug 27, 2024
docs: Add `@details` and @import*` tags

refs: #97
egouldo added a commit that referenced this issue Aug 27, 2024
egouldo added a commit that referenced this issue Aug 27, 2024
bug!: #118 ensure `estimate_type` column is added back in using argument value if existing col is replaced and stop grouping on returned data frame
egouldo added a commit that referenced this issue Aug 27, 2024
egouldo added a commit that referenced this issue Aug 28, 2024
- rm commented out `poss_fit_*()` (now exported internally in 7dabe6d) #97
- replace name of data arg to `data` #97
- switch to rlang::is_null for arg checking #116 / conditional behaviour
- Add arg checking for `filter_vars`, `data`, and checking wither required columns, incl. those in `filter_vars` exist in `data` #116
- expose user-supplied arguments `outcom_variable` / `outcome_SE` and match values to arg conditions in new columns
- update supply of colnames arg to meta-analysis functions

docs!: update corresponding docs #102

- switch to `@importFrom` for `cli::`, add missing `@importFrom` calls
- Add `@details` on user-specified exclusion of outcome variable / outcome variable SE

style: spacing indentation, rm inline TODO comments #97
egouldo added a commit that referenced this issue Aug 28, 2024
…118

- `fit_MA_mv()` switch from `Z_colname` to `outcome_colname` and `VZ_colname` to `outcome_SE_colname` #118
- `calculate_deviation_score()` #118:  expose colname selection column to user , return meta-analytic mean in column, add `outcome_colname` to specify relevant outcome column name, add argument checking #116
- `apply_slice_conditionally()` create column `exclusion_set` if does not exist and switch to `se_log` as `VZ_colname` in example for eucalyptus` #188
- `box_cox_transform()` expose `outcome_SE_colname` arg, add relevant arg checks, update cli output, parse outcome_SE_columns` to `folded_params()` function call #188
- replace `std.error_log` arg with `se_log` for any logged `yi` data #188
- and update wrapper function calls in `meta_analyse_datasets()`, provide NULL default for new arg `outcome_SE` #188
- `fit_box_cox_ratings_cat()`: add arg checks #116, replace arg name `.data` with `data`, switch to `inject` approach as per `fit_box_cox_ratings_cont()` #97
- fit_box_cox_ratings_cont()` switch to `data` arg from `.data`, add arg checks #116
- add arg checks to `standardise_response()`, `fit_sorensen_glm()`, `fit_multivar_MA()` , `fit_uni_mixed_effects()` #116

docs!: update corresponding docs

- delete obsolete `@examples` code #102
- add #TODO comments #97
- add missing `@import` calls
- switch to `@importFrom` from `@import` for `purrr::` `rlang::` and `tidyr::` et al
- don't import `rlang::` in package.R

bug!: minor bug fixes

- unquote bare colname in pointblank check for `exclude_extreme_VZ()`
- `fit_metafor_mv_reduced()` replace obs_id with study_id as random effect
egouldo added a commit that referenced this issue Aug 28, 2024
- style: use comments to structure function. rearrange condition checks, and helper functions. update indentation. #97
egouldo added a commit that referenced this issue Aug 28, 2024
style: fix indentation and spacing #97
egouldo added a commit that referenced this issue Aug 29, 2024
feat!: add threshold for executing function in line with preregistered threshold (5 in each category of `mixed_model`)

style: move cli output after argument checking #97

docs: capitalise Box-Cox #102
egouldo added a commit that referenced this issue Aug 29, 2024
---

Whenever mapped functions were called inside `ifelse()` statements in mutate calls without grouping, the same dataset (i.e. the first value) of the list-column was getting passed over and over again. I think that's because `ifelse()` isn't vectorised... switched to rowwise approach described at <https://cran.r-project.org/web/packages/dplyr/vignettes/rowwise.html> to avoid this problem, but also to explicitly enforce rowwise functionality without having to explicitly group to permit generalisability #97
egouldo added a commit that referenced this issue Sep 6, 2024
egouldo added a commit that referenced this issue Sep 6, 2024
(note has since been replaced by `compute_MA_inputs()`)
egouldo added a commit that referenced this issue Sep 6, 2024
egouldo added a commit that referenced this issue Sep 6, 2024
egouldo added a commit that referenced this issue Sep 9, 2024
…s_yi()`, update call of function within `prepare_response_variables_yi()` #97

And update associated roxygen code, especially imports #102
egouldo added a commit that referenced this issue Sep 9, 2024
egouldo added a commit that referenced this issue Sep 9, 2024
egouldo added a commit that referenced this issue Sep 10, 2024
egouldo added a commit that referenced this issue Sep 10, 2024
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