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Upkeep for ManyEcoEvo (2024) #97
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- 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
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style: remove todo comments #97, shutup noisy joins by supplying `by` arg in join call.
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style: linespacing / and indentation #97
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- 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
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- 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
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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
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- 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
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…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
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- style: use comments to structure function. rearrange condition checks, and helper functions. update indentation. #97
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--- 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
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(note has since been replaced by `compute_MA_inputs()`)
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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()
dataset
checks aren't hard-coded for ManyAnalysts datasetsc("eucalyptus", "blue tit")
.2020
usethis::use_package_doc()
usethis::use_testthat(3)
R/
files andtest/
files2021
cran-comments.md
2022
master
-->main
issuesusethis:::use_codecov_badge("egouldo/ManyEcoEvo")
usethis::use_lifecycle()
2023
usethis::use_tidy_logo(); pkgdown::build_favicons(overwrite = TRUE)
usethis::use_tidy_coc()
use_citation()
pak::pak("egouldo/ManyEcoEvo")
in READMEusethis::use_tidy_dependencies()
and/or replace compat files withuse_standalone()
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
To finish
usethis::use_package("R", "Depends", "4.0")
usethis::use_tidy_description()
usethis::use_tidy_github_actions()
devtools::build_readme()
Created on 2024-08-10 with
usethis::use_tidy_upkeep_issue()
, using usethis v2.2.3, edited by hand in issueThe text was updated successfully, but these errors were encountered: