Defensive programming / argument checks #116

egouldo · 2024-08-15T03:02:47Z

https://adv-r.hadley.nz/conditions.html

- #116 add checks for param table argument - update default behaviour description #102 - line linting / indentation #97 - #88 change default behaviour to `process_response()`, not `standardise_response()` when `is.null(dataset_standardise)`, otherwise function did not allow for case when all datasets should not be Z-standardised

- #118 adapt response variable preparation to accept additional argument `dataset_log_transform` apply argument checks #116, add roxygen param #102 - #118 adapt response variable processing to accept either/or/none for dataset standardisation/log-transformation.

- #102 add import, return, and see also roxygen doc tags, replace note with details tag, rename fn doc title - #116 update argument checks conditional expression - #118 match output to `log_transform_yi()` (now returns additional cols `lower` and `upper`, not only `c("Z","VZ")`) - #118 match process to `log_transform_yi()` and #97 generalise processing to both euc/bt datasets without hard-coding dataset names in fns, and remove associated dataset-specific argument checking #116

- #116 check appropriate required variable (i.e. function needs `back_transformed_data`, but checked for `augmented_data` in `dat` arg, wouldn't throw required error because `augmented_data` was present in `dat`

style: remove todo comments #97, shutup noisy joins by supplying `by` arg in join call.

…rceded and add arg checking #116

- 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

- 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

…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

- Added conditional behaviour for when character vector supplied - feat!: added arg checks #116 and cli output for when this condition is triggered --- But wasn't failing for `yi` because `yi` received `rlang::expressions()` while `Zr` call used single length character variable for `outcome_variable` and `outcome_SE`

After discarding NA values if the length is less than the number of inputs (4) THEN trigger the warning / early exit from fn. Threshold check was too low (3).

#102

- and add details explaining model structure and required data structure in roxygen documentation #102 - don't pointblank check for box_cox column, let user's value be checked #116 - update data checks to match required model structure #116

egouldo mentioned this issue Aug 15, 2024

Upkeep for ManyEcoEvo (2024) #97

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egouldo self-assigned this Aug 15, 2024

egouldo added the upkeep maintenance, infrastructure, and similar label Aug 15, 2024

egouldo added this to the pkgdown milestone Aug 15, 2024

egouldo linked a pull request Aug 15, 2024 that will close this issue

Fix bug in prpare_response_variables() #117

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egouldo closed this as completed in #117 Aug 15, 2024

egouldo removed a link to a pull request Aug 15, 2024

Fix bug in prpare_response_variables() #117

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egouldo reopened this Aug 15, 2024

egouldo added a commit that referenced this issue Aug 15, 2024

#116 #97 update argument checks

89947c1

egouldo added a commit that referenced this issue Aug 26, 2024

feat: Add pointblank:: column checks and user warnings #116

6841a89

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

fix: wrap column names in c() when checking if exist #116

7515021

egouldo added a commit that referenced this issue Aug 26, 2024

style!: replace call to pointblank::cars() with c() since is supe…

8869ca2

…rceded and add arg checking #116

egouldo added a commit that referenced this issue Aug 27, 2024

feat: add argument checks #116 #97

421e02f

egouldo mentioned this issue Aug 28, 2024

118 log transform yi #121

Merged

egouldo added a commit that referenced this issue Sep 6, 2024

- bug fix in arg checking #116

20d7449

After discarding NA values if the length is less than the number of inputs (4) THEN trigger the warning / early exit from fn. Threshold check was too low (3).

egouldo added a commit that referenced this issue Sep 10, 2024

- add argument checking for summary fns #116 and update roxygen imports

416ff44

#102

egouldo added a commit that referenced this issue Sep 10, 2024

- #116 add argument check

1e9ea1e

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Defensive programming / argument checks #116

Defensive programming / argument checks #116

egouldo commented Aug 15, 2024 •

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Defensive programming / argument checks #116

Defensive programming / argument checks #116

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egouldo commented Aug 15, 2024 • edited Loading

egouldo commented Aug 15, 2024 •

edited

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