roxygen2 documentation for all functions #102

egouldo · 2024-08-11T02:21:53Z

function name
description
details
all params
Ensure all exported, where relevant otherwise, set to internal function
ensure all fns have @import or @importFrom calls
- ensure not mix and matching @importFrom and @import across functions
Examples, where relevant
- replace ManyEcoEvo::data object calls with data(data object) after switching away from lazy loading data

The text was updated successfully, but these errors were encountered:

…n()` call

- rename fn title, - give more detail in `@returns`, - explain mechanics in `@details`, - switch to `@import` instead of `@importFrom`, - add `@family` and `@seealso tags`

…umentation for `_back()` family \document

… title

- https://stackoverflow.com/questions/73911723/how-to-have-pkgdown-use-figure-numbers-and-cross-references-in-vignettes - https://forum.posit.co/t/cross-references-in-r-vignettes/138463/2

- #102 rm duplicate tidyselect import - required for 02151e5

…akagawa (2023)

egouldo · 2024-08-12T05:14:57Z

/document

- #42 #102 functionalise + document forest plot extraction - #42 mv plot_forest into pkg and document #102

…re_response_variables()` #88

…_response()

- #102 Add `@details` section for `process_response()` and add heading for `@details` in `standardise_response()`

Switch to `@importFrom` tags from `@import` Add `@seealso`, `@details` and some `@examples` Reorganise index manual grouping structure with `@family` and `@describeIn` tags `devtools::document()` Refs: #97 #102

style: linespacing / and indentation #97

- 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

- 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

- add import tag for `purrr::transpose()` in `fit_multivar_MA()` #102 - defuse argument `outcome` in `cli()` call in `fit_boxcox_ratings_cont()` - `meta_analyse_datasets()`: - use correct argument in calls to `fit_boxcox_ratings_*()` (`data` from `.data`) - apply coalesce on list-cols only and `@import` `tidyselect::where()` (previously non-list-cols were ignored because character columns were explicitly grouped, however current approach in pipeline is ungrouped in order to allow for generalisability / scalability #87. Can't caoalesce a character vector and list, must be of same type). build!: update calls in targets `yi` pipeline

- style: use comments to structure function. rearrange condition checks, and helper functions. update indentation. #97

style: fix indentation and spacing #97

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

…s_yi()`, update call of function within `prepare_response_variables_yi()` #97 And update associated roxygen code, especially imports #102

…e_vars_yi()` in vignette and roxygen examples #102 #97

#102

… review data cols are all re-nested #102 add note in documentation explaining data requirements

- 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 added the documentation label Aug 11, 2024

egouldo added this to the Software Manuscript Submit milestone Aug 11, 2024

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egouldo added a commit that referenced this issue Aug 11, 2024

#102 update roxygen examples and doc /document

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egouldo added a commit that referenced this issue Aug 11, 2024

#102 add examples, seealso and explicit by = argument in `left_joi…

34bb7fa

…n()` call

egouldo added a commit that referenced this issue Aug 11, 2024

#102 update function roxygen

5b3540b

- rename fn title, - give more detail in `@returns`, - explain mechanics in `@details`, - switch to `@import` instead of `@importFrom`, - add `@family` and `@seealso tags`

egouldo added a commit that referenced this issue Aug 11, 2024

#102 combine @Rdname and @describeIn approach to merging function doc…

c31e7ee

…umentation for `_back()` family \document

egouldo added a commit that referenced this issue Aug 11, 2024

#102 add @import packages to documentation and update descriotion /…

99badef

… title

egouldo added a commit that referenced this issue Aug 11, 2024

#102 add @import calls to function doc

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egouldo added a commit that referenced this issue Aug 11, 2024

#102 add @seealso entry

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egouldo added a commit that referenced this issue Aug 12, 2024

#102 update namespace

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egouldo added a commit that referenced this issue Aug 12, 2024

#102 update and add @import calls

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#102 #59 add rmarkdown and bookdown to pkg depends

77154df

- #102 rm duplicate tidyselect import - required for 02151e5

egouldo added a commit that referenced this issue Aug 12, 2024

#97 #59 #102 add snapshot bookdown to renv

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Roxygen / Pkgdown documentation overhaul #106

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Roxygen / Pkgdown documentation overhaul #106

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egouldo closed this as completed in #106 Aug 12, 2024

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#59 #102 add .bib for vignettes add link to alt. outcome measures / N…

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…akagawa (2023)

egouldo added a commit that referenced this issue Aug 12, 2024

#97 #102 move @examples tag to correct line /document

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egouldo added a commit that referenced this issue Aug 12, 2024

#102 #97 replace @importFrom calls with @import

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egouldo reopened this Aug 12, 2024

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#102 #97 replace md equation syntax with roxygen

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Move forest plot fun into pkg

3c21b5a

- #42 #102 functionalise + document forest plot extraction - #42 mv plot_forest into pkg and document #102

egouldo added a commit that referenced this issue Aug 14, 2024

#102 add @imports call and document new param for new arg in `prepa…

c58621d

…re_response_variables()` #88

egouldo added a commit that referenced this issue Aug 14, 2024

#102 devtools::document()

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egouldo added a commit that referenced this issue Aug 14, 2024

#102 #97 combine documentation for standardise_response() and process…

772bdc2

…_response()

egouldo added a commit that referenced this issue Aug 14, 2024

#97 #102 rebuild documentation

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egouldo added a commit that referenced this issue Aug 14, 2024

#88 rm unused args in process_response() and replace with ...

4d556d0

- #102 Add `@details` section for `process_response()` and add heading for `@details` in `standardise_response()`

egouldo added a commit that referenced this issue Aug 23, 2024

#102 #118 devtools::document()

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egouldo added a commit that referenced this issue Aug 23, 2024

#118 #102 export log_transform_response()

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

docs!: switch to import from importFrom #102

29cfbdf

style: linespacing / and indentation #97

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

bug!: fix @imports #97 #102

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egouldo added a commit that referenced this issue Aug 28, 2024

- docs!: update @imports #102

a0d5b14

- 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

docs!: #102 add @import* calls

045ec1a

style: fix indentation and spacing #97

egouldo added a commit that referenced this issue Aug 28, 2024

docs!: devtools::document() #102

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egouldo mentioned this issue Aug 28, 2024

118 log transform yi #121

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- #97 rename first data argument #102 update roxygen doc, add imports

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#102 devtools::document()

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#102 delete redundant data() call in examples

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#97 #102 replace first argument with data

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docs: #102 update documentation

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- docs!: #102 add roxygen imports to function doc

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- refactor!: rm unnecessary arguments to `back_transform_response_var…

bc8ae03

…s_yi()`, update call of function within `prepare_response_variables_yi()` #97 And update associated roxygen code, especially imports #102

egouldo mentioned this issue Sep 9, 2024

Extreme precision introduced into yi plots after fixing standardisation #151

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egouldo added a commit that referenced this issue Sep 9, 2024

- docs!: rm redundant arguments from calls to `back_transform_respons…

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…e_vars_yi()` in vignette and roxygen examples #102 #97

egouldo added a commit that referenced this issue Sep 9, 2024

- #102 devtools::document()

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

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#102

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- fix #75 ensure columns not rm in rating subset generation, and that…

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… review data cols are all re-nested #102 add note in documentation explaining data requirements

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- [docs]: #102 wrap equations in \eqn{} instead of $ $

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#102 minor docs typos / formatting

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roxygen2 documentation for all functions #102

roxygen2 documentation for all functions #102

egouldo commented Aug 11, 2024 •

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egouldo commented Aug 12, 2024

roxygen2 documentation for all functions #102

roxygen2 documentation for all functions #102

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egouldo commented Aug 11, 2024 •

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