Fix #88 conditionally apply standardisation to datasets

[egouldo]

• Write vignettes #59 roxygen2 documentation for all functions #102 add .bib for vignettes add link to alt. outcome measures / Nakagawa (2023)
• Upkeep for ManyEcoEvo (2024) #97 roxygen2 documentation for all functions #102 move @examples tag to correct line /document
• Upkeep for ManyEcoEvo (2024) #97 add pkgdown favicons
• roxygen2 documentation for all functions #102 Upkeep for ManyEcoEvo (2024) #97 replace @importFrom calls with @import
• Upkeep for ManyEcoEvo (2024) #97 devtools::document(), devtools::build_vignettes()
• roxygen example code error fit_metafor_mv #9 namespace targets::
• roxygen2 documentation for all functions #102 Upkeep for ManyEcoEvo (2024) #97 replace md equation syntax with roxygen
• Upkeep for ManyEcoEvo (2024) #97 devtools::document()
• Fix prepare back-transformation analysis pipeline needs reorganising - duplicated components #104 reorganise yi computational pipeline in prep for Ensure euc yi vars not erroneously being back-transformed #88 - prepare back-transformation analysis pipeline needs reorganising - duplicated components #104 mv assign_transformation_type() and convert_predictions() out of standardise_response() into back_transform_response_vars_yi() - Call back_transform_response_vars_yi() in prepare_response_variables() for yi workflow (was not being called currently) prepare back-transformation analysis pipeline needs reorganising - duplicated components #104 - prepare back-transformation analysis pipeline needs reorganising - duplicated components #104 keep addition of param_table inside standardise_response()
• Increment version number to 2.3.0.9004
• Constructed Variables are ignored when standardising (no average values in param table) #82 add comment
• fix raw data columns misnamed #107 misnamed cols
• prepare back-transformation analysis pipeline needs reorganising - duplicated components #104 group by id_col
• prepare back-transformation analysis pipeline needs reorganising - duplicated components #104 Upkeep for ManyEcoEvo (2024) #97 make join_by argument explicit
• prepare back-transformation analysis pipeline needs reorganising - duplicated components #104 fix bugs in prepare_response_variable() - don't return out early (after backtransformation, need to standardise still!) prepare back-transformation analysis pipeline needs reorganising - duplicated components #104 - standardise on the results of backtransformation out, if applied, and if not, use out prior to backtransformation, and backtransform on original out prepare back-transformation analysis pipeline needs reorganising - duplicated components #104
• prepare back-transformation analysis pipeline needs reorganising - duplicated components #104 fix conditional evaluation to trigger convert_predictions() / standardise_response() - incorrect use of pipe operator returned TRUE when one expression eval'd to TRUE, but we want it to return FALSE if any exprs eval to FALSE.
• #204 rm duplicate cli header
• prepare back-transformation analysis pipeline needs reorganising - duplicated components #104 update comment
• prepare back-transformation analysis pipeline needs reorganising - duplicated components #104 ungroup results of back_transform_response_vars_yi() and standardise_response()
• prepare back-transformation analysis pipeline needs reorganising - duplicated components #104 use input argument dataset, not column in input arg dat, as dat may or may not have the required dataset column.
• prepare back-transformation analysis pipeline needs reorganising - duplicated components #104 update pointblank data check - don't expect any identifier col other than id_col exists - don't expect transformation, or response_transformation_status exists - expect response_variable_name exists
• Write vignettes #59 update vignette to reflect prepare back-transformation analysis pipeline needs reorganising - duplicated components #104 updates
• prepare back-transformation analysis pipeline needs reorganising - duplicated components #104 Upkeep for ManyEcoEvo (2024) #97 devtools::document()
• Increment version number to 2.3.0.9005
• Upkeep for ManyEcoEvo (2024) #97 prepare back-transformation analysis pipeline needs reorganising - duplicated components #104 tar_make()
• Increment version number to 2.4.0
• Ensure euc yi vars not erroneously being back-transformed #88 add argument for selectively standardising - NOTE: dummy function for datasets not selected for standardising is currently applied - TODO: update dummy function - TODO: apply functions with map2
• Increment version number to 2.4.0.9000
• Move forest plot fun into pkg - Investigate and fix rating analysis weights #42 roxygen2 documentation for all functions #102 functionalise + document forest plot extraction - Investigate and fix rating analysis weights #42 mv plot_forest into pkg and document roxygen2 documentation for all functions #102
• roxygen2 documentation for all functions #102 add @imports call and document new param for new arg in prepare_response_variables() Ensure euc yi vars not erroneously being back-transformed #88
• roxygen2 documentation for all functions #102 devtools::document()
• update renv
• Ensure euc yi vars not erroneously being back-transformed #88 switch to alternative approach for assigning fns to list-col - prev approach with rlang::as_function() was taking the entire set of all previous input code including the wrapping mutate() calls
• Increment version number to 2.4.0.9001
• Ensure euc yi vars not erroneously being back-transformed #88 conditionally apply standardisation - 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() - Upkeep for ManyEcoEvo (2024) #97 delete comment
• Increment version number to 2.4.0.9002
• Ensure euc yi vars not erroneously being back-transformed #88 add function arg checks Upkeep for ManyEcoEvo (2024) #97 delete comment Upkeep for ManyEcoEvo (2024) #97 lint
• Increment version number to 2.4.0.9003
• Upkeep for ManyEcoEvo (2024) #97 add comment
• Upkeep for ManyEcoEvo (2024) #97 update _pkgdown.yaml to capture new forest plotting funs
• Ensure euc yi vars not erroneously being back-transformed #88 add process_response() - for alternate to standardise_response()
• roxygen2 documentation for all functions #102 Upkeep for ManyEcoEvo (2024) #97 combine documentation for standardise_response() and process_response()
• Upkeep for ManyEcoEvo (2024) #97 roxygen2 documentation for all functions #102 rebuild documentation
• Increment version number to 2.4.0.9004
• Ensure euc yi vars not erroneously being back-transformed #88 rm unused args in process_response() and replace with ... - roxygen2 documentation for all functions #102 Add @details section for process_response() and add heading for @details in standardise_response()
• Upkeep for ManyEcoEvo (2024) #97 indentation
• close Ensure euc yi vars not erroneously being back-transformed #88 update function call to prepare_response_variables() in targets - only standardise blue tit yi Ensure euc yi vars not erroneously being back-transformed #88
• Increment version number to 2.4.1
• devtools::document() Upkeep for ManyEcoEvo (2024) #97 roxygen2 documentation for all functions #102 Ensure euc yi vars not erroneously being back-transformed #88
• Upkeep for ManyEcoEvo (2024) #97 linelength linting
• Constructed Variables are ignored when standardising (no average values in param table) #82 delete code that excluded all constructed variables
• Upkeep for ManyEcoEvo (2024) #97 linelength spacing / linting
• Upkeep for ManyEcoEvo (2024) #97 update project settings to roxygenise on build
• Upkeep for ManyEcoEvo (2024) #97 update renv
• Upkeep for ManyEcoEvo (2024) #97 update packages
• Upkeep for ManyEcoEvo (2024) #97 delete comment
• Ensure euc yi vars not erroneously being back-transformed #88 tar_make.R error - rm left over line from Constructed Variables are ignored when standardising (no average values in param table) #82
• Upkeep for ManyEcoEvo (2024) #97 reindent after fixing prev commit
• Fix Ensure euc yi vars not erroneously being back-transformed #88 rebuild targets
• Increment version number to 2.4.1.9000