Rebuild manuscript #82

egouldo · 2024-09-17T00:11:07Z

Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42 rm functions from ManyAnalysts after functionalise manuscript code in SM3 ManyEcoEvo#29
rm hack fn since performance:: pkg update, see Add check_convergence method for parsnip _glm model easystats/performance#605
- Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42 switch to latest ManyEcoEvo, see https://github.com/egouldo/ManyEcoEvo/releases/tag/v2.1.0
- Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42 rm multivariate model code since upgrading ManyEcoEvo
- Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42 extract updated model object rather than coding in manuscript
switch to round pluck and semantically extract in-text outputs
Fix Explain yi exclusions due to missing param data for constructed variables #61 explain yi exclusions when can't standardize constructed variables
explicitly call object from ManyEcoEvo::
Add rm whitespace
replace explicit arg name call with correct arg name in fit_MA_mv() Mv multivariate MA code into ManyEcoEvo and update #44
Explain yi exclusions due to missing param data for constructed variables #61 add fontawesome extensions
update argument name, see argument name incorrect in fit_MA_mv ManyEcoEvo#89
Add library call explicitly
Update SM3_ExplainingDeviation.qmd
update figure crossref
Update equation / text in SM2 for yi standardisation
fix for quarto cross-reference not rendering
fix citation
add shared functions to pre-render script - note that quarto preview ignores the pre-render script, so have inserted source() calls for interactive dev, as per Pre render for quarto preview quarto-dev/quarto-cli#4841
quarto cross-reference not rendering #50 box label and cross-ref now renders but heading separate to note label, so switch to using double hash headers in all .callout boxes
fix update calls to ManyEcoEvo:: objects after lazy-loading rm'd #73 call data() to load ManyEcoEvo objects - data is no longer lazy-loaded in ManyEcoEvo
renv.lock upgrade to current dev ManyEcoEvo (v2.3.0)
re-render freeze
mv shared functions into shared pre-render script, set execution directory to project
update calls to ManyEcoEvo:: objects after lazy-loading rm'd #73 ensure cross-ref renders by adding caption to table.
Update equation / text in SM2 for yi standardisation #64 switch to back-slash for bar command
Update equation / text in SM2 for yi standardisation #64 add in missing subscript
Update equation / text in SM2 for yi standardisation #64 re-insert calculation of variance for Zj that was removed
Update equation / text in SM2 for yi standardisation #64 revert filtering of models, and add MA_mod_mv to list to filter out
Update equation / text in SM2 for yi standardisation #64 permit SD_calc == NA generated on binding with - code erroneously filtered out Sorensen's / mixed effects univarirate models which didn't have their SD_calc check performed
source utils.R for previewing
Fix equation alignment, syntax, subscripts - switch to \begin{alignat*} environment from amsmath:: - ensure Sorensen is wrapped in \mathrm{} or \text{} - add missing subscript - add missing definition of Deviation Score to eq-deviation-multivar
linting, add spaces around =
fix duplicate meta-analytic mean values in forest plot #77 - rm mean value introduced from collinearity analyses that weren't filtered out
duplicate meta-analytic mean values in forest plot #77 filter out, not for!
Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42 don't re-run broom::tidy now that is in ManyEcoEvo::
style: lint indentation
Table 3.2, 3.4 update table structure #51 change structure of input data for tables
Table 3.2, 3.4 update table structure #51 remove collinearity analysis gt col manipulation, and add grouping col for collinearity removed subset
bug!: fix switch back to lazy loading of data #76 don't call data(*) after reverting to lazy loading data in ManyEcoEvo::
bug!: upgrade to latest ManyEcoEvo 2.7.3 after fix Table 3.2, 3.4 update table structure #51
Fix Table 3.2, 3.4 update table structure #51 table 3.4
- Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42 update ManyEcoEvo:: to v.2.7.4
- Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42 reinstall ManyEcoEvo:: as prev release did not have correct targets data build
- Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42 update data wrangling and gt table code for tbl-model-summary-stats-ratings-cont
- Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42 update data wrangling and gt table code for tbl-yi-heterogeneity
- Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42 update data wrangling and gt table code for tbl-deviation-rating-estimates
lint: indentation and whitespaces
- bug!: Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42 subset correct object for getting mean deviation values
Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42 check back-transformation on yi euc meta-analysis #63 move plot function creation immediately before call
- bug!: Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42 check back-transformation on yi euc meta-analysis #63 update eucalyptus yi results / viz extraction now that logged model fitting is in ManyEcoEvo::
- Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42 update data extraction for plotting model means from uni_mixed_effects model
- bug: update preregistration deviation section for yi standardisation / transformation check back-transformation on yi euc meta-analysis #63
build!: update to v2.7.5 ManyEcoEvo:: Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42
feat!: Add citations for yi euc transformation prereg deviation check back-transformation on yi euc meta-analysis #63
Add gt::as_raw_html() to end of gt table
bug!: update downstream plotting for yi Euc check back-transformation on yi euc meta-analysis #63
linespacing
bug: extract meta-analytic mean estimates only for Table B1 SM2 Table B1 needs individual term parameters removed #78
feat!: update downstream code after Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42
bug!: correctly return favicon icon for constructed variables included in yi meta-analysis Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42
feat!: don't rerun model fitting + extraction for euc yi, pull from pkg object Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42
feat!: update strip plot labels
remove redundant commented code Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42
bug: suppress dplyr lifecycle warning generated from create_model_workflow()
bug!: update pkg data extraction code Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42
feat!: add separate check and reporting for CI calculation on model selection investigation
bug!: update downstream code for singularity / convergence checking of yi deviation models Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42
bug!: update downstream code for extracting summary stats from yi meta-analysis models Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42
feat!: check that RE CI's can becalculated in Zr analyses
bug!: update convergence / singularity check tables ~ peer-ratings Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42
bug!: update downstream code in fig-yi-deviation-cat-rating Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42
feat!: set names of plots in fig-yi-deviation-cont-rating Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42
bug!: update downstream code in tbl-yi-deviation-model-params Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42
bug!: update downstream code in calc-yi-sorensen-plots Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42
feat!: set names in yi_sorensen_plots Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42
bug!: update downstream code in tbl-deviation-similarity-convergence-singularity-yi Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42
style: update line indentation
bug!: update downstream yi_deviation_RE_plot_ data, plots + captions Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42*
feat!: delete commented out redundant code Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42
bug!: replace all SD_calc with SE_calc cols for semantic accuracy
style: indentation and linespacing
bug: don't replace NA's with TRUE for singularity, only do so for convergence Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42
feat!: update downstream code for reporting model fits Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42
feat: don't replace missing values in model checking report tables with 'no" Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42
bug: multivariate model fit checking analysis should not use 'mixed_effects' as predictor for BT #79 delete redundant unused code
bug: multivariate model fit checking analysis should not use 'mixed_effects' as predictor for BT #79 regenerate model formulas grid with predicor set excluding mixed_model
bug!: delete redundant subsetting on ManyEcoEvo results object Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42
bug!: multivariate model fit checking analysis should not use 'mixed_effects' as predictor for BT #79 update multivar analysis model fitting workflow
bug!: multivariate model fit checking analysis should not use 'mixed_effects' as predictor for BT #79 switch to pulling ManyEcoEvo:: multivariate model fits for reporting
bug!: fix typos
bug!: multivariate model fit checking analysis should not use 'mixed_effects' as predictor for BT #79 Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42 properly calculate and report convergence / singularity for multivar analyses
substitute NA's with empty values in gt tables
line spacing and indentation
use round_pluck() to round values for reporting
linespacing and indentation
bug!: Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42 update model summary metrics table for all yi deviations
bug: fix table formatting, capitalise cat ratings, rm repeated values
bug: check back-transformation on yi euc meta-analysis #63 fix digit / sci formatting
bug!: multivariate model fit checking analysis should not use 'mixed_effects' as predictor for BT #79 add missing function create_model_formulas()
Ensure italicisation matching is correctly string matched
bug: gt tables rm scientific notation, or constrain to only large numbers at least! #65 sci / digit formatting
Hide effect column, and rename group column to random effects in model param reporting
bug: switch to fmt_icon() instead of gtExtras::gt_fa_column()
bug: fix sci formatting in A.2 gt tables rm scientific notation, or constrain to only large numbers at least! #65
gt tables rm scientific notation, or constrain to only large numbers at least! #65 update numeric formatting in table
bug!: Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline #42 correctly subset ManyEcoEvo_viz post-updates and subset in text more succinctly
feat: format yi column in heterogeneity metric data, drop trailing 0 and decimal for 100% values
bug: turn off warning where model can't be found in environment
merge column Effects and Group, rename
bug!: round decimal places using round_pluck()
bug: fix table caption, and format row groups with capitals, italicise sample size
bug!: Fix extra numbers - deletion needed #46 subset for only single number
fix!: Update equation / text in SM2 for yi standardisation #64 update equation explanation.
fix typo
update table formatting with md code for variable names
fix plural typo
rm quarto document author names
fix gt tables rm scientific notation, or constrain to only large numbers at least! #65 scientific / numeric formatting in tables and update indentation
fix Low-priority table caption formatting #1 table caption justificaiton
fix gt tables rm scientific notation, or constrain to only large numbers at least! #65 for C3, C5, C9
fix gt tables rm scientific notation, or constrain to only large numbers at least! #65 table sci notation + p value col name
fix indentation
gt tables rm scientific notation, or constrain to only large numbers at least! #65 relocate Nobs after dataset inline with other tables
gt tables rm scientific notation, or constrain to only large numbers at least! #65 scientific / numeric table formtting fix and italicise column p
update table caption latex formatting and sci notation
-build!: update to latest ManyEcoEvo https://github.com/egouldo/ManyEcoEvo/releases/tag/v2.7.6
- Fix math expressions
Fix Euc variable incorrectly included in Table B2 #81
Fix Euc variable incorrectly included in Table B2 #81
capitalise and italicise 'Eucalyptus' in table caption
wrap math df in \mathit{}
wrap math text in \text{} or \mathit{}
Euc variable incorrectly included in Table B2 #81 ensure excluded analyses aren't counted in dropped yi
Euc variable incorrectly included in Table B2 #81 updates
Fix fig B6 - calculate upper x axis lim dynamically
fix typo
wrap SE and SD in inline math syntax and \text{}
Check have used correct random effect in Deviation ~ Continuous Ratings... #80 update to latest ManyEcoEvo and upgrade all other pkg versions
linting
delete duplicate function creation
Check have used correct random effect in Deviation ~ Continuous Ratings... #80 namespace ManyEcoEvo data call
linespace linting and add namespace
Delete redundant code chunk in this supp mat
Check have used correct random effect in Deviation ~ Continuous Ratings... #80 switch to any_of in case changes in variable name
lint spacing
add set seed
switch to ManyEcoEvo 2.7.6.9004
namespace fn
gt table calls wrap column label equations in gt::md()
fix awk expression
lint spacing
Move markdown caption content out of gt call and into quarto chunk caption
don't leave spaces in chunk name
- update YAML options across all quarto documents
update text formatting
Update text explaining random effects for peer rating models Check have used correct random effect in Deviation ~ Continuous Ratings... #80
update ManyEcoEvo:: renv
update chunk echos in supp mat
fix Check have used correct random effect in Deviation ~ Continuous Ratings... #80 update systematic model checking and rewrite results
rerender manuscript

…yEcoEvo/releases/tag/v2.1.0

…ables

Fix #61 explain yi exclusions

As per issue #26 I have added sorensen and random effects results to this table - note that I haven't been able to check this because I cant seem to run any many analysts stuff on my computer anymore.

see issue #28 I have added the right crossref for this... I couldn't find the placeholder though so it's possible that still exists somewhere

as per #64 updated the equation as suggested dictated by Shinichi (I hope)

As per issue #50 fixed reference not rendering (I hope) by adding the prefix nte- to the name as recommended here https://quarto.org/docs/authoring/cross-references.html#:~:text=To%20cross%2Dreference%20a%20callout,%3A%3A%3A%20%7B%23tip%2Dexample%20. I have not checked as I cant render

added nte- to the reference to the box-weight deviation

fix citation #50

fix for quarto cross-reference not rendering #50

- note that quarto preview ignores the pre-render script, so have inserted source() calls for interactive dev, as per quarto-dev/quarto-cli#4841

but heading separate to note label, so switch to using double hash headers in all .callout boxes

- data is no longer lazy-loaded in ManyEcoEvo

…ctory to project

Update to latest ManyEcoEvo and ensure #50 cross-refs render

bar command

delete old comment

```r remotes::install_github("egouldo/ManyEcoEvo", ref = "50d0fbf") ```

…ption

Ensure that freeze isn't set to false, and that code is echoed and folded in supplementary material documents. link code in html where possible.

egouldo and others added 30 commits July 29, 2024 20:24

#42 rm functions from ManyAnalysts after egouldo/ManyEcoEvo#29

a968e27

rm hack fn since performance:: pkg update, see easystats/performance#605

05dd513

- #42 switch to latest ManyEcoEvo, see https://github.com/egouldo/Man…

11a54bb

…yEcoEvo/releases/tag/v2.1.0

- #42 rm multivariate model code since upgrading ManyEcoEvo

67f618f

- #42 extract updated model object rather than coding in manuscript

375b1e5

switch to round pluck and semantically extract in-text outputs

7c31a81

Fix #61 explain yi exclusions when can't standardize constructed vari…

17e21a7

…ables

explicitly call object from ManyEcoEvo::

88a12c6

Add rm whitespace

4cdbb70

replace explicit arg name call with correct arg name in fit_MA_mv() #44

fd485ce

#61 add fontawesome extensions

2115a02

Merge pull request #62 from egouldo/61-explain-yi-exclusions

fea6e7b

Fix #61 explain yi exclusions

update argument name, see egouldo/ManyEcoEvo#89

74966af

Add library call explicitly

3b0b52a

Update SM3_ExplainingDeviation.qmd

8b5a464

As per issue #26 I have added sorensen and random effects results to this table - note that I haven't been able to check this because I cant seem to run any many analysts stuff on my computer anymore.

update figure crossref

af284dc

see issue #28 I have added the right crossref for this... I couldn't find the placeholder though so it's possible that still exists somewhere

Update equation / text in SM2 for yi standardisation

576d11d

as per #64 updated the equation as suggested dictated by Shinichi (I hope)

fix citation

22b8ae0

added nte- to the reference to the box-weight deviation

Merge pull request #72 from egouldo/hannahsfraser-patch-9-1

f97ed3a

fix citation #50

Merge pull request #71 from egouldo/hannahsfraser-patch-9

c767bb6

fix for quarto cross-reference not rendering #50

add shared functions to pre-render script

7cc8c55

- note that quarto preview ignores the pre-render script, so have inserted source() calls for interactive dev, as per quarto-dev/quarto-cli#4841

#50 box label and cross-ref now renders

2f72697

but heading separate to note label, so switch to using double hash headers in all .callout boxes

fix #73 call data() to load ManyEcoEvo objects

3cd56f7

- data is no longer lazy-loaded in ManyEcoEvo

renv.lock upgrade to current dev ManyEcoEvo (v2.3.0)

d2c9d21

re-render freeze

3171e5b

mv shared functions into shared pre-render script, set execution dire…

a1fb71d

…ctory to project

Merge pull request #75 from egouldo/no-lazy-data-loading

0e87517

Update to latest ManyEcoEvo and ensure #50 cross-refs render

#73 ensure cross-ref renders by adding caption to table.

31412e0

#64 switch to back-slash for

b366680

bar command

egouldo added 26 commits September 14, 2024 15:01

Fix fig B6 - calculate upper x axis lim dynamically

8bdf009

delete old comment

fix typo

200c54b

wrap SE and SD in inline math syntax and \text{}

eacd6c3

#80 update to latest ManyEcoEvo and upgrade all other pkg versions

52a9fae

```r remotes::install_github("egouldo/ManyEcoEvo", ref = "50d0fbf") ```

linting

f99b348

delete duplicate function creation

7f70033

#80 namespace ManyEcoEvo data call

e0ecfe4

linespace linting and add namespace

408d7ac

Delete redundant code chunk in this supp mat

d1b96ec

#80 switch to any_of in case changes in variable name

02c88c8

lint spacing

dc66da5

add set seed

83bcf4f

switch to ManyEcoEvo 2.7.6.9004

f6f75b4

namespace fn

0572b88

gt table calls wrap column label equations in gt::md()

b11b373

fix awk expression

fbf134d

lint spacing

a62c88f

Move markdown caption content out of gt call and into quarto chunk ca…

27c8d85

…ption

don't leave spaces in chunk name

df3d7c6

- update YAML options across all quarto documents

0ce9f2d

Ensure that freeze isn't set to false, and that code is echoed and folded in supplementary material documents. link code in html where possible.

update text formatting

b077395

Update text explaining random effects for peer rating models #80

c088696

update ManyEcoEvo:: renv

f49445b

update chunk echos in supp mat

3e26e84

fix #80 update systematic model checking and rewrite results

1b83b55

rerender manuscript

4f72c2c

egouldo linked an issue Sep 17, 2024 that may be closed by this pull request

gt tables rm scientific notation, or constrain to only large numbers at least! #65

Closed

egouldo merged commit 09c048f into main Sep 17, 2024
1 check passed

egouldo linked an issue Sep 17, 2024 that may be closed by this pull request

Rm analyses that shouldn't be run (BT random effects models) #23

Closed

egouldo deleted the 42-mv-fns-2-pkg branch September 17, 2024 00:11

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Rebuild manuscript #82

Rebuild manuscript #82

egouldo commented Sep 17, 2024

Rebuild manuscript #82

Rebuild manuscript #82

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egouldo commented Sep 17, 2024