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Rebuild manuscript #82

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merged 171 commits into from
Sep 17, 2024
Merged

Rebuild manuscript #82

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a968e27
#42 rm functions from ManyAnalysts after https://github.com/egouldo/M…
egouldo Jul 29, 2024
05dd513
rm hack fn since performance:: pkg update, see https://github.com/eas…
egouldo Jul 29, 2024
11a54bb
- #42 switch to latest ManyEcoEvo, see https://github.com/egouldo/Man…
egouldo Jul 31, 2024
67f618f
- #42 rm multivariate model code since upgrading ManyEcoEvo
egouldo Jul 31, 2024
375b1e5
- #42 extract updated model object rather than coding in manuscript
egouldo Jul 31, 2024
7c31a81
switch to round pluck and semantically extract in-text outputs
egouldo Jul 31, 2024
17e21a7
Fix #61 explain yi exclusions when can't standardize constructed vari…
egouldo Aug 5, 2024
88a12c6
explicitly call object from ManyEcoEvo::
egouldo Aug 5, 2024
4cdbb70
Add rm whitespace
egouldo Aug 5, 2024
fd485ce
replace explicit arg name call with correct arg name in fit_MA_mv() #44
egouldo Aug 5, 2024
2115a02
#61 add fontawesome extensions
egouldo Aug 5, 2024
fea6e7b
Merge pull request #62 from egouldo/61-explain-yi-exclusions
egouldo Aug 5, 2024
74966af
update argument name, see https://github.com/egouldo/ManyEcoEvo/issue…
egouldo Aug 7, 2024
3b0b52a
Add library call explicitly
egouldo Aug 7, 2024
8b5a464
Update SM3_ExplainingDeviation.qmd
hannahsfraser Aug 8, 2024
af284dc
update figure crossref
hannahsfraser Aug 8, 2024
576d11d
Update equation / text in SM2 for yi standardisation
hannahsfraser Aug 8, 2024
1c1544a
fix for quarto cross-reference not rendering
hannahsfraser Aug 8, 2024
22b8ae0
fix citation
hannahsfraser Aug 8, 2024
f97ed3a
Merge pull request #72 from egouldo/hannahsfraser-patch-9-1
egouldo Aug 10, 2024
c767bb6
Merge pull request #71 from egouldo/hannahsfraser-patch-9
egouldo Aug 10, 2024
7cc8c55
add shared functions to pre-render script
egouldo Aug 10, 2024
2f72697
#50 box label and cross-ref now renders
egouldo Aug 10, 2024
3cd56f7
fix #73 call data() to load ManyEcoEvo objects
egouldo Aug 10, 2024
d2c9d21
renv.lock upgrade to current dev ManyEcoEvo (v2.3.0)
egouldo Aug 10, 2024
3171e5b
re-render freeze
egouldo Aug 10, 2024
a1fb71d
mv shared functions into shared pre-render script, set execution dire…
egouldo Aug 10, 2024
0e87517
Merge pull request #75 from egouldo/no-lazy-data-loading
egouldo Aug 10, 2024
31412e0
#73 ensure cross-ref renders by adding caption to table.
egouldo Aug 10, 2024
b366680
#64 switch to back-slash for
egouldo Aug 10, 2024
8cfb5c7
#64 add in missing subscript
egouldo Aug 10, 2024
c264b31
#64 re-insert calculation of variance for Zj that was removed
egouldo Aug 10, 2024
aee7c5d
#64 revert filtering of models, and add MA_mod_mv to list to filter out
egouldo Aug 10, 2024
ef78952
#64 permit SD_calc == NA generated on binding with
egouldo Aug 10, 2024
fc854d5
Merge branch '42-mv-fns-2-pkg' into hannahsfraser-patch-3
egouldo Aug 10, 2024
b793938
Merge pull request #66 from egouldo/hannahsfraser-patch-3
egouldo Aug 10, 2024
4cb4dbc
Merge branch '42-mv-fns-2-pkg' into hannahsfraser-patch-8
egouldo Aug 10, 2024
95c138f
Merge pull request #70 from egouldo/hannahsfraser-patch-8
egouldo Aug 10, 2024
ccb06af
Merge branch '42-mv-fns-2-pkg' into hannahsfraser-patch-4-1
egouldo Aug 10, 2024
73daf5f
Merge pull request #67 from egouldo/hannahsfraser-patch-4-1
egouldo Aug 10, 2024
1d62998
source utils.R for previewing
egouldo Aug 12, 2024
d40fe2f
Fix equation alignment, syntax, subscripts
egouldo Aug 12, 2024
7f8e17d
linting, add spaces around `=`
egouldo Sep 1, 2024
6d1fbc7
fix #77 - rm mean value introduced from collinearity analyses that we…
egouldo Sep 1, 2024
00ef777
#77 filter *out*, not *for*!
egouldo Sep 1, 2024
ddb7471
#42 don't re-run broom::tidy now that is in `ManyEcoEvo::`
egouldo Sep 1, 2024
9699fbd
style: lint indentation
egouldo Sep 1, 2024
9688b73
#51 change structure of input data for tables
egouldo Sep 1, 2024
36651f2
#51 remove collinearity analysis gt col manipulation, and add groupin…
egouldo Sep 1, 2024
e7c8bce
bug!: fix #76 don't call `data(*)` after reverting to lazy loading da…
egouldo Sep 1, 2024
01caa42
bug!: upgrade to latest ManyEcoEvo 2.7.3 after fix #51
egouldo Sep 1, 2024
5c12ef7
Fix #51 table 3.4
egouldo Sep 1, 2024
af74156
- #42 update `ManyEcoEvo::` to v.2.7.4
egouldo Sep 2, 2024
9d4d469
- #42 reinstall `ManyEcoEvo::` as prev release did not have correct t…
egouldo Sep 2, 2024
a2f974c
- #42 update data wrangling and gt table code for `tbl-model-summary-…
egouldo Sep 2, 2024
2ae64bf
- #42 update data wrangling and gt table code for `tbl-yi-heterogeneity`
egouldo Sep 2, 2024
6dde962
- #42 update data wrangling and gt table code for `tbl-deviation-rati…
egouldo Sep 2, 2024
23011cc
lint: indentation and whitespaces
egouldo Sep 2, 2024
7f7c9c6
- bug!: #42 subset correct object for getting mean deviation values
egouldo Sep 2, 2024
5cffaca
#42 #63 move plot function creation immediately before call
egouldo Sep 2, 2024
217dc48
- bug!: #42 #63 update eucalyptus yi results / viz extraction now tha…
egouldo Sep 2, 2024
41886b6
- #42 update data extraction for plotting model means from `uni_mixed…
egouldo Sep 2, 2024
8064da7
- bug: update preregistration deviation section for `yi` standardisat…
egouldo Sep 2, 2024
12c3aaf
build!: update to v2.7.5 `ManyEcoEvo::` #42
egouldo Sep 2, 2024
517e266
feat!: Add citations for yi euc transformation prereg deviation #63
egouldo Sep 2, 2024
6bf82bb
Add gt::as_raw_html() to end of gt table
egouldo Sep 2, 2024
bcf3b3a
bug!: update downstream plotting for yi Euc #63
egouldo Sep 2, 2024
225d2f4
linespacing
egouldo Sep 2, 2024
bc0f595
bug: extract meta-analytic mean estimates only for Table B1 #78
egouldo Sep 2, 2024
64c2937
feat!: update downstream code after #42
egouldo Sep 2, 2024
e01cf99
bug!: correctly return favicon icon for constructed variables include…
egouldo Sep 2, 2024
ba802ed
feat!: don't rerun model fitting + extraction for euc yi, pull from p…
egouldo Sep 2, 2024
a53e024
feat!: update strip plot labels
egouldo Sep 2, 2024
2105e2b
remove redundant commented code #42
egouldo Sep 2, 2024
97aa884
bug: suppress dplyr lifecycle warning generated from `create_model_wo…
egouldo Sep 2, 2024
73d54b0
bug!: update pkg data extraction code #42
egouldo Sep 2, 2024
c5eda69
feat!: add separate check and reporting for CI calculation on model s…
egouldo Sep 2, 2024
4aa58b2
bug!: update downstream code for singularity / convergence checking o…
egouldo Sep 2, 2024
ce119b8
bug!: update downstream code for extracting summary stats from yi met…
egouldo Sep 2, 2024
40b4c1c
feat!: check that RE CI's can becalculated in Zr analyses
egouldo Sep 2, 2024
48520d1
bug!: update convergence / singularity check tables ~ peer-ratings #42
egouldo Sep 2, 2024
8c3cdbf
bug!: update downstream code in fig-yi-deviation-cat-rating #42
egouldo Sep 2, 2024
e14400e
feat!: set names of plots in fig-yi-deviation-cont-rating #42
egouldo Sep 2, 2024
bf10918
bug!: update downstream code in tbl-yi-deviation-model-params #42
egouldo Sep 2, 2024
a84e0af
bug!: update downstream code in calc-yi-sorensen-plots #42
egouldo Sep 2, 2024
bcba166
feat!: set names in yi_sorensen_plots #42
egouldo Sep 2, 2024
9d83744
bug!: update downstream code in tbl-deviation-similarity-convergence-…
egouldo Sep 2, 2024
284568c
style: update line indentation
egouldo Sep 2, 2024
e8f9dc1
bug!: update downstream yi_deviation_RE_plot_* data, plots + captions…
egouldo Sep 2, 2024
90d3645
feat!: delete commented out redundant code #42
egouldo Sep 2, 2024
1fc5b7f
bug!: replace all `SD_calc` with `SE_calc` cols for semantic accuracy
egouldo Sep 2, 2024
0662c87
style: indentation and linespacing
egouldo Sep 4, 2024
065154d
bug: don't replace NA's with TRUE for singularity, only do so for con…
egouldo Sep 4, 2024
6354099
feat!: update downstream code for reporting model fits #42
egouldo Sep 4, 2024
42365f8
feat: don't replace missing values in model checking report tables wi…
egouldo Sep 4, 2024
ea647e1
bug: #79 delete redundant unused code
egouldo Sep 4, 2024
d7f1b12
bug: #79 regenerate model formulas grid with predicor set excluding m…
egouldo Sep 4, 2024
06fc2c0
bug!: delete redundant subsetting on ManyEcoEvo results object #42
egouldo Sep 4, 2024
43180bb
bug!: #79 update multivar analysis model fitting workflow
egouldo Sep 4, 2024
ed969f0
bug!: #79 switch to pulling ManyEcoEvo:: multivariate model fits for …
egouldo Sep 4, 2024
dbe9363
bug!: fix typos
egouldo Sep 4, 2024
7f24d5d
bug!: #79 #42 properly calculate and report convergence / singularity…
egouldo Sep 4, 2024
5cc234c
substitute NA's with empty values in gt tables
egouldo Sep 4, 2024
dc914b7
line spacing and indentation
egouldo Sep 4, 2024
824b9c3
use round_pluck() to round values for reporting
egouldo Sep 4, 2024
a78da90
linespacing and indentation
egouldo Sep 4, 2024
0a0031c
bug!: #42 update model summary metrics table for all yi deviations
egouldo Sep 4, 2024
6b6eccd
bug: fix table formatting, capitalise cat ratings, rm repeated values
egouldo Sep 4, 2024
dc024fb
bug: #63 fix digit / sci formatting
egouldo Sep 4, 2024
d050e6f
bug!: #79 add missing function `create_model_formulas()`
egouldo Sep 4, 2024
017eb36
Ensure italicisation matching is correctly string matched
egouldo Sep 4, 2024
c24d0c8
bug: #65 sci / digit formatting
egouldo Sep 4, 2024
f73658f
Hide effect column, and rename group column to random effects in mode…
egouldo Sep 4, 2024
13b6f4a
bug: switch to `fmt_icon()` instead of `gtExtras::gt_fa_column()`
egouldo Sep 4, 2024
5f00d3f
bug: fix sci formatting in A.2 #65
egouldo Sep 4, 2024
cc9fc06
#65 update numeric formatting in table
egouldo Sep 4, 2024
3f1e0ab
bug!: #42 correctly subset ManyEcoEvo_viz post-updates and subset in …
egouldo Sep 4, 2024
6a82b36
feat: format yi column in heterogeneity metric data, drop trailing 0 …
egouldo Sep 4, 2024
a657431
bug: turn off warning where model can't be found in environment
egouldo Sep 4, 2024
c91cfc0
merge column Effects and Group, rename
egouldo Sep 4, 2024
740077b
bug!: round decimal places using `round_pluck()`
egouldo Sep 4, 2024
93dc912
bug: fix table caption, and format row groups with capitals, italicis…
egouldo Sep 4, 2024
4b4611d
bug!: Fix #46 subset for only single number
egouldo Sep 4, 2024
660549f
fix!: #64 update equation explanation.
egouldo Sep 4, 2024
6d33bd9
fix typo
egouldo Sep 4, 2024
b63e358
update table formatting with md code for variable names
egouldo Sep 4, 2024
f531b8e
fix plural typo
egouldo Sep 4, 2024
f0eb4fb
rm quarto document author names
egouldo Sep 4, 2024
0b346a3
fix #65 scientific / numeric formatting in tables and update indentation
egouldo Sep 4, 2024
b4a4b9b
fix #1 table caption justificaiton
egouldo Sep 4, 2024
528e0db
fix #65 for C3, C5, C9
egouldo Sep 4, 2024
0655424
fix #65 table sci notation + p value col name
egouldo Sep 4, 2024
49ebd32
fix indentation
egouldo Sep 4, 2024
434d3f6
#65 relocate Nobs after dataset inline with other tables
egouldo Sep 4, 2024
b2dcd31
#65 scientific / numeric table formtting fix and italicise column p
egouldo Sep 4, 2024
4b7e6bd
update table caption latex formatting and sci notation
egouldo Sep 4, 2024
be0ae12
-build!: update to latest ManyEcoEvo https://github.com/egouldo/ManyE…
egouldo Sep 5, 2024
faa895e
- Fix math expressions
egouldo Sep 14, 2024
eb758d5
Fix #81
egouldo Sep 14, 2024
82f6130
Fix #81
egouldo Sep 14, 2024
d47c107
capitalise and italicise 'Eucalyptus' in table caption
egouldo Sep 14, 2024
cd19df7
wrap math `df` in `\mathit{}`
egouldo Sep 14, 2024
78ac538
wrap math text in `\text{}` or `\mathit{}`
egouldo Sep 14, 2024
98faac4
#81 ensure excluded analyses aren't counted in dropped yi
egouldo Sep 14, 2024
e963054
#81 updates
egouldo Sep 14, 2024
8bdf009
Fix fig B6 - calculate upper x axis lim dynamically
egouldo Sep 14, 2024
200c54b
fix typo
egouldo Sep 14, 2024
eacd6c3
wrap SE and SD in inline math syntax and `\text{}`
egouldo Sep 14, 2024
52a9fae
#80 update to latest ManyEcoEvo and upgrade all other pkg versions
egouldo Sep 16, 2024
f99b348
linting
egouldo Sep 16, 2024
7f70033
delete duplicate function creation
egouldo Sep 16, 2024
e0ecfe4
#80 namespace ManyEcoEvo data call
egouldo Sep 16, 2024
408d7ac
linespace linting and add namespace
egouldo Sep 16, 2024
d1b96ec
Delete redundant code chunk in this supp mat
egouldo Sep 16, 2024
02c88c8
#80 switch to any_of in case changes in variable name
egouldo Sep 16, 2024
dc66da5
lint spacing
egouldo Sep 16, 2024
83bcf4f
add set seed
egouldo Sep 16, 2024
f6f75b4
switch to ManyEcoEvo 2.7.6.9004
egouldo Sep 16, 2024
0572b88
namespace fn
egouldo Sep 16, 2024
b11b373
gt table calls wrap column label equations in `gt::md()`
egouldo Sep 16, 2024
fbf134d
fix awk expression
egouldo Sep 16, 2024
a62c88f
lint spacing
egouldo Sep 16, 2024
27c8d85
Move markdown caption content out of gt call and into quarto chunk ca…
egouldo Sep 16, 2024
df3d7c6
don't leave spaces in chunk name
egouldo Sep 16, 2024
0ce9f2d
- update YAML options across all quarto documents
egouldo Sep 17, 2024
b077395
update text formatting
egouldo Sep 17, 2024
c088696
Update text explaining random effects for peer rating models #80
egouldo Sep 17, 2024
f49445b
update ManyEcoEvo:: renv
egouldo Sep 17, 2024
3e26e84
update chunk echos in supp mat
egouldo Sep 17, 2024
1b83b55
fix #80 update systematic model checking and rewrite results
egouldo Sep 17, 2024
4f72c2c
rerender manuscript
egouldo Sep 17, 2024
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4 changes: 3 additions & 1 deletion .Rprofile
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Original file line number Diff line number Diff line change
@@ -1 +1,3 @@
source("renv/activate.R")
if (Sys.getenv("R_BUILD_CHECK") != "TRUE") {
source("renv/activate.R")
}
7 changes: 7 additions & 0 deletions _extensions/quarto-ext/fontawesome/_extension.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
title: Font Awesome support
author: Carlos Scheidegger
version: 1.1.0
quarto-required: ">=1.2.269"
contributes:
shortcodes:
- fontawesome.lua
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