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26f87d6
large file is messing with synching, perhaps?
dustinfife Nov 20, 2019
19fb700
post reclone
dustinfife Nov 20, 2019
6aca268
more stuff
dustinfife Nov 20, 2019
0ef04c5
finished running custom bayes
dustinfife Nov 21, 2019
52c69ac
update from computer
dustinfife Nov 21, 2019
061fc4a
first draft of deriving trace plots
dustinfife Nov 21, 2019
1411d28
wrote document explaining overview of project
dustinfife Nov 21, 2019
6e1028f
added description/namespace
dustinfife Nov 25, 2019
a88fc7c
converting to R package, developing tests
dustinfife Nov 25, 2019
ac24e3a
visualize can compare fits between two models
dustinfife Nov 26, 2019
0391791
test plots showing actual factor scores for two models
dustinfife Nov 26, 2019
24f46ab
dinking around and failing...need to extract MCMC output from bayesian
dustinfife Nov 26, 2019
7ebc57e
tidybayes test
dustinfife Nov 27, 2019
cf9bf88
fixed several bugs with visualize.lavaan
dustinfife Nov 27, 2019
1b1cdfc
worked on bayes and failed
dustinfife Nov 27, 2019
d775394
have a good approximation for bayesian trace line
dustinfife Nov 28, 2019
5460dbd
bayesian visualization with jags model
dustinfife Nov 29, 2019
54be6d6
failure
dustinfife Nov 29, 2019
b7b5d2f
reorganized folders and started creating datasets
dustinfife Nov 29, 2019
136f3c0
bayesian estimation with hogwarts data seems to work
dustinfife Nov 29, 2019
5b0f149
ynew and ynew2 were the same (because they were scaled after correcti…
dustinfife Nov 29, 2019
572db74
grumble
dustinfife Dec 1, 2019
8ea7361
loess lines between latent and observed serve as proxies for nonlinea…
dustinfife Dec 2, 2019
8f2ec32
wrapped jags model in visualize function - success!
dustinfife Dec 2, 2019
ea0808a
plot exports
dustinfife Dec 2, 2019
c2fe942
cleaned up the R files in scratch
dustinfife Dec 5, 2019
7d33f81
updating method explanation writeup
dustinfife Dec 12, 2019
706b49d
First draft of document
dustinfife Dec 13, 2019
2cfa564
moved writeup into README
dustinfife Dec 16, 2019
1018886
added .md for github?
dustinfife Dec 16, 2019
84482b9
README wasn't built with cross-referencing
dustinfife Dec 16, 2019
fa275d0
readme wasn't rendering equations
dustinfife Dec 16, 2019
a8e5b28
github doesn't read latex...
dustinfife Dec 16, 2019
ff761fa
asdf
dustinfife Dec 16, 2019
f779d60
trying index.html
dustinfife Dec 16, 2019
7773ba8
a
dustinfife Dec 16, 2019
f65f70b
Final updates to readme before sending to collaborators
dustinfife Dec 17, 2019
22dfa99
exported visualize methods
dustinfife Sep 16, 2020
0e43540
Added ability to subset based on NAMES, instead of numbers
dustinfife Oct 14, 2020
1e0e977
if a dataset had the name "y2", it conflicted with this function
dustinfife Oct 14, 2020
8622783
added get_subset function + tests
dustinfife Oct 21, 2020
aa027e8
finishing fix on variables named y
dustinfife Oct 21, 2020
0c75730
visualize was showing generic model names when comparing models
dustinfife Oct 21, 2020
db6e560
added measurement plots with unit tests
dustinfife Oct 22, 2020
a559dfa
visualize can now do measurement plots
dustinfife Oct 22, 2020
8bac463
added latent variable plots (with automatic flexplot functionality)
dustinfife Oct 22, 2020
4acd6f5
added ability to visualize latents in visualize function
dustinfife Oct 22, 2020
4b3525f
added ability to sort axes for visualize using block modeling
dustinfife Oct 23, 2020
9226335
Create .travis.yml
dustinfife Oct 23, 2020
b6af285
adding codecov
dustinfife Oct 23, 2020
7806d44
Update README.md
dustinfife Oct 23, 2020
2456d64
Update README.md
dustinfife Oct 23, 2020
31cfa21
reran README file
dustinfife Oct 23, 2020
24107b8
Trying to get readme to work....
dustinfife Oct 23, 2020
0b84ada
readme
dustinfife Oct 23, 2020
b7dfcf5
added residual correlation matrix plots
dustinfife Oct 24, 2020
49c343d
Update visualize.lavaan.Rd
dustinfife Oct 24, 2020
e64cddf
r cmd checks (not all taken care of)
dustinfife Oct 24, 2020
3519228
blockmodeling columns wasn't working
dustinfife Oct 26, 2020
8ed8817
diagonals of plots should be RESIDUALS not raw data
dustinfife Oct 26, 2020
46c170d
when observed had NO latents, residual_from_latents errored
dustinfife Oct 26, 2020
8d7f461
unit tests for last error
dustinfife Oct 26, 2020
db91cf7
measurement_plot errored bc it was using names, not indices
dustinfife Oct 28, 2020
56ff11a
when observed was endogenous, latent_plot failed bc it couldn't find …
dustinfife Oct 28, 2020
adf9b20
got stuck on Rubin's pooling rules for the latent variables
dustinfife Oct 28, 2020
e108a6e
latent_plot: changed to crosshairs and added transparency
dustinfife Oct 29, 2020
17ac716
Added documents from our paper
dustinfife Nov 3, 2020
ab1456f
Second round of uploads from the paper
dustinfife Nov 3, 2020
11727a2
ABCT presentation images
dustinfife Nov 3, 2020
58980a3
modifications to ABCT presentation
dustinfife Nov 4, 2020
44972f6
modified measurement_plot to ensure fitting line is last layer
dustinfife Nov 6, 2020
769e3ac
presentation images
dustinfife Nov 6, 2020
1ea8ec6
created implied measurement plots (hastily)
dustinfife Nov 12, 2020
d035eaa
implied measurement seems to work
dustinfife Nov 12, 2020
5f027ca
needed to standardize BOTH latents and observed for lines to line up
dustinfife Nov 12, 2020
7ec496f
ordering implied_measurement by deviation from regression slope
dustinfife Nov 13, 2020
41323de
added ability to limit implied_measurement plots
dustinfife Nov 13, 2020
7f3b811
Added documentation for implied_measurement
dustinfife Nov 13, 2020
ef105a5
allow user to NOT sort by differences in slopes for implied_measurement
dustinfife Nov 13, 2020
82b4987
observed names were set to numbers so produced an error with implied_…
dustinfife Nov 23, 2020
11a3549
Increment version number
dustinfife Nov 23, 2020
ee0eb48
beta_to_flexplot assumed there were endogenous variables
dustinfife Nov 24, 2020
b21b5ed
added error for when there's only one latent variable
dustinfife Nov 24, 2020
b2a96c6
had an error when only one latent plot was produced
dustinfife Nov 24, 2020
86ddc06
finished generating fits
dustinfife Nov 24, 2020
e6155ff
increment version number
dustinfife Nov 24, 2020
5779c57
finalized fitted objects
dustinfife Nov 25, 2020
c93f1f9
20201128a
Nov 28, 2020
f46c8f1
20201129a
Nov 29, 2020
066cc15
20201129b
Nov 29, 2020
aeef4f4
Merge pull request #1 from brunwasser/master
dustinfife Dec 1, 2020
ffe32c9
create flexplavaan object to save on time calculating standard errors
dustinfife Dec 1, 2020
be53d90
added labels to plots for red/blue lines
dustinfife Dec 2, 2020
f947603
remove browser
dustinfife Dec 4, 2020
ffe7b4e
edits on flexplavaan paper
dustinfife Dec 5, 2020
2040ceb
more work on paper
dustinfife Dec 6, 2020
663ebb3
more work on paper
dustinfife Dec 8, 2020
b2ed71e
more paper changes
dustinfife Dec 9, 2020
1273bc1
added documentation for residual_plots
dustinfife Dec 9, 2020
3e8d826
added ability to visually compare models in implied_measurement
dustinfife Dec 9, 2020
d6939d9
debugging implied_measurement
dustinfife Dec 9, 2020
7e2797d
passed tests for implied_measurement
dustinfife Dec 9, 2020
f5ac6be
started working on latent_plot showing multiple graphs
dustinfife Dec 9, 2020
0675027
enable latent_measurement to use flexplavaan object
dustinfife Dec 9, 2020
940f6b7
flexplavaan as a class now passes tests
dustinfife Dec 10, 2020
6edc920
visualize method wasn't specified correctly
dustinfife Dec 11, 2020
09b6406
moved vignette location
dustinfife Dec 11, 2020
3d5aae9
more work on paper
dustinfife Dec 15, 2020
72b2a15
more modifications to flexplavaan document
dustinfife Dec 15, 2020
b2ce394
updates to draft
brunwasser Jan 3, 2021
79ccaa1
Merge pull request #2 from brunwasser/master
dustinfife Jan 6, 2021
7a80ee5
modification to allow steve's changes to work on my machine.
dustinfife Jan 6, 2021
522f032
Update flexplavaan_draft.Rmd
dustinfife Jan 6, 2021
f94f9e8
Updates to applied example & discussion
brunwasser Jan 13, 2021
80fe433
added quick note about modeling blind
dustinfife Jan 20, 2021
6ffcef9
Merge branch 'master' of https://github.com/brunwasser/flexplavaan in…
dustinfife Jan 20, 2021
8d69340
resolved conflicts with Steve's branch
dustinfife Jan 20, 2021
0fb34b8
Merge branch 'brunwasser-master'
dustinfife Jan 20, 2021
f32fb34
Update flexplavaan_draft.Rmd
brunwasser Jan 20, 2021
7ad8838
just-identified
brunwasser Jan 27, 2021
a2b4270
updates 01/29/2021
brunwasser Jan 29, 2021
7289390
steven changes
dustinfife Feb 2, 2021
111c14c
erge branch 'brunwasser-master2'
dustinfife Feb 2, 2021
71c783b
Final edits on first draft
dustinfife Feb 2, 2021
7b0b4ee
Feb 6th text revisions
brunwasser Feb 6, 2021
743c946
Create Merkle.txt
dustinfife Feb 10, 2021
7c78ec8
Post Ed Review Feedback
dustinfife Feb 10, 2021
06a3179
Merge branch 'brunwasser-master'
dustinfife Feb 10, 2021
2647471
Finalized Ed Commentary
dustinfife Feb 10, 2021
b6b5702
Residual plots' text was running off the page
dustinfife Feb 11, 2021
ad12616
FInal edits of flexplavaan before sending to Ed.
dustinfife Feb 11, 2021
1e5f122
Final version of manuscript
dustinfife Feb 19, 2021
50308c8
Replaced README with simplified readme
dustinfife Feb 19, 2021
bdf3579
SubmissionDocuments
dustinfife Feb 19, 2021
54bafb1
Residual plots flipped over/under estimates labels. Also, changed to …
dustinfife Apr 27, 2021
d908d5b
Minor changes to manuscript post review
dustinfife Oct 20, 2021
45e4037
final changes to psych methods manuscript
dustinfife Oct 20, 2021
5cbae1d
final submission to psych methods
dustinfife Oct 22, 2021
b0f9a8f
modifications to prepare for videos
dustinfife Nov 3, 2021
3971317
added ability to use visualize function for measurement/residual plots
dustinfife Nov 3, 2021
31e9a53
There was an error when the user tried to specify an alpha for latent…
dustinfife Nov 3, 2021
b17d054
working on rebuilding tests for macbook
dustinfife Nov 3, 2021
c60d986
all warnings/messages are suppressed in tests
dustinfife Nov 3, 2021
bdf4f49
mid-change on flexplavaan
dustinfife Nov 3, 2021
5fc00ad
plot_scatter_matrix works with simple object
dustinfife Nov 4, 2021
62b5592
not working, but get_subset isn't returning the right variables
dustinfife Nov 4, 2021
42dd55a
creating plot/data/helper model
dustinfife Nov 4, 2021
e60687b
plot isn't needed until specific functions+
dustinfife Nov 4, 2021
1589e70
converted scatterplot matrix functions to methods
dustinfife Nov 4, 2021
abaf94a
simplified set_model_class to fewer arguments for testing
dustinfife Nov 4, 2021
c911948
modified tests because I changed the arguments order
dustinfife Nov 4, 2021
85cbb4b
mid-modification -- tests are passing now
dustinfife Nov 4, 2021
d5e8d43
removing tests from git
dustinfife Nov 4, 2021
9cc246d
organizing R scripts based on plot/helper/data model
dustinfife Nov 5, 2021
c3fa3ad
migrated model_names option to its own function
dustinfife Nov 5, 2021
d0513c4
cleaning up helper functions
dustinfife Nov 5, 2021
0504374
cleaning arguments to visualize functions
dustinfife Nov 5, 2021
cf2d449
mid migration of creating separate modify formula argument
dustinfife Nov 5, 2021
f267326
finished modify_formula option
dustinfife Nov 6, 2021
ce0a7e2
letting modify_formula borrow helper functions
dustinfife Nov 6, 2021
23e4502
all tests are passing
dustinfife Nov 6, 2021
2e920f2
created tests for all data_functions functions
dustinfife Nov 6, 2021
6c40ff4
organizing helper_functions and tests
dustinfife Nov 6, 2021
7da4584
modified the block modeling algorithm
dustinfife Nov 6, 2021
ac6f0a1
removed sna import (because I'm not using blockmodeling anymore)
dustinfife Nov 6, 2021
78f8376
passing tests
dustinfife Nov 6, 2021
4d99cff
cleaned up output for visualize functions
dustinfife Nov 6, 2021
fca422d
changed function "checked_data_has_observed" to be "create_se_for_end…
dustinfife Nov 7, 2021
26bd464
created small datasets for faster testing
dustinfife Nov 7, 2021
2331b8d
created more small objects for testing
dustinfife Nov 7, 2021
f22cf90
Create test-helper_flexplavaan.R
dustinfife Nov 7, 2021
3f59dc9
Update helper_flexplavaan.R
dustinfife Nov 7, 2021
9eac1ac
moved sequencing functions to archive
dustinfife Nov 8, 2021
897fc16
cleaned up plot_diagnostics file
dustinfife Nov 8, 2021
9c475ff
fix links in README
ecmerkle Nov 8, 2021
caddf1b
tests for helper_implied_measurement
dustinfife Nov 9, 2021
70d3971
added plot modifer modify_latent
dustinfife Nov 9, 2021
9ec85e0
added ability to add a smoother modifier
dustinfife Nov 9, 2021
9150bff
implied measurement no longer returns a list of plots
dustinfife Nov 9, 2021
4c7a2a9
added tests for modify_latent and modify_smooth
dustinfife Nov 9, 2021
b0a0fcb
working on getting modify_smooth to work for ggmatrix
dustinfife Nov 9, 2021
efd7cca
modify_smooth now works for ggmatrix
dustinfife Nov 10, 2021
bd1e7a0
if subset wasn't specified, there was an error with visualizing scatt…
dustinfife Nov 10, 2021
c83f3fd
choosing not to sort slopes was making implied_measurement plots look…
dustinfife Nov 10, 2021
afe31bf
implied_measurement was unnecessarily split up
dustinfife Nov 10, 2021
5295464
creating functions to find common latent variables between two models
dustinfife Nov 10, 2021
2c4a483
implied_measurement now works for non-nested models
dustinfife Nov 10, 2021
cdbd2cc
forgot that latent_flexplot needed to be its own function
dustinfife Nov 10, 2021
e8fe96f
added dataset that has no endogenous variables
dustinfife Nov 11, 2021
aab1214
creating helper tests for plot_latent
dustinfife Nov 11, 2021
934ce24
updated the second argument in beta_to_flexplot which caused an error…
dustinfife Nov 11, 2021
84196c3
scatterplot matrix of ddp's wasn't inputting legend correctly
dustinfife Nov 11, 2021
fd941c4
updating tests posts helper_visualize tests
dustinfife Nov 11, 2021
6920384
get_and_checked_names changed its arguments, so I updated it here
dustinfife Nov 11, 2021
4ebfd1b
changed name of tests for plot_latent
dustinfife Nov 11, 2021
9e98480
created one-factor dataset for testing
dustinfife Nov 11, 2021
493cf81
manuscript changes
dustinfife Jan 30, 2022
c338017
Updated description to have a depends for flexplot
dustinfife Jan 30, 2022
77ee932
Merge branch 'master' into cleanup_functions
dustinfife Jan 31, 2022
46a3399
updated vignette based on new stuff
dustinfife Jan 31, 2022
6fca9e8
added dataset with missing values
dustinfife Jan 31, 2022
6480370
added error message if they don't put second model as lavaan object
dustinfife Jan 31, 2022
ab44954
implied measurement wasn't working for single factor models
dustinfife Jan 31, 2022
beb2edc
created/modified datasets for tests
dustinfife Jan 31, 2022
038e0b4
Merge pull request #8 from ecmerkle/master
dustinfife Jan 31, 2022
6421989
visualize didn't work with missing data
dustinfife Feb 2, 2022
0afd74f
subset in visualize function wasn't allowing strings
dustinfife Feb 4, 2022
d6ef28f
When lavaan model has negative variances it can't compute factor scores
dustinfife Jul 29, 2022
ab0ab48
Merge pull request #11 from dustinfife/development
dustinfife Sep 27, 2022
a18ac2b
add timeout option to installation instructions
moritzketzer Dec 19, 2024
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8 changes: 8 additions & 0 deletions .Rbuildignore
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^.*\.Rproj$
^\.Rproj\.user$
writing/
^.*\.csv$
R/scratch/
^codecov\.yml$
R/justidentified.R
^README\.Rmd$
5 changes: 5 additions & 0 deletions .Rbuildignore (1)
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^.*\.Rproj$
^\.Rproj\.user$
writing/
^.*\.csv$
R/scratch/
3 changes: 3 additions & 0 deletions .gitignore
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Expand Up @@ -2,3 +2,6 @@
.Rhistory
.RData
.Ruserdata
*.svg
tests/fits/deps.txt
data/custom_bayes_fit_linear.rds
21 changes: 21 additions & 0 deletions .travis.yml
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language: r
cache: packages
warnings_are_errors: false

r:
- oldrel
- release
- devel

notifications:
email:
on_success: change
on_failure: change

# for codecov
r_packages:
- covr

# only report coverage after build is successful
after_success:
- Rscript -e 'covr::codecov()'
35 changes: 35 additions & 0 deletions DESCRIPTION
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Package: flexplavaan
Title: Visualizing Latent Variable Models Using Flexplot
Version: 0.2.4
Authors@R:
person(given = "Dustin",
family = "Fife",
role = c("aut", "cre"),
email = "[email protected]")
Description: `flexplavaan` is a package designed to visualize latent variable models
with raw data. Basic functionality includes disturbance dependence plots, trail plots,
model-implied plots, and the ability to compare fits between two latent variable models.
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports:
ggplot2,
lavaan,
blavaan,
flexplot,
GGally,
purrr,
dplyr,
semTools,
tidyr,
tibble,
ggforce
Suggests:
MASS,
testthat,
covr,
vdiffr
RoxygenNote: 7.1.2
Depends:
R (>= 2.10),
flexplot
18 changes: 18 additions & 0 deletions NAMESPACE
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# Generated by roxygen2: do not edit by hand

S3method(visualize,flexplavaan)
S3method(visualize,lavaan)
S3method(visualize,runjags)
export(flexplavaan)
export(implied_measurement)
export(measurement_plot)
export(residual_plots)
export(viz_diagnostics)
import(GGally)
import(dplyr)
import(flexplot)
import(ggplot2)
import(lavaan)
import(tidyr)
importFrom(purrr,map)
importFrom(semTools,plausibleValues)
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