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make edits to remove import lavaan and import ggplot2 #80

Merged
merged 3 commits into from
Feb 20, 2024
Merged

make edits to remove import lavaan and import ggplot2 #80

merged 3 commits into from
Feb 20, 2024

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jrosen48
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this should address the remaining NAMESPACE issues in #50

@jrosen48 jrosen48 merged commit f499f10 into master Feb 20, 2024
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this should address #50

@jrosen48 jrosen48 deleted the addressing-namespace-issue branch February 20, 2024 19:30
jrosen48 added a commit that referenced this pull request Feb 21, 2024
@jrosen48
edits to the paper and .bib to related to issues 3 and 5 in #80
09c675f
qinyun-lin added a commit that referenced this pull request Mar 19, 2024
@qinyun-lin @jrosen48
@bretsw @wwang93 @olivroy @JihoonChoi26
Newitcv output (#83)
bcc0cf2 
* add missing dois

* Update README.md to include coding team meeting note link

* fix typo in title

* Update README.md

* change default to control group throughout

* fixed formatting issues with output

* Update helper_output_dataframe.R

The default assignment of function parameters retains the value "=", and when assigning values to the columns of the dplyr::tibble I chose to replace the assignment "=" with the value "<-", (this change can be retained or not).

* Update nonlinear_auxiliary.R

The main change comes from the assignment of variables with T changed to "TRUE", not all = changed to <-, the main principle is: function parameter assignment with "=", variable assignment for "<-". "

In addition, for the definition of the matrix "byrow = TRUE" this way usually use "=", instead of the assignment symbol <-. This is a way of passing a function parameter without using the assignment "<-" symbol.

* Update helper_plot_threshold.R

 change“ est_eff = est_eff,
  beta_threshold = beta_threshold”

to
  est_eff <- est_eff,
      beta_threshold <- beta_threshold

* Update test_cop.R

Maintain "=" for function parameter assignments and "<-" for variable assignments.

* Update test_pse.R

 Maintain "=" for function parameter assignments and "<-" for variable assignments.

* Update test_sensitivity_ln.R

T to TRUE;F to FALSE

* Update tkonfound.R

T to TRUE

* Update tkonfound_fig.R

T to TRUE; F to FALSE

* update nrow issue

* add CONTRIBUTING and update README; also change email for JR

* add CONTRIBUTING and update README; also change email for S narvaiz

* fix the bug pkonfound error #64

* fix bug error with thresh_plot output #63

* Update links in DESCRIPTION

* remove rounding in itcv calculation

* work on tests

* move

* minor edits to tests

* to close #65 and to close #70

* add tests

* update docs

* update docs

* update README

* add check badges

* setting covr up again

* undo lme4 edits

trying another approach

* Revert "undo lme4 edits"

This reverts commit 2810fd0.

* update Matrix depends

* update lme4 version

* update README

* edit description

* update tests and docs

* update testing with Qinyun

* get rid of test_all = TRUE

* remove test_all = TRUE

* remove test_all = TRUE

* patch to konfound to address test_all = TRUE error

* add pkgdown action

* address warnings in tests that were due to an unititialized column

* iterate version

* fix minor discrepancy with package name

* continue to update tests, remove unused code

* further enhancing tests

* add badges and update README

* address error in vignette

* remove mention of functionality to call multiple forms of output at once

* address error in mkonfound

* remove calling of multiple forms of output

* remove commented out code

* address NOTES in R CMD CHECK

* add a few more tests

* address note about class(flag_cov)

* work on documentation to address imports issue

* edits to JOSS paper in response to feedback from @fartist and @wjakethompson

* simplify the function test_sensitivity_ln

now almost all calculations are moved to subfunctions in nonlinear_auxiliary

* minor edits to DESCRIPTION, removing aes_string and data_frame to address warnings, and moving print output out of test_sensitivity_ln

* Update helper_output_print.R

round up 'r_con' for ITCV

* Update helper_output_print.R

* Update cop_pse_auxiliary.R（F - FALSE） (#78)

* Update cop_pse_auxiliary.R

* Update cop_pse_auxiliary.R

* Update concord1.R

* Update cop_pse_auxiliary.R

* Update helper_output_print.R

* Update helper_output_dataframe.R

* Update helper_plot_correlation.R

* Update helper_plot_threshold.R

* Update konfound-glm-dichotomous.R

* Update konfound-glm.R

* Update konfound-lm.R

* Update konfound-lmer.R

* Update konfound.R

* Update mkonfound-data.R

* Update mkonfound.R

* Update core-sensitivity-mkonfound.R

* Update pkonfound.R

* Update test_cop.R

* Update test_cop.R

* Update test_pse.R

* Update test_sensitivity.R

* Update test_sensitivity_ln.R

* Update tkonfound.R

* Update tkonfound_fig.R

* Update zzz.R

* Update helper_output_table.R

* Update nonlinear_auxiliary.R

* Update test_cop.R

* Update test_pse.R

* Update test_sensitivity_ln.R

* Update test_pse.R

* Update test_cop.R

* Update cop_pse_auxiliary.R

* Update concord1.R

* Update cop_pse_auxiliary.R

* Update core-sensitivity-mkonfound.R

* Update konfound-glm.R

* Update konfound-lmer.R

* Update mkonfound.R

* Update nonlinear_auxiliary.R

* Update zzz.R

* Update DESCRIPTION

* addressing namespace issue - trying to rewrite the NAMESPACE and docs

* delete dup doc file

* remove glue and lifecycle

* make edits to remove import lavaan and import ggplot2

* remove summary function

* remove summary function to simplify codebase and address remaining NAMESPACE issue

* Update paper.md

* Update paper.bib

* Update paper.bib

* Update paper.bib

* Update paper.bib

* Update paper.bib

* edits to paper.bib to address APA issues

* edits to the paper and .bib to related to issues 3 and 5 in #80

* minor edits to .bib

* Update CONTRIBUTING.md

* a few more edits to address formatting issues with the paper

* a few more minor edits to the paper after viewing the rendered PDF

* update README to link to CONTRIBUTING.md and minor edits to paper.md based on Ken's feedback

* Update helper_output_print.R

* Update CONTRIBUTING.md

* edits to paper.bib and paper.md in response to request from @fabian-s: openjournals/joss-reviews#5779 (comment)

* minor edit to .bib

* additional edits to .bib

* fix bug when single predictor and test_all == T

* minor copy edits to paper

* Update helper_output_print.R

* a few more edits in response to Ken's feedback

* Update test_sensitivity_ln.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* remove mice and tibble as they are not used

* Revert "remove mice and tibble as they are not used"

This reverts commit 16cad9f.

* updates to links

* add Wei to DESCRIPTION, remove unused license

* edit license

* rename license

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update konfound-lm.R

* Update konfound-lm.R

* Update konfound-lm.R

* Update konfound-lm.R

* Update konfound-lm.R

* Update helper_output_print.R

* edits in response to @fabian-s feedback on the paper

* Update helper_output_print.R

* Update helper_output_print.R

* Update helper_output_print.R

* Update test_sensitivity_ln.R

* Update test_sensitivity_ln.R

* Update test_sensitivity_ln.R

* Update test_sensitivity_ln.R

* super small edit to the paper - changing &beta so it appears correctly as β

* fix the bug when est_eff_start = 0 and needtworows

fix the bug when est_eff_start = 0 and needtworows

* update URL in README

* update urls

* CRAN submission

* Update CONTRIBUTING.md

* Update konfound.R

revised warning message for non-linear model in konfound

* update testing

no errors now in devtools::check()

* Revert "Merge branch 'master' into newitcv_output"

This reverts commit fc199f7, reversing
changes made to 04fbc43.

---------

Co-authored-by: jrosen48 <jmrosen48@gmail.com>
Co-authored-by: Bret Staudt Willet <bret.staudt.willet@gmail.com>
Co-authored-by: wwang93 <142034236+wwang93@users.noreply.github.com>
Co-authored-by: Joshua Rosenberg <jmrosenberg@utk.edu>
Co-authored-by: olivroy <52606734+olivroy@users.noreply.github.com>
Co-authored-by: Jihoon_Choi <50298939+JihoonChoi26@users.noreply.github.com>
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