Merge branch 'master' of https://github.com/konfound-project/konfound

Author: JihoonChoi26

.DS_Store

@@ -15,3 +15,9 @@
 ^\.github$
 ^codecov\.yml$
 ^CODE_OF_CONDUCT\.md$
+^joss-paper$
+^CRAN-SUBMISSION$
+^doc$
+^Meta$
+^_pkgdown\.yml$
+^pkgdown$

.Rbuildignore

@@ -1,7 +1,6 @@
 # Contributing to konfound
 
 This outlines how to propose a change to konfound.
-For a detailed discussion on contributing to this and other tidyverse packages, please see the [development contributing guide](https://rstd.io/tidy-contrib) and our [code review principles](https://code-review.tidyverse.org/).
 
 ## Fixing typos
 
@@ -11,7 +10,8 @@ You can find the `.R` file that generates the `.Rd` by reading the comment in th
 
 ## Bigger changes
 
-If you want to make a bigger change, it's a good idea to first file an issue and make sure someone from the team agrees that it’s needed. 
+If you want to make a bigger change, it's a good idea to first file an issue to notify the team.
+
 If you’ve found a bug, please file an issue that illustrates the bug with a minimal 
 [reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed).
 See our guide on [how to create a great issue](https://code-review.tidyverse.org/issues/) for more advice.
@@ -23,12 +23,25 @@ You may also wish to contact the development team for bigger changes. Please see
 *   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("konfound-project/konfound", fork = TRUE)`.
 
 *   Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. 
-    If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. 
-*   Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`.
+    If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing.
+    
+*   Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`. This is important: **even for team members, please make commits to branches, first**.
+
+*   Ensure that all checks are passing. You can see this information within your PR (on GitHub). It will say passing or failing, and if failing, you can see what is the cause. If a check is not passing, correct the issue or contact a package maintainer for help.
+
+*   Please run `goodpractice::gp()` to ensure code quality compliance. Some markers from this can justifiably be ignored, whereas others must be addressed. See a discussion [here](https://github.com/konfound-project/konfound/issues/50). Some things to be aware of:
+    * avoiding long code lines (more than 80 characters)
+    * using TRUE and FALSE instead of T and F
+    * using roxygen2 syntax to import specific functions from packages
+    * avoiding functions that are overly complex (i.e., avoiding high cyclomatic complexity)
+ 
+*   For new functions or functionality, write examples and tests to cover the core of the functionality. Aim for 80% or higher test coverage for new functions. Check with `covr::package_coverage()`. 
 
 *   Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser.
     The title of your PR should briefly describe the change.
     The body of your PR should contain `Fixes #issue-number`.
+    
+*   A member of the team will then review your PR.
 
 *  For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style described in <https://style.tidyverse.org/news.html>.
 

.github/CONTRIBUTING.md

@@ -14,7 +14,7 @@ jobs:
           # This should be the path to the paper within your repo.
           paper-path: joss-paper/paper.md
       - name: Upload
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v4
         with:
           name: paper
           # This is the output path where Pandoc will write the compiled

.github/workflows/draft-pdf.yml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/pkgdown.yaml

@@ -18,3 +18,6 @@ notes.md
 table-of-features.xlsx
 .DS_Store
 .DS_Store
+docs
+/doc/
+/Meta/

.gitignore

@@ -0,0 +1,3 @@
+Version: 1.0.2
+Date: 2024-10-17 14:47:16 UTC
+SHA: 24e277cde428c3af5fc3884966c5bb16d0fb46aa

CRAN-SUBMISSION

@@ -1,37 +1,44 @@
 Type: Package
 Package: konfound
 Title: Quantify the Robustness of Causal Inferences
-Version: 0.4.0
+Version: 1.0.3
 Authors@R: c(
     person(c("Joshua", "M"), "Rosenberg", , "jmrosen48@gmail.com", role = c("aut", "cre")),
     person("Ran", "Xu", , "ranxu@msu.edu", role = "ctb"),
     person("Qinyun", "Lin", , "linqinyun1001@gmail.com", role = "ctb"),
     person("Spiro", "Maroulis", , "Spiro.Maroulis@asu.edu", role = "ctb"),
     person("Sarah", "Narvaiz", , "snarvaiz@alum.utk.edu", role = "ctb"),
-    person(c("Kenneth", "A"), "Frank", , "kenfrank@msu.edu", role = "ctb")
+    person(c("Kenneth", "A"), "Frank", , "kenfrank@msu.edu", role = "ctb"),
+    person("Wei", "Wang", , "wwang93@vols.utk.edu", role = "ctb"),
+    person("Yunhe", "Cui", , "yunhe.cui@uconn.edu", role = "ctb"),
+    person("Gaofei", "Zhang", , "gaofei.2.zhang@uconn.edu", role = "ctb"),
+    person("Xuesen", "Cheng", , "chengxu3@msu.edu", role = "ctb"),
+    person("JiHoon", "Choi", , "choijih3@msu.edu", role = "ctb"),
+    person("Guan", "Saw", , "guan.saw@cgu.edu", role = "ctb")
   )
 Description: Statistical methods that quantify the conditions necessary to
     alter inferences, also known as sensitivity analysis, are becoming
     increasingly important to a variety of quantitative sciences. A series
     of recent works, including Frank (2000)
-    <doi:10.1177/0049124100029002001> and Frank et al.  (2013)
+    <doi:10.1177/0049124100029002001> and Frank et al. (2013)
     <doi:10.3102/0162373713493129> extend previous sensitivity analyses by
     considering the characteristics of omitted variables or unobserved
     cases that would change an inference if such variables or cases were
     observed. These analyses generate statements such as "an omitted
     variable would have to be correlated at xx with the predictor of
-    interest (e.g., treatment) and outcome to invalidate an inference of a
+    interest (e.g., the treatment) and outcome to invalidate an inference of a
     treatment effect". Or "one would have to replace pp percent of the
-    observed data with null hypothesis cases to invalidate the inference".
+    observed data with nor which the treatment had no effect to invalidate the 
+    inference".
     We implement these recent developments of sensitivity analysis and
     provide modules to calculate these two robustness indices and generate
     such statements in R. In particular, the functions konfound(),
     pkonfound() and mkonfound() allow users to calculate the robustness of
     inferences for a user's own model, a single published study and
     multiple studies respectively.
 License: MIT + file LICENSE
-URL: https://github.com/jrosen48/konfound
-BugReports: https://github.com/jrosen48/konfound/issues
+URL: https://github.com/konfound-project/konfound, https://konfound-it.org/konfound/
+BugReports: https://github.com/konfound-project/konfound/issues
 Depends: 
     R (>= 2.10)
 Imports: 
@@ -41,27 +48,27 @@ Imports:
     dplyr,
     ggplot2,
     lavaan,
-    mice,
     purrr,
     rlang,
+    tidyr,
+    lme4 (>= 1.1-35.1),
     tibble,
-    tidyr
+    ggrepel,
+    pbkrtest
 Suggests: 
     covr,
     devtools,
     forcats,
-    ggrepel,
     knitr,
-    lme4,
-    margins,
-    pbkrtest,
     rmarkdown,
+    mice,
     roxygen2,
-    testthat
+    testthat,
+    Matrix (>= 1.6-2)
 VignetteBuilder: 
     knitr
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Roxygen: list(roclets = c("collate", "rd", "namespace", 
               "doctest::dt_roclet"), packages = "doctest")

DESCRIPTION

@@ -1,2 +1,2 @@
-YEAR: 2019
-COPYRIGHT HOLDER: Joshua Rosenberg; Ran Xu; Kenneth Frank
+YEAR: 2024
+COPYRIGHT HOLDER: konfound authors

LICENSE

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2019 Joshua Rosenberg; Ran Xu; Kenneth Frank
+Copyright (c) 2024 konfound authors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

LICENSE.md

@@ -1,16 +1,66 @@
 # Generated by roxygen2: do not edit by hand
 
 export(konfound)
-export(launch_shiny)
 export(mkonfound)
 export(pkonfound)
-export(summary.konfound)
+export(tkonfound)
 export(tkonfound_fig)
-import(dplyr)
-import(ggplot2)
-import(lavaan)
-import(rlang)
+importFrom(broom,glance)
+importFrom(broom,tidy)
+importFrom(broom.mixed,tidy)
+importFrom(crayon,bold)
+importFrom(crayon,italic)
+importFrom(crayon,underline)
+importFrom(dplyr,bind_cols)
+importFrom(dplyr,case_when)
+importFrom(dplyr,filter)
+importFrom(dplyr,mutate)
+importFrom(dplyr,pull)
+importFrom(dplyr,rename)
 importFrom(dplyr,select)
-importFrom(rlang,.data)
+importFrom(dplyr,tibble)
+importFrom(ggplot2,aes)
+importFrom(ggplot2,aes_string)
+importFrom(ggplot2,annotate)
+importFrom(ggplot2,element_blank)
+importFrom(ggplot2,element_line)
+importFrom(ggplot2,facet_grid)
+importFrom(ggplot2,geom_col)
+importFrom(ggplot2,geom_curve)
+importFrom(ggplot2,geom_histogram)
+importFrom(ggplot2,geom_hline)
+importFrom(ggplot2,geom_line)
+importFrom(ggplot2,geom_point)
+importFrom(ggplot2,geom_segment)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,ggtitle)
+importFrom(ggplot2,scale_fill_manual)
+importFrom(ggplot2,scale_shape_manual)
+importFrom(ggplot2,scale_x_continuous)
+importFrom(ggplot2,scale_y_continuous)
+importFrom(ggplot2,theme)
+importFrom(ggplot2,theme_bw)
+importFrom(ggplot2,theme_void)
+importFrom(ggplot2,xlab)
+importFrom(ggplot2,ylab)
+importFrom(ggrepel,geom_label_repel)
+importFrom(lavaan,parameterEstimates)
+importFrom(lavaan,sem)
+importFrom(lme4,fixef)
+importFrom(lme4,lmer)
+importFrom(pbkrtest,get_Lb_ddf)
+importFrom(purrr,map2_dfr)
+importFrom(purrr,map_dbl)
+importFrom(purrr,modify_if)
+importFrom(rlang,"!!")
+importFrom(rlang,enquo)
+importFrom(rlang,quo_name)
 importFrom(stats,chisq.test)
+importFrom(stats,cor)
 importFrom(stats,fisher.test)
+importFrom(stats,glm)
+importFrom(stats,pt)
+importFrom(stats,qt)
+importFrom(stats,var)
+importFrom(tidyr,gather)
+importFrom(utils,globalVariables)

Meta/vignette.rds

@@ -1,3 +1,36 @@
+# konfound 1.0.3 (IN DEVELOPMENT)
+
+* fix sign problems in print output for some cases 
+
+# konfound 1.0.2
+
+* edits to README and vignette
+* small edit to DESCRIPTION
+
+# konfound 1.0.1
+
+* minor edits in advance of CRAN submit
+
+# konfound 1.0.0
+
+* major release of changes that were being made in the "newitcv" branch:
+   * Includes option to specify non-zero null hypotheses
+   * Includes option to directly specify threshold for inference
+   * Improved output statements
+   * Includes full raw results for RIR and ITCV
+   * Calculation for unconditional ITCV when possible
+
+# konfound 0.5.1
+
+* minor patch for CRAN
+
+# konfound 0.5.0
+
+* edits in response to JOSS feedback, specifically:
+    * improved testing suite
+    * removal of test_all = TRUE to deal with high cyclomatic complexity
+    * improvement of coding style to be consistent and in accordance with good practice
+
 # konfound 0.4.0
 
 * major updates in advance of initial submission to the R Journal

NAMESPACE

@@ -4,5 +4,5 @@
 #'
 #' @docType data
 #' @name binary_dummy_data
-#' @format A data.frame with 107 rows and 2 variables.
+#' @format A data.frame with 107 rows and 3 variables.
 NULL

NEWS.md

@@ -4,6 +4,8 @@
 #'
 #' @docType data
 #' @name concord1
-#' @references Hamilton, Lawrence C. 1983. Saving water: A causal model of household conservation. Sociological Perspectives 26(4):355-374.
+#' @references Hamilton, Lawrence C. 1983. Saving water: 
+#' A causal model of household conservation. 
+#' Sociological Perspectives 26(4):355-374.
 #' @format A data.frame with 496 rows and 10 variables.
-NULL
+NULL