From f156137afbfaf49833a43876d077f000da4ed398 Mon Sep 17 00:00:00 2001 From: Nima Hejazi Date: Sat, 13 Mar 2021 14:45:48 -0800 Subject: [PATCH 1/4] bump version; add DOI; fix txshift dep --- DESCRIPTION | 24 ++++++++++----------- README.Rmd | 19 ++++++++++++++++ inst/CITATION | 2 +- man/LF_shift.Rd | 4 +++- man/Param_MSM_linear.Rd | 4 +++- tests/testthat/test-shift_additive_simple.R | 4 ++-- 6 files changed, 39 insertions(+), 18 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index ab64d24..54a8c36 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: tmle3shift Title: Targeted Learning of the Causal Effects of Stochastic Interventions -Version: 0.1.9 +Version: 0.2.0 Authors@R: c( person("Nima", "Hejazi", email = "nh@nimahejazi.org", role = c("aut", "cre", "cph"), @@ -18,10 +18,10 @@ Description: Targeted maximum likelihood estimation (TMLE) of population-level variable importance analyses. Tools are provided for TML estimation of the counterfactual mean under a stochastic intervention characterized as a modified treatment policy, such as treatment policies that shift the natural - value of the exposure. The methodology implemented was first - described by I. Díaz and M.J. van der Laan (2013; - ) and expanded upon in I. Díaz and - M.J. van der Laan (2018). + value of the exposure. The causal parameter and estimation were described in + Díaz and van der Laan (2013) and an + improved estimation approach was given by Díaz and van der Laan (2018) + . Depends: R (>= 3.4.0) License: GPL-3 @@ -31,7 +31,7 @@ Imports: methods, data.table, assertthat, - tmle3 + tmle3 (>= 0.2.0) Suggests: testthat, knitr, @@ -39,24 +39,22 @@ Suggests: covr, stats, ggplot2, - sl3 (>= 1.3.7), - txshift (>= 0.3.1), + sl3 (>= 1.4.2), + txshift (>= 0.3.5), haldensify (>= 0.0.5), hal9001, xgboost, ranger, Rsolnp, - nnls, + nnls Remotes: github::tlverse/sl3, - github::tlverse/tmle3@devel, - github::nhejazi/haldensify, - github::nhejazi/txshift + github::tlverse/tmle3 URL: https://tlverse.org/tmle3shift BugReports: https://github.com/tlverse/tmle3shift/issues Encoding: UTF-8 LazyData: true LazyLoad: yes VignetteBuilder: knitr -RoxygenNote: 7.0.2 +RoxygenNote: 7.1.1 Roxygen: list(markdown = TRUE, r6 = FALSE) diff --git a/README.Rmd b/README.Rmd index f6c7eb0..d947620 100644 --- a/README.Rmd +++ b/README.Rmd @@ -21,6 +21,7 @@ knitr::opts_chunk$set( [![Coverage Status](https://img.shields.io/codecov/c/github/tlverse/tmle3shift/master.svg)](https://codecov.io/github/tlverse/tmle3shift?branch=master) [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](http://www.gnu.org/licenses/gpl-3.0) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4603372.svg)](https://doi.org/10.5281/zenodo.4603372) > Targeted Learning of the Causal Effects of Stochastic Interventions @@ -75,6 +76,24 @@ issue](https://github.com/tlverse/tmle3shift/issues). --- +## Citation + +After using the `tmle3shift` R package, please cite the following: + + @software{hejazi2021tmle3shift-rpkg, + author = {Hejazi, Nima S and Coyle, Jeremy R and {van der Laan}, Mark + J}, + title = {{tmle3shift}: {Targeted Learning} of the Causal Effects of + Stochastic Interventions}, + year = {2021}, + howpublished = {\url{https://github.com/tlverse/tmle3shift}}, + note = {{R} package version 0.2.0}, + url = {https://doi.org/10.5281/zenodo.4603372}, + doi = {10.5281/zenodo.4603372} + } + +--- + ## Related * [R/`txshift`](https://github.com/nhejazi/txshift) - An R package providing an diff --git a/inst/CITATION b/inst/CITATION index 5fdc3e8..aab5dff 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -12,5 +12,5 @@ bibentry(bibtype = "Manual", person("Mark", "van der Laan", "J")), year = year, note = note, - doi = "", + doi = "10.5281/zenodo.4603372", url = "https://github.com/tlverse/tmle3shift") diff --git a/man/LF_shift.Rd b/man/LF_shift.Rd index 0c6ac54..31b39ec 100644 --- a/man/LF_shift.Rd +++ b/man/LF_shift.Rd @@ -3,7 +3,9 @@ \name{LF_shift} \alias{LF_shift} \title{Shifted Likelihood Factor} -\format{\code{\link{R6Class}} object.} +\format{ +\code{\link{R6Class}} object. +} \value{ \code{LF_base} object } diff --git a/man/Param_MSM_linear.Rd b/man/Param_MSM_linear.Rd index d42fbdd..9cc99c3 100644 --- a/man/Param_MSM_linear.Rd +++ b/man/Param_MSM_linear.Rd @@ -3,7 +3,9 @@ \name{Param_MSM_linear} \alias{Param_MSM_linear} \title{Parameter for Linear Working Marginal Structural Model} -\format{\code{\link{R6Class}} object.} +\format{ +\code{\link{R6Class}} object. +} \value{ \code{Param_base} object } diff --git a/tests/testthat/test-shift_additive_simple.R b/tests/testthat/test-shift_additive_simple.R index f3c5e33..ca3e2f3 100644 --- a/tests/testthat/test-shift_additive_simple.R +++ b/tests/testthat/test-shift_additive_simple.R @@ -87,9 +87,9 @@ txshift_sl_tmle <- txshift( W = W, A = A, Y = Y, delta = delta_value, fluctuation = "standard", - g_fit_args = list( + g_exp_fit_args = list( fit_type = "sl", - sl_learners = g_learner + sl_learners_density = g_learner ), Q_fit_args = list( fit_type = "sl", From fd80fb266dc5c50d0f5de12291c17f5d855325bb Mon Sep 17 00:00:00 2001 From: Nima Hejazi Date: Sat, 13 Mar 2021 14:48:37 -0800 Subject: [PATCH 2/4] update CI deps + rebuild pkgdown --- .travis.yml | 2 +- README.md | 38 +- appveyor.yml | 5 +- docs/404.html | 34 +- docs/LICENSE-text.html | 34 +- docs/articles/index.html | 38 +- docs/articles/shift_tmle.html | 246 +++++--- docs/articles/vimshift.html | 586 +++++++++++++----- docs/authors.html | 45 +- docs/bootstrap-toc.css | 60 ++ docs/bootstrap-toc.js | 159 +++++ docs/index.html | 87 +-- docs/news/index.html | 77 ++- docs/pkgdown.css | 125 +++- docs/pkgdown.js | 5 - docs/pkgdown.yml | 5 +- docs/reference/LF_shift.html | 51 +- docs/reference/Param_MSM_linear.html | 48 +- docs/reference/additive_shifting.html | 50 +- docs/reference/additive_shifting_bounded.html | 86 +-- docs/reference/index.html | 42 +- docs/reference/msm_linear_factory.html | 43 +- docs/reference/tmle3_Spec_shift.html | 40 +- docs/reference/tmle3_Spec_vimshift_delta.html | 40 +- docs/reference/tmle3_Spec_vimshift_msm.html | 40 +- docs/reference/tmle_shift.html | 55 +- docs/reference/tmle_vimshift_delta.html | 57 +- docs/reference/tmle_vimshift_msm.html | 57 +- docs/reference/trend_msm.html | 53 +- 29 files changed, 1472 insertions(+), 736 deletions(-) create mode 100644 docs/bootstrap-toc.css create mode 100644 docs/bootstrap-toc.js diff --git a/.travis.yml b/.travis.yml index 92359f6..1bcef69 100644 --- a/.travis.yml +++ b/.travis.yml @@ -30,13 +30,13 @@ r_packages: - delayed - origami - hal9001 + - haldensify r_github_packages: - r-lib/covr - r-lib/sessioninfo - tlverse/sl3 - tlverse/tmle3 - - nhejazi/haldensify - nhejazi/txshift after_success: diff --git a/README.md b/README.md index 8f2fa8e..4e60441 100644 --- a/README.md +++ b/README.md @@ -14,6 +14,7 @@ state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](http://www.gnu.org/licenses/gpl-3.0) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4603372.svg)](https://doi.org/10.5281/zenodo.4603372) > Targeted Learning of the Causal Effects of Stochastic Interventions @@ -34,11 +35,12 @@ builds upon the core `tlverse` grammar introduced by `tmle3`, a general framework that supports the implementation of a range of TMLE parameters through a unified interface. For a detailed description of the target parameter, TML estimator, and algorithm implemented in `tmle3shift`, the -interested reader is invited to consult Díaz and van der Laan (2012) and -Díaz and van der Laan (2018). For a general discussion of the framework -of targeted minimum loss-based estimation and the role this methodology -plays in statistical and causal inference, the canonical references are -van der Laan and Rose (2011) and van der Laan and Rose (2018). +interested reader is invited to consult Dı́az and van der Laan (2012) +and Dı́az and van der Laan (2018). For a general discussion of the +framework of targeted minimum loss-based estimation and the role this +methodology plays in statistical and causal inference, the canonical +references are van der Laan and Rose (2011) and van der Laan and Rose +(2018). Building on the original work surrounding the TML estimator for the aforementioned target parameter, `tmle3shift` additionally implements a @@ -70,6 +72,26 @@ If you encounter any bugs or have any specific feature requests, please ----- +## Citation + +After using the `tmle3shift` R package, please cite the following: + +``` + @software{hejazi2021tmle3shift-rpkg, + author = {Hejazi, Nima S and Coyle, Jeremy R and {van der Laan}, Mark + J}, + title = {{tmle3shift}: {Targeted Learning} of the Causal Effects of + Stochastic Interventions}, + year = {2021}, + howpublished = {\url{https://github.com/tlverse/tmle3shift}}, + note = {{R} package version 0.2.0}, + url = {https://doi.org/10.5281/zenodo.4603372}, + doi = {10.5281/zenodo.4603372} + } +``` + +----- + ## Related - [R/`txshift`](https://github.com/nhejazi/txshift) - An R package @@ -100,9 +122,9 @@ See file `LICENSE` for details.
-Díaz, Iván, and Mark J van der Laan. 2012. “Population Intervention -Causal Effects Based on Stochastic Interventions.” *Biometrics* 68 (2). -Wiley Online Library: 541–49. +Dı́az, Iván, and Mark J van der Laan. 2012. “Population Intervention +Causal Effects Based on Stochastic Interventions.” *Biometrics* 68 (2): +541–49.
diff --git a/appveyor.yml b/appveyor.yml index f559c53..0029570 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -36,9 +36,8 @@ build_script: - echo Current directory=%CD% - travis-tool.sh install_r base64 - travis-tool.sh install_github r-lib/sessioninfo r-lib/covr - - travis-tool.sh install_github tlverse/delayed tlverse/origami - - travis-tool.sh install_github tlverse/hal9001 tlverse/sl3 tlverse/tmle3 - - travis-tool.sh install_github nhejazi/haldensify nhejazi/txshift + - travis-tool.sh install_github tlverse/sl3 tlverse/tmle3 + - travis-tool.sh install_github nhejazi/txshift - travis-tool.sh install_deps test_script: diff --git a/docs/404.html b/docs/404.html index 4ddf723..407e0c5 100644 --- a/docs/404.html +++ b/docs/404.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -63,7 +67,7 @@ - +
@@ -102,7 +106,7 @@
  • - +
    • @@ -126,6 +130,12 @@

    Page not found (404)

+ + @@ -136,7 +146,7 @@

Page not found (404)

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 3899ab8..1219c0d 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -63,7 +67,7 @@ - +
@@ -102,7 +106,7 @@
  • - +
    • @@ -800,6 +804,12 @@

    License

+ + @@ -810,7 +820,7 @@

License

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/articles/index.html b/docs/articles/index.html index 98a058e..8459266 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -63,7 +67,7 @@ - +
@@ -102,7 +106,7 @@
@@ -141,7 +147,7 @@

All vignettes

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/articles/shift_tmle.html b/docs/articles/shift_tmle.html index e82dece..a7b3935 100644 --- a/docs/articles/shift_tmle.html +++ b/docs/articles/shift_tmle.html @@ -6,13 +6,13 @@ Targeted Learning with Stochastic Treatment Regimes • tmle3shift - - - - + + + + + - - + - - - + + + + + - - + - + - + - + + + + + - - + + - + - - + + @@ -63,7 +67,7 @@ - +
@@ -102,7 +106,7 @@
  • - +
    • @@ -120,18 +124,19 @@

    Citation

    - + Source: inst/CITATION
    -

    Hejazi NS, Coyle JR, van der Laan MJ (2020). +

    Hejazi NS, Coyle JR, van der Laan MJ (2021). tmle3shift: Targeted Learning of the Causal Effects of Stochastic Interventions. -R package version 0.1.9, https://github.com/tlverse/tmle3shift. +doi: 10.5281/zenodo.4603372, R package version 0.2.0, https://github.com/tlverse/tmle3shift. 

    @Manual{,
   title = {{tmle3shift}: Targeted Learning of the Causal Effects of Stochastic Interventions},
   author = {Nima S Hejazi and Jeremy R Coyle and Mark J {van der Laan}},
-  year = {2020},
-  note = {R package version 0.1.9},
+  year = {2021},
+  note = {R package version 0.2.0},
+  doi = {10.5281/zenodo.4603372},
   url = {https://github.com/tlverse/tmle3shift},
 }
    @@ -141,15 +146,15 @@

    Authors

    • -

      Nima Hejazi. Author, maintainer, copyright holder. ORCID +

      Nima Hejazi. Author, maintainer, copyright holder.

    • -

      Jeremy Coyle. Author. ORCID +

      Jeremy Coyle. Author.

    • -

      Mark van der Laan. Author, thesis advisor. ORCID +

      Mark van der Laan. Author, thesis advisor.

    @@ -166,7 +171,7 @@

    Authors

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.6.1.

    diff --git a/docs/bootstrap-toc.css b/docs/bootstrap-toc.css new file mode 100644 index 0000000..5a85941 --- /dev/null +++ b/docs/bootstrap-toc.css @@ -0,0 +1,60 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ + +/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */ + +/* All levels of nav */ +nav[data-toggle='toc'] .nav > li > a { + display: block; + padding: 4px 20px; + font-size: 13px; + font-weight: 500; + color: #767676; +} +nav[data-toggle='toc'] .nav > li > a:hover, +nav[data-toggle='toc'] .nav > li > a:focus { + padding-left: 19px; + color: #563d7c; + text-decoration: none; + background-color: transparent; + border-left: 1px solid #563d7c; +} +nav[data-toggle='toc'] .nav > .active > a, +nav[data-toggle='toc'] .nav > .active:hover > a, +nav[data-toggle='toc'] .nav > .active:focus > a { + padding-left: 18px; + font-weight: bold; + color: #563d7c; + background-color: transparent; + border-left: 2px solid #563d7c; +} + +/* Nav: second level (shown on .active) */ +nav[data-toggle='toc'] .nav .nav { + display: none; /* Hide by default, but at >768px, show it */ + padding-bottom: 10px; +} +nav[data-toggle='toc'] .nav .nav > li > a { + padding-top: 1px; + padding-bottom: 1px; + padding-left: 30px; + font-size: 12px; + font-weight: normal; +} +nav[data-toggle='toc'] .nav .nav > li > a:hover, +nav[data-toggle='toc'] .nav .nav > li > a:focus { + padding-left: 29px; +} +nav[data-toggle='toc'] .nav .nav > .active > a, +nav[data-toggle='toc'] .nav .nav > .active:hover > a, +nav[data-toggle='toc'] .nav .nav > .active:focus > a { + padding-left: 28px; + font-weight: 500; +} + +/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */ +nav[data-toggle='toc'] .nav > .active > ul { + display: block; +} diff --git a/docs/bootstrap-toc.js b/docs/bootstrap-toc.js new file mode 100644 index 0000000..1cdd573 --- /dev/null +++ b/docs/bootstrap-toc.js @@ -0,0 +1,159 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ +(function() { + 'use strict'; + + window.Toc = { + helpers: { + // return all matching elements in the set, or their descendants + findOrFilter: function($el, selector) { + // http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/ + // http://stackoverflow.com/a/12731439/358804 + var $descendants = $el.find(selector); + return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])'); + }, + + generateUniqueIdBase: function(el) { + var text = $(el).text(); + var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-'); + return anchor || el.tagName.toLowerCase(); + }, + + generateUniqueId: function(el) { + var anchorBase = this.generateUniqueIdBase(el); + for (var i = 0; ; i++) { + var anchor = anchorBase; + if (i > 0) { + // add suffix + anchor += '-' + i; + } + // check if ID already exists + if (!document.getElementById(anchor)) { + return anchor; + } + } + }, + + generateAnchor: function(el) { + if (el.id) { + return el.id; + } else { + var anchor = this.generateUniqueId(el); + el.id = anchor; + return anchor; + } + }, + + createNavList: function() { + return $('
      '); + }, + + createChildNavList: function($parent) { + var $childList = this.createNavList(); + $parent.append($childList); + return $childList; + }, + + generateNavEl: function(anchor, text) { + var $a = $(''); + $a.attr('href', '#' + anchor); + $a.text(text); + var $li = $('
    • '); + $li.append($a); + return $li; + }, + + generateNavItem: function(headingEl) { + var anchor = this.generateAnchor(headingEl); + var $heading = $(headingEl); + var text = $heading.data('toc-text') || $heading.text(); + return this.generateNavEl(anchor, text); + }, + + // Find the first heading level (`

      `, then `

      `, etc.) that has more than one element. Defaults to 1 (for `

      `). + getTopLevel: function($scope) { + for (var i = 1; i <= 6; i++) { + var $headings = this.findOrFilter($scope, 'h' + i); + if ($headings.length > 1) { + return i; + } + } + + return 1; + }, + + // returns the elements for the top level, and the next below it + getHeadings: function($scope, topLevel) { + var topSelector = 'h' + topLevel; + + var secondaryLevel = topLevel + 1; + var secondarySelector = 'h' + secondaryLevel; + + return this.findOrFilter($scope, topSelector + ',' + secondarySelector); + }, + + getNavLevel: function(el) { + return parseInt(el.tagName.charAt(1), 10); + }, + + populateNav: function($topContext, topLevel, $headings) { + var $context = $topContext; + var $prevNav; + + var helpers = this; + $headings.each(function(i, el) { + var $newNav = helpers.generateNavItem(el); + var navLevel = helpers.getNavLevel(el); + + // determine the proper $context + if (navLevel === topLevel) { + // use top level + $context = $topContext; + } else if ($prevNav && $context === $topContext) { + // create a new level of the tree and switch to it + $context = helpers.createChildNavList($prevNav); + } // else use the current $context + + $context.append($newNav); + + $prevNav = $newNav; + }); + }, + + parseOps: function(arg) { + var opts; + if (arg.jquery) { + opts = { + $nav: arg + }; + } else { + opts = arg; + } + opts.$scope = opts.$scope || $(document.body); + return opts; + } + }, + + // accepts a jQuery object, or an options object + init: function(opts) { + opts = this.helpers.parseOps(opts); + + // ensure that the data attribute is in place for styling + opts.$nav.attr('data-toggle', 'toc'); + + var $topContext = this.helpers.createChildNavList(opts.$nav); + var topLevel = this.helpers.getTopLevel(opts.$scope); + var $headings = this.helpers.getHeadings(opts.$scope, topLevel); + this.helpers.populateNav($topContext, topLevel, $headings); + } + }; + + $(function() { + $('nav[data-toggle="toc"]').each(function(i, el) { + var $nav = $(el); + Toc.init($nav); + }); + }); +})(); diff --git a/docs/index.html b/docs/index.html index c24cc55..cc55c98 100644 --- a/docs/index.html +++ b/docs/index.html @@ -6,21 +6,21 @@ Targeted Learning of the Causal Effects of Stochastic Interventions • tmle3shift - - - - + + + + + - + value of the exposure. The causal parameter and estimation were described in + Díaz and van der Laan (2013) <doi:10.1111/j.1541-0420.2011.01685.x> and an + improved estimation approach was given by Díaz and van der Laan (2018) + <doi:10.1007/978-3-319-65304-4_14>."> - + - + - + + + + + - - + + - + - - + + @@ -63,7 +67,7 @@ - +
      @@ -102,7 +106,7 @@
      • - +
        • @@ -119,13 +123,13 @@
        -

        Changelog

        - +

        Changelog

        + Source: NEWS.md
        -
        -

        -tmle3shift 0.1.9

        +
        +

        +tmle3shift 0.1.9

        • Change Spec_shift object to use point treatment helpers from tmle3.
        • Support missing data functionality based on updates to tmle3.
          • @@ -133,26 +137,26 @@

        • Remove reliance on Lrnr_rfcde since package appears unstable.

        -
        -

        -tmle3shift 0.1.8

        +
        +

        +tmle3shift 0.1.8

        • Change default for MSMs to use identity-based weighting over variance-based, improving stability of estimates.
        • Bug fixes for cross-validation: cv_fold -> fold_number.
        -
        -

        -tmle3shift 0.1.7

        +
        +

        +tmle3shift 0.1.7

        • Addition of cvtmle = TRUE in Updater objects as the default.
        • Bug fixes to bounding of conditional densities at the natural exposure value.
        • Tweaks to cvtmle option and fold_number argument to match tmle3 updates.
        -
        -

        -tmle3shift 0.1.6

        +
        +

        +tmle3shift 0.1.6

        • Addition of HAL-based conditional density estimation as an option.
        • Addition of random forest-based conditional density estimation as an option.
          • @@ -161,26 +165,19 @@

        • Minor bug fixes, including to vignettes.

        -
        -

        -tmle3shift 0.1.5

        +
        +

        +tmle3shift 0.1.5

        • An initial stable release of the package.
        - @@ -192,7 +189,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.

        +

        Site built with pkgdown 1.6.1.

        diff --git a/docs/pkgdown.css b/docs/pkgdown.css index 9145958..1273238 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -17,6 +17,10 @@ html, body { height: 100%; } +body { + position: relative; +} + body > .container { display: flex; height: 100%; @@ -67,6 +71,10 @@ summary { margin-top: calc(-60px + 1em); } +dd { + margin-left: 3em; +} + /* Section anchors ---------------------------------*/ a.anchor { @@ -100,29 +108,132 @@ a.anchor { margin-top: -40px; } +/* Navbar submenu --------------------------*/ + +.dropdown-submenu { + position: relative; +} + +.dropdown-submenu>.dropdown-menu { + top: 0; + left: 100%; + margin-top: -6px; + margin-left: -1px; + border-radius: 0 6px 6px 6px; +} + +.dropdown-submenu:hover>.dropdown-menu { + display: block; +} + +.dropdown-submenu>a:after { + display: block; + content: " "; + float: right; + width: 0; + height: 0; + border-color: transparent; + border-style: solid; + border-width: 5px 0 5px 5px; + border-left-color: #cccccc; + margin-top: 5px; + margin-right: -10px; +} + +.dropdown-submenu:hover>a:after { + border-left-color: #ffffff; +} + +.dropdown-submenu.pull-left { + float: none; +} + +.dropdown-submenu.pull-left>.dropdown-menu { + left: -100%; + margin-left: 10px; + border-radius: 6px 0 6px 6px; +} + /* Sidebar --------------------------*/ -#sidebar { +#pkgdown-sidebar { margin-top: 30px; position: -webkit-sticky; position: sticky; top: 70px; } -#sidebar h2 { + +#pkgdown-sidebar h2 { font-size: 1.5em; margin-top: 1em; } -#sidebar h2:first-child { +#pkgdown-sidebar h2:first-child { margin-top: 0; } -#sidebar .list-unstyled li { +#pkgdown-sidebar .list-unstyled li { margin-bottom: 0.5em; } +/* bootstrap-toc tweaks ------------------------------------------------------*/ + +/* All levels of nav */ + +nav[data-toggle='toc'] .nav > li > a { + padding: 4px 20px 4px 6px; + font-size: 1.5rem; + font-weight: 400; + color: inherit; +} + +nav[data-toggle='toc'] .nav > li > a:hover, +nav[data-toggle='toc'] .nav > li > a:focus { + padding-left: 5px; + color: inherit; + border-left: 1px solid #878787; +} + +nav[data-toggle='toc'] .nav > .active > a, +nav[data-toggle='toc'] .nav > .active:hover > a, +nav[data-toggle='toc'] .nav > .active:focus > a { + padding-left: 5px; + font-size: 1.5rem; + font-weight: 400; + color: inherit; + border-left: 2px solid #878787; +} + +/* Nav: second level (shown on .active) */ + +nav[data-toggle='toc'] .nav .nav { + display: none; /* Hide by default, but at >768px, show it */ + padding-bottom: 10px; +} + +nav[data-toggle='toc'] .nav .nav > li > a { + padding-left: 16px; + font-size: 1.35rem; +} + +nav[data-toggle='toc'] .nav .nav > li > a:hover, +nav[data-toggle='toc'] .nav .nav > li > a:focus { + padding-left: 15px; +} + +nav[data-toggle='toc'] .nav .nav > .active > a, +nav[data-toggle='toc'] .nav .nav > .active:hover > a, +nav[data-toggle='toc'] .nav .nav > .active:focus > a { + padding-left: 15px; + font-weight: 500; + font-size: 1.35rem; +} + +/* orcid ------------------------------------------------------------------- */ + .orcid { - height: 16px; + font-size: 16px; + color: #A6CE39; /* margins are required by official ORCID trademark and display guidelines */ margin-left:4px; margin-right:4px; @@ -133,14 +244,14 @@ a.anchor { .ref-index th {font-weight: normal;} -.ref-index td {vertical-align: top;} +.ref-index td {vertical-align: top; min-width: 100px} .ref-index .icon {width: 40px;} .ref-index .alias {width: 40%;} .ref-index-icons .alias {width: calc(40% - 40px);} .ref-index .title {width: 60%;} .ref-arguments th {text-align: right; padding-right: 10px;} -.ref-arguments th, .ref-arguments td {vertical-align: top;} +.ref-arguments th, .ref-arguments td {vertical-align: top; min-width: 100px} .ref-arguments .name {width: 20%;} .ref-arguments .desc {width: 80%;} diff --git a/docs/pkgdown.js b/docs/pkgdown.js index 087a762..7e7048f 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -9,11 +9,6 @@ $('body').css('padding-top', $('.navbar').height() + 10); }); - $('body').scrollspy({ - target: '#sidebar', - offset: 60 - }); - $('[data-toggle="tooltip"]').tooltip(); var cur_path = paths(location.pathname); diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index a3735de..99d3cd9 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,9 +1,10 @@ -pandoc: 2.2.1 -pkgdown: 1.4.1 +pandoc: '2.5' +pkgdown: 1.6.1 pkgdown_sha: ~ articles: shift_tmle: shift_tmle.html vimshift: vimshift.html +last_built: 2021-03-13T22:47Z urls: reference: https://tlverse.org/tmle3shift/reference article: https://tlverse.org/tmle3shift/articles diff --git a/docs/reference/LF_shift.html b/docs/reference/LF_shift.html index e3a578c..aaf5c09 100644 --- a/docs/reference/LF_shift.html +++ b/docs/reference/LF_shift.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -41,7 +45,6 @@ get_likelihood(tmle_task) from tmle3 will instead be the likelihood from the original_lf, but for a shifted value \(A'=\)shift_function\((A, W)\)." /> - @@ -69,7 +72,7 @@ - +
        @@ -108,7 +111,7 @@
        • - +
          • @@ -126,7 +129,7 @@

          Shifted Likelihood Factor

          - + Source: R/LF_shift.R
          @@ -152,7 +155,7 @@

          define_lf(LF_shift, name, type = "density", original_lf, shift_function, ...)

          -
          +
          name

          character, the name of the factor. Should match a node name in the specification in tmle3_Task$npsem.

          original_lf

          LF_base object, the likelihood @@ -176,7 +179,7 @@

          Fields +
          original_lf

          LF_base object, the likelihood factor to shift.

          shift_function

          function, defines the shift.

          @@ -197,7 +200,7 @@

          FieldsReferences

          -
          +
          "Stochastic Treatment Regimes."

          Díaz, Iván and van der Laan, Mark (2018). In Targeted Learning in Data Science: Causal Inference for Complex Longitudinal Studies, 167–80. Springer Science & Business @@ -210,16 +213,10 @@

          R

          - @@ -230,7 +227,7 @@

          Contents

        -

        Site built with pkgdown 1.4.1.

        +

        Site built with pkgdown 1.6.1.

        diff --git a/docs/reference/Param_MSM_linear.html b/docs/reference/Param_MSM_linear.html index fbd1a57..beea6b7 100644 --- a/docs/reference/Param_MSM_linear.html +++ b/docs/reference/Param_MSM_linear.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -39,7 +43,6 @@ - @@ -67,7 +70,7 @@ - +
        @@ -106,7 +109,7 @@
        • - +
          • @@ -124,7 +127,7 @@

          Parameter for Linear Working Marginal Structural Model

          - + Source: R/Param_MSM_linear.R
          @@ -148,7 +151,7 @@

          define_param(Param_MSM_linear, observed_likelihood, intervention_list, ..., outcome_node)

          -
          +
          observed_likelihood

          A Likelihood corresponding to the observed likelihood.

          intervention_list

          A list of objects inheriting from @@ -163,7 +166,7 @@

          Fields +
          cf_likelihood

          the counterfactual likelihood for this treatment.

          intervention_list

          A list of objects inheriting from @@ -173,15 +176,10 @@

          Fields - @@ -192,7 +190,7 @@

          Contents

          -

          Site built with pkgdown 1.4.1.

          +

          Site built with pkgdown 1.6.1.

          diff --git a/docs/reference/additive_shifting.html b/docs/reference/additive_shifting.html index 171212a..4c2427c 100644 --- a/docs/reference/additive_shifting.html +++ b/docs/reference/additive_shifting.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -37,7 +41,6 @@ - @@ -65,7 +68,7 @@ - +
          @@ -104,7 +107,7 @@
          • - +
            • @@ -122,7 +125,7 @@

            Additive Shifts of Continuous-Valued Interventions Without Bounds

            - + Source: R/shift_additive.R
            @@ -130,9 +133,9 @@

            Additive Shifts of Continuous-Valued Interventions Without Bounds

            Additive Shifts of Continuous-Valued Interventions Without Bounds

            - 
            shift_additive(tmle_task, delta = 0, ...)
+    
            shift_additive(tmle_task, delta = 0, ...)
 
-shift_additive_inv(tmle_task, delta = 0, ...)
            
+shift_additive_inv(tmle_task, delta = 0, ...)

            Arguments

            @@ -160,18 +163,15 @@

            Arg

            See also

            Other shifting_interventions: -shift_additive_bounded()

            +shift_additive_bounded()

            Other shifting_interventions: -shift_additive_bounded()

            +shift_additive_bounded()

            - @@ -182,7 +182,7 @@

            Contents

            -

            Site built with pkgdown 1.4.1.

            +

            Site built with pkgdown 1.6.1.

            diff --git a/docs/reference/additive_shifting_bounded.html b/docs/reference/additive_shifting_bounded.html index 0ae834c..0884603 100644 --- a/docs/reference/additive_shifting_bounded.html +++ b/docs/reference/additive_shifting_bounded.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -38,7 +42,6 @@ - @@ -66,7 +69,7 @@ - +
            @@ -105,7 +108,7 @@
            • - +
              • @@ -123,7 +126,7 @@

              Additive Shifts of Continuous-Valued Interventions based on Bounded Densities

              - + Source: R/shift_density_bounded.R
              @@ -132,25 +135,25 @@

              Additive Shifts of Continuous-Valued Interventions based on Bounded Densitie

              Compute Ratio of Observed and Counterfactual Intervention Densities

              - 
              shift_additive_bounded(
-  tmle_task,
-  delta,
-  likelihood_base,
-  max_shifted_ratio,
-  fold_number,
-  ...
-)
-
-shift_additive_bounded_inv(
-  tmle_task,
-  delta,
-  likelihood_base,
-  max_shifted_ratio,
-  fold_number,
-  ...
-)
-
-get_density_ratio(tmle_task, delta, likelihood_base, fold_number)
              + 
              shift_additive_bounded(
+  tmle_task,
+  delta,
+  likelihood_base,
+  max_shifted_ratio,
+  fold_number,
+  ...
+)
+
+shift_additive_bounded_inv(
+  tmle_task,
+  delta,
+  likelihood_base,
+  max_shifted_ratio,
+  fold_number,
+  ...
+)
+
+get_density_ratio(tmle_task, delta, likelihood_base, fold_number)

              Arguments

            @@ -198,20 +201,17 @@

            Arg

            See also

            Other shifting_interventions: -shift_additive()

            +shift_additive()

            Other shifting_interventions: -shift_additive()

            +shift_additive()

            Other shifting_interventions: -shift_additive()

            +shift_additive()

            - @@ -222,7 +222,7 @@

            Contents

            -

            Site built with pkgdown 1.4.1.

            +

            Site built with pkgdown 1.6.1.

            diff --git a/docs/reference/index.html b/docs/reference/index.html index eefb00b..8721b6b 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -63,7 +67,7 @@ - +
            @@ -102,7 +106,7 @@
            + +
            @@ -202,11 +211,10 @@

            -

            Contents

            -             + @@ -217,7 +225,7 @@

            Contents

            -

            Site built with pkgdown 1.4.1.

            +

            Site built with pkgdown 1.6.1.

            diff --git a/docs/reference/msm_linear_factory.html b/docs/reference/msm_linear_factory.html index 231cf09..5fc934f 100644 --- a/docs/reference/msm_linear_factory.html +++ b/docs/reference/msm_linear_factory.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -37,7 +41,6 @@ - @@ -65,7 +68,7 @@ - +
            @@ -104,7 +107,7 @@
            • - +
              • @@ -122,7 +125,7 @@

              Function factory for computing linear working MSM delta method functions

              - + Source: R/delta_msm_functions.R
              @@ -130,7 +133,7 @@

              Function factory for computing linear working MSM delta method functions

              Function factory for computing linear working MSM delta method functions

              - 
              msm_linear_factory(design_matrix, weighting = c("identity", "variance"))
              + 
              msm_linear_factory(design_matrix, weighting = c("identity", "variance"))

              Arguments

              @@ -154,12 +157,10 @@

              Arg - @@ -170,7 +171,7 @@

              Contents

              -

              Site built with pkgdown 1.4.1.

              +

              Site built with pkgdown 1.6.1.

              diff --git a/docs/reference/tmle3_Spec_shift.html b/docs/reference/tmle3_Spec_shift.html index 162edf7..d1a650e 100644 --- a/docs/reference/tmle3_Spec_shift.html +++ b/docs/reference/tmle3_Spec_shift.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -37,7 +41,6 @@ - @@ -65,7 +68,7 @@ - +
              @@ -104,7 +107,7 @@
              • - +
                • @@ -122,7 +125,7 @@

                Defines a TML Estimator for the Outcome under a Shifted Treatment

                - + Source: R/tmle3_Spec_shift.R
                @@ -134,11 +137,10 @@

                Defines a TML Estimator for the Outcome under a Shifted Treatment

                - @@ -149,7 +151,7 @@

                Contents

              -

              Site built with pkgdown 1.4.1.

              +

              Site built with pkgdown 1.6.1.

              diff --git a/docs/reference/tmle3_Spec_vimshift_delta.html b/docs/reference/tmle3_Spec_vimshift_delta.html index 5e0ea50..8b533f4 100644 --- a/docs/reference/tmle3_Spec_vimshift_delta.html +++ b/docs/reference/tmle3_Spec_vimshift_delta.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -37,7 +41,6 @@ - @@ -65,7 +68,7 @@ - +
              @@ -104,7 +107,7 @@
              • - +
                • @@ -122,7 +125,7 @@

                Defines a TML Estimator for Variable Importance for Continuous Interventions

                - + Source: R/tmle3_Spec_vimshift_delta.R
                @@ -134,11 +137,10 @@

                Defines a TML Estimator for Variable Importance for Continuous Interventions

                - @@ -149,7 +151,7 @@

                Contents

              -

              Site built with pkgdown 1.4.1.

              +

              Site built with pkgdown 1.6.1.

              diff --git a/docs/reference/tmle3_Spec_vimshift_msm.html b/docs/reference/tmle3_Spec_vimshift_msm.html index ecc85ec..4f4acaf 100644 --- a/docs/reference/tmle3_Spec_vimshift_msm.html +++ b/docs/reference/tmle3_Spec_vimshift_msm.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -37,7 +41,6 @@ - @@ -65,7 +68,7 @@ - +
              @@ -104,7 +107,7 @@
              • - +
                • @@ -122,7 +125,7 @@

                Defines a TML Estimator for Variable Importance for Continuous Interventions

                - + Source: R/tmle3_Spec_vimshift_msm.R
                @@ -134,11 +137,10 @@

                Defines a TML Estimator for Variable Importance for Continuous Interventions

                - @@ -149,7 +151,7 @@

                Contents

              -

              Site built with pkgdown 1.4.1.

              +

              Site built with pkgdown 1.6.1.

              diff --git a/docs/reference/tmle_shift.html b/docs/reference/tmle_shift.html index 4e56345..9ef684f 100644 --- a/docs/reference/tmle_shift.html +++ b/docs/reference/tmle_shift.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -40,7 +44,6 @@ W = Covariates A = Treatment (binary or categorical) Y = Outcome (binary or bounded continuous)" /> - @@ -68,7 +71,7 @@ - +
              @@ -107,7 +110,7 @@
              • - +
                • @@ -125,7 +128,7 @@

                Outcome under Shifted Treatment

                - + Source: R/tmle3_Spec_shift.R
                @@ -136,13 +139,13 @@

                Outcome under Shifted Treatment

                Y = Outcome (binary or bounded continuous)

                - 
                tmle_shift(
-  shift_fxn = shift_additive_bounded,
-  shift_fxn_inv = shift_additive_bounded_inv,
-  shift_val = 1,
-  max_shifted_ratio = 2,
-  ...
-)
                + 
                tmle_shift(
+  shift_fxn = shift_additive_bounded,
+  shift_fxn_inv = shift_additive_bounded_inv,
+  shift_val = 1,
+  max_shifted_ratio = 2,
+  ...
+)

                Arguments

              @@ -180,12 +183,10 @@

              Arg - @@ -196,7 +197,7 @@

              Contents

              -

              Site built with pkgdown 1.4.1.

              +

              Site built with pkgdown 1.6.1.

              diff --git a/docs/reference/tmle_vimshift_delta.html b/docs/reference/tmle_vimshift_delta.html index 58e00fc..018cc84 100644 --- a/docs/reference/tmle_vimshift_delta.html +++ b/docs/reference/tmle_vimshift_delta.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -40,7 +44,6 @@ W = Covariates A = Treatment (binary or categorical) Y = Outcome (binary or bounded continuous)" /> - @@ -68,7 +71,7 @@ - +
              @@ -107,7 +110,7 @@
              • - +
                • @@ -125,7 +128,7 @@

                Outcome Under a Grid of Shifted Interventions via Delta Method

                - + Source: R/tmle3_Spec_vimshift_delta.R
                @@ -136,14 +139,14 @@

                Outcome Under a Grid of Shifted Interventions via Delta Method

                Y = Outcome (binary or bounded continuous)

                - 
                tmle_vimshift_delta(
-  shift_fxn = shift_additive_bounded,
-  shift_fxn_inv = shift_additive_bounded_inv,
-  shift_grid = seq(-1, 1, by = 0.5),
-  max_shifted_ratio = 2,
-  weighting = c("identity", "variance"),
-  ...
-)
                + 
                tmle_vimshift_delta(
+  shift_fxn = shift_additive_bounded,
+  shift_fxn_inv = shift_additive_bounded_inv,
+  shift_grid = seq(-1, 1, by = 0.5),
+  max_shifted_ratio = 2,
+  weighting = c("identity", "variance"),
+  ...
+)

                Arguments

              @@ -191,12 +194,10 @@

              Arg - @@ -207,7 +208,7 @@

              Contents

              -

              Site built with pkgdown 1.4.1.

              +

              Site built with pkgdown 1.6.1.

              diff --git a/docs/reference/tmle_vimshift_msm.html b/docs/reference/tmle_vimshift_msm.html index 30fd0b7..568886f 100644 --- a/docs/reference/tmle_vimshift_msm.html +++ b/docs/reference/tmle_vimshift_msm.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -40,7 +44,6 @@ W = Covariates A = Treatment (binary or categorical) Y = Outcome (binary or bounded continuous)" /> - @@ -68,7 +71,7 @@ - +
              @@ -107,7 +110,7 @@
              • - +
                • @@ -125,7 +128,7 @@

                Outcome Under a Grid of Shifted Interventions via Targeted Working MSM

                - + Source: R/tmle3_Spec_vimshift_msm.R
                @@ -136,14 +139,14 @@

                Outcome Under a Grid of Shifted Interventions via Targeted Working MSM

                Y = Outcome (binary or bounded continuous)

                - 
                tmle_vimshift_msm(
-  shift_fxn = shift_additive_bounded,
-  shift_fxn_inv = shift_additive_bounded_inv,
-  shift_grid = seq(-1, 1, by = 0.5),
-  max_shifted_ratio = 2,
-  weighting = c("identity", "variance"),
-  ...
-)
                + 
                tmle_vimshift_msm(
+  shift_fxn = shift_additive_bounded,
+  shift_fxn_inv = shift_additive_bounded_inv,
+  shift_grid = seq(-1, 1, by = 0.5),
+  max_shifted_ratio = 2,
+  weighting = c("identity", "variance"),
+  ...
+)

                Arguments

              @@ -191,12 +194,10 @@

              Arg - @@ -207,7 +208,7 @@

              Contents

              -

              Site built with pkgdown 1.4.1.

              +

              Site built with pkgdown 1.6.1.

              diff --git a/docs/reference/trend_msm.html b/docs/reference/trend_msm.html index 1b437fe..e8e1683 100644 --- a/docs/reference/trend_msm.html +++ b/docs/reference/trend_msm.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -37,7 +41,6 @@ - @@ -65,7 +68,7 @@ - +
              @@ -104,7 +107,7 @@
              • - +
                • @@ -122,7 +125,7 @@

                Test for a trend in the effect of shift interventions via working MSM

                - + Source: R/msm_trend_test.R
                @@ -130,12 +133,12 @@

                Test for a trend in the effect of shift interventions via working MSM

                Test for a trend in the effect of shift interventions via working MSM

                - 
                trend_msm(
-  tmle_fit_estimates,
-  delta_grid,
-  level = 0.95,
-  weighting = c("identity", "variance")
-)
                + 
                trend_msm(
+  tmle_fit_estimates,
+  delta_grid,
+  level = 0.95,
+  weighting = c("identity", "variance")
+)

                Arguments

              @@ -168,12 +171,10 @@

              Arg - @@ -184,7 +185,7 @@

              Contents

              -

              Site built with pkgdown 1.4.1.

              +

              Site built with pkgdown 1.6.1.

              From 0d49a07fd6fb7372dc1b82d4eb15e1f3edde9c0d Mon Sep 17 00:00:00 2001 From: Nima Hejazi Date: Sat, 13 Mar 2021 14:52:40 -0800 Subject: [PATCH 3/4] add contributing note --- CONTRIBUTING.md | 104 +++++++++++++++++++ README.Rmd | 9 ++ README.md | 9 ++ docs/CONTRIBUTING.html | 224 +++++++++++++++++++++++++++++++++++++++++ docs/index.html | 12 +++ docs/pkgdown.yml | 2 +- 6 files changed, 359 insertions(+), 1 deletion(-) create mode 100644 CONTRIBUTING.md create mode 100644 docs/CONTRIBUTING.html diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..f8f5bf8 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,104 @@ +# Contributing to `tmle3shift` development + +We, the authors of the `tmle3shift` R package, use the same guide as is used for +contributing to the development of the popular `ggplot2` R package. This +document is simply a formal re-statement of that fact. + +The goal of this guide is to help you get up and contributing to `tmle3shift` as +quickly as possible. The guide is divided into two main pieces: + +* Filing a bug report or feature request in an issue. +* Suggesting a change via a pull request. + +## Issues + +When filing an issue, the most important thing is to include a minimal +reproducible example so that we can quickly verify the problem, and then figure +out how to fix it. There are three things you need to include to make your +example reproducible: required packages, data, code. + +1. **Packages** should be loaded at the top of the script, so it's easy to + see which ones the example needs. + +2. The easiest way to include **data** is to use `dput()` to generate the R + code to recreate it. For example, to recreate the `mtcars` dataset in R, + I'd perform the following steps: + + 1. Run `dput(mtcars)` in R + 2. Copy the output + 3. In my reproducible script, type `mtcars <- ` then paste. + + But even better is if you can create a `data.frame()` with just a handful + of rows and columns that still illustrates the problem. + +3. Spend a little bit of time ensuring that your **code** is easy for others to + read: + + * make sure you've used spaces and your variable names are concise, but + informative + + * use comments to indicate where your problem lies + + * do your best to remove everything that is not related to the problem. + The shorter your code is, the easier it is to understand. + +You can check you have actually made a reproducible example by starting up a +fresh R session and pasting your script in. + +(Unless you've been specifically asked for it, please don't include the output +of `sessionInfo()`.) + +## Pull requests + +To contribute a change to `tmle3shift`, you follow these steps: + +1. Create a branch in git and make your changes. +2. Push branch to github and issue pull request (PR). +3. Discuss the pull request. +4. Iterate until either we accept the PR or decide that it's not a good fit for + `tmle3shift`. + +Each of these steps are described in more detail below. This might feel +overwhelming the first time you get set up, but it gets easier with practice. + +If you're not familiar with git or GitHub, please start by reading + + +Pull requests will be evaluated against the a checklist: + +1. __Motivation__. Your pull request should clearly and concisely motivates the + need for change. Plesae describe the problem your PR addresses and show + how your pull request solves it as concisely as possible. + + Also include this motivation in `NEWS` so that when a new release of + ggplot2 comes out it's easy for users to see what's changed. Add your + item at the top of the file and use markdown for formatting. The + news item should end with `(@yourGithubUsername, #the_issue_number)`. + +2. __Only related changes__. Before you submit your pull request, please + check to make sure that you haven't accidentally included any unrelated + changes. These make it harder to see exactly what's changed, and to + evaluate any unexpected side effects. + + Each PR corresponds to a git branch, so if you expect to submit + multiple changes make sure to create multiple branches. If you have + multiple changes that depend on each other, start with the first one + and don't submit any others until the first one has been processed. + +3. __Use `tmle3shift` coding style__. Please follow the + [official ggplot2 style](http://adv-r.had.co.nz/Style.html). Maintaing + a consistent style across the whole code base makes it much easier to + jump into the code. If you're modifying existing ggplot2 code that + doesn't follow the style guide, a separate pull request to fix the + style would be greatly appreciated. + +4. If you're adding new parameters or a new function, you'll also need + to document them with [roxygen](https://github.com/klutometis/roxygen). + Make sure to re-run `devtools::document()` on the code before submitting. + +This seems like a lot of work but don't worry if your pull request isn't +perfect. It's a learning process. A pull request is a process, and unless +you've submitted a few in the past it's unlikely that your pull request will be +accepted as is. Please don't submit pull requests that change existing +behaviour. Instead, think about how you can add a new feature in a minimally +invasive way. diff --git a/README.Rmd b/README.Rmd index d947620..e6727ea 100644 --- a/README.Rmd +++ b/README.Rmd @@ -76,6 +76,15 @@ issue](https://github.com/tlverse/tmle3shift/issues). --- +## Contributions + +Contributions are very welcome. Interested contributors should consult our +[contribution +guidelines](https://github.com/tlverse/tmle3shift/blob/master/CONTRIBUTING.md) +prior to submitting a pull request. + +--- + ## Citation After using the `tmle3shift` R package, please cite the following: diff --git a/README.md b/README.md index 4e60441..b6a37e5 100644 --- a/README.md +++ b/README.md @@ -72,6 +72,15 @@ If you encounter any bugs or have any specific feature requests, please ----- +## Contributions + +Contributions are very welcome. Interested contributors should consult +our [contribution +guidelines](https://github.com/tlverse/tmle3shift/blob/master/CONTRIBUTING.md) +prior to submitting a pull request. + +----- + ## Citation After using the `tmle3shift` R package, please cite the following: diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html new file mode 100644 index 0000000..4239fff --- /dev/null +++ b/docs/CONTRIBUTING.html @@ -0,0 +1,224 @@ + + + + + + + + +Contributing to tmle3shift development • tmle3shift + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
              +
              + + + + +
              + +
              +
              +
              +

              Contributing to tmle3shift development

              +
              + +
              + +

              We, the authors of the tmle3shift R package, use the same guide as is used for contributing to the development of the popular ggplot2 R package. This document is simply a formal re-statement of that fact.

              +

              The goal of this guide is to help you get up and contributing to tmle3shift as quickly as possible. The guide is divided into two main pieces:

              +
                +
              • Filing a bug report or feature request in an issue.
                • +
              • Suggesting a change via a pull request.
                • +
              +
              +

              +Issues

              +

              When filing an issue, the most important thing is to include a minimal reproducible example so that we can quickly verify the problem, and then figure out how to fix it. There are three things you need to include to make your example reproducible: required packages, data, code.

              +
                +

              1. Packages should be loaded at the top of the script, so it’s easy to see which ones the example needs.

                2. +
              2. +

                The easiest way to include data is to use dput() to generate the R code to recreate it. For example, to recreate the mtcars dataset in R, I’d perform the following steps:

                +
                  +
                1. Run dput(mtcars) in R
                  2. +
                2. Copy the output
                  3. +
                3. In my reproducible script, type mtcars <- then paste.
                  4. +
                +

                But even better is if you can create a data.frame() with just a handful of rows and columns that still illustrates the problem.

                +
                3. +
              3. +

                Spend a little bit of time ensuring that your code is easy for others to read:

                +
                  +

                • make sure you’ve used spaces and your variable names are concise, but informative

                  • +

                • use comments to indicate where your problem lies

                  • +

                • do your best to remove everything that is not related to the problem. The shorter your code is, the easier it is to understand.

                  • +
                +
                4. +
              +

              You can check you have actually made a reproducible example by starting up a fresh R session and pasting your script in.

              +

              (Unless you’ve been specifically asked for it, please don’t include the output of sessionInfo().)

              +
              +
              +

              +Pull requests

              +

              To contribute a change to tmle3shift, you follow these steps:

              +
                +
              1. Create a branch in git and make your changes.
                2. +
              2. Push branch to github and issue pull request (PR).
                3. +
              3. Discuss the pull request.
                4. +
              4. Iterate until either we accept the PR or decide that it’s not a good fit for tmle3shift.
                5. +
              +

              Each of these steps are described in more detail below. This might feel overwhelming the first time you get set up, but it gets easier with practice.

              +

              If you’re not familiar with git or GitHub, please start by reading http://r-pkgs.had.co.nz/git.html

              +

              Pull requests will be evaluated against the a checklist:

              +
                +
              1. +Motivation. Your pull request should clearly and concisely motivates the need for change. Plesae describe the problem your PR addresses and show how your pull request solves it as concisely as possible.
                2. +
              +

              Also include this motivation in NEWS so that when a new release of ggplot2 comes out it’s easy for users to see what’s changed. Add your item at the top of the file and use markdown for formatting. The news item should end with (@yourGithubUsername, #the_issue_number).

              +
                +
              1. +

                Only related changes. Before you submit your pull request, please check to make sure that you haven’t accidentally included any unrelated changes. These make it harder to see exactly what’s changed, and to evaluate any unexpected side effects.

                +

                Each PR corresponds to a git branch, so if you expect to submit multiple changes make sure to create multiple branches. If you have multiple changes that depend on each other, start with the first one and don’t submit any others until the first one has been processed.

                +
                2. +

              2. Use tmle3shift coding style. Please follow the official ggplot2 style. Maintaing a consistent style across the whole code base makes it much easier to jump into the code. If you’re modifying existing ggplot2 code that doesn’t follow the style guide, a separate pull request to fix the style would be greatly appreciated.

                3. +

              3. If you’re adding new parameters or a new function, you’ll also need to document them with roxygen. Make sure to re-run devtools::document() on the code before submitting.

                4. +
              +

              This seems like a lot of work but don’t worry if your pull request isn’t perfect. It’s a learning process. A pull request is a process, and unless you’ve submitted a few in the past it’s unlikely that your pull request will be accepted as is. Please don’t submit pull requests that change existing behaviour. Instead, think about how you can add a new feature in a minimally invasive way.

              +
              +
              + +
              + + + +
              + + + +
              +
              +

              Developed by Nima Hejazi, Jeremy Coyle, Mark van der Laan.

              +
              + +
              +

              Site built with pkgdown 1.6.1.

              +
              + +
              +
              + + + + + + + + diff --git a/docs/index.html b/docs/index.html index cc55c98..9837885 100644 --- a/docs/index.html +++ b/docs/index.html @@ -117,6 +117,12 @@

              If you encounter any bugs or have any specific feature requests, please file an issue.

              +
              +

              +Contributions

              +

              Contributions are very welcome. Interested contributors should consult our contribution guidelines prior to submitting a pull request.

              +
              +

              Citation

              @@ -192,6 +198,12 @@

              License

            • GPL-3
              • +
              +

              Community

              + +

              Citation

                diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 99d3cd9..246cd45 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -4,7 +4,7 @@ pkgdown_sha: ~ articles: shift_tmle: shift_tmle.html vimshift: vimshift.html -last_built: 2021-03-13T22:47Z +last_built: 2021-03-13T22:49Z urls: reference: https://tlverse.org/tmle3shift/reference article: https://tlverse.org/tmle3shift/articles From 136778b174be3776250703de4c181e0b5b20e122 Mon Sep 17 00:00:00 2001 From: Nima Hejazi Date: Sat, 13 Mar 2021 14:55:20 -0800 Subject: [PATCH 4/4] rm PATs from CI --- .travis.yml | 4 ---- appveyor.yml | 2 -- 2 files changed, 6 deletions(-) diff --git a/.travis.yml b/.travis.yml index 1bcef69..95cbaab 100644 --- a/.travis.yml +++ b/.travis.yml @@ -5,7 +5,6 @@ branches: env: global: - RGL_USE_NULL=TRUE - - secure: TF4+d5Jj4KrwoEt7a8z0kk0+Y0K6ScKQpuAnGFFp/dSuNLPX76UmIIbKNWA/JhDpgdNyecHdwV+HRPgMj5/wDfokLX7IUMFdpWldDy84Df/m38T2fogspjFa7k3eMeucoOL8q79IUayuRq3g8qGaxa0Sm/JhFJcpqSdyrjAk5qNBDCrt9EcQB92PpiZnWCg4GHHAnegAFEtmmB2QLve6dwhPMS2kAa0mqRWNJVFhpnaNIn1A5rn3FfShtc4ccVfbYqSt7wMAKttjz+FnVSj42zR4IftoHXB1Jvfvdrh1K5iGuiSmiQoS4sxG1ktzqvkRDbRbxZ4GKT8VQ9DsISL3sALbpAyafLjdmxf76YGMldRztPAvkdgZMBPpvBer6x2fEkLgpq4MEnTwfhBABMwMoXUt/p3ed/HtrjTtlzUttZpQHvL+OgOguo6ZzfDSCWbChGU5v/d3at0xRCO0QJoClxZ1lhNn+5jpaH2VcTRidel4Yr3Y7HfJOumHO21mFjC87lHKqZZBcWd33s3Y2Km9AuYcy3pLM3BfU7BlAyUsEhUniaFFVC9yMj4LOuYTG1xjFkuvM7ZAn80bcXfz4JKmEDjzG9DxQDaETARdJfyIG+vsx+xmej1LaoHBeuIxfCRcMKZJzvXlq9aZCwSl8Ps/RequfJWRsyn2TXieDxGOP4Q= language: r sudo: required @@ -19,9 +18,6 @@ r: - release - devel -before_install: - - Rscript -e 'update.packages(ask = FALSE)' - r_packages: - devtools - sessioninfo diff --git a/appveyor.yml b/appveyor.yml index 0029570..3fcfc49 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -25,8 +25,6 @@ environment: PKGTYPE: both R_REMOTES_STANDALONE: true R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - GITHUB_PAT: - secure: Nu6c5CmcVdYHDUVGej5ZIXGKOXVPBwqUwjrLV8d6UlbUaAtYuUhgpNuv9oLztAQQ matrix: - R_VERSION: release