merge pr #322: v0.5.3 on CRAN!

Author: simonpcouch

.github/workflows/check-standard.yaml

@@ -20,10 +20,10 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: '3.6'}
-          - {os: macOS-latest, r: '3.6'}
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
           - {os: macOS-latest, r: 'devel'}
-          - {os: ubuntu-16.04, r: '3.6', rspm: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04, r: 'release', rspm: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

CONDUCT.md

@@ -1,25 +1,128 @@
-# Contributor Code of Conduct
+# Contributor Covenant Code of Conduct
 
-As contributors and maintainers of this project, we pledge to respect all people who
-contribute through reporting issues, posting feature requests, updating documentation,
-submitting pull requests or patches, and other activities.
+## Our Pledge
 
-We are committed to making participation in this project a harassment-free experience for
-everyone, regardless of level of experience, gender, gender identity and expression,
-sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
 
-Examples of unacceptable behavior by participants include the use of sexual language or
-imagery, derogatory comments or personal attacks, trolling, public or private harassment,
-insults, or other unprofessional conduct.
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
 
-Project maintainers have the right and responsibility to remove, edit, or reject comments,
-commits, code, wiki edits, issues, and other contributions that are not aligned to this
-Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed
-from the project team.
+## Our Standards
 
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by
-opening an issue or contacting one or more of the project maintainers.
+Examples of behavior that contributes to a positive environment for our
+community include:
 
-This Code of Conduct is adapted from the Contributor Covenant
-(http://contributor-covenant.org), version 1.0.0, available at
-http://contributor-covenant.org/version/1/0/0/.
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards
+of acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies
+when an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement listed as package
+authors. All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0,
+available at https://www.contributor-covenant.org/version/2/0/
+code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at https://
+www.contributor-covenant.org/translations.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: infer
 Type: Package
 Title: Tidy Statistical Inference
-Version: 0.5.2
+Version: 0.5.3
 Authors@R: c(
     person("Andrew", "Bray", email = "[email protected]", role = c("aut", "cre")),
     person("Chester", "Ismay", email = "[email protected]", role = "aut"),
@@ -32,7 +32,7 @@ Imports:
     grDevices,
     purrr
 Depends:
-    R (>= 3.1.2)
+    R (>= 3.5.0)
 Suggests: 
     broom,
     devtools (>= 1.12.0),
@@ -43,10 +43,11 @@ Suggests:
     stringr,
     testthat,
     covr,
-    vdiffr
+    vdiffr,
+    fs
 URL: https://github.com/tidymodels/infer,
      https://infer.netlify.com/
 BugReports: https://github.com/tidymodels/infer/issues
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.0.9000
+RoxygenNote: 7.1.1
 VignetteBuilder: knitr

NEWS.md

@@ -1,3 +1,20 @@
+# infer 0.5.3
+
+## Breaking changes
+
+- `get_confidence_interval()` now uses column names ('lower_ci' and 'upper_ci') 
+in output that are consistent with other infer functionality (#317).
+
+## New functionality
+
+- `get_confidence_interval()` can now produce bias-corrected confidence intervals
+by setting `type = "bias-corrected"`. Thanks to @davidbaniadam for the 
+initial implementation (#237, #318)!
+
+## Other
+
+- Fix CRAN check failures related to long double errors.
+
 # infer 0.5.2
 
 - Warn the user when a p-value of 0 is reported (#257, #273)

R/get_confidence_interval.R

@@ -14,12 +14,14 @@
 #'   Default value is 0.95.
 #' @param type A string giving which method should be used for creating the
 #'   confidence interval. The default is `"percentile"` with `"se"`
-#'   corresponding to (multiplier * standard error) as the other option.
+#'   corresponding to (multiplier * standard error) and `"bias-corrected"` for
+#'   bias-corrected interval as other options.
 #' @param point_estimate A numeric value or a 1x1 data frame set to `NULL` by
-#'   default. Needed to be provided if `type = "se"`.
+#'   default. Needed to be provided if `type` is `"se"` or `"bias-corrected"`.
+#'
+#' @return A 1 x 2 tibble with 'lower_ci' and 'upper_ci' columns. Values
+#'   correspond to lower and upper bounds of the confidence interval.
 #'
-#' @return A 1 x 2 tibble with values corresponding to lower and upper values in
-#'   the confidence interval.
 #' @section Aliases:
 #' `get_ci()` is an alias of `get_confidence_interval()`.
 #' `conf_int()` is a deprecated alias of `get_confidence_interval()`.
@@ -43,11 +45,13 @@
 #'   # finding the null distribution
 #'   calculate(stat = "mean") %>%
 #    # calculate the confidence interval around the point estimate
-#'   get_confidence_interval(point_estimate = point_estimate,
-#'                           # at the 95% confidence level
-#'                           level = .95,
-#'                           # using the standard error method
-#'                           type = "se")
+#'   get_confidence_interval(
+#'     point_estimate = point_estimate,
+#'     # at the 95% confidence level
+#'     level = 0.95,
+#'     # using the standard error method
+#'     type = "se"
+#'   )
 #'   
 #' # More in-depth explanation of how to use the infer package
 #' \dontrun{
@@ -57,59 +61,90 @@
 #' @name get_confidence_interval
 #' @export
 get_confidence_interval <- function(x, level = 0.95, type = "percentile",
-  point_estimate = NULL){
-
+                                    point_estimate = NULL) {
   check_ci_args(x, level, type, point_estimate)
-
-  if(type == "percentile") {
-    ci_vec <- stats::quantile(x[["stat"]],
-      probs = c((1 - level) / 2, level + (1 - level) / 2))
-
-    ci <- tibble::tibble(ci_vec[1], ci_vec[2])
-    names(ci) <- names(ci_vec)
-  } else {
-    point_estimate <- check_obs_stat(point_estimate)
-    multiplier <- stats::qnorm(1 - (1 - level) / 2)
-    ci <- tibble::tibble(
-      lower = point_estimate - multiplier * stats::sd(x[["stat"]]),
-      upper = point_estimate + multiplier * stats::sd(x[["stat"]]))
+  
+  # Inform if no `level` was explicitly supplied
+  if (!("level" %in% rlang::call_args_names(match.call()))) {
+    message_glue("Using `level = {level}` to compute confidence interval.")
   }
-
-  return(ci)
+  
+  switch(
+    type,
+    percentile = ci_percentile(x, level),
+    se = ci_se(x, level, point_estimate),
+    `bias-corrected` = ci_bias_corrected(x, level, point_estimate)
+  )
 }
 
 #' @rdname get_confidence_interval
 #' @export
 get_ci <- function(x, level = 0.95, type = "percentile",
-  point_estimate = NULL) {
+                   point_estimate = NULL) {
   get_confidence_interval(
     x, level = level, type = type, point_estimate = point_estimate
   )
 }
 
-check_ci_args <- function(x, level, type, point_estimate){
+ci_percentile <- function(x, level) {
+  ci_vec <- stats::quantile(x[["stat"]], probs = (1 + c(-level, level)) / 2)
+  
+  make_ci_df(ci_vec)
+}
 
-  if(!is.null(point_estimate)){
-    if(!is.data.frame(point_estimate))
+ci_se <- function(x, level, point_estimate) {
+  point_estimate <- check_obs_stat(point_estimate)
+  
+  multiplier <- stats::qnorm((1 + level) / 2)
+  ci_vec <- point_estimate + c(-multiplier, multiplier) * stats::sd(x[["stat"]])
+  
+  make_ci_df(ci_vec)
+}
+
+ci_bias_corrected <- function(x, level, point_estimate) {
+  point_estimate <- check_obs_stat(point_estimate)
+  
+  p <- mean(x[["stat"]] <= point_estimate)
+  z0 <- stats::qnorm(p) 
+  # z_alpha_2 is z_(alpha/2)
+  z_alpha_2 <- stats::qnorm((1 + c(-level, level)) / 2)
+  new_probs <- stats::pnorm(2*z0 + z_alpha_2)
+  
+  ci_vec <- stats::quantile(x[["stat"]], probs = new_probs)
+  
+  make_ci_df(ci_vec)
+}
+
+check_ci_args <- function(x, level, type, point_estimate){
+  if (!is.null(point_estimate)) {
+    if (!is.data.frame(point_estimate)) {
       check_type(point_estimate, is.numeric)
-    else
+    } else {
       check_type(point_estimate, is.data.frame)
+      check_type(point_estimate[[1]][[1]], is.numeric)
+    }
   }
   check_type(x, is.data.frame)
   check_type(level, is.numeric)
-  if(level <= 0 || level >= 1){
+  
+  if ((level <= 0) || (level >= 1)) {
     stop_glue("The value of `level` must be between 0 and 1 non-inclusive.")
   }
 
-  if(!(type %in% c("percentile", "se"))){
-    stop_glue('The options for `type` are "percentile" or "se".')
+  if (!(type %in% c("percentile", "se", "bias-corrected"))) {
+    stop_glue(
+      'The options for `type` are "percentile", "se", or "bias-corrected".'
+    )
   }
 
-  if(type == "se" && is.null(point_estimate))
-    stop_glue('A numeric value needs to be given for `point_estimate` ',
-      'for `type = "se"')
-
-  if(type == "se" && is.vector(point_estimate))
-    check_type(point_estimate, is.numeric)
+  if ((type %in% c("se", "bias-corrected")) && is.null(point_estimate)) {
+    stop_glue(
+      'A numeric value needs to be given for `point_estimate` ',
+      'for `type` "se" or "bias-corrected".'
+    )
+  }
 }
 
+make_ci_df <- function(ci_vec) {
+  tibble::tibble(lower_ci = ci_vec[[1]], upper_ci = ci_vec[[2]])
+}

R/utils.R

@@ -343,6 +343,7 @@ sanitize_hypothesis_params_point <- function(dots, x) {
 }
 
 sanitize_hypothesis_params_proportion <- function(p, x) {
+  eps <- if (capabilities("long.double")) {sqrt(.Machine$double.eps)} else {0.01}
   if(anyNA(p)) {
     stop_glue('`p` should not contain missing values.')
   }
@@ -359,7 +360,7 @@ sanitize_hypothesis_params_proportion <- function(p, x) {
     p <- c(p, 1 - p)
     names(p) <- get_success_then_response_levels(x)
   } else {
-    if (sum(p) != 1) {
+    if (sum(p) < 1 - eps | sum(p) > 1 + eps) {
       stop_glue(
         "Make sure the hypothesized values for the `p` parameters sum to 1. ",
         "Please try again."