test coverage ~70%

.Rbuildignore

@@ -11,3 +11,5 @@
 ^README\.html$
 ^pkgdown$
 ^Makefile$
+^codemeta\.json$
+^CODE_OF_CONDUCT\.md$

.github/CONTRIBUTING.md

@@ -0,0 +1,43 @@
+# Contributing to capybara
+
+This outlines how to propose a change to capybara. For more detailed
+info about contributing to this, and other tidyverse packages, please see the
+[**development contributing guide**](https://rstd.io/tidy-contrib).
+
+### Fixing typos
+
+Small typos or grammatical errors in documentation may be edited directly using
+the GitHub web interface, so long as the changes are made in the _source_ file.
+
+*  YES: you edit a roxygen comment in a `.R` file below `R/`.
+*  NO: you edit an `.Rd` file below `man/`.
+
+### Prerequisites
+
+Before you make a substantial pull request, you should always file an issue and
+make sure someone from the team agrees that it’s a problem. If you’ve found a
+bug, create an associated issue and illustrate the bug with a minimal 
+[reprex](https://www.tidyverse.org/help/#reprex).
+
+### Pull request process
+
+*  We recommend that you create a Git branch for each pull request (PR).  
+*  Look at the Travis and AppVeyor build status before and after making changes.
+The `README` should contain badges for any continuous integration services used
+by the package.  
+*  New code should follow the tidyverse [style guide](https://style.tidyverse.org).
+You can use the [styler](https://CRAN.R-project.org/package=styler) package to
+apply these styles, but please don't restyle code that has nothing to do with 
+your PR.  
+*  We use [roxygen2](https://cran.r-project.org/package=roxygen2), with
+[Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/markdown.html), 
+for documentation.  
+*  We use [testthat](https://cran.r-project.org/package=testthat). Contributions
+with test cases included are easier to accept.  
+*  For user-facing changes, add a bullet to the top of `NEWS.md` below the
+current development version header describing the changes made followed by your
+GitHub username, and links to relevant issue(s)/PR(s).
+
+### Code of Conduct
+
+Please note that the capybara project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.

CODE_OF_CONDUCT.md

@@ -0,0 +1,126 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+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, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* 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 at . 
+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 2.1, available at
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
+
+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>.
+
+[homepage]: https://www.contributor-covenant.org

NAMESPACE

@@ -32,7 +32,6 @@ export(apes)
 export(augment)
 export(bias_corr)
 export(feglm)
-export(feglm_control)
 export(felm)
 export(fenegbin)
 export(fepoisson)

R/cpp11.R

@@ -75,7 +75,3 @@ solve_eta2_ <- function(yadj, myadj, offset, eta) {
 sqrt_ <- function(w) {
   .Call(`_capybara_sqrt_`, w)
 }
-
-pairwise_cor_ <- function(y, yhat) {
-  .Call(`_capybara_pairwise_cor_`, y, yhat)
-}

R/feglm_control.R

@@ -32,8 +32,6 @@
 #' @return A named list of control parameters.
 #'
 #' @seealso \code{\link{feglm}}
-#'
-#' @export
 feglm_control <- function(
     dev.tol = 1.0e-08,
     center.tol = 1.0e-08,

R/fenegbin.R

@@ -14,6 +14,9 @@
 #' )
 #'
 #' summary(mod)
+#' 
+#' @return A named list of class \code{"feglm"}.
+#' 
 #' @export
 fenegbin <- function(
     formula = NULL,

R/fepoisson.R

@@ -10,6 +10,9 @@
 #' )
 #'
 #' summary(mod)
+#' 
+#' @return A named list of class \code{"feglm"}.
+#' 
 #' @export
 fepoisson <- function(
     formula = NULL,

R/generics_print.R

@@ -124,14 +124,14 @@ summary_r2_ <- function(x, digits) {
   )
 }
 
-summary_pseudo_rsq_ <- function(x, digits) {
-  if (x[["family"]][["family"]] == "poisson") {
-    cat(
-      "\nPseudo R-squared:",
-      format(x[["pseudo.rsq"]], digits = digits, nsmall = 2L), "\n"
-    )
-  }
-}
+# summary_pseudo_rsq_ <- function(x, digits) {
+#   if (x[["family"]][["family"]] == "poisson") {
+#     cat(
+#       "\nPseudo R-squared:",
+#       format(x[["pseudo.rsq"]], digits = digits, nsmall = 2L), "\n"
+#     )
+#   }
+# }
 
 summary_nobs_ <- function(x) {
   cat(
@@ -202,7 +202,7 @@ print.summary.feglm <- function(
 
   summary_estimates_(x, digits)
 
-  summary_pseudo_rsq_(x, digits)
+  # summary_pseudo_rsq_(x, digits)
 
   summary_nobs_(x)
 

R/generics_summary.R

@@ -1,6 +1,7 @@
 #' @title Summary method for fixed effects APEs
 #' @inherit vcov.apes
 #' @export
+#' @noRd
 summary.apes <- function(object, ...) {
   # Compute coefficent matrix
   est <- object[["delta"]]
@@ -18,6 +19,7 @@ summary.apes <- function(object, ...) {
 #' @title Summary method for fixed effects GLMs
 #' @inherit vcov.feglm
 #' @export
+#' @noRd
 summary.feglm <- function(
     object,
     type = c("hessian", "outer.product", "sandwich", "clustered"),
@@ -43,14 +45,13 @@ summary.feglm <- function(
     family        = object[["family"]]
   )
 
-  if (object[["family"]][["family"]] == "poisson") {
-    # Compute pseudo R-squared
-    # http://personal.lse.ac.uk/tenreyro/r2.do
-    y <- unlist(object$data[, 1], use.names = FALSE)
-    yhat <- predict(object, type = "response")
-    res[["pseudo.rsq"]] <- (pairwise_cor_(y, yhat))^2
-    # res[["pseudo.rsq"]] <- 0
-  }
+  # if (object[["family"]][["family"]] == "poisson") {
+  #   # Compute pseudo R-squared
+  #   # http://personal.lse.ac.uk/tenreyro/r2.do
+  #   y <- unlist(object$data[, 1], use.names = FALSE)
+  #   yhat <- predict(object, type = "response")
+  #   # res[["pseudo.rsq"]] <- (pairwise_cor_(y, yhat))^2
+  # }
 
   if (inherits(object, "fenegbin")) {
     res[["theta"]] <- object[["theta"]]
@@ -64,6 +65,7 @@ summary.feglm <- function(
 #' @title Summary method for fixed effects LMs
 #' @inherit vcov.felm
 #' @export
+#' @noRd
 summary.felm <- function(
     object,
     type = "hessian",

R/generics_vcov.R

@@ -6,6 +6,7 @@
 #' @return A named matrix of covariance estimates.
 #' @seealso \code{\link{apes}}
 #' @export
+#' @noRd
 vcov.apes <- function(object, ...) {
   object[["vcov"]]
 }
@@ -26,6 +27,16 @@ vcov.apes <- function(object, ...) {
 #' @references Cameron, C., J. Gelbach, and D. Miller (2011). "Robust Inference
 #'  With Multiway Clustering". Journal of Business & Economic Statistics 29(2).
 #' @seealso \code{\link{feglm}}
+#' @examples 
+#' mod <- fepoisson(
+#'  trade ~ log_dist + lang + cntg + clny | exp_year + imp_year | pair,
+#'  trade_panel
+#' )
+#' 
+#' vcov(mod, type = "clustered")
+#' 
+#' @return A named matrix of covariance estimates.
+#' 
 #' @export
 vcov.feglm <- function(
     object,
@@ -150,7 +161,7 @@ vcov.feglm <- function(
   V
 }
 
-#' @title Covariance matrix for GLMs
+#' @title Covariance matrix for LMs
 #' @inherit vcov.feglm
 #' @seealso \code{\link{felm}}
 #' @export

README.Rmd

@@ -223,3 +223,7 @@ create memory leaks.
 initialized values and all kinds of problems that result in memory leaks.
 
 When you are ready testing, you need to remove `-UDEGUG` from `src/Makevars`.
+
+## Code of Conduct
+
+Please note that the capybara project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.