capybara 0.4.6

pachadotdev · May 19, 2024 · bb177b8 · bb177b8
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -31,7 +31,6 @@ jobs:
           # Use older ubuntu to maximise backward compatibility
           - {os: ubuntu-20.04,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-20.04,   r: 'release'}
-          - {os: ubuntu-20.04,   r: 'release', custom: 'gcc 4.8'}
           - {os: ubuntu-20.04,   r: 'oldrel-1'}
           - {os: ubuntu-20.04,   r: 'oldrel-2'}
           - {os: ubuntu-20.04,   r: 'oldrel-3'}
@@ -52,24 +51,6 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - name : Install compiler version
-        # We check on this old compiler specifically to support CentOS 7,
-        # which uses this gcc version. RStudio products support CentOS 7 through
-        # June 2024.
-        # https://github.com/r-lib/cpp11/pull/78
-        # https://www.rstudio.com/about/platform-support/
-        # Ubuntu 20.04 technically dropped support for gcc 4.8, so we have to
-        # add old archives back in manually to install it
-        # https://github.com/r-lib/cpp11/pull/279
-        if: matrix.config.custom == 'gcc 4.8'
-        run: |
-          echo "deb http://dk.archive.ubuntu.com/ubuntu/ xenial main" | sudo tee -a /etc/apt/sources.list
-          echo "deb http://dk.archive.ubuntu.com/ubuntu/ xenial universe" | sudo tee -a /etc/apt/sources.list
-          sudo apt update
-          sudo apt-get install -y g++-4.8 libgfortran-*
-          mkdir ~/.R/
-          echo $'CXX1X=g++-4.8\nCXX11=g++-4.8\nCC=gcc-4.8 -std=c99\nCXX=g++-4.8 -std=gnu++11' >> ~/.R/Makevars
-
       - name: Install macOS system dependencies
         if: runner.os == 'macOS'
         run: brew install --cask xquartz

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: capybara
 Type: Package
 Title: Fast and Memory Efficient Fitting of Linear Models With High-Dimensional
     Fixed Effects
-Version: 0.4.5
+Version: 0.4.6
 Authors@R: c(
     person(
         given = "Mauricio",
@@ -42,5 +42,5 @@ LinkingTo: cpp11, cpp11armadillo
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 Remotes: 
-    pachadotdev/cpp11armadillo
+    ropenscilabs/srr
 Roxygen: list(markdown = TRUE, roclets = c("namespace", "rd", "srr::srr_stats_roclet"))
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# capybara 0.4.6
+
+* Fixes notes from tidyselect regarding the use of `all_of()`.
+* The C++ code follows a more consistent style.
+* The GH-Actions do not test gcc 4.8 anymore.
+
 # capybara 0.4.5
 
 * Ungroups the data to avoid issues with the model matrix

diff --git a/R/generics_vcov.R b/R/generics_vcov.R
@@ -131,7 +131,7 @@ vcov.feglm <- function(
                 as.matrix(
                   G %>%
                     group_by(!!sym(cl)) %>%
-                    summarise(across(sp.vars, sum), .groups = "drop") %>%
+                    summarise(across(all_of(sp.vars), sum), .groups = "drop") %>%
                     select(-!!sym(cl))
                 ),
                 NA_real_, FALSE, FALSE

diff --git a/R/srr-stats-standards.R b/R/srr-stats-standards.R
@@ -11,7 +11,7 @@
 #'
 #' @srrstats {G1.0} *Statistical Software should list at least one primary reference from published academic literature.*
 #' @srrstats {G1.1} *Statistical Software should document whether the algorithm(s) it implements are:* - *The first implementation of a novel algorithm*; or - *The first implementation within **R** of an algorithm which has previously been implemented in other languages or contexts*; or - *An improvement on other implementations of similar algorithms in **R***.
-#' @srrstatsTODO {G1.2} *Statistical Software should include a* Life Cycle Statement *describing current and anticipated future states of development.*
+#' @srrstats {G1.2} *Statistical Software should include a* Life Cycle Statement *describing current and anticipated future states of development.*
 #' @srrstats {G1.3} *All statistical terminology should be clarified and unambiguously defined.*
 #' @srrstats {G1.4} *Software should use [`roxygen2`](https://roxygen2.r-lib.org/) to document all functions.*
 #' @srrstatsTODO {G1.4a} *All internal (non-exported) functions should also be documented in standard [`roxygen2`](https://roxygen2.r-lib.org/) format, along with a final `@noRd` tag to suppress automatic generation of `.Rd` files.*
@@ -23,13 +23,13 @@
 #' @srrstats {G2.1a} *Provide explicit secondary documentation of expectations on data types of all vector inputs.*
 #' @srrstatsTODO {G2.2} *Appropriately prohibit or restrict submission of multivariate input to parameters expected to be univariate.*
 #' @srrstatsTODO {G2.3} *For univariate character input:*
-#' @srrstatsTODO {G2.3a} *Use `match.arg()` or equivalent where applicable to only permit expected values.*
+#' @srrstats {G2.3a} *Use `match.arg()` or equivalent where applicable to only permit expected values.*
 #' @srrstatsTODO {G2.3b} *Either: use `tolower()` or equivalent to ensure input of character parameters is not case dependent; or explicitly document that parameters are strictly case-sensitive.*
-#' @srrstatsTODO {G2.4} *Provide appropriate mechanisms to convert between different data types, potentially including:*
-#' @srrstatsTODO {G2.4a} *explicit conversion to `integer` via `as.integer()`*
-#' @srrstatsTODO {G2.4b} *explicit conversion to continuous via `as.numeric()`*
+#' @srrstats {G2.4} *Provide appropriate mechanisms to convert between different data types, potentially including:*
+#' @srrstats {G2.4a} *explicit conversion to `integer` via `as.integer()`*
+#' @srrstats {G2.4b} *explicit conversion to continuous via `as.numeric()`*
 #' @srrstatsTODO {G2.4c} *explicit conversion to character via `as.character()` (and not `paste` or `paste0`)*
-#' @srrstatsTODO {G2.4d} *explicit conversion to factor via `as.factor()`*
+#' @srrstats {G2.4d} *explicit conversion to factor via `as.factor()`*
 #' @srrstatsTODO {G2.4e} *explicit conversion from factor via `as...()` functions*
 #' @srrstatsTODO {G2.5} *Where inputs are expected to be of `factor` type, secondary documentation should explicitly state whether these should be `ordered` or not, and those inputs should provide appropriate error or other routines to ensure inputs follow these expectations.*
 #' @srrstats {G2.6} *Software which accepts one-dimensional input should ensure values are appropriately pre-processed regardless of class structures.*
@@ -57,9 +57,9 @@
 #' @srrstatsTODO {G5.2b} *Explicit tests should demonstrate conditions which trigger every one of those messages, and should compare the result with expected values.*
 #' @srrstatsTODO {G5.3} *For functions which are expected to return objects containing no missing (`NA`) or undefined (`NaN`, `Inf`) values, the absence of any such values in return objects should be explicitly tested.*
 #' @srrstatsTODO {G5.4} **Correctness tests** *to test that statistical algorithms produce expected results to some fixed test data sets (potentially through comparisons using binding frameworks such as [RStata](https://github.com/lbraglia/RStata)).*
-#' @srrstatsTODO {G5.4a} *For new methods, it can be difficult to separate out correctness of the method from the correctness of the implementation, as there may not be reference for comparison. In this case, testing may be implemented against simple, trivial cases or against multiple implementations such as an initial R implementation compared with results from a C/C++ implementation.*
+#' @srrstats {G5.4a} *For new methods, it can be difficult to separate out correctness of the method from the correctness of the implementation, as there may not be reference for comparison. In this case, testing may be implemented against simple, trivial cases or against multiple implementations such as an initial R implementation compared with results from a C/C++ implementation.*
 #' @srrstats {G5.4b} *For new implementations of existing methods, correctness tests should include tests against previous implementations. Such testing may explicitly call those implementations in testing, preferably from fixed-versions of other software, or use stored outputs from those where that is not possible.*
-#' @srrstatsTODO {G5.4c} *Where applicable, stored values may be drawn from published paper outputs when applicable and where code from original implementations is not available*
+#' @srrstats {G5.4c} *Where applicable, stored values may be drawn from published paper outputs when applicable and where code from original implementations is not available*
 #' @srrstatsTODO {G5.5} *Correctness tests should be run with a fixed random seed*
 #' @srrstatsTODO {G5.6} **Parameter recovery tests** *to test that the implementation produce expected results given data with known properties. For instance, a linear regression algorithm should return expected coefficient values for a simulated data set generated from a linear model.*
 #' @srrstatsTODO {G5.6a} *Parameter recovery tests should generally be expected to succeed within a defined tolerance rather than recovering exact values.*

diff --git a/README.Rmd b/README.Rmd
@@ -19,6 +19,7 @@ knitr::opts_chunk$set(
 [![R-CMD-check](https://github.com/pachadotdev/capybara/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/pachadotdev/capybara/actions/workflows/R-CMD-check.yaml)
 [![codecov](https://codecov.io/gh/pachadotdev/capybara/graph/badge.svg?token=kDP0pWmfRk)](https://codecov.io/gh/pachadotdev/capybara)
 [![BuyMeACoffee](https://raw.githubusercontent.com/pachadotdev/buymeacoffee-badges/main/bmc-donate-yellow.svg)](https://www.buymeacoffee.com/pacha)
+[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 <!-- badges: end -->
 
 ## About

diff --git a/README.md b/README.md
@@ -8,6 +8,8 @@
 [![R-CMD-check](https://github.com/pachadotdev/capybara/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/pachadotdev/capybara/actions/workflows/R-CMD-check.yaml)
 [![codecov](https://codecov.io/gh/pachadotdev/capybara/graph/badge.svg?token=kDP0pWmfRk)](https://codecov.io/gh/pachadotdev/capybara)
 [![BuyMeACoffee](https://raw.githubusercontent.com/pachadotdev/buymeacoffee-badges/main/bmc-donate-yellow.svg)](https://www.buymeacoffee.com/pacha)
+[![Lifecycle:
+stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 <!-- badges: end -->
 
 ## About

diff --git a/dev/bench_endogeneity.rds b/dev/bench_endogeneity.rds
diff --git a/dev/bench_globalization.rds b/dev/bench_globalization.rds
diff --git a/dev/bench_phasing.rds b/dev/bench_phasing.rds
diff --git a/dev/bench_ppml.rds b/dev/bench_ppml.rds
diff --git a/dev/bench_reverse_causality.rds b/dev/bench_reverse_causality.rds
diff --git a/dev/bench_trade_diversion.rds b/dev/bench_trade_diversion.rds
diff --git a/dev/cass_bug.r b/dev/cass_bug.r
diff --git a/dev/cass_bug.txt b/dev/cass_bug.txt