From 084ed2e6105bbfda35a7e13e0b40844f126cfaad Mon Sep 17 00:00:00 2001
From: Etienne Bacher <52219252+etiennebacher@users.noreply.github.com>
Date: Tue, 10 Dec 2024 02:16:37 +0100
Subject: [PATCH] Fix a couple of lints (#469)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* init

* document, styler

---------

Co-authored-by: Daniel <mail@danielluedecke.de>
Co-authored-by: Rémi Thériault <13123390+rempsyc@users.noreply.github.com>
---
 R/report.BFBayesFactor.R           |  1 -
 R/report.R                         |  1 -
 R/report.aov.R                     |  5 -----
 R/report.bayesfactor_models.R      |  2 --
 R/report.brmsfit.R                 |  1 -
 R/report.character.R               |  7 -------
 R/report.data.frame.R              | 15 ---------------
 R/report.factor.R                  |  3 ---
 R/report.lavaan.R                  |  2 --
 R/report.lm.R                      |  5 -----
 R/report.numeric.R                 |  4 ----
 R/report.sessionInfo.R             |  5 -----
 R/report_effectsize.R              |  2 --
 R/report_htest_cor.R               |  1 -
 R/report_info.R                    |  2 --
 R/report_intercept.R               |  1 -
 R/report_misc.R                    |  1 -
 R/report_model.R                   |  1 -
 R/report_parameters.R              |  2 --
 R/report_performance.R             |  2 --
 R/report_priors.R                  |  1 -
 R/report_random.R                  |  1 -
 R/report_sample.R                  |  3 ---
 R/report_table.R                   |  4 ----
 R/utils_combine_tables.R           |  2 --
 man/report-package.Rd              | 12 ++++++------
 tests/testthat/test-format_model.R |  2 --
 tests/testthat/test-report.aov.R   |  4 ++--
 tests/testthat/test-report.lmer.R  |  4 ++--
 29 files changed, 10 insertions(+), 86 deletions(-)

diff --git a/R/report.BFBayesFactor.R b/R/report.BFBayesFactor.R
index b6f597c9..2f7fc65b 100644
--- a/R/report.BFBayesFactor.R
+++ b/R/report.BFBayesFactor.R
@@ -63,7 +63,6 @@ report.BFBayesFactor <- function(x, h0 = "H0", h1 = "H1", ...) {
 }
 
 
-
 #' @rdname report.BFBayesFactor
 #' @export
 report_statistics.BFBayesFactor <- function(x, table = NULL, ...) {
diff --git a/R/report.R b/R/report.R
index 73073b17..70b8fe31 100644
--- a/R/report.R
+++ b/R/report.R
@@ -141,7 +141,6 @@ as.report <- function(text, table = NULL, plot = NULL, ...) {
 }
 
 
-
 #' @rdname as.report
 #' @export
 is.report <- function(x) inherits(x, "report")
diff --git a/R/report.aov.R b/R/report.aov.R
index f5ce5286..e810127e 100644
--- a/R/report.aov.R
+++ b/R/report.aov.R
@@ -83,7 +83,6 @@ report_effectsize.aov <- function(x, ...) {
   parameters <- paste0(interpretation, " (", statistics, ")")
 
 
-
   as.report_effectsize(parameters,
     summary = parameters,
     table = table,
@@ -211,9 +210,6 @@ report_statistics.anova <- report_statistics.aov
 report_statistics.aovlist <- report_statistics.aov
 
 
-
-
-
 # report_parameters ------------------------------------------------------------
 
 
@@ -319,7 +315,6 @@ report_info.anova <- report_info.aov
 report_info.aovlist <- report_info.aov
 
 
-
 # report_text ------------------------------------------------------------
 
 #' @rdname report.aov
diff --git a/R/report.bayesfactor_models.R b/R/report.bayesfactor_models.R
index 2547ff8f..d76fd9a2 100644
--- a/R/report.bayesfactor_models.R
+++ b/R/report.bayesfactor_models.R
@@ -99,7 +99,6 @@ report_text.bayesfactor_models <- function(x,
 }
 
 
-
 #' @keywords internal
 .report.bayesfactor_models <- function(model,
                                        interpretation = "jeffreys1961",
@@ -211,7 +210,6 @@ report_text.bayesfactor_models <- function(x,
 }
 
 
-
 # bayesfactor_inclusion ---------------------------------------------------
 
 #' @rdname report.bayesfactor_models
diff --git a/R/report.brmsfit.R b/R/report.brmsfit.R
index 0ffee6db..057c5cd2 100644
--- a/R/report.brmsfit.R
+++ b/R/report.brmsfit.R
@@ -53,7 +53,6 @@ report_text.brmsfit <- report_text.lm
 # ==================== Specific to Bayes ===================================
 
 
-
 # report_priors -----------------------------------------------------------
 
 #' @export
diff --git a/R/report.character.R b/R/report.character.R
index 16fe8fc3..39f999a4 100644
--- a/R/report.character.R
+++ b/R/report.character.R
@@ -25,13 +25,9 @@ report.character <- function(x,
 }
 
 
-
-
-
 # report_table ------------------------------------------------------------
 
 
-
 #' @export
 report_table.character <- function(x,
                                    n_entries = 3,
@@ -68,7 +64,6 @@ report_table.character <- function(x,
 }
 
 
-
 # report_parameters -------------------------------------------------------
 
 #' @export
@@ -102,7 +97,6 @@ report_parameters.character <- function(x,
 }
 
 
-
 # report_text -------------------------------------------------------------
 
 #' @export
@@ -175,7 +169,6 @@ report_text.character <- function(x,
 }
 
 
-
 # report_statistics -------------------------------------------------------
 
 
diff --git a/R/report.data.frame.R b/R/report.data.frame.R
index d5a97bf5..22d910ac 100644
--- a/R/report.data.frame.R
+++ b/R/report.data.frame.R
@@ -100,7 +100,6 @@ report.data.frame <- function(x,
 # report_table ------------------------------------------------------------
 
 
-
 #' @export
 report_table.data.frame <- function(x,
                                     n = FALSE,
@@ -178,12 +177,9 @@ report_table.data.frame <- function(x,
 }
 
 
-
-
 # report_parameters -------------------------------------------------------
 
 
-
 #' @export
 report_parameters.data.frame <- function(x,
                                          table = NULL,
@@ -224,7 +220,6 @@ report_parameters.data.frame <- function(x,
 }
 
 
-
 # report_text -------------------------------------------------------------
 
 #' @export
@@ -272,7 +267,6 @@ report_text.data.frame <- function(x,
 }
 
 
-
 # report_statistics -------------------------------------------------------
 
 
@@ -401,8 +395,6 @@ report_table.grouped_df <- function(x,
 }
 
 
-
-
 #' @export
 report_parameters.grouped_df <- function(x,
                                          table = NULL,
@@ -494,7 +486,6 @@ report_text.grouped_df <- function(x,
 report.grouped_df <- report.data.frame
 
 
-
 #' @export
 report_statistics.grouped_df <- function(x,
                                          table = NULL,
@@ -538,12 +529,6 @@ report_statistics.grouped_df <- function(x,
 }
 
 
-
-
-
-
-
-
 # Utils -------------------------------------------------------------------
 
 #' @keywords internal
diff --git a/R/report.factor.R b/R/report.factor.R
index acdf2502..2a805862 100644
--- a/R/report.factor.R
+++ b/R/report.factor.R
@@ -20,7 +20,6 @@ report.Date <- report.factor
 # report_table ------------------------------------------------------------
 
 
-
 #' @export
 report_table.factor <- function(x, levels_percentage = "auto", ...) {
   if (!is.factor(x)) {
@@ -56,7 +55,6 @@ report_table.Date <- report_table.factor
 # report_parameters -------------------------------------------------------
 
 
-
 #' @export
 report_parameters.factor <- function(x, table = NULL, levels_percentage = "auto", ...) {
   if (!is.factor(x)) {
@@ -140,7 +138,6 @@ report_text.logical <- report_text.factor
 report_text.Date <- report_text.factor
 
 
-
 # report_statistics -------------------------------------------------------
 
 
diff --git a/R/report.lavaan.R b/R/report.lavaan.R
index a2fc8b42..9a5dddc5 100644
--- a/R/report.lavaan.R
+++ b/R/report.lavaan.R
@@ -34,7 +34,6 @@ report.lavaan <- function(x, ...) {
 }
 
 
-
 #' @export
 report_table.lavaan <- function(x, ...) {
   parameters <- parameters::model_parameters(x, ci_random = FALSE, ...)
@@ -80,7 +79,6 @@ report_table.lavaan <- function(x, ...) {
 }
 
 
-
 #' @rdname report.lavaan
 #' @export
 report_performance.lavaan <- function(x, table = NULL, ...) {
diff --git a/R/report.lm.R b/R/report.lm.R
index 69df2167..239fd111 100644
--- a/R/report.lm.R
+++ b/R/report.lm.R
@@ -65,7 +65,6 @@ report.lm <- function(x, include_effectsize = TRUE, effectsize_method = "refit",
 }
 
 
-
 # report_effectsize -------------------------------------------------------
 
 #' @rdname report.lm
@@ -124,7 +123,6 @@ report_effectsize.lm <- function(x, effectsize_method = "refit", ...) {
 }
 
 
-
 # report_table ------------------------------------------------------------
 
 
@@ -278,7 +276,6 @@ report_statistics.lm <- function(x,
 }
 
 
-
 # report_statistics ------------------------------------------------------------
 
 #' @rdname report.lm
@@ -475,7 +472,6 @@ report_performance.lm <- function(x, table = NULL, ...) {
 }
 
 
-
 # report_info ------------------------------------------------------------
 
 #' @rdname report.lm
@@ -518,7 +514,6 @@ report_info.lm <- function(x,
 }
 
 
-
 # report_text ------------------------------------------------------------
 
 #' @rdname report.lm
diff --git a/R/report.numeric.R b/R/report.numeric.R
index 631698bf..49bfcab5 100644
--- a/R/report.numeric.R
+++ b/R/report.numeric.R
@@ -51,7 +51,6 @@ report.numeric <- function(x,
 }
 
 
-
 # report_table ------------------------------------------------------------
 
 #' @export
@@ -132,8 +131,6 @@ report_table.numeric <- function(x,
 }
 
 
-
-
 # report_parameters -------------------------------------------------------
 
 #' @export
@@ -258,7 +255,6 @@ report_parameters.numeric <- function(x,
 }
 
 
-
 # report_text -------------------------------------------------------------
 
 #' @export
diff --git a/R/report.sessionInfo.R b/R/report.sessionInfo.R
index 8dae6db5..63264b7c 100644
--- a/R/report.sessionInfo.R
+++ b/R/report.sessionInfo.R
@@ -37,7 +37,6 @@ report.sessionInfo <- function(x, ...) {
 }
 
 
-
 # Aliases -----------------------------------------------------------------
 
 
@@ -67,7 +66,6 @@ cite_packages <- function(session = NULL, include_R = TRUE, ...) {
 }
 
 
-
 # report_system --------------------------------------------------------------
 
 
@@ -104,7 +102,6 @@ report_system <- function(session = NULL) {
 }
 
 
-
 # report_table ------------------------------------------------------------
 
 #' @export
@@ -141,7 +138,6 @@ report_table.sessionInfo <- function(x, include_R = TRUE, ...) {
 }
 
 
-
 # report_parameters -------------------------------------------------------
 
 #' @export
@@ -179,7 +175,6 @@ report_parameters.sessionInfo <- function(x, table = NULL, include_R = TRUE, ...
 }
 
 
-
 # report_text -------------------------------------------------------------
 
 #' @export
diff --git a/R/report_effectsize.R b/R/report_effectsize.R
index 421e7d3e..ac62bea4 100644
--- a/R/report_effectsize.R
+++ b/R/report_effectsize.R
@@ -83,11 +83,9 @@ print.report_effectsize <- function(x, ...) {
 }
 
 
-
 # Utilities ---------------------------------------------------------------
 
 
-
 #' @keywords internal
 .text_effectsize <- function(interpretation) {
   # Effect size
diff --git a/R/report_htest_cor.R b/R/report_htest_cor.R
index 1cf31e48..d8e1d95c 100644
--- a/R/report_htest_cor.R
+++ b/R/report_htest_cor.R
@@ -24,7 +24,6 @@
 }
 
 
-
 # report_effectsize ---------------------
 
 .report_effectsize_correlation <- function(x, table, dot_args) {
diff --git a/R/report_info.R b/R/report_info.R
index 395674d8..f73af600 100644
--- a/R/report_info.R
+++ b/R/report_info.R
@@ -46,7 +46,6 @@ report_info <- function(x, ...) {
 }
 
 
-
 # METHODS -----------------------------------------------------------------
 
 
@@ -78,7 +77,6 @@ print.report_info <- function(x, ...) {
 }
 
 
-
 # Utils -------------------------------------------------------------------
 
 #' @keywords internal
diff --git a/R/report_intercept.R b/R/report_intercept.R
index 884034b6..74e4f9c3 100644
--- a/R/report_intercept.R
+++ b/R/report_intercept.R
@@ -99,7 +99,6 @@ print.report_intercept <- function(x, ...) {
 }
 
 
-
 .find_reference_level <- function(f) {
   tryCatch(
     {
diff --git a/R/report_misc.R b/R/report_misc.R
index 09bce460..173c9fa9 100644
--- a/R/report_misc.R
+++ b/R/report_misc.R
@@ -22,7 +22,6 @@ report_date <- function(...) {
 }
 
 
-
 #' @rdname report_date
 #' @export
 report_story <- function(...) {
diff --git a/R/report_model.R b/R/report_model.R
index c9598084..bc2fd7ed 100644
--- a/R/report_model.R
+++ b/R/report_model.R
@@ -46,7 +46,6 @@ report_model <- function(x, table = NULL, ...) {
 }
 
 
-
 # METHODS -----------------------------------------------------------------
 
 
diff --git a/R/report_parameters.R b/R/report_parameters.R
index bd0102f7..12e537a7 100644
--- a/R/report_parameters.R
+++ b/R/report_parameters.R
@@ -104,7 +104,6 @@ print.report_parameters <- function(x, ...) {
 }
 
 
-
 # Utils -------------------------------------------------------------------
 
 #' @keywords internal
@@ -158,7 +157,6 @@ print.report_parameters <- function(x, ...) {
 }
 
 
-
 #' @keywords internal
 .parameters_diagnostic_bayesian <- function(diagnostic, only_when_insufficient = FALSE, ...) {
   # Convergence
diff --git a/R/report_performance.R b/R/report_performance.R
index 1d5b2efc..2f60e37e 100644
--- a/R/report_performance.R
+++ b/R/report_performance.R
@@ -52,7 +52,6 @@ report_performance <- function(x, table = NULL, ...) {
 }
 
 
-
 # METHODS -----------------------------------------------------------------
 
 
@@ -85,7 +84,6 @@ print.report_performance <- print.report_text
 # Utils -------------------------------------------------------------------
 
 
-
 #' @keywords internal
 .text_r2 <- function(x, info, performance, ...) {
   text <- ""
diff --git a/R/report_priors.R b/R/report_priors.R
index 11cbd564..8a287c40 100644
--- a/R/report_priors.R
+++ b/R/report_priors.R
@@ -25,7 +25,6 @@ report_priors <- function(x, ...) {
 }
 
 
-
 # METHODS -----------------------------------------------------------------
 
 
diff --git a/R/report_random.R b/R/report_random.R
index 51efe567..74a7d513 100644
--- a/R/report_random.R
+++ b/R/report_random.R
@@ -47,7 +47,6 @@ report_random <- function(x, ...) {
 }
 
 
-
 # METHODS -----------------------------------------------------------------
 
 
diff --git a/R/report_sample.R b/R/report_sample.R
index 83b95115..14918e28 100644
--- a/R/report_sample.R
+++ b/R/report_sample.R
@@ -325,7 +325,6 @@ report_sample <- function(data,
 }
 
 
-
 .report_sample_row.factor <- function(x,
                                       column,
                                       weights = NULL,
@@ -388,7 +387,6 @@ report_sample <- function(data,
 .report_sample_row.character <- .report_sample_row.factor
 
 
-
 # Standard error for confidence interval of proportions ----
 
 .ci_proportion <- function(x, table_proportions, weights, ci, ci_method, ci_correct) {
@@ -446,7 +444,6 @@ report_sample <- function(data,
 }
 
 
-
 # print-method --------------------------------------------
 
 #' @export
diff --git a/R/report_table.R b/R/report_table.R
index 4a77098e..faa2ae0f 100644
--- a/R/report_table.R
+++ b/R/report_table.R
@@ -63,7 +63,6 @@ report_table <- function(x, ...) {
 }
 
 
-
 # METHODS -----------------------------------------------------------------
 
 #' @rdname as.report
@@ -104,9 +103,6 @@ as.report_table.report <- function(x, summary = NULL, ...) {
 }
 
 
-
-
-
 #' @export
 summary.report_table <- function(object, ...) {
   if (is.null(attributes(object)$summary)) {
diff --git a/R/utils_combine_tables.R b/R/utils_combine_tables.R
index 7c342db7..05fac632 100644
--- a/R/utils_combine_tables.R
+++ b/R/utils_combine_tables.R
@@ -14,7 +14,6 @@
 }
 
 
-
 #' @keywords internal
 .combine_tables_performance <- function(parameters, performance) {
   table <- parameters
@@ -67,7 +66,6 @@
 }
 
 
-
 #' @keywords internal
 .remove_performance <- function(table) {
   if ("Fit" %in% names(table)) {
diff --git a/man/report-package.Rd b/man/report-package.Rd
index 43f8fa51..ce41d492 100644
--- a/man/report-package.Rd
+++ b/man/report-package.Rd
@@ -24,15 +24,15 @@ Useful links:
 
 }
 \author{
-\strong{Maintainer}: Rémi Thériault \email{remi.theriault@mail.mcgill.ca} (\href{https://orcid.org/0000-0003-4315-6788}{ORCID}) (@rempsyc)
+\strong{Maintainer}: Rémi Thériault \email{remi.theriault@mail.mcgill.ca} (\href{https://orcid.org/0000-0003-4315-6788}{ORCID})
 
 Authors:
 \itemize{
-  \item Dominique Makowski \email{dom.makowski@gmail.com} (\href{https://orcid.org/0000-0001-5375-9967}{ORCID}) (@Dom_Makowski)
-  \item Daniel Lüdecke \email{d.luedecke@uke.de} (\href{https://orcid.org/0000-0002-8895-3206}{ORCID}) (@strengejacke)
-  \item Indrajeet Patil \email{patilindrajeet.science@gmail.com} (\href{https://orcid.org/0000-0003-1995-6531}{ORCID}) (@patilindrajeets)
-  \item Mattan S. Ben-Shachar \email{matanshm@post.bgu.ac.il} (\href{https://orcid.org/0000-0002-4287-4801}{ORCID}) (@mattansb)
-  \item Brenton M. Wiernik \email{brenton@wiernik.org} (\href{https://orcid.org/0000-0001-9560-6336}{ORCID}) (@bmwiernik)
+  \item Dominique Makowski \email{dom.makowski@gmail.com} (\href{https://orcid.org/0000-0001-5375-9967}{ORCID})
+  \item Daniel Lüdecke \email{d.luedecke@uke.de} (\href{https://orcid.org/0000-0002-8895-3206}{ORCID})
+  \item Indrajeet Patil \email{patilindrajeet.science@gmail.com} (\href{https://orcid.org/0000-0003-1995-6531}{ORCID})
+  \item Mattan S. Ben-Shachar \email{matanshm@post.bgu.ac.il} (\href{https://orcid.org/0000-0002-4287-4801}{ORCID})
+  \item Brenton M. Wiernik \email{brenton@wiernik.org} (\href{https://orcid.org/0000-0001-9560-6336}{ORCID})
 }
 
 Other contributors:
diff --git a/tests/testthat/test-format_model.R b/tests/testthat/test-format_model.R
index 3f569a45..a429edde 100644
--- a/tests/testthat/test-format_model.R
+++ b/tests/testthat/test-format_model.R
@@ -20,8 +20,6 @@ test_that("format_model", {
 })
 
 
-
-
 test_that("format_model", {
   skip_if_not_installed("rstanarm")
   expect_identical(
diff --git a/tests/testthat/test-report.aov.R b/tests/testthat/test-report.aov.R
index 01f33e5c..f25a0b6c 100644
--- a/tests/testthat/test-report.aov.R
+++ b/tests/testthat/test-report.aov.R
@@ -32,8 +32,8 @@ test_that("report.aov", {
   expect_equal(sum(as.report_table(r3, summary = TRUE)$Mean_Square), 5.787854, tolerance = 0.01)
 
   data <- iris
-  data$Cat1 <- rep(c("X", "X", "Y"), length.out = nrow(data))
-  data$Cat2 <- rep(c("A", "B"), length.out = nrow(data))
+  data$Cat1 <- rep_len(c("X", "X", "Y"), nrow(data))
+  data$Cat2 <- rep_len(c("A", "B"), nrow(data))
 
   model <- aov(Sepal.Length ~ Species * Cat1 * Cat2, data = data)
   r4 <- report(model)
diff --git a/tests/testthat/test-report.lmer.R b/tests/testthat/test-report.lmer.R
index 53421b15..d3a27687 100644
--- a/tests/testthat/test-report.lmer.R
+++ b/tests/testthat/test-report.lmer.R
@@ -3,12 +3,12 @@ skip_if_not_installed("lme4")
 test_that("report-lmer", {
   df <- lme4::sleepstudy
   set.seed(123)
-  df$mygrp <- sample(1:5, size = 180, replace = TRUE)
+  df$mygrp <- sample.int(5, size = 180, replace = TRUE)
   df$mysubgrp <- NA
   for (i in 1:5) {
     filter_group <- df$mygrp == i
     df$mysubgrp[filter_group] <-
-      sample(1:30, size = sum(filter_group), replace = TRUE)
+      sample.int(30, size = sum(filter_group), replace = TRUE)
   }
 
   set.seed(123)