From 9494db7209e560fa81fd8ed6377002e6a4b47b22 Mon Sep 17 00:00:00 2001 From: Indrajeet Patil Date: Wed, 28 Dec 2022 20:28:50 +0100 Subject: [PATCH] Get rid of `numeric_leading_zero_linter()` lints https://github.com/easystats/easystats/issues/334 --- R/compute_variances.R | 2 +- R/get_loglikelihood.R | 2 +- R/get_statistic.R | 2 +- tests/testthat/test-BayesFactorBF.R | 6 ++-- tests/testthat/test-GLMMadaptive.R | 2 +- tests/testthat/test-Gam2.R | 2 +- tests/testthat/test-LORgee.R | 2 +- tests/testthat/test-MCMCglmm.R | 4 +-- tests/testthat/test-aovlist.R | 4 +-- tests/testthat/test-betabin.R | 4 +-- tests/testthat/test-betareg.R | 2 +- tests/testthat/test-bigglm.R | 2 +- tests/testthat/test-blmer.R | 4 +-- tests/testthat/test-censReg.R | 2 +- tests/testthat/test-clm.R | 6 ++-- tests/testthat/test-clm2.R | 2 +- tests/testthat/test-clmm.R | 10 ++----- tests/testthat/test-coxme.R | 4 +-- tests/testthat/test-coxph.R | 2 +- tests/testthat/test-cpglmm.R | 4 +-- tests/testthat/test-crch.R | 2 +- tests/testthat/test-crq.R | 4 +-- tests/testthat/test-feis.R | 2 +- tests/testthat/test-felm.R | 2 +- .../testthat/test-find_predictor_nested_re.R | 2 +- tests/testthat/test-find_terms.R | 2 +- tests/testthat/test-find_weights.R | 4 +-- tests/testthat/test-fixest.R | 16 +++++----- tests/testthat/test-format.R | 30 ++++++++++++------- tests/testthat/test-format_table_ci.R | 2 +- tests/testthat/test-gam.R | 10 +++---- tests/testthat/test-gamlss.R | 4 +-- tests/testthat/test-gamm.R | 6 ++-- tests/testthat/test-gamm4.R | 4 +-- tests/testthat/test-gbm.R | 2 +- tests/testthat/test-gee.R | 2 +- tests/testthat/test-geeglm.R | 2 +- tests/testthat/test-get_predicted.R | 2 +- tests/testthat/test-get_residuals.R | 6 ++-- tests/testthat/test-get_weights.R | 2 +- tests/testthat/test-glm.R | 4 +-- tests/testthat/test-glmmTMB.R | 4 +-- tests/testthat/test-glmrob_base.R | 4 +-- tests/testthat/test-gls.R | 2 +- tests/testthat/test-gmnl.R | 2 +- tests/testthat/test-hurdle.R | 2 +- tests/testthat/test-iv_robust.R | 4 +-- tests/testthat/test-ivreg.R | 2 +- tests/testthat/test-ivreg_AER.R | 2 +- tests/testthat/test-lm.R | 4 +-- tests/testthat/test-lm_robust.R | 6 ++-- tests/testthat/test-lme.R | 2 +- tests/testthat/test-lmer.R | 4 +-- tests/testthat/test-lmrob_base.R | 4 +-- tests/testthat/test-logistf.R | 2 +- tests/testthat/test-metaBMA.R | 7 ++++- tests/testthat/test-mixed.R | 4 +-- tests/testthat/test-mlogit.R | 4 +-- tests/testthat/test-multinom.R | 2 +- tests/testthat/test-namespace.R | 4 +-- tests/testthat/test-negbin.R | 4 +-- tests/testthat/test-ols.R | 4 +-- tests/testthat/test-panelr.R | 2 +- tests/testthat/test-plm.R | 2 +- tests/testthat/test-polr.R | 2 +- tests/testthat/test-psm.R | 4 +-- tests/testthat/test-rlmer.R | 4 +-- tests/testthat/test-rms.R | 2 +- tests/testthat/test-rq.R | 6 ++-- tests/testthat/test-rqss.R | 6 ++-- tests/testthat/test-rstanarm.R | 4 +-- tests/testthat/test-spatial.R | 2 +- tests/testthat/test-speedglm.R | 4 +-- tests/testthat/test-speedlm.R | 4 +-- tests/testthat/test-survey.R | 2 +- tests/testthat/test-survfit.R | 2 +- tests/testthat/test-survreg.R | 2 +- tests/testthat/test-tidymodels.R | 4 +-- tests/testthat/test-tobit.R | 2 +- tests/testthat/test-truncreg.R | 2 +- tests/testthat/test-vgam.R | 4 +-- tests/testthat/test-vglm.R | 6 ++-- tests/testthat/test-zeroinfl.R | 2 +- vignettes/display.Rmd | 6 ++-- 84 files changed, 166 insertions(+), 159 deletions(-) diff --git a/R/compute_variances.R b/R/compute_variances.R index c494cba18..d3cf07771 100644 --- a/R/compute_variances.R +++ b/R/compute_variances.R @@ -953,7 +953,7 @@ # we here check if random slopes from correlated and uncorrelated # are duplicated (i.e. their difference is 0 - including a tolerance) # and then remove duplicated elements - the_same <- which(abs(outer(out[j], rndslopes, `-`)) < .0001) + the_same <- which(abs(outer(out[j], rndslopes, `-`)) < 0.0001) if (length(the_same) && grepl(dn[the_same], names(out[j]), fixed = TRUE)) { to_remove <- c(to_remove, j) } diff --git a/R/get_loglikelihood.R b/R/get_loglikelihood.R index ebc39224e..5625acf2a 100644 --- a/R/get_loglikelihood.R +++ b/R/get_loglikelihood.R @@ -459,7 +459,7 @@ get_loglikelihood.cpglm <- get_loglikelihood.plm } else if (trans == "expm1") { .weighted_sum((get_response(x, as_proportion = TRUE) - 1), w = model_weights) } else if (trans == "sqrt") { - .weighted_sum(log(.5 / sqrt(get_response(x, as_proportion = TRUE))), w = model_weights) + .weighted_sum(log(0.5 / sqrt(get_response(x, as_proportion = TRUE))), w = model_weights) } else if (is.null(model_weights)) { .ll_log_adjustment(x) } else { diff --git a/R/get_statistic.R b/R/get_statistic.R index 44d0aa352..e9fcb4482 100644 --- a/R/get_statistic.R +++ b/R/get_statistic.R @@ -2304,7 +2304,7 @@ get_statistic.metaplus <- function(x, ...) { ci_low <- as.vector(x$results[, "95% ci.lb"]) ci_high <- as.vector(x$results[, "95% ci.ub"]) cis <- apply(cbind(ci_low, ci_high), MARGIN = 1, diff) - se <- cis / (2 * stats::qnorm(.975)) + se <- cis / (2 * stats::qnorm(0.975)) out <- data.frame( Parameter = params$Parameter, diff --git a/tests/testthat/test-BayesFactorBF.R b/tests/testthat/test-BayesFactorBF.R index 6b985dea0..42e9abb2b 100644 --- a/tests/testthat/test-BayesFactorBF.R +++ b/tests/testthat/test-BayesFactorBF.R @@ -66,7 +66,7 @@ test_that("find_parameters", { expect_equal(find_parameters(t2d)[[1]], "Difference") }) -t <- c(-.15, 2.39, 2.42, 2.43) +t <- c(-0.15, 2.39, 2.42, 2.43) N <- c(100, 150, 97, 99) x <- meta.ttestBF(t = t, n1 = N, rscale = 1) test_that("get_data", { @@ -303,9 +303,9 @@ ttest_BFk <- ttestBF(sleep$extra[sleep$group == 1], sleep$extra[sleep$group == 2 nullInterval = c(-3, 0) ) -prop_BF1 <- proportionBF(y = 15, N = 25, p = .5, progress = FALSE) +prop_BF1 <- proportionBF(y = 15, N = 25, p = 0.5, progress = FALSE) prop_BFk <- proportionBF( - y = 15, N = 25, p = .5, progress = FALSE, + y = 15, N = 25, p = 0.5, progress = FALSE, nullInterval = c(0, 0.3) ) diff --git a/tests/testthat/test-GLMMadaptive.R b/tests/testthat/test-GLMMadaptive.R index b0cae643b..5cbcd5450 100644 --- a/tests/testthat/test-GLMMadaptive.R +++ b/tests/testthat/test-GLMMadaptive.R @@ -155,7 +155,7 @@ if (.runThisTest) { }) test_that("link_inverse", { - expect_identical(link_inverse(m)(.2), exp(.2)) + expect_identical(link_inverse(m)(0.2), exp(0.2)) }) test_that("clean_names", { diff --git a/tests/testthat/test-Gam2.R b/tests/testthat/test-Gam2.R index 763a8dc8c..564e8eeda 100644 --- a/tests/testthat/test-Gam2.R +++ b/tests/testthat/test-Gam2.R @@ -28,7 +28,7 @@ if (.runThisTest && }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), plogis(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), plogis(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-LORgee.R b/tests/testthat/test-LORgee.R index 238c3a5ee..287408e58 100644 --- a/tests/testthat/test-LORgee.R +++ b/tests/testthat/test-LORgee.R @@ -49,7 +49,7 @@ if (requiet("multgee")) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), plogis(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), plogis(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-MCMCglmm.R b/tests/testthat/test-MCMCglmm.R index 314a4cf3b..12b20efc4 100644 --- a/tests/testthat/test-MCMCglmm.R +++ b/tests/testthat/test-MCMCglmm.R @@ -47,7 +47,7 @@ if (.Platform$OS.type == "windows" && }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.5), .5, tolerance = 1e-1) + expect_equal(link_inverse(m1)(0.5), 0.5, tolerance = 1e-1) }) test_that("get_data", { @@ -84,7 +84,7 @@ if (.Platform$OS.type == "windows" && }) test_that("linkfun", { - expect_equal(link_function(m1)(.5), .5, tolerance = 1e-1) + expect_equal(link_function(m1)(0.5), 0.5, tolerance = 1e-1) }) test_that("find_parameters", { diff --git a/tests/testthat/test-aovlist.R b/tests/testthat/test-aovlist.R index d335ebc3c..fa254e705 100644 --- a/tests/testthat/test-aovlist.R +++ b/tests/testthat/test-aovlist.R @@ -39,8 +39,8 @@ test_that("get_predictors", { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) - expect_equal(link_inverse(m2)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) + expect_equal(link_inverse(m2)(0.2), 0.2, tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-betabin.R b/tests/testthat/test-betabin.R index 13d154dde..ec1975d76 100644 --- a/tests/testthat/test-betabin.R +++ b/tests/testthat/test-betabin.R @@ -49,11 +49,11 @@ if (requiet("aod")) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), plogis(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), plogis(0.2), tolerance = 1e-5) }) test_that("link_function", { - expect_equal(link_function(m1)(.2), qlogis(.2), tolerance = 1e-5) + expect_equal(link_function(m1)(0.2), qlogis(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-betareg.R b/tests/testthat/test-betareg.R index 9c7081ab3..798b2c374 100644 --- a/tests/testthat/test-betareg.R +++ b/tests/testthat/test-betareg.R @@ -35,7 +35,7 @@ if ( }) test_that("link_inverse", { - expect_identical(link_inverse(m1)(.2), plogis(.2)) + expect_identical(link_inverse(m1)(0.2), plogis(0.2)) }) test_that("get_data", { diff --git a/tests/testthat/test-bigglm.R b/tests/testthat/test-bigglm.R index 9bb18e89b..998386938 100644 --- a/tests/testthat/test-bigglm.R +++ b/tests/testthat/test-bigglm.R @@ -54,7 +54,7 @@ if (.runThisTest && requiet("glmmTMB") && requiet("biglm")) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), exp(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), exp(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-blmer.R b/tests/testthat/test-blmer.R index aad4dfe25..1f7119632 100644 --- a/tests/testthat/test-blmer.R +++ b/tests/testthat/test-blmer.R @@ -101,8 +101,8 @@ if (requiet("blme")) { }) test_that("link_inverse", { - expect_identical(link_inverse(m1)(.2), .2) - expect_identical(link_inverse(m2)(.2), .2) + expect_identical(link_inverse(m1)(0.2), 0.2) + expect_identical(link_inverse(m2)(0.2), 0.2) }) test_that("get_data", { diff --git a/tests/testthat/test-censReg.R b/tests/testthat/test-censReg.R index 7d74cc847..6ed17eeca 100644 --- a/tests/testthat/test-censReg.R +++ b/tests/testthat/test-censReg.R @@ -67,7 +67,7 @@ if (requiet("censReg") && requiet("AER")) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-clm.R b/tests/testthat/test-clm.R index 26fccf4f5..f330eba81 100644 --- a/tests/testthat/test-clm.R +++ b/tests/testthat/test-clm.R @@ -1,6 +1,4 @@ -if ( - - requiet("ordinal")) { +if (requiet("ordinal")) { data(wine, package = "ordinal") m1 <- clm(rating ~ temp * contact, data = wine) @@ -37,7 +35,7 @@ if ( }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), plogis(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), plogis(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-clm2.R b/tests/testthat/test-clm2.R index 939eb9493..46f9f4b0b 100644 --- a/tests/testthat/test-clm2.R +++ b/tests/testthat/test-clm2.R @@ -41,7 +41,7 @@ if ( }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), plogis(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), plogis(0.2), tolerance = 1e-5) }) test_that("find_weights", { diff --git a/tests/testthat/test-clmm.R b/tests/testthat/test-clmm.R index 00fc61405..f8ce27974 100644 --- a/tests/testthat/test-clmm.R +++ b/tests/testthat/test-clmm.R @@ -14,11 +14,7 @@ osx <- tryCatch( .runThisTest <- Sys.getenv("RunAllinsightTests") == "yes" -if (.runThisTest && - - - requiet("lme4") && - requiet("ordinal")) { +if (.runThisTest && requiet("lme4") && requiet("ordinal")) { data(wine, package = "ordinal") data(soup) @@ -92,8 +88,8 @@ if (.runThisTest && }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), plogis(.2), tolerance = 1e-5) - expect_equal(link_inverse(m2)(.2), pnorm(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), plogis(0.2), tolerance = 1e-5) + expect_equal(link_inverse(m2)(0.2), pnorm(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-coxme.R b/tests/testthat/test-coxme.R index 41cc6aa0e..21342e7ff 100644 --- a/tests/testthat/test-coxme.R +++ b/tests/testthat/test-coxme.R @@ -36,8 +36,8 @@ if ( }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), plogis(.2), tolerance = 1e-5) - expect_equal(link_inverse(m2)(.2), plogis(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), plogis(0.2), tolerance = 1e-5) + expect_equal(link_inverse(m2)(0.2), plogis(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-coxph.R b/tests/testthat/test-coxph.R index e07a91f1a..22c6bf09a 100644 --- a/tests/testthat/test-coxph.R +++ b/tests/testthat/test-coxph.R @@ -25,7 +25,7 @@ test_that("find_response", { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), plogis(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), plogis(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-cpglmm.R b/tests/testthat/test-cpglmm.R index c83b42968..3b7560850 100644 --- a/tests/testthat/test-cpglmm.R +++ b/tests/testthat/test-cpglmm.R @@ -85,11 +85,11 @@ if ( test_that("link_function", { - expect_equal(link_function(m1)(.2), log(.2), tolerance = 1e-3) + expect_equal(link_function(m1)(0.2), log(0.2), tolerance = 1e-3) }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), exp(.2), tolerance = 1e-3) + expect_equal(link_inverse(m1)(0.2), exp(0.2), tolerance = 1e-3) }) diff --git a/tests/testthat/test-crch.R b/tests/testthat/test-crch.R index 7441932e4..eac89d90d 100644 --- a/tests/testthat/test-crch.R +++ b/tests/testthat/test-crch.R @@ -39,7 +39,7 @@ if ( }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-crq.R b/tests/testthat/test-crq.R index eb6b898dc..60490b924 100644 --- a/tests/testthat/test-crq.R +++ b/tests/testthat/test-crq.R @@ -72,11 +72,11 @@ if (requiet("quantreg")) { }) test_that("link_function", { - expect_equal(link_function(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_function(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("find_parameters", { diff --git a/tests/testthat/test-feis.R b/tests/testthat/test-feis.R index b0f6817c9..4ff43b9a9 100644 --- a/tests/testthat/test-feis.R +++ b/tests/testthat/test-feis.R @@ -67,7 +67,7 @@ if (!osx && requiet("plm") && requiet("feisr")) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-felm.R b/tests/testthat/test-felm.R index 1a282a2db..8f306595b 100644 --- a/tests/testthat/test-felm.R +++ b/tests/testthat/test-felm.R @@ -65,7 +65,7 @@ if ( }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-find_predictor_nested_re.R b/tests/testthat/test-find_predictor_nested_re.R index 80615efa9..5aa6569e9 100644 --- a/tests/testthat/test-find_predictor_nested_re.R +++ b/tests/testthat/test-find_predictor_nested_re.R @@ -1,7 +1,7 @@ if (requiet("lme4")) { set.seed(1984) dat <- data.frame( - y = rnorm(1000 * 5, sd = 1 - .20), + y = rnorm(1000 * 5, sd = 1 - 0.20), time = rep(1:10, 100 * 5), g1 = sort(rep(1:100, 10 * 5)), g2 = sort(rep(1:10, 100 * 5)) diff --git a/tests/testthat/test-find_terms.R b/tests/testthat/test-find_terms.R index 3d615f53a..4d82d6052 100644 --- a/tests/testthat/test-find_terms.R +++ b/tests/testthat/test-find_terms.R @@ -28,7 +28,7 @@ if (requiet("lme4")) { set.seed(1984) dat <- data.frame( - y = rnorm(100 * 5, sd = 1 - .20), + y = rnorm(100 * 5, sd = 1 - 0.20), time = rep(1:10, 10 * 5), g1 = sort(rep(1:100, 5)), g2 = sort(rep(1:10, 10 * 5)) diff --git a/tests/testthat/test-find_weights.R b/tests/testthat/test-find_weights.R index c1f757eed..41db6eb58 100644 --- a/tests/testthat/test-find_weights.R +++ b/tests/testthat/test-find_weights.R @@ -1,13 +1,13 @@ if (requiet("lme4")) { test_that("find_weights", { data(mtcars) - mtcars$weight <- rnorm(nrow(mtcars), 1, .3) + mtcars$weight <- rnorm(nrow(mtcars), 1, 0.3) m <- lm(mpg ~ wt + cyl + vs, data = mtcars, weights = weight) expect_equal(find_weights(m), "weight") }) test_that("find_weights", { data(iris) - iris$wgt <- rnorm(nrow(iris), 1, .3) + iris$wgt <- rnorm(nrow(iris), 1, 0.3) m <- lmer(Sepal.Width ~ Sepal.Length + (1 | Species), data = iris, weights = wgt) expect_equal(find_weights(m), "wgt") }) diff --git a/tests/testthat/test-fixest.R b/tests/testthat/test-fixest.R index c621b9ebf..27532dac6 100644 --- a/tests/testthat/test-fixest.R +++ b/tests/testthat/test-fixest.R @@ -107,15 +107,15 @@ test_that("get_predictors", { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), exp(.2), tolerance = 1e-4) - expect_equal(link_inverse(m2)(.2), .2, tolerance = 1e-4) - expect_equal(link_inverse(m3)(.2), exp(.2), tolerance = 1e-4) + expect_equal(link_inverse(m1)(0.2), exp(0.2), tolerance = 1e-4) + expect_equal(link_inverse(m2)(0.2), 0.2, tolerance = 1e-4) + expect_equal(link_inverse(m3)(0.2), exp(0.2), tolerance = 1e-4) }) test_that("link_function", { - expect_equal(link_function(m1)(.2), log(.2), tolerance = 1e-4) - expect_equal(link_function(m2)(.2), .2, tolerance = 1e-4) - expect_equal(link_function(m3)(.2), log(.2), tolerance = 1e-4) + expect_equal(link_function(m1)(0.2), log(0.2), tolerance = 1e-4) + expect_equal(link_function(m2)(0.2), 0.2, tolerance = 1e-4) + expect_equal(link_function(m3)(0.2), log(0.2), tolerance = 1e-4) }) test_that("get_data", { @@ -264,14 +264,14 @@ test_that("get_predicted", { b <- get_predicted(m1, type = "link", predict = NULL) expect_equal(a, b) # these used to raise warnings - expect_warning(get_predicted(m1, ci = .4), NA) + expect_warning(get_predicted(m1, ci = 0.4), NA) expect_warning(get_predicted(m1, predict = NULL, type = "link"), NA) }) test_that("get_data works when model data has name of reserved words", { ## NOTE check back every now and then and see if tests still work skip("works interactively") - rep <- data.frame(Y = runif(100) > .5, X = rnorm(100)) + rep <- data.frame(Y = runif(100) > 0.5, X = rnorm(100)) m <- feglm(Y ~ X, data = rep, family = binomial) out <- get_data(m) expect_s3_class(out, "data.frame") diff --git a/tests/testthat/test-format.R b/tests/testthat/test-format.R index 830d04fa1..6502fbf18 100644 --- a/tests/testthat/test-format.R +++ b/tests/testthat/test-format.R @@ -63,29 +63,37 @@ test_that("format_p", { }) test_that("format_table, other CI columns", { - x <- data.frame(test_CI = .9, test_CI_low = .1, test_CI_high = 1.3) + x <- data.frame(test_CI = 0.9, test_CI_low = 0.1, test_CI_high = 1.3) test <- utils::capture.output(format_table(x)) expect_equal(test, c(" test 90% CI", "1 [0.10, 1.30]")) x <- data.frame( - CI = .8, CI_low = 2.43, CI_high = 5.453, - test_CI = .9, test_CI_low = .1, test_CI_high = 1.3 + CI = 0.8, + CI_low = 2.43, + CI_high = 5.453, + test_CI = 0.9, + test_CI_low = 0.1, + test_CI_high = 1.3 ) test <- utils::capture.output(format_table(x)) expect_equal(test, c(" 80% CI test 90% CI", "1 [2.43, 5.45] [0.10, 1.30]")) - x <- data.frame(CI_low = 2.43, CI_high = 5.453, test_CI_low = .1, test_CI_high = 1.3) - attr(x, "ci") <- .8 - attr(x, "ci_test") <- .9 + x <- data.frame(CI_low = 2.43, CI_high = 5.453, test_CI_low = 0.1, test_CI_high = 1.3) + attr(x, "ci") <- 0.8 + attr(x, "ci_test") <- 0.9 test <- utils::capture.output(format_table(x)) expect_equal(test, c(" 80% CI test 90% CI", "1 [2.43, 5.45] [0.10, 1.30]")) x <- data.frame( - CI_low = 2.43, CI_high = 5.453, test_CI_low = .1, test_CI_high = 1.3, - other_CI_low = .12, other_CI_high = 1.4 + CI_low = 2.43, + CI_high = 5.453, + test_CI_low = 0.1, + test_CI_high = 1.3, + other_CI_low = 0.12, + other_CI_high = 1.4 ) - attr(x, "ci") <- .8 - attr(x, "ci_test") <- .9 + attr(x, "ci") <- 0.8 + attr(x, "ci_test") <- 0.9 test <- utils::capture.output(format_table(x)) expect_equal(test, c(" 80% CI test 80% CI other 80% CI", "1 [2.43, 5.45] [0.10, 1.30] [0.12, 1.40]")) }) @@ -104,7 +112,7 @@ test_that("format_table, multiple CI columns", { df_error = c(29, 29, 29), stringsAsFactors = FALSE ) - attr(d, "ci") <- c(.8, .9) + attr(d, "ci") <- c(0.8, 0.9) expect_equal( format_table(d), data.frame( diff --git a/tests/testthat/test-format_table_ci.R b/tests/testthat/test-format_table_ci.R index cc0b7bc6b..adb3ddf40 100644 --- a/tests/testthat/test-format_table_ci.R +++ b/tests/testthat/test-format_table_ci.R @@ -55,7 +55,7 @@ if (.runThisTest && requiet("bayestestR")) { set.seed(1234) test_that("format_table with multiple si-levels", { d <- bayestestR::distribution_normal(1000) - x <- bayestestR::hdi(d, ci = c(.80, .90)) + x <- bayestestR::hdi(d, ci = c(0.80, 0.90)) out <- capture.output(print(x)) expect_equal( out, diff --git a/tests/testthat/test-gam.R b/tests/testthat/test-gam.R index 233c11d24..7daf48b0e 100644 --- a/tests/testthat/test-gam.R +++ b/tests/testthat/test-gam.R @@ -102,9 +102,9 @@ if (.runThisTest) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) - expect_equal(link_inverse(m2)(.2), .2, tolerance = 1e-5) - expect_equal(link_inverse(m3)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) + expect_equal(link_inverse(m2)(0.2), 0.2, tolerance = 1e-5) + expect_equal(link_inverse(m3)(0.2), 0.2, tolerance = 1e-5) }) test_that("get_data", { @@ -263,7 +263,7 @@ if (.runThisTest) { # poisson void <- capture.output( - dat <<- gamSim(1, n = 400, dist = "poisson", scale = .25) + dat <<- gamSim(1, n = 400, dist = "poisson", scale = 0.25) ) b4 <- gam( y ~ s(x0) + s(x1) + s(x2) + s(x3), @@ -290,7 +290,7 @@ if (.runThisTest) { expect_equal(as.vector(p1), as.vector(p2), tolerance = 1e-4, ignore_attr = TRUE) void <- capture.output( - dat <<- gamSim(1, n = 400, dist = "poisson", scale = .25) + dat <<- gamSim(1, n = 400, dist = "poisson", scale = 0.25) ) b4 <- gam( y ~ s(x0) + s(x1) + s(x2) + s(x3), diff --git a/tests/testthat/test-gamlss.R b/tests/testthat/test-gamlss.R index 91e21e5dd..99d29336f 100644 --- a/tests/testthat/test-gamlss.R +++ b/tests/testthat/test-gamlss.R @@ -92,11 +92,11 @@ if ( }) test_that("link_function", { - expect_equal(link_function(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_function(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("find_parameters", { diff --git a/tests/testthat/test-gamm.R b/tests/testthat/test-gamm.R index 519655cc7..bc570d754 100644 --- a/tests/testthat/test-gamm.R +++ b/tests/testthat/test-gamm.R @@ -4,7 +4,7 @@ if (.runThisTest) { unloadNamespace("gam") if (requiet("mgcv")) { set.seed(0) - void <- capture.output(dat <- gamSim(6, n = 200, scale = .2, dist = "poisson")) + void <- capture.output(dat <- gamSim(6, n = 200, scale = 0.2, dist = "poisson")) m1 <- gamm( y ~ s(x0) + s(x1) + s(x2), @@ -45,7 +45,7 @@ if (.runThisTest) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), exp(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), exp(0.2), tolerance = 1e-5) }) test_that("get_data", { @@ -142,7 +142,7 @@ if (.runThisTest) { set.seed(0) void <- capture.output( - dat <- gamSim(6, n = 200, scale = .2, dist = "poisson") + dat <- gamSim(6, n = 200, scale = 0.2, dist = "poisson") ) m2 <- gamm( diff --git a/tests/testthat/test-gamm4.R b/tests/testthat/test-gamm4.R index 4df8e9f56..b9326e106 100644 --- a/tests/testthat/test-gamm4.R +++ b/tests/testthat/test-gamm4.R @@ -20,7 +20,7 @@ if (.runThisTest && !osx && requiet("gamm4")) { set.seed(0) void <- capture.output(dat <- gamSim(1, n = 400, scale = 2)) ## simulate 4 term additive truth dat$fac <- fac <- as.factor(sample(1:20, 400, replace = TRUE)) - dat$y <- dat$y + model.matrix(~ fac - 1) %*% rnorm(20) * .5 + dat$y <- dat$y + model.matrix(~ fac - 1) %*% rnorm(20) * 0.5 m1 <- gamm4(y ~ s(x0) + x1 + s(x2), data = dat, @@ -50,7 +50,7 @@ if (.runThisTest && !osx && requiet("gamm4")) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-gbm.R b/tests/testthat/test-gbm.R index 13c9a0c5d..ac5baf580 100644 --- a/tests/testthat/test-gbm.R +++ b/tests/testthat/test-gbm.R @@ -56,7 +56,7 @@ if (.runThisTest) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-gee.R b/tests/testthat/test-gee.R index 05ee0fd1d..91b1f83d9 100644 --- a/tests/testthat/test-gee.R +++ b/tests/testthat/test-gee.R @@ -44,7 +44,7 @@ if ( }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-geeglm.R b/tests/testthat/test-geeglm.R index c9b15d046..2e9d0a326 100644 --- a/tests/testthat/test-geeglm.R +++ b/tests/testthat/test-geeglm.R @@ -55,7 +55,7 @@ if ( }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), exp(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), exp(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-get_predicted.R b/tests/testthat/test-get_predicted.R index 92321fc7a..6f5bf5903 100644 --- a/tests/testthat/test-get_predicted.R +++ b/tests/testthat/test-get_predicted.R @@ -567,7 +567,7 @@ test_that("brms: `type` in ellipsis used to produce the wrong intervals", { y <- get_predicted(mod, predict = "expectation", ci = 0.95) z <- get_predicted(mod, predict = NULL, type = "response", ci = 0.95, verbose = FALSE) expect_equal(round(x[1], 1), -1.5, tolerance = 1e-1) - expect_equal(round(y[1], 1), .2, tolerance = 1e-1) + expect_equal(round(y[1], 1), 0.2, tolerance = 1e-1) expect_equal(y, z, ignore_attr = TRUE) data <- mtcars diff --git a/tests/testthat/test-get_residuals.R b/tests/testthat/test-get_residuals.R index b093213d3..2a3ddca4d 100644 --- a/tests/testthat/test-get_residuals.R +++ b/tests/testthat/test-get_residuals.R @@ -3,9 +3,9 @@ if (requiet("lme4")) { data(sleepstudy) data(cbpp) set.seed(123) - mtcars$w <- abs(rnorm(nrow(mtcars), mean = 1, .3)) - sleepstudy$w <- abs(rnorm(nrow(sleepstudy), mean = 1, .3)) - cbpp$w <- abs(rnorm(nrow(cbpp), mean = 1, .3)) + mtcars$w <- abs(rnorm(nrow(mtcars), mean = 1, 0.3)) + sleepstudy$w <- abs(rnorm(nrow(sleepstudy), mean = 1, 0.3)) + cbpp$w <- abs(rnorm(nrow(cbpp), mean = 1, 0.3)) test_that("get_residuals - lm", { m <- lm(am ~ cyl, weights = w, data = mtcars) diff --git a/tests/testthat/test-get_weights.R b/tests/testthat/test-get_weights.R index e37153432..48371c56e 100644 --- a/tests/testthat/test-get_weights.R +++ b/tests/testthat/test-get_weights.R @@ -9,7 +9,7 @@ if (requiet("lme4")) { }) set.seed(123) - mtcars$w <- abs(rnorm(nrow(mtcars), sd = .5)) + mtcars$w <- abs(rnorm(nrow(mtcars), sd = 0.5)) m1 <- lmer(mpg ~ am + (1 | cyl), data = mtcars, weights = w) m2 <- lm(mpg ~ am, data = mtcars, weights = w) diff --git a/tests/testthat/test-glm.R b/tests/testthat/test-glm.R index 9e908db7c..6f191a055 100644 --- a/tests/testthat/test-glm.R +++ b/tests/testthat/test-glm.R @@ -76,11 +76,11 @@ if ( }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), exp(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), exp(0.2), tolerance = 1e-5) }) test_that("linkfun", { - expect_equal(link_function(m1)(.2), -1.609438, tolerance = 1e-4) + expect_equal(link_function(m1)(0.2), -1.609438, tolerance = 1e-4) }) test_that("get_data", { diff --git a/tests/testthat/test-glmmTMB.R b/tests/testthat/test-glmmTMB.R index 14d66659d..fd302160e 100644 --- a/tests/testthat/test-glmmTMB.R +++ b/tests/testthat/test-glmmTMB.R @@ -218,8 +218,8 @@ if ( }) test_that("link_inverse", { - expect_identical(link_inverse(m1)(.2), exp(.2)) - expect_identical(link_inverse(m2)(.2), exp(.2)) + expect_identical(link_inverse(m1)(0.2), exp(0.2)) + expect_identical(link_inverse(m2)(0.2), exp(0.2)) }) test_that("get_data", { diff --git a/tests/testthat/test-glmrob_base.R b/tests/testthat/test-glmrob_base.R index a4e4af72d..a54b8386a 100644 --- a/tests/testthat/test-glmrob_base.R +++ b/tests/testthat/test-glmrob_base.R @@ -93,11 +93,11 @@ if ( }) test_that("link_function", { - expect_equal(link_function(m1)(.2), qlogis(.2), tolerance = 1e-5) + expect_equal(link_function(m1)(0.2), qlogis(0.2), tolerance = 1e-5) }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), plogis(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), plogis(0.2), tolerance = 1e-5) }) test_that("find_parameters", { diff --git a/tests/testthat/test-gls.R b/tests/testthat/test-gls.R index 9930bee37..60fb0f109 100644 --- a/tests/testthat/test-gls.R +++ b/tests/testthat/test-gls.R @@ -39,7 +39,7 @@ if ( }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-gmnl.R b/tests/testthat/test-gmnl.R index 9f8705bae..3f07fc7d2 100644 --- a/tests/testthat/test-gmnl.R +++ b/tests/testthat/test-gmnl.R @@ -33,7 +33,7 @@ if ( }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), plogis(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), plogis(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-hurdle.R b/tests/testthat/test-hurdle.R index c843bccee..8b1814f2b 100644 --- a/tests/testthat/test-hurdle.R +++ b/tests/testthat/test-hurdle.R @@ -35,7 +35,7 @@ if ( }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), exp(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), exp(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-iv_robust.R b/tests/testthat/test-iv_robust.R index cb19dbce0..ce9c56123 100644 --- a/tests/testthat/test-iv_robust.R +++ b/tests/testthat/test-iv_robust.R @@ -85,11 +85,11 @@ if (requiet("estimatr")) { }) test_that("link_function", { - expect_equal(link_function(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_function(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("find_parameters", { diff --git a/tests/testthat/test-ivreg.R b/tests/testthat/test-ivreg.R index 8687053a3..b187a71eb 100644 --- a/tests/testthat/test-ivreg.R +++ b/tests/testthat/test-ivreg.R @@ -47,7 +47,7 @@ if (requiet("ivreg")) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-ivreg_AER.R b/tests/testthat/test-ivreg_AER.R index 23637582f..ef8595fa7 100644 --- a/tests/testthat/test-ivreg_AER.R +++ b/tests/testthat/test-ivreg_AER.R @@ -55,7 +55,7 @@ if (requiet("AER")) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-lm.R b/tests/testthat/test-lm.R index 14a51df6e..574c54cf5 100644 --- a/tests/testthat/test-lm.R +++ b/tests/testthat/test-lm.R @@ -43,8 +43,8 @@ test_that("find_response", { }) test_that("link_inverse", { - expect_identical(link_inverse(m1)(.2), .2) - expect_identical(link_inverse(m2)(.2), .2) + expect_identical(link_inverse(m1)(0.2), 0.2) + expect_identical(link_inverse(m2)(0.2), 0.2) }) test_that("loglik", { diff --git a/tests/testthat/test-lm_robust.R b/tests/testthat/test-lm_robust.R index 5329bdf5a..b24a5fcad 100644 --- a/tests/testthat/test-lm_robust.R +++ b/tests/testthat/test-lm_robust.R @@ -35,7 +35,7 @@ if ( }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("get_data", { @@ -65,11 +65,11 @@ if ( }) test_that("link_function", { - expect_equal(link_function(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_function(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("find_parameters", { diff --git a/tests/testthat/test-lme.R b/tests/testthat/test-lme.R index 3755533d6..2bf79f62e 100644 --- a/tests/testthat/test-lme.R +++ b/tests/testthat/test-lme.R @@ -84,7 +84,7 @@ if ( }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-lmer.R b/tests/testthat/test-lmer.R index 799328ad8..637c7c11a 100644 --- a/tests/testthat/test-lmer.R +++ b/tests/testthat/test-lmer.R @@ -173,8 +173,8 @@ if (.runThisTest && }) test_that("link_inverse", { - expect_identical(link_inverse(m1)(.2), .2) - expect_identical(link_inverse(m2)(.2), .2) + expect_identical(link_inverse(m1)(0.2), 0.2) + expect_identical(link_inverse(m2)(0.2), 0.2) }) test_that("get_data", { diff --git a/tests/testthat/test-lmrob_base.R b/tests/testthat/test-lmrob_base.R index fec9dd522..e4e0ffdc9 100644 --- a/tests/testthat/test-lmrob_base.R +++ b/tests/testthat/test-lmrob_base.R @@ -61,11 +61,11 @@ if ( }) test_that("link_function", { - expect_equal(link_function(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_function(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("find_parameters", { diff --git a/tests/testthat/test-logistf.R b/tests/testthat/test-logistf.R index bb29a0c86..6f876ba36 100644 --- a/tests/testthat/test-logistf.R +++ b/tests/testthat/test-logistf.R @@ -47,7 +47,7 @@ if ( }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), plogis(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), plogis(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-metaBMA.R b/tests/testthat/test-metaBMA.R index 6b209b0a5..b25e77de8 100644 --- a/tests/testthat/test-metaBMA.R +++ b/tests/testthat/test-metaBMA.R @@ -3,7 +3,12 @@ if (.runThisTest && requiet("metaBMA")) { data(towels) set.seed(123) - mf <- meta_fixed(logOR, SE, study, data = towels, d = prior("norm", c(mean = 0, sd = .3), lower = 0)) + mf <- meta_fixed(logOR, + SE, + study, + data = towels, + d = prior("norm", c(mean = 0, sd = 0.3), lower = 0) + ) test_that("get_priors-metaBMA", { priors <- get_priors(mf) diff --git a/tests/testthat/test-mixed.R b/tests/testthat/test-mixed.R index f3c98a40d..2ede4cb1c 100644 --- a/tests/testthat/test-mixed.R +++ b/tests/testthat/test-mixed.R @@ -102,8 +102,8 @@ if ( }) test_that("link_inverse", { - expect_identical(link_inverse(m1)(.2), .2) - expect_identical(link_inverse(m2)(.2), .2) + expect_identical(link_inverse(m1)(0.2), 0.2) + expect_identical(link_inverse(m2)(0.2), 0.2) }) test_that("get_data", { diff --git a/tests/testthat/test-mlogit.R b/tests/testthat/test-mlogit.R index a31c828db..caae9714f 100644 --- a/tests/testthat/test-mlogit.R +++ b/tests/testthat/test-mlogit.R @@ -85,8 +85,8 @@ if ( } test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), plogis(.2), tolerance = 1e-5) - expect_equal(link_inverse(m2)(.2), plogis(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), plogis(0.2), tolerance = 1e-5) + expect_equal(link_inverse(m2)(0.2), plogis(0.2), tolerance = 1e-5) }) diff --git a/tests/testthat/test-multinom.R b/tests/testthat/test-multinom.R index 4bec47353..c2d0119f5 100644 --- a/tests/testthat/test-multinom.R +++ b/tests/testthat/test-multinom.R @@ -33,7 +33,7 @@ if ( }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), plogis(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), plogis(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-namespace.R b/tests/testthat/test-namespace.R index 5895d55e5..246dec0d2 100644 --- a/tests/testthat/test-namespace.R +++ b/tests/testthat/test-namespace.R @@ -30,11 +30,11 @@ if ( }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-4) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-4) }) test_that("link_function", { - expect_equal(link_function(m1)(.2), .2, tolerance = 1e-4) + expect_equal(link_function(m1)(0.2), 0.2, tolerance = 1e-4) }) test_that("get_data", { diff --git a/tests/testthat/test-negbin.R b/tests/testthat/test-negbin.R index 00b3d2be7..469598700 100644 --- a/tests/testthat/test-negbin.R +++ b/tests/testthat/test-negbin.R @@ -71,11 +71,11 @@ if (.runThisTest && Sys.getenv("USER") != "travis") { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), exp(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), exp(0.2), tolerance = 1e-5) }) test_that("link_function", { - expect_equal(link_function(m1)(.2), log(.2), tolerance = 1e-5) + expect_equal(link_function(m1)(0.2), log(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-ols.R b/tests/testthat/test-ols.R index e038c7f8f..709bae674 100644 --- a/tests/testthat/test-ols.R +++ b/tests/testthat/test-ols.R @@ -64,11 +64,11 @@ if ( }) test_that("linkfun", { - expect_equal(link_function(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_function(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("find_parameters", { diff --git a/tests/testthat/test-panelr.R b/tests/testthat/test-panelr.R index e9d3cacdb..fd298f595 100644 --- a/tests/testthat/test-panelr.R +++ b/tests/testthat/test-panelr.R @@ -64,7 +64,7 @@ if (requiet("panelr")) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("clean_parameters", { diff --git a/tests/testthat/test-plm.R b/tests/testthat/test-plm.R index d52dc8185..7d20fccd5 100644 --- a/tests/testthat/test-plm.R +++ b/tests/testthat/test-plm.R @@ -56,7 +56,7 @@ if (.runThisTest && getRversion() > "3.5") { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-polr.R b/tests/testthat/test-polr.R index 64295412b..d6cbd8cda 100644 --- a/tests/testthat/test-polr.R +++ b/tests/testthat/test-polr.R @@ -22,7 +22,7 @@ if (requiet("MASS")) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), plogis(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), plogis(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-psm.R b/tests/testthat/test-psm.R index 40c1d2751..93a29a109 100644 --- a/tests/testthat/test-psm.R +++ b/tests/testthat/test-psm.R @@ -4,7 +4,7 @@ if (requiet("rms")) { age <- rnorm(n, 50, 12) sex <- factor(sample(c("Female", "Male"), n, TRUE)) # Population hazard function: - h <- .02 * exp(.06 * (age - 50) + .8 * (sex == "Female")) + h <- 0.02 * exp(0.06 * (age - 50) + 0.8 * (sex == "Female")) d.time <- -log(runif(n)) / h cens <- 15 * runif(n) death <- ifelse(d.time <= cens, 1, 0) @@ -50,7 +50,7 @@ if (requiet("rms")) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), exp(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), exp(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-rlmer.R b/tests/testthat/test-rlmer.R index aa1dd932a..24829265b 100644 --- a/tests/testthat/test-rlmer.R +++ b/tests/testthat/test-rlmer.R @@ -110,8 +110,8 @@ if (.runThisTest && requiet("robustlmm") && utils::packageVersion("robustlmm") > }) test_that("link_inverse", { - expect_identical(link_inverse(m1)(.2), .2) - expect_identical(link_inverse(m2)(.2), .2) + expect_identical(link_inverse(m1)(0.2), 0.2) + expect_identical(link_inverse(m2)(0.2), 0.2) }) test_that("get_data", { diff --git a/tests/testthat/test-rms.R b/tests/testthat/test-rms.R index 4056c8c05..686bcd884 100644 --- a/tests/testthat/test-rms.R +++ b/tests/testthat/test-rms.R @@ -37,7 +37,7 @@ if (.runThisTest && requiet("rms")) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), plogis(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), plogis(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-rq.R b/tests/testthat/test-rq.R index 9c01f0db6..87f8b244a 100644 --- a/tests/testthat/test-rq.R +++ b/tests/testthat/test-rq.R @@ -5,7 +5,7 @@ if (requiet("quantreg")) { m1 <- rq(stack.loss ~ Air.Flow + Water.Temp, data = stackloss, - tau = .25 + tau = 0.25 ) test_that("model_info", { @@ -80,11 +80,11 @@ if (requiet("quantreg")) { }) test_that("link_function", { - expect_equal(link_function(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_function(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("find_parameters", { diff --git a/tests/testthat/test-rqss.R b/tests/testthat/test-rqss.R index ac79a65ce..c2a9663c3 100644 --- a/tests/testthat/test-rqss.R +++ b/tests/testthat/test-rqss.R @@ -10,7 +10,7 @@ if (FALSE && CobarOre$w <- rnorm(nrow(CobarOre)) # model - m1 <- rqss(z ~ w + qss(cbind(x, y), lambda = .08), data = CobarOre) + m1 <- rqss(z ~ w + qss(cbind(x, y), lambda = 0.08), data = CobarOre) test_that("model_info", { @@ -66,11 +66,11 @@ if (FALSE && }) test_that("link_function", { - expect_equal(link_function(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_function(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("find_parameters", { diff --git a/tests/testthat/test-rstanarm.R b/tests/testthat/test-rstanarm.R index dbf86cf60..d0ececdf9 100644 --- a/tests/testthat/test-rstanarm.R +++ b/tests/testthat/test-rstanarm.R @@ -76,7 +76,7 @@ if (.runThisTest && .runStanTest) { ybar <- mean(y) s_y <- sd(y) m11 <- suppressWarnings(stan_biglm.fit(b, R, SSR, N, xbar, ybar, s_y, - prior = R2(.75), + prior = R2(0.75), # the next line is only to make the example go fast chains = 1, iter = 500, seed = 12345 )) @@ -370,7 +370,7 @@ if (.runThisTest && .runStanTest) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), plogis(.2), tolerance = 1e-4) + expect_equal(link_inverse(m1)(0.2), plogis(0.2), tolerance = 1e-4) }) test_that("get_data", { diff --git a/tests/testthat/test-spatial.R b/tests/testthat/test-spatial.R index bf30a3e28..7449db143 100644 --- a/tests/testthat/test-spatial.R +++ b/tests/testthat/test-spatial.R @@ -49,7 +49,7 @@ if (.runThisTest && requiet("glmmTMB") && requiet("geoR")) { }) test_that("link_inverse", { - expect_identical(link_inverse(m1)(.2), .2) + expect_identical(link_inverse(m1)(0.2), 0.2) }) test_that("get_data", { diff --git a/tests/testthat/test-speedglm.R b/tests/testthat/test-speedglm.R index 6fa00b24d..0399596f6 100644 --- a/tests/testthat/test-speedglm.R +++ b/tests/testthat/test-speedglm.R @@ -45,11 +45,11 @@ if (requiet("speedglm") && requiet("glmmTMB")) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), exp(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), exp(0.2), tolerance = 1e-5) }) test_that("linkfun", { - expect_equal(link_function(m1)(.2), log(.2), tolerance = 1e-5) + expect_equal(link_function(m1)(0.2), log(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-speedlm.R b/tests/testthat/test-speedlm.R index 80262182f..9ef24b005 100644 --- a/tests/testthat/test-speedlm.R +++ b/tests/testthat/test-speedlm.R @@ -42,11 +42,11 @@ if (requiet("speedglm")) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("linkfun", { - expect_equal(link_function(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_function(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-survey.R b/tests/testthat/test-survey.R index a749763e3..23b2d6045 100644 --- a/tests/testthat/test-survey.R +++ b/tests/testthat/test-survey.R @@ -29,7 +29,7 @@ if (requiet("survey")) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-survfit.R b/tests/testthat/test-survfit.R index d0be38e21..ca7b22645 100644 --- a/tests/testthat/test-survfit.R +++ b/tests/testthat/test-survfit.R @@ -17,7 +17,7 @@ if (requiet("survival")) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), plogis(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), plogis(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-survreg.R b/tests/testthat/test-survreg.R index c57fad5e1..bc3e0c093 100644 --- a/tests/testthat/test-survreg.R +++ b/tests/testthat/test-survreg.R @@ -40,7 +40,7 @@ if (requiet("survival")) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), exp(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), exp(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-tidymodels.R b/tests/testthat/test-tidymodels.R index 246694446..458f77e6d 100644 --- a/tests/testthat/test-tidymodels.R +++ b/tests/testthat/test-tidymodels.R @@ -64,11 +64,11 @@ if (.runThisTest && requiet("parsnip")) { # }) # # test_that("link_inverse", { - # expect_equal(link_inverse(m1)(.2), exp(.2), tolerance = 1e-5) + # expect_equal(link_inverse(m1)(0.2), exp(0.2), tolerance = 1e-5) # }) # # test_that("linkfun", { - # expect_equal(link_function(m1)(.2), -1.609438, tolerance = 1e-4) + # expect_equal(link_function(m1)(0.2), -1.609438, tolerance = 1e-4) # }) # # test_that("get_data", { diff --git a/tests/testthat/test-tobit.R b/tests/testthat/test-tobit.R index a1ad7c06f..64eebfdc2 100644 --- a/tests/testthat/test-tobit.R +++ b/tests/testthat/test-tobit.R @@ -63,7 +63,7 @@ if (requiet("AER")) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-truncreg.R b/tests/testthat/test-truncreg.R index 6628190aa..615df7520 100644 --- a/tests/testthat/test-truncreg.R +++ b/tests/testthat/test-truncreg.R @@ -17,7 +17,7 @@ if (requiet("truncreg") && requiet("survival")) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), .2, tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), 0.2, tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-vgam.R b/tests/testthat/test-vgam.R index 6f55c794d..088fff550 100644 --- a/tests/testthat/test-vgam.R +++ b/tests/testthat/test-vgam.R @@ -58,8 +58,8 @@ if (.runThisTest && Sys.getenv("USER") != "travis") { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), plogis(.2), tolerance = 1e-5) - expect_equal(link_inverse(m2)(.2), plogis(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), plogis(0.2), tolerance = 1e-5) + expect_equal(link_inverse(m2)(0.2), plogis(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/tests/testthat/test-vglm.R b/tests/testthat/test-vglm.R index 80d7d3067..1065086d1 100644 --- a/tests/testthat/test-vglm.R +++ b/tests/testthat/test-vglm.R @@ -51,10 +51,10 @@ if (requiet("VGAM")) { expect_equal(colnames(get_predictors(m1)), c("outcome", "treatment")) }) - li <- suppressWarnings(link_inverse(m1)(.2)[1, 1]) + li <- suppressWarnings(link_inverse(m1)(0.2)[1, 1]) test_that("link_inverse", { - expect_equal(li, exp(.2), tolerance = 1e-5) - expect_warning(link_inverse(m1)(.2)) + expect_equal(li, exp(0.2), tolerance = 1e-5) + expect_warning(link_inverse(m1)(0.2)) }) test_that("get_data", { diff --git a/tests/testthat/test-zeroinfl.R b/tests/testthat/test-zeroinfl.R index 1b689f730..c464e31e6 100644 --- a/tests/testthat/test-zeroinfl.R +++ b/tests/testthat/test-zeroinfl.R @@ -36,7 +36,7 @@ if (requiet("pscl")) { }) test_that("link_inverse", { - expect_equal(link_inverse(m1)(.2), exp(.2), tolerance = 1e-5) + expect_equal(link_inverse(m1)(0.2), exp(0.2), tolerance = 1e-5) }) test_that("get_data", { diff --git a/vignettes/display.Rmd b/vignettes/display.Rmd index 7f69cf7a6..85d7f8edc 100644 --- a/vignettes/display.Rmd +++ b/vignettes/display.Rmd @@ -92,9 +92,9 @@ With `use_symbols = TRUE`, it is possible to render certain effect size names as ```{r eval=.Platform$OS.type == "windows"} x <- data.frame( - phi_adjusted = .3, - Glass_delta = .4, - Epsilon2 = .7, + phi_adjusted = 0.3, + Glass_delta = 0.4, + Epsilon2 = 0.7, R2 = 0.4 )