Merge branch 'coef_plot'

R/plot_fixefs.R

@@ -132,3 +132,4 @@ plot_fixefs.merMod <- function(model,
   }
 }
 
+# plot_fixefs.glmerMod <- plot_fixefs.merMod

tests/testthat/helper_load_data.R

@@ -0,0 +1 @@
+load('brms_res.RData')

tests/testthat/test_plot_coefficients.R

@@ -0,0 +1,136 @@
+context('test coefficient plots')
+
+
+test_lm = lm(mpg ~ ., mtcars)
+
+x = rnorm(100)
+q = rnorm(100)
+z = rnorm(100)
+y = rpois(100, exp(.25*x + .1*q - .5*z))
+test_glm = glm(y ~ x + q + z, family = poisson)
+
+fit_mer = lme4::lmer(Reaction ~ Days + (Days|Subject), lme4::sleepstudy)
+fit_mer2 = lme4::lmer(count ~ log_Age_c + log_Base4_c * Trt + (1 | patient), brms::epilepsy)
+mer_re = plot_coefficients(fit_mer, ranef = T, which_ranef = 'Subject')
+
+test_that('It works', {
+  expect_s3_class(mer_re[[1]], 'ggplot')
+})
+
+test_that('It works', {
+  expect_s3_class(plot_coefficients(test_lm, plot = FALSE), 'data.frame')
+})
+
+
+
+# test lm glm coefficients ------------------------------------------------
+
+test_that('test plot_coefficients.lm', {
+  expect_s3_class(plot_coefficients(test_lm), 'ggplot')
+})
+
+test_that('test palette', {
+  expect_s3_class(plot_coefficients(test_lm, palette = 'oslo'), 'ggplot')
+})
+
+test_that('test order numeric', {
+  expect_s3_class(plot_coefficients(test_lm, order = sample(1:10)), 'ggplot')
+})
+
+test_that('test order increasing', {
+  expect_s3_class(plot_coefficients(test_lm, order = 'increasing'), 'ggplot')
+})
+
+
+test_that('test plot_coefficients.glm and trans', {
+  expect_s3_class(plot_coefficients(test_glm, trans = exp, ref_line = 1), 'ggplot')
+})
+
+
+
+
+
+# test lme4 ---------------------------------------------------------------
+
+# test fixed effects plots ------------------------------------------------
+test_that('test fixef options', {
+  test_fe = plot_coefficients(fit_mer, ranef = F)
+  expect_s3_class(test_fe, 'ggplot')
+})
+
+test_that('test fixef options order increasing', {
+  test_fe = plot_coefficients(fit_mer, order = 'increasing')
+  expect_s3_class(test_fe, 'ggplot')
+})
+
+test_that('test fixef options order numeric', {
+  test_fe = plot_coefficients(fit_mer2, order = 4:1)
+  expect_s3_class(test_fe, 'ggplot')
+})
+
+test_that('no plot works', {
+  expect_s3_class(plot_coefficients(fit_mer, plot = FALSE), 'data.frame')
+})
+
+
+# test random effect plots ------------------------------------------------
+
+test_that('test ranef options', {
+  expect_s3_class(mer_re[[1]], 'ggplot')
+})
+
+test_that('test error with wrong ranef', {
+  expect_error(plot_coefficients(fit_mer, ranef = T, which_ranef = 'blah'))
+})
+
+test_that('test error with null ranef', {
+  expect_error(plot_coefficients(fit_mer, ranef = T, which_ranef = NULL))
+})
+
+test_that('test can return data', {
+  expect_s3_class(plot_coefficients(fit_mer, ranef = T, which_ranef = 'Subject', plot=F)[[1]], 'data.frame')
+})
+
+# test brms ---------------------------------------------------------------
+
+
+# test fixed effects plots ------------------------------------------------
+
+test_that('test fixef options', {
+  test_fe = plot_coefficients(fit1, ranef = F)
+  expect_s3_class(test_fe, 'ggplot')
+})
+
+test_that('test fixef options order increasing', {
+  test_fe = plot_coefficients(fit1, order = 'increasing')
+  expect_s3_class(test_fe, 'ggplot')
+})
+
+test_that('test fixef options order numeric', {
+  test_fe = plot_coefficients(fit1, order = 4:1)
+  expect_s3_class(test_fe, 'ggplot')
+})
+
+test_that('no plot works', {
+  expect_s3_class(plot_coefficients(fit1, plot = FALSE), 'data.frame')
+})
+
+
+# test random effect plots ------------------------------------------------
+
+
+test_that('test ranef options', {
+  expect_s3_class(plot_coefficients(fit1, ranef = T, which_ranef='patient')[[1]], 'ggplot')
+})
+
+test_that('test error with wrong ranef', {
+  expect_error(plot_coefficients(fit1, ranef = T, which_ranef = 'blah'))
+})
+
+test_that('test error with null ranef', {
+  expect_error(plot_coefficients(fit1, ranef = T, which_ranef = NULL))
+})
+
+test_that('test can return data', {
+  expect_s3_class(plot_coefficients(fit1, ranef = T, which_ranef = 'patient', plot=F)[[1]], 'data.frame')
+})