Merge pull request #79 from svteichman/check_zero_categories

Address points 2 and 3 in issue #78

DESCRIPTION

@@ -19,6 +19,7 @@ Depends:
     methods,
     dplyr,
     ggplot2,
+    rlang,
     R (>= 2.10)
 Suggests: 
     testthat (>= 3.0.0),
@@ -30,4 +31,4 @@ Suggests:
     parallel,
     rmarkdown
 Config/testthat/edition: 3
-VignetteBuilder: knitr
+VignetteBuilder: knitr

NAMESPACE

@@ -1,13 +1,17 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(plot,radEmu)
 S3method(print,emuFit)
 export(emuFit)
 export(emuFit_micro)
 export(score_test)
 export(simulate_data)
 import(MASS)
 import(Matrix)
+import(dplyr)
+import(ggplot2)
 importFrom(methods,as)
+importFrom(rlang,.data)
 importFrom(stats,cov)
 importFrom(stats,median)
 importFrom(stats,model.matrix)

R/emuFit.R

@@ -681,6 +681,7 @@ and the corresponding gradient function to constraint_grad_fn.")
   if (!is.null(zero_comparison_res)) {
     coefficients <- dplyr::full_join(coefficients, zero_comparison_res, 
                                      by = c("covariate", "category")) 
+    coefficients$zero_comparison[is.na(coefficients$zero_comparison)] <- FALSE
 
     if (remove_zero_comparison_pvals == TRUE | is.numeric(remove_zero_comparison_pvals)) {
       pval_cols <- which(grepl("pval", names(coefficients)))

R/zero_comparison_check.R

@@ -34,7 +34,7 @@ zero_comparison_check <- function(X, Y) {
         }
 
         # get matrix that is (p - 1) x J that gives whether or not parameter is zero-comparison
-        zero_comp <- matrix(NA, nrow = n_groups - 1, J)
+        zero_comp <- matrix(FALSE, nrow = n_groups - 1, J)
         for (i in 1:(n_groups - 1)) {
           zero_comp[i, ] <- (group_counts[1, ] == 0) * (group_counts[i + 1, ] == 0) == 1
         }

tests/testthat/test-zero_comparison_check.R

@@ -103,7 +103,7 @@ test_that("zero_comparison column is added to coef when it should be, model.matr
   emuRes5 <- emuFit(Y = Y0, X = X5, run_score_tests = FALSE, compute_cis = FALSE)
   expect_true("zero_comparison" %in% names(emuRes5$coef))
   expect_true(emuRes5$coef$zero_comparison[1])
-  expect_true(is.na(emuRes5$coef$zero_comparison[13]))
+  expect_false(emuRes5$coef$zero_comparison[13])
   expect_true(emuRes5$coef$zero_comparison[31])
   expect_false(emuRes5$coef$zero_comparison[32])
 })