continuing to debug examples on rhub platforms

bertcarnell · Dec 12, 2022 · d5ad16b · d5ad16b
1 parent 1af7ded
commit d5ad16b
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Showing 8 changed files with 41 additions and 25 deletions.
diff --git a/R/cdfe.R b/R/cdfe.R
@@ -16,7 +16,9 @@
 #' print(cdfe)
 #' summary(cdfe)
 #' coef(cdfe)
-#' if (isNamespaceLoaded("MASS")) confint(cdfe)
+#' \dontrun{
+#'   MASS::confint(cdfe)
+#' }
 triangle_cdfe <- function(x)
 {
   # x <- rtriangle(100, 0, 1, .3)

diff --git a/R/mle-utils.R b/R/mle-utils.R
@@ -29,11 +29,14 @@
 #' \dontrun{
 #'   prof <- profile(mle1)
 #'   stats4::plot(prof)
+#'   confint(mle1, 1:3, level = 0.95)
 #' }
-#' confint(mle1, 1:3, level = 0.95)
 summary.triangle_mle <- function(object, ...)
 {
-  cmat <- cbind(Estimate = object$coef, `Std. Error` = sqrt(diag(object$vcov)))
+  vars <- diag(object$vcov)
+  # it is possible to have negative numbers in the vcov because of numerical precision
+  vars[which(vars < 0)] <- NA
+  cmat <- cbind(Estimate = object$coef, `Std. Error` = sqrt(vars))
   m2logL <- 2 * object$min
   methods::new("summary.mle", call = object$call, coef = cmat, m2logL = m2logL)
 }
@@ -46,10 +49,13 @@ summary.triangle_mle <- function(object, ...)
 #' @importFrom stats4 coef vcov
 print.triangle_mle <- function(x, ...)
 {
+  vars <- diag(stats4::vcov(x))
+  # it is possible to have negative numbers in the vcov because of numerical precision
+  vars[which(vars < 0)] <- NA
   cat("Triangle Maximum Likelihood Estimates")
   cat("\n\nCall: ", deparse(x$call), "\n")
   cat("\nEstimates:\n")
-  cmat <- cbind(stats4::coef(x), sqrt(diag(stats4::vcov(x))))
+  cmat <- cbind(stats4::coef(x), sqrt(vars))
   colnames(cmat) <- c("Estimate", "Std.Err")
   stats::printCoefmat(cmat, ...)
   cat("\nConvergence Code: ", ifelse(all(is.na(x$details)), NA, x$details$convergence))

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.6
 pkgdown_sha: ~
 articles:
   triangledistributionmath: triangledistributionmath.html
-last_built: 2022-12-12T01:03Z
+last_built: 2022-12-12T02:13Z
 
diff --git a/docs/reference/mle-utils.html b/docs/reference/mle-utils.html
diff --git a/docs/reference/triangle_cdfe.html b/docs/reference/triangle_cdfe.html
diff --git a/man/mle-utils.Rd b/man/mle-utils.Rd
diff --git a/man/triangle_cdfe.Rd b/man/triangle_cdfe.Rd
diff --git a/tests/testthat/test-mle-utils.R b/tests/testthat/test-mle-utils.R
@@ -1,5 +1,6 @@
 test_that("summary works", {
-  xtest <- c(0.1, 0.25, 0.3, 0.4, 0.45, 0.6, 0.75, 0.8)
+  set.seed(39854)
+  xtest <- rtriangle(200, 0, 1, 0.5)
 
   mle1 <- triangle_mle(xtest)
   summ <- summary(mle1)
@@ -12,14 +13,16 @@ test_that("summary works", {
 })
 
 test_that("print works", {
-  xtest <- c(0.1, 0.25, 0.3, 0.4, 0.45, 0.6, 0.75, 0.8)
+  set.seed(39854)
+  xtest <- rtriangle(200, 0, 1, 0.5)
 
   mle1 <- triangle_mle(xtest)
   expect_output(print(mle1))
 })
 
 test_that("coef works", {
-  xtest <- c(0.1, 0.25, 0.3, 0.4, 0.45, 0.6, 0.75, 0.8)
+  set.seed(39854)
+  xtest <- rtriangle(200, 0, 1, 0.5)
 
   mle1 <- triangle_mle(xtest)
   cf <- coef(mle1)
@@ -28,7 +31,8 @@ test_that("coef works", {
 })
 
 test_that("logLik works", {
-  xtest <- c(0.1, 0.25, 0.3, 0.4, 0.45, 0.6, 0.75, 0.8)
+  set.seed(39854)
+  xtest <- rtriangle(200, 0, 1, 0.5)
 
   mle1 <- triangle_mle(xtest)
   ll <- logLik(mle1)
@@ -40,7 +44,8 @@ test_that("logLik works", {
 })
 
 test_that("AIC works", {
-  xtest <- c(0.1, 0.25, 0.3, 0.4, 0.45, 0.6, 0.75, 0.8)
+  set.seed(39854)
+  xtest <- rtriangle(200, 0, 1, 0.5)
 
   mle1 <- triangle_mle(xtest)
   aic <- AIC(mle1)
@@ -50,7 +55,8 @@ test_that("AIC works", {
 })
 
 test_that("BIC works", {
-  xtest <- c(0.1, 0.25, 0.3, 0.4, 0.45, 0.6, 0.75, 0.8)
+  set.seed(39854)
+  xtest <- rtriangle(200, 0, 1, 0.5)
 
   mle1 <- triangle_mle(xtest)
   bic <- BIC(mle1)
@@ -60,7 +66,8 @@ test_that("BIC works", {
 })
 
 test_that("vcov works", {
-  xtest <- c(0.1, 0.25, 0.3, 0.4, 0.45, 0.6, 0.75, 0.8)
+  set.seed(39854)
+  xtest <- rtriangle(200, 0, 1, 0.5)
 
   mle1 <- triangle_mle(xtest)
   v <- vcov(mle1)
@@ -69,7 +76,8 @@ test_that("vcov works", {
 })
 
 test_that("profile works", {
-  xtest <- c(0.1, 0.25, 0.3, 0.4, 0.45, 0.6, 0.75, 0.8)
+  set.seed(39854)
+  xtest <- rtriangle(200, 0, 1, 0.5)
 
   mle1 <- triangle_mle(xtest)
   prof <- profile(mle1)
@@ -87,20 +95,20 @@ test_that("profile works", {
 })
 
 test_that("confint works", {
-  xtest <- c(0.1, 0.25, 0.3, 0.4, 0.45, 0.6, 0.75, 0.8)
+  set.seed(39854)
+  xtest <- rtriangle(200, 0, 1, 0.5)
 
   mle1 <- triangle_mle(xtest)
   cfi <- confint(mle1, level = 0.95)
 
   expect_equal(c(3,2), dim(cfi))
-  expect_true(all(is.na(cfi[3,])))
   expect_true(cfi[1,1] < 0 & 0 < cfi[1,2])
   expect_true(cfi[2,1] < 1 & 1 < cfi[2,2])
 
-  cfi <- confint(mle1, level = 0.6)
+  cfi <- confint(mle1, level = 0.9)
 
   expect_true(cfi[1,1] < 0 & 0 < cfi[1,2])
   expect_true(cfi[2,1] < 1 & 1 < cfi[2,2])
-  expect_true(cfi[3,1] < 0.3 & 0.3 < cfi[3,2])
+  expect_true(cfi[3,1] < 0.5 & 0.5 < cfi[3,2])
 })