Fixed bug in confint.boot related to car::Confint

NEWS.md

@@ -3,6 +3,7 @@
 * Updated `pkgdown.yaml` GitHub action to [v2](https://github.com/r-lib/actions/tree/v2-branch/examples#build-pkgdown-site). Changed action to only run on a release (rather than a push) but it can be [run manually](https://docs.github.com/en/actions/managing-workflow-runs/manually-running-a-workflow) as well.
 * Updated `R-CMD-check.yaml` GitHub action to [v2](https://github.com/r-lib/actions/tree/v2-branch/examples#standard-ci-workflow). Note that I had to add the [extra code for dealing with graphics on the Mac version](https://github.com/r-lib/actions#common-questions).
 * `alkIndivAge()`: Modified. Added a catch for `NA`s in the length sample. Also added a test. This addresses [#88](https://github.com/fishR-Core-Team/FSA/issues/88)).
+* `confint.boot()`: Modified. Changed hard-coding of columns that contained the confidence interval values to find those columns by `grep()`ing for the `%` sign. This fixes an issue related to `car::Confint()` returning the `coef()` results for functions that have a `coef()` method but not for those that do not. Also updated tests to use results from `car::Boot()` rather than the old `car::bootCase()`.
 
 # FSA 0.9.3 15-Feb-21
 * Moved `dplyr` from `imports` to `suggests` (needed because functions were removed in last version; however it is still used in some examples; partially addresses [#87](https://github.com/fishR-Core-Team/FSA/issues/87)).

R/bootstrap.R

@@ -74,7 +74,8 @@
 #' 
 #' @rdname boot
 #' @export
-confint.boot <- function(object,parm=NULL,level=conf.level,conf.level=0.95,
+confint.boot <- function(object,parm=NULL,
+                         level=conf.level,conf.level=0.95,
                          type=c("bca","norm","basic","perc"),
                          plot=FALSE,err.col="black",err.lwd=2,
                          rows=NULL,cols=NULL,...) {
@@ -95,7 +96,7 @@ confint.boot <- function(object,parm=NULL,level=conf.level,conf.level=0.95,
     }
   }
   res <- car::Confint(object,parm=parm,level=conf.level,type=type)
-  colnames(res)[2:3] <- iCILabel(conf.level)
+  colnames(res)[grep("%",colnames(res))] <- iCILabel(conf.level)
   if (plot) {
     tmp <- object$t
     np <- ncol(tmp)

tests/testthat/testthat_bootstrap.R

@@ -12,11 +12,14 @@ fnx <- function(days,B1,B2,B3) {
 # Fit the nonlinear model
 nl1 <- nls(cells~fnx(days,B1,B2,B3),data=Ecoli,start=list(B1=6,B2=7.2,B3=-1.45))
 
-# Get the bootstrap results saved previously because nlsBoot() and bootCase()
-#   will not run within a testing environment
+# Get the results saved previously because nlsBoot() and bootCase() will not
+#   run within a testing environment. This is the code to create the files.
+#      nlsBoot1 <- nlstools::nlsBoot(nl1)
+#      save(nlsBoot1,file="inst/extdata/nlsBoot1.RData")
+#      Boot1 <- car::Boot(nl1)
+#      save(Boot1,file="inst/extdata/Boot1.RData")
 load(system.file("extdata", "nlsBoot1.RData", package="FSA"))
-load(system.file("extdata", "bootCase1.RData", package="FSA"))
-
+load(system.file("extdata", "Boot1.RData", package="FSA"))
 
 
 ## Test Messages ----
@@ -46,53 +49,53 @@ test_that("nlsBoot() methods messages",{
   expect_error(predict(nlsBoot1,fnx,days=2,digits=0),"must be positive")
 })
 
-test_that("bootCase() methods messages",{
+test_that("Boot() methods messages",{
   # testing confint()
-  expect_error(confint(bootCase1,"derek"),
+  expect_error(confint(Boot1,"derek"),
                "does not exist in")
-  expect_error(confint(bootCase1,c("B1","derek")),
+  expect_error(confint(Boot1,c("B1","derek")),
                "does not exist in")
-  expect_error(confint(bootCase1,4),
+  expect_error(confint(Boot1,4),
                "exceeds number of columns")
-  expect_error(confint(bootCase1,-4),
+  expect_error(confint(Boot1,-4),
                "exceeds number of columns")
-  expect_error(confint(bootCase1,c(1,4)),
+  expect_error(confint(Boot1,c(1,4)),
                "exceeds number of columns")
-  expect_error(confint(bootCase1,-c(1,4)),
+  expect_error(confint(Boot1,-c(1,4)),
                "exceeds number of columns")
-  expect_error(confint(bootCase1,c(-1,2)),
+  expect_error(confint(Boot1,c(-1,2)),
                "cannot be both positive and negative")
-  expect_error(confint(bootCase1,conf.level=0),
+  expect_error(confint(Boot1,conf.level=0),
                "must be between 0 and 1")
-  expect_error(confint(bootCase1,conf.level=1),
+  expect_error(confint(Boot1,conf.level=1),
                "must be between 0 and 1")
-  expect_error(confint(bootCase1,conf.level="R"),
+  expect_error(confint(Boot1,conf.level="R"),
                "must be numeric")
   # testing htest()
-  expect_error(htest(bootCase1,"derek"),
+  expect_error(htest(Boot1,"derek"),
                "does not exist in")
-  expect_error(htest(bootCase1,c("B1","derek")),
+  expect_error(htest(Boot1,c("B1","derek")),
                "must be of length 1")
-  expect_error(htest(bootCase1,4),
+  expect_error(htest(Boot1,4),
                "exceeds number of columns")
-  expect_error(htest(bootCase1,-4),
+  expect_error(htest(Boot1,-4),
                "must be positive")
-  expect_error(htest(bootCase1,c(1,4)),
+  expect_error(htest(Boot1,c(1,4)),
                "must be of length 1")
-  expect_error(htest(bootCase1),
+  expect_error(htest(Boot1),
                "must select a parameter")
   # testing predict()
-  expect_error(predict(bootCase1,1:7,days=2),
+  expect_error(predict(Boot1,1:7,days=2),
                "is not a function")
-  expect_error(predict(bootCase1,fnx,derek=2),
+  expect_error(predict(Boot1,fnx,derek=2),
                "unused argument")
-  expect_error(predict(bootCase1,fnx,days=2,conf.level=0),
+  expect_error(predict(Boot1,fnx,days=2,conf.level=0),
                "must be between 0 and 1")
-  expect_error(predict(bootCase1,fnx,days=2,conf.level=1),
+  expect_error(predict(Boot1,fnx,days=2,conf.level=1),
                "must be between 0 and 1")
-  expect_error(predict(bootCase1,fnx,days=2,conf.level="R"),
+  expect_error(predict(Boot1,fnx,days=2,conf.level="R"),
                "must be numeric")
-  expect_error(predict(bootCase1,fnx,days=2,digits=0),
+  expect_error(predict(Boot1,fnx,days=2,digits=0),
                "must be positive")
 })
 
@@ -161,61 +164,61 @@ test_that("nlsBoot() methods output types",{
   expect_equal(tmp[,"days"],1:5)
 })
 
-test_that("bootCase() methods output types",{
+test_that("Boot() methods output types",{
   # testing confint()
-  tmp <- confint(bootCase1)
+  tmp <- confint(Boot1)
   expect_is(tmp,"matrix")
   expect_equal(mode(tmp),"numeric")
   expect_equal(colnames(tmp),c("Estimate","95% LCI","95% UCI"))
   expect_equal(rownames(tmp),c("B1","B2","B3"))
   expect_equal(nrow(tmp),3)
   expect_equal(ncol(tmp),3)
-  tmp <- confint(bootCase1,"B1")
+  tmp <- confint(Boot1,"B1")
   expect_is(tmp,"matrix")
   expect_equal(mode(tmp),"numeric")
   expect_equal(colnames(tmp),c("Estimate","95% LCI","95% UCI"))
   expect_equal(rownames(tmp),c("B1"))
   expect_equal(nrow(tmp),1)
   expect_equal(ncol(tmp),3)
-  tmp <- confint(bootCase1,c(1,3))
+  tmp <- confint(Boot1,c(1,3))
   expect_is(tmp,"matrix")
   expect_equal(mode(tmp),"numeric")
   expect_equal(colnames(tmp),c("Estimate","95% LCI","95% UCI"))
   expect_equal(rownames(tmp),c("B1","B3"))
   expect_equal(nrow(tmp),2)
   expect_equal(ncol(tmp),3)
   # testing htest()
-  tmp <- htest(bootCase1,"B1")
+  tmp <- htest(Boot1,"B1")
   expect_is(tmp,"matrix")
   expect_equal(mode(tmp),"numeric")
   expect_equal(colnames(tmp),c("Ho Value","p value"))
   expect_equal(rownames(tmp),c("B1"))
   expect_equal(nrow(tmp),1)
   expect_equal(ncol(tmp),2)
-  tmp <- htest(bootCase1,1)
+  tmp <- htest(Boot1,1)
   expect_is(tmp,"matrix")
   expect_equal(mode(tmp),"numeric")
   expect_equal(colnames(tmp),c("Ho Value","p value"))
   expect_equal(rownames(tmp),c("B1"))
   expect_equal(nrow(tmp),1)
   expect_equal(ncol(tmp),2)
   # testing predict()
-  tmp <- predict(bootCase1,fnx,days=3)
+  tmp <- predict(Boot1,fnx,days=3)
   expect_is(tmp,"matrix")
   expect_equal(mode(tmp),"numeric")
   expect_equal(colnames(tmp),c("days","Median","95% LCI","95% UCI"))
   expect_equal(nrow(tmp),1)
   expect_equal(ncol(tmp),4)
   expect_equal(tmp[,"days"],c(days=3))
-  tmp <- predict(bootCase1,fnx,days=1:5)
+  tmp <- predict(Boot1,fnx,days=1:5)
   expect_is(tmp,"matrix")
   expect_equal(mode(tmp),"numeric")
   expect_equal(colnames(tmp),c("days","Median","95% LCI","95% UCI"))
   expect_equal(nrow(tmp),5)
   expect_equal(ncol(tmp),4)
   expect_equal(tmp[,"days"],1:5)
   # get same output when digits are used?
-  tmp <- predict(bootCase1,fnx,days=1:5,digits=2)
+  tmp <- predict(Boot1,fnx,days=1:5,digits=2)
   expect_is(tmp,"matrix")
   expect_equal(mode(tmp),"numeric")
   expect_equal(colnames(tmp),c("days","Median","95% LCI","95% UCI"))