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| author | Ken Kellner <ken@kenkellner.com> | 2023-12-11 15:09:59 -0500 |
|---|---|---|
| committer | Ken Kellner <ken@kenkellner.com> | 2023-12-11 15:09:59 -0500 |
| commit | 851b783c93a7b64798189fdde506e874b6071593 (patch) | |
| tree | ae296b01319b09543a09d41aeeead0bac384e635 | |
| parent | b4234c9934a114f8ae86a423b363e595081ae868 (diff) | |
confint should only show fixed effects, fixes #268
| -rw-r--r-- | R/unmarkedEstimate.R | 2 | ||||
| -rw-r--r-- | R/unmarkedFit.R | 2 | ||||
| -rw-r--r-- | tests/testthat/test_occu.R | 7 |
3 files changed, 9 insertions, 2 deletions
diff --git a/R/unmarkedEstimate.R b/R/unmarkedEstimate.R index 86caf40..71f8716 100644 --- a/R/unmarkedEstimate.R +++ b/R/unmarkedEstimate.R @@ -294,7 +294,7 @@ setMethod("vcov", "unmarkedEstimate", setMethod("confint", "unmarkedEstimate", function(object, parm, level = 0.95) { - if(missing(parm)) parm <- 1:length(object@estimates) + if(missing(parm)) parm <- object@fixed ests <- object@estimates[parm] ses <- SE(object)[parm] z <- qnorm((1-level)/2, lower.tail = FALSE) diff --git a/R/unmarkedFit.R b/R/unmarkedFit.R index 95c832c..97ccfe4 100644 --- a/R/unmarkedFit.R +++ b/R/unmarkedFit.R @@ -363,7 +363,7 @@ setMethod("confint", "unmarkedFit", function(object, parm, level = 0.95, if(missing(type)) stop(paste("Must specify type as one of (", paste(names(object), collapse=", "),").",sep="")) if(missing(parm)) - parm <- 1:length(object[type]@estimates) + parm <- object[type]@fixed if(method == "normal") { callGeneric(object[type],parm = parm, level = level) } else { diff --git a/tests/testthat/test_occu.R b/tests/testthat/test_occu.R index 043bc59..8bb603e 100644 --- a/tests/testthat/test_occu.R +++ b/tests/testthat/test_occu.R @@ -374,6 +374,13 @@ test_that("occu can handle random effects",{ pb <- parboot(fm, nsim=1) expect_is(pb, "parboot") + # confint should only show fixed effects + ci <- confint(fm, type = 'state') + expect_equal(nrow(ci), 2) + + ci <- confint(fm['state']) + expect_equal(nrow(ci), 2) + # Check custom initial values expect_equal(fm@TMB$starts_order[1], "beta_det") fmi <- occu(~1~cov1 + (1|site_id), umf, starts=c(10,0,0,0)) |