diff options
| author | Ken Kellner <ken@kenkellner.com> | 2022-07-27 10:28:17 -0400 |
|---|---|---|
| committer | Ken Kellner <ken@kenkellner.com> | 2022-07-27 10:28:17 -0400 |
| commit | be8b9eb76ed14b85a395ab718c6bc8f467118865 (patch) | |
| tree | 16090b877b4778c7dabc7fd1d160b5744d23a4db | |
| parent | 9213a62c177ce9556a7a55fb87e900557e434e5f (diff) | |
Allow : notation for interactions among fixed effects
| -rw-r--r-- | DESCRIPTION | 4 | ||||
| -rw-r--r-- | R/stanmodels.R | 2 | ||||
| -rw-r--r-- | R/submodel.R | 2 | ||||
| -rw-r--r-- | tests/testthat/test_distsamp.R | 2 | ||||
| -rw-r--r-- | tests/testthat/test_submodel.R | 9 |
5 files changed, 14 insertions, 5 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 318d80a..4bf4d22 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: ubms -Version: 1.1.9004 -Date: 2022-03-31 +Version: 1.1.9005 +Date: 2022-07-27 Title: Bayesian Models for Data from Unmarked Animals using 'Stan' Authors@R: person("Ken", "Kellner", email="contact@kenkellner.com", role=c("cre","aut")) diff --git a/R/stanmodels.R b/R/stanmodels.R index 016113d..e78fcd4 100644 --- a/R/stanmodels.R +++ b/R/stanmodels.R @@ -23,5 +23,5 @@ stanmodels <- sapply(stanmodels, function(model_name) { model_name = stanfit$model_name, model_code = stanfit$model_code, model_cpp = stanfit$model_cpp, - mk_cppmodule = function(x) get(paste0("model_", model_name))) + mk_cppmodule = function(x) get(paste0("rstantools_model_", model_name))) }) diff --git a/R/submodel.R b/R/submodel.R index 29e9911..f7b6c8d 100644 --- a/R/submodel.R +++ b/R/submodel.R @@ -164,7 +164,7 @@ check_formula <- function(formula, data){ rand <- lme4::findbars(formula) if(is.null(rand)) return(invisible()) - char <- paste(formula, collapse=" ") + char <- paste(lme4::findbars(formula)[[1]], collapse=" ") if(grepl(":|/", char)){ stop("Nested random effects (using / and :) are not supported", call.=FALSE) diff --git a/tests/testthat/test_distsamp.R b/tests/testthat/test_distsamp.R index 101d22f..8a8c22a 100644 --- a/tests/testthat/test_distsamp.R +++ b/tests/testthat/test_distsamp.R @@ -95,7 +95,7 @@ test_that("stan_distsamp produces accurate results",{ stan_mod <- suppressWarnings(stan_distsamp(~1~1, ltUMF_big, keyfun="exp", chains=2, iter=200, refresh=0)) um_mod <- distsamp(~1~1, ltUMF_big, keyfun="exp") - expect_RMSE(coef(stan_mod), coef(um_mod), 0.01) + expect_RMSE(coef(stan_mod), coef(um_mod), 0.02) stan_mod <- suppressWarnings(stan_distsamp(~1~1, ltUMF_big, output="abund", chains=2, iter=200, refresh=0)) diff --git a/tests/testthat/test_submodel.R b/tests/testthat/test_submodel.R index b57f03b..484026d 100644 --- a/tests/testthat/test_submodel.R +++ b/tests/testthat/test_submodel.R @@ -387,6 +387,15 @@ test_that("check_formula identifies unsupported formulas",{ expect_error(check_formula(~(1|x1 : x2), dat)) }) +test_that("check_formula allows : in non-random effects part of formula",{ + dat <- data.frame(y=rnorm(10), x1=rnorm(10), x2=rnorm(10), + x3=sample(letters[1:3], 10, replace=T), + x4=sample(letters[4:6], 10, replace=T)) + expect_error(check_formula(~x1*x2 + (1|x3), dat), NA) + expect_error(check_formula(~x1:x2 + (1|x3), dat), NA) + expect_error(check_formula(~x1:x2 + (1|x3:x2), dat)) +}) + test_that("check_formula handles very long formulas",{ dat <- data.frame(y=rnorm(10), longcovariate1=rnorm(10), longcovariate2=rnorm(10), longcovariate3=rnorm(10), longcovariate4=rnorm(10), |