CRAN fixes

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: birdie
 Title: Bayesian Instrumental Regression for Disparity Estimation
-Version: 0.6.0
+Version: 0.6.1
 Authors@R: c(
     person("Cory", "McCartan", role=c("aut", "cre"), email="mccartan@psu.edu"),
     person("Kosuke", "Imai", role="ctb", email="imai@harvard.edu"),

NAMESPACE

@@ -94,6 +94,7 @@ importFrom(stringr,str_remove)
 importFrom(stringr,str_remove_all)
 importFrom(stringr,str_replace_all)
 importFrom(stringr,str_starts)
+importFrom(utils,capture.output)
 importFrom(utils,head)
 importFrom(utils,packageVersion)
 importFrom(utils,relist)

NEWS.md

@@ -1,4 +1,4 @@
-# birdie 0.6.0
+# birdie 0.6.1
 
 * Switch to an inverse-gamma prior for the random effects scale parameter in 
   the mixed model.

R/birdie-package.R

@@ -21,7 +21,7 @@
 #' @importFrom stats weighted.mean rnorm rgamma median sd cov dnorm optim
 #' @importFrom stats terms get_all_vars model.frame model.matrix setNames
 #' @importFrom stats formula update.formula as.formula nobs family vcov residuals
-#' @importFrom utils tail unstack relist head packageVersion
+#' @importFrom utils tail unstack relist head packageVersion capture.output
 #' @importFrom graphics barplot par arrows
 #' @importFrom grDevices colorRampPalette
 #' @useDynLib birdie, .registration=TRUE

R/bisg.R

@@ -355,13 +355,13 @@ make_gx_tbl_vec <- function(vars, p_r, p_rgx) {
 
         # if there is just one ID column we can easily fill in "<none>"
         if (length(GX_names) > 1) {
-            d_miss <- anti_join(vars$GX, p_rgx, by=names(vars$GX))
+            d_miss <- distinct(anti_join(vars$GX, p_rgx, by=names(vars$GX)))
             if (nrow(d_miss) > 0) {
-                cli::cli_text("Missing from {.arg p_rgx}:")
-                print(head(d_miss, 10))
-                if (nrow(d_miss) > 10) cat("...")
-                cli_abort("Some predictor combinations are missing from {.arg p_rgx}.",
-                          call=parent.frame())
+                str_miss = capture.output(head(d_miss, 10))
+                if (nrow(d_miss) > 10) str_miss = c(str_miss, "  ...")
+                msg = c("Some predictor combinations are missing from {.arg p_rgx}:", str_miss) |>
+                    str_replace_all(" ", "\ua0")
+                rlang::abort(msg, use_cli_format=TRUE, call=parent.frame())
             }
         }
     }
@@ -419,7 +419,6 @@ make_gx_tbl_vec <- function(vars, p_r, p_rgx) {
         p_gxr[, i] = p_gxr[, i] / sum(p_gxr[, i])
     }
 
-
     if (est_p_r) {
         p_r = colSums(p_rgx)
         p_r = p_r / sum(p_r)

R/census.R

@@ -3,10 +3,11 @@
 #'
 #' Downloads and prepares race-by-geography tables from U.S. census data, using
 #' the [`easycensus`][easycensus::easycensus] package. Requires that an api key
-#' be set up through [easycensus::cens_auth()] in that package. Supports data
-#' from the decennial census and the American Community Survey at a variety of
-#' levels of geographic detail. The output of this function can be used directly
-#' in [bisg()].
+#' be set up through [easycensus::cens_auth()] in that package, usually by
+#' storing it in the `CENSUS_API_KEY` environment variable. Supports data from
+#' the decennial census and the American Community Survey at a variety of levels
+#' of geographic detail. The output of this function can be used directly in
+#' [bisg()].
 #'
 #' @param geo The geographic level to return. Common options are listed in the
 #'   function signature, but any of the geographies listed at
@@ -26,11 +27,13 @@
 #'   `white`, `black`, etc. containing the counts or proportion of
 #'   residents in each racial group.
 #'
-#' @examples \dontrun{
+#' @examples
+#' census_race_geo_table("zcta", year=2010)
+#' \dontrun{
+#' # Census API key required
 #' census_race_geo_table("us", year=2010)
 #' census_race_geo_table("state", year=2021, survey="acs1")
-#' census_race_geo_table("state", year=2021, survey="acs1", GEOIDs=FALSE)
-#' }
+#' census_race_geo_table("state", year=2021, survey="acs1", GEOIDs=FALSE) }
 #' @concept preproc
 #' @export
 census_race_geo_table <- function(geo=c("us", "state", "county", "zcta", "tract"),

cran-comments.md

@@ -10,15 +10,20 @@
 
 0 errors | 0 warnings | 2 notes
 
-* This is a new release.
+* This is a resubmission of a new release.
 
 * GNU make is a SystemRequirement in order to compile Stan models.
 
 * C++17 is a requirement in order to compile Stan models as well.
   This is noted in src/Makevars and in SystemRequirements.
 
-* Examples are \dontrun{} in census_race_geo_table() since they require an API
-  key and may take some time to run. This function is tested locally in 
-  tests/testthat/test-census.R.
+* Three examples are \dontrun{} in census_race_geo_table() since they require an 
+  API key. Since last submission, the API key requirement is now documented in 
+  the examples, not just in the function documentation. This function is tested
+  locally in tests/testthat/test-census.R.
+
 * Examples are \donttest{} in birdie() since they generally take more than 5
   seconds to run. 
+
+* I have removed the use of cat() to print additional error information in 
+  bisg.R that was flagged on previous submission.