Fix bugs 20-24

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: cicalc
 Title: Calculate Confidence Intervals
-Version: 0.2.1
+Version: 0.2.2
 Authors@R: c(
     person("Christina", "Fillmore", , "christina.e.fillmore@gsk.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0595-2302")),

NEWS.md

@@ -1,3 +1,9 @@
+# cicalc 0.2.2
+* Fix issue with factor conversion in Miettinen-Nurminen CI calculation #20 
+* Fix issue with ci_prop_diff_mh_strata() for z statistic calculation
+* Fix issue with ci_prop_wilson_strata() when datasets are provided [#22](https://github.com/GSK-Biostatistics/cicalc/issues/22)
+* Fix non-logical [#23](https://github.com/GSK-Biostatistics/cicalc/issues/23) and dataset issue [#24](https://github.com/GSK-Biostatistics/cicalc/issues/24) for ci_prop_diff_nc_strata()
+
 # cicalc 0.2.1 
 * Fix bug in Miettinen-Nurminen CI calculation when non-rootable conditions occur
 

R/prop_ci.R

@@ -439,7 +439,7 @@ ci_prop_wilson_strata <- function(x,
   # if data was passed, evaluate in the context of the data frame
   if (is.data.frame(data)) {
     return(
-      ci_prop_jeffreys(
+      ci_prop_wilson_strata(
         x = x ,
         conf.level = conf.level
       ) |>

R/prop_ci_common_risk.R

@@ -127,7 +127,7 @@ ci_prop_diff_mh_strata <- function(x, by, strata, conf.level = 0.95, sato_var =
   lower_ci <- d_mh - z_alpha*sqrt(est_var)
   upper_ci <- d_mh + z_alpha*sqrt(est_var)
 
-  z_stat <- d_mh/sqrt(sato_var)
+  z_stat <- d_mh/sqrt(est_var)
 
   p.value <- 2 * (1 - stats::pnorm(abs(z_stat)))
 
@@ -334,9 +334,11 @@ ci_prop_diff_nc_strata <- function(x,
   # if data was passed, evaluate in the context of the data frame
   if (is.data.frame(data)) {
     return(
-      ci_prop_diff_nc(
+      ci_prop_diff_nc_strata(
         x = x,
         by = by,
+        strata = strata,
+        weights_method = weights_method,
         conf.level = conf.level,
         correct = correct
       ) |>
@@ -353,7 +355,7 @@ ci_prop_diff_nc_strata <- function(x,
   check_scalar(correct)
   check_range(conf.level, range = c(0, 1), include_bounds = c(FALSE, FALSE))
   check_scalar(conf.level)
-
+  x<- as.logical(x)
 
   if (any(tapply(x, strata, length) < 5)) {
     cli::cli_warn("Less than 5 observations in some strata.")
@@ -439,6 +441,6 @@ ci_prop_diff_nc_strata <- function(x,
       method =
         glue::glue("Stratified Newcombe Confidence Interval {ifelse(correct, 'with', 'without')} continuity correction, {weights_method}")
     ),
-    class = c("stratified_newcombe", "stratified_wilson", "cicada")
+    class = c("ci_prop_diff_nc_strata", "stratified_wilson", "cicalc")
   )
 }

R/prop_ci_mn.R

@@ -419,7 +419,7 @@ ci_prop_diff_mn_strata <- function(x, by, strata, method = c("score", "summary s
 
     estimate_df <- dplyr::tibble(
       x = x,
-      by = as.numeric(as.factor(by)),
+      by = as.numeric(forcats::as_factor(by)),
       strata = strata
     ) |>
       dplyr::group_by(strata) |>

tests/testthat/_snaps/prop_ci_common_risk.md

@@ -109,9 +109,9 @@
       * 50 responses out of 80
       * Weights: a.x = 0.211, b.x = 0.189, a.y = 0.118, b.y = 0.154, a.z = 0.174, b.z
       = 0.153
-      * Estimate: 0
+      * Estimate: 0.259
       * 95% Confidence Interval:
-        (0, 0)
+        (0.0392, 0.4502)
 
 ---
 
@@ -124,9 +124,9 @@
       * 50 responses out of 80
       * Weights: a.x = 0.195, b.x = 0.163, a.y = 0.135, b.y = 0.138, a.z = 0.202, b.z
       = 0.167
-      * Estimate: 0
+      * Estimate: 0.254
       * 95% Confidence Interval:
-        (0, 0)
+        (0.0347, 0.4454)
 
 ---
 
@@ -138,9 +138,9 @@
       * 50 responses out of 80
       * Weights: a.x = 0.211, b.x = 0.189, a.y = 0.118, b.y = 0.154, a.z = 0.174, b.z
       = 0.153
-      * Estimate: 0
+      * Estimate: 0.259
       * 95% Confidence Interval:
-        (0, 0)
+        (0.0392, 0.4502)
 
 ---