update tests and snapshots (#49)

* update tests and snapshots * update word list * fix typo * update fda guidance link
openpharma · Oct 23, 2024 · aa7cf6e · aa7cf6e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -12,7 +12,7 @@ Authors@R:
     )
 Description: Performs robust estimation and inference when using covariate adjustment
   and/or covariate-adaptive randomization in randomized controlled trials.
-  This package is trimmed to reduce the depdendencies and validated to be used across industry.
+  This package is trimmed to reduce the dependencies and validated to be used across industry.
 License: Apache License 2.0
 URL: https://github.com/openpharma/RobinCar2/
 BugReports: https://github.com/openpharma/RobinCar2/issues

diff --git a/R/robin_glm.R b/R/robin_glm.R
@@ -42,11 +42,11 @@ robin_glm <- function(
     )
   }
   if (identical(contrast, "difference")) {
-    difference(pc)
+    difference(pc, variance = vcov, vcov_args = vcov_args)
   } else if (identical(contrast, "risk_ratio")) {
-    risk_ratio(pc)
+    risk_ratio(pc, variance = vcov, vcov_args = vcov_args)
   } else if (identical(contrast, "odds_ratio")) {
-    odds_ratio(pc)
+    odds_ratio(pc, variance = vcov, vcov_args = vcov_args)
   } else {
     assert_function(contrast)
     assert_function(contrast_jac, null.ok = TRUE)

diff --git a/R/treatment_effect.R b/R/treatment_effect.R
@@ -73,15 +73,15 @@ treatment_effect.prediction_cf <- function(
 #' @export
 #' @inheritParams predict_counterfactual
 treatment_effect.lm <- function(
-    object, pair, variance = gvcov, eff_measure, eff_jacobian,
+    object, pair, variance = "gvcov", eff_measure, eff_jacobian,
     vcov_args = list(), treatment, data = find_data(object), ...) {
   pc <- predict_counterfactual(object, data = data, treatment)
   treatment_effect(pc, pair = pair, variance = variance, eff_measure = eff_measure, eff_jacobian = eff_jacobian, ...)
 }
 
 #' @export
 treatment_effect.glm <- function(
-    object, pair, variance = gvcov, eff_measure, eff_jacobian,
+    object, pair, variance = "gvcov", eff_measure, eff_jacobian,
     vcov_args = list(), treatment, data = find_data(object), ...) {
   pc <- predict_counterfactual(object, treatment, data)
   treatment_effect(pc, pair = pair, variance = variance, eff_measure = eff_measure, eff_jacobian = eff_jacobian, ...)
@@ -201,7 +201,7 @@ print.treatment_effect <- function(x, ...) {
     ),
     nrow = length(x)
   )
-  colnames(coef_mat) <- c("Estimate", "Std.Err", "Z Value", "Pr(>z)")
+  colnames(coef_mat) <- c("Estimate", "Std.Err", "Z Value", "Pr(>|z|)")
   row.names(coef_mat) <- attr(x, "name")
   stats::printCoefmat(
     coef_mat,

diff --git a/README.Rmd b/README.Rmd
@@ -24,7 +24,7 @@ knitr::opts_chunk$set(
 \
 
 RobinCar2 is a package to provide robust inference of covariate adjusted analysis under stratified randomization.
-The methods implemented are recommended by [FDA guidance on covariate adjustment]().
+The methods implemented are recommended by [FDA guidance on covariate adjustment](https://www.fda.gov/regulatory-information/search-fda-guidance-documents/adjusting-covariates-randomized-clinical-trials-drugs-and-biological-products).
 The methods are based on the work of [Ye, Shao, Yi and Zhao (2023)](doi:10.1080/01621459.2022.2049278),
 [Ye, Bannick, Yi and Shao (2023)](doi:10.1080/24754269.2023.2205802), 
 [Ye, Shao, Yi (2023)](doi:10.1093/biomet/asad045>) and

diff --git a/README.md b/README.md
@@ -21,8 +21,9 @@ Coverage](https://raw.githubusercontent.com/openpharma/RobinCar2/_xml_coverage_r
 
 RobinCar2 is a package to provide robust inference of covariate adjusted
 analysis under stratified randomization. The methods implemented are
-recommended by [FDA guidance on covariate adjustment](). The methods are
-based on the work of [Ye, Shao, Yi and Zhao
+recommended by [FDA guidance on covariate
+adjustment](https://www.fda.gov/regulatory-information/search-fda-guidance-documents/adjusting-covariates-randomized-clinical-trials-drugs-and-biological-products).
+The methods are based on the work of [Ye, Shao, Yi and Zhao
 (2023)](doi:10.1080/01621459.2022.2049278), [Ye, Bannick, Yi and Shao
 (2023)](doi:10.1080/24754269.2023.2205802), [Ye, Shao, Yi
 (2023)](doi:10.1093/biomet/asad045%3E) and [Bannick, Shao, Liu, Du, Yi,

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -1,5 +1,13 @@
 ANHECOVA
+INference
+Liu
+ORCID
+Pocock
+ROBust
 RobinCar
+Shao
+Yi
+Zhao
 glm
 jacobian
 jacobians

diff --git a/tests/testthat/_snaps/treatment_effect.md b/tests/testthat/_snaps/treatment_effect.md
@@ -13,11 +13,11 @@
             pbo      trt1      trt2 
       0.3560965 0.5806957 0.6213865 
       
-      Variance Type:  function 
-                  Estimate Std.Err Z Value  Pr(>z)    
-      trt1 - pbo    0.2246  0.0477    4.71 2.5e-06 ***
-      trt2 - pbo    0.2653  0.0475    5.58 2.4e-08 ***
-      trt2 - trt1   0.0407  0.0479    0.85     0.4    
+      Variance Type:  gvcov 
+                  Estimate Std.Err Z Value Pr(>|z|)    
+      trt1 - pbo    0.2246  0.0477    4.71  2.5e-06 ***
+      trt2 - pbo    0.2653  0.0475    5.58  2.4e-08 ***
+      trt2 - trt1   0.0407  0.0479    0.85      0.4    
       ---
       Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
 
@@ -36,11 +36,11 @@
             pbo      trt1      trt2 
       0.2003208 0.7639709 0.9712499 
       
-      Variance Type:  function 
-                  Estimate Std.Err Z Value  Pr(>z)    
-      trt1 - pbo     0.564   0.101    5.60 2.2e-08 ***
-      trt2 - pbo     0.771   0.101    7.61 2.8e-14 ***
-      trt2 - trt1    0.207   0.107    1.94   0.052 .  
+      Variance Type:  gvcov 
+                  Estimate Std.Err Z Value Pr(>|z|)    
+      trt1 - pbo     0.564   0.101    5.60  2.2e-08 ***
+      trt2 - pbo     0.771   0.101    7.61  2.8e-14 ***
+      trt2 - trt1    0.207   0.107    1.94    0.052 .  
       ---
       Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
 
@@ -61,10 +61,10 @@
       0.3560965 0.5806957 0.6213865 
       
       Variance Type:  none 
-                  Estimate Std.Err Z Value Pr(>z)
-      trt1 - pbo    0.2246      NA      NA     NA
-      trt2 - pbo    0.2653      NA      NA     NA
-      trt2 - trt1   0.0407      NA      NA     NA
+                  Estimate Std.Err Z Value Pr(>|z|)
+      trt1 - pbo    0.2246      NA      NA       NA
+      trt2 - pbo    0.2653      NA      NA       NA
+      trt2 - trt1   0.0407      NA      NA       NA
 
 # treatment_effect works if pair is integer
 
@@ -82,9 +82,9 @@
             pbo      trt1      trt2 
       0.3560965 0.5806957 0.6213865 
       
-      Variance Type:  function 
-                 Estimate Std.Err Z Value  Pr(>z)    
-      trt1 - pbo   0.2246  0.0477    4.71 2.5e-06 ***
+      Variance Type:  gvcov 
+                 Estimate Std.Err Z Value Pr(>|z|)    
+      trt1 - pbo   0.2246  0.0477    4.71  2.5e-06 ***
       ---
       Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1