update output

R/helper_output_print.R

@@ -48,7 +48,7 @@ output_print <- function(n_covariates,
       cat("\n")
       cat(paste0("The estimated effect is ", round(est_eff, 3), ". To invalidate the inference of an effect using"))
       cat("\n")
-      cat(paste0("the threshold of ", round(beta_threshhold, 3), " for statistical significance with alpha = ", alpha, ", ", round(bias, 3), "% of"))
+      cat(paste0("the threshold of ", round(beta_threshhold, 3), " for statistical significance (with alpha = ", alpha, "), ", round(bias, 3), "% of"))
       cat("\n")
       cat(paste0("the (", round(est_eff, 3), ") estimate would have to be due to bias. This implies that to invalidate"))
       cat("\n")
@@ -134,7 +134,7 @@ output_print <- function(n_covariates,
       cat("\n")
       cat("on all observed covariates in the model; signs are interchangeable). This is")
       cat("\n")
-      cat(paste0("based on a threshold of ", round(critical_r, 3), " for statistical significance (alpha = ", alpha, ").\n"))
+      cat(paste0("based on a threshold effect of ", round(critical_r, 3), " for statistical significance (alpha = ", alpha, ").\n"))
       cat("\n")
       cat("Correspondingly the impact of an omitted variable (as defined in Frank 2000) must be ") 
       cat("\n")
@@ -148,7 +148,7 @@ output_print <- function(n_covariates,
       cat("\n")
       cat("of interest (conditioning on all observed covariates in the model;")
       cat("\n")
-      cat(paste0("signs are interchangeable). This is based on a threshold of ", round(critical_r, 3), " for"))
+      cat(paste0("signs are interchangeable). This is based on a threshold effect of ", round(critical_r, 3), " for"))
       cat("\n")
       cat("statistical significance (alpha = ", alpha, ").\n", sep = "")
       cat("\n")
@@ -164,7 +164,7 @@ output_print <- function(n_covariates,
       cat("\n")
       cat("of interest (conditioning on all observed covariates in the model;")
       cat("\n")
-      cat(paste0("signs are interchangeable). This is based on a threshold of ", round(beta_threshhold, 3)))
+      cat(paste0("signs are interchangeable). This is based on a threshold effect of ", round(beta_threshhold, 3)))
       cat("\n")
       cat("for statistical significance (alpha = ", alpha, ").\n", sep = "")
       cat("\n")
@@ -180,7 +180,7 @@ output_print <- function(n_covariates,
       cat("\n")
       cat("on all observed covariates in the model; signs are interchageable).")
       cat("\n")
-      cat(paste0("This is based on a threshold of ", round(beta_threshhold, 3), " for statistical significance (alpha = ", alpha, ").\n"))
+      cat(paste0("This is based on a threshold effect of ", round(beta_threshhold, 3), " for statistical significance (alpha = ", alpha, ").\n"))
       cat("\n")
       cat("Correspondingly the impact of an omitted variable (as defined in Frank 2000) must be ")
       cat("\n")

R/test_cop.R

@@ -342,6 +342,7 @@ fig <- ggplot2::ggplot(figTable, ggplot2::aes(x = figTable$ModelLabel)) +
     cat("\n")
     cat(sprintf("Delta* is %.3f (assuming no covariates in the baseline model M1),\nthe correlation-based delta is %.3f, with a bias of %.3f%%.\n", 
               delta_star, delta_exact, delta_pctbias))
+    cat("Note that %bias = (delta* - delta) / delta.\n")
     cat("\n")
     cat(sprintf("With delta*, the coefficient in the final model will be %.3f.\nWith the correlation-based delta, the coefficient will be %.3f.\n",  
               eff_x_M3_oster, eff_x_M3))

R/test_pse.R

@@ -143,10 +143,10 @@ test_pse <- function(est_eff,
     }
 
     if (to_return == "print") {
-        cat("This function calculates the conditions that set the estimated effect\napproximately equal to the threshold while preserving the standard error.\n\n")
+        cat("This function calculates the correlations associated with the confound that \ngenerate an estimated effect that is approximately equal to the threshold \nwhile preserving the standard error.\n\n")
         cat(sprintf("The correlation between X and CV is %.3f, and the correlation between\nY and CV is %.3f.\n\n", rxcv, rycv))
         cat(sprintf("Conditional on the covariates, the correlation between X and CV is %.3f,\nand the correlation between Y and CV is %.3f.\n\n", rxcvGz, rycvGz))
-        cat(sprintf("Including such CV, the coefficient changes to %.3f, and standard error\nis %.3f.\n\n", eff_x_M3, se_x_M3))
+        cat(sprintf("Including such a CV, the coefficient changes to %.3f, and standard error\nis %.3f.\n\n", eff_x_M3, se_x_M3))
         cat("Use to_return = \"raw_output\" to see more specific results.")
     }
 

R/tkonfound.R

@@ -202,7 +202,7 @@ total_rate_final <- total_success_final / (total_fail_final + total_success_fina
 
   if (!allnotenough & final > 1) {
     conclusion1 <- paste0(
-      change, sprintf("one would need to replace %d ", RIR), RIRway, "data points")
+      change, sprintf("one would need to replace %d ", RIR), RIRway, " data points with data points")
 
     if (replace == "control") {
       conclusion1b <- paste0(
@@ -214,13 +214,13 @@ total_rate_final <- total_success_final / (total_fail_final + total_success_fina
 
     conclusion1c <- paste0(
       sprintf("This is equivalent to transferring %d", final),
-      " data points from ", transferway, "."
-    )
+      " data points from ", transferway, " (Fragility = ", final, ")."
+      )
   }
 
   if (!allnotenough & final == 1) {
     conclusion1 <- paste0(
-      change, sprintf("one would need to replace %d ", RIR), RIRway, "data points")
+      change, sprintf("one would need to replace %d ", RIR), RIRway, " data points with data points")
 
     if (replace == "control") {
       conclusion1b <- paste0(
@@ -232,7 +232,7 @@ total_rate_final <- total_success_final / (total_fail_final + total_success_fina
 
     conclusion1c <- paste0(
       sprintf("This is equivalent to transferring %d", final),
-      " data points from ", transferway, ".")
+      " data points from ", transferway, " (Fragility = ", final, ").")
   }
 
   if (allnotenough){
@@ -265,7 +265,7 @@ total_rate_final <- total_success_final / (total_fail_final + total_success_fina
   info1 <- "This function calculates the number of data points that would have to be replaced with"
   info2 <- "zero effect data points (RIR) to invalidate an inference made about the association"
   info3 <- "between the rows and columns in a 2x2 table."
-  info4 <- "One can also interpret this as switches from one cell to another, such as from the"
+  info4 <- "One can also interpret this as switches (Fragility) from one cell to another, such as from the"
   info5 <- "treatment success cell to the treatment failure cell."
 
   if (to_return == "raw_output") {

tests/testthat/test-test_cop.R

@@ -88,7 +88,8 @@ test_that("test_cop outputs the correct language and values when to_return is 'p
         "proportionality (delta) as well as Oster's delta*.",
         "",
         "Delta* is 0.387 (assuming no covariates in the baseline model M1),", 
-        "the correlation-based delta is 1.172, with a bias of -66.980%.",  
+        "the correlation-based delta is 1.172, with a bias of -66.980%.",
+        "Note that %bias = (delta* - delta) / delta.",
         "",
         "With delta*, the coefficient in the final model will be 0.447.",     
         "With the correlation-based delta, the coefficient will be 0.300.",

tests/testthat/test-test_pse.R

@@ -78,16 +78,17 @@ test_that("test_pse print output is correct", {
 
     # Expected string
     expected_output <- c(
-        "This function calculates the conditions that set the estimated effect",
-        "approximately equal to the threshold while preserving the standard error.",
+        "This function calculates the correlations associated with the confound that ",
+        "generate an estimated effect that is approximately equal to the threshold ",
+        "while preserving the standard error.",
         "",
         "The correlation between X and CV is 0.214, and the correlation between",
         "Y and CV is 0.313.",
         "",
         "Conditional on the covariates, the correlation between X and CV is 0.248,",
         "and the correlation between Y and CV is 0.372.",
         "",
-        "Including such CV, the coefficient changes to 0.097, and standard error",
+        "Including such a CV, the coefficient changes to 0.097, and standard error",
         "is 0.054.",
         "",
         "Use to_return = \"raw_output\" to see more specific results."