Update test_sensitivity_ln.R

R/test_sensitivity_ln.R

@@ -17,22 +17,22 @@
 
     ## error message if input is inappropriate
     if (!(std_err > 0)) {
       stop("Did not run! Standard error needs to be greater than zero.")}
     if (!(n_obs > n_covariates + 3)) {
       stop("Did not run! There are too few observations relative to 
            the number of observations and covariates. Please specify a 
            less complex model to use KonFound-It.")}
 
     thr_t <- cal_thr_t(est_eff, alpha, tails, n_obs, n_covariates)
 
     # stop message
     if (n_obs <= 0 || n_treat <= 0) {
         stop("Please enter positive integers for sample size 
              and number of treatment group cases.")
     }
     if (n_obs <= n_treat) {
         stop("The total sample size should be larger than 
              the number of treatment group cases.")
     }
 
     odds_ratio <- exp(est_eff)
@@ -63,18 +63,18 @@
     # to record the original treatment cases in case we need to adjust it
     # user_ntrm <- n_treat
     # check if the implied table solution may contain imaginary numbers
-    # haveimaginary <- F
-    # changepi <- F
+    # haveimaginary <- FALSE
+    # changepi <- FALSE
     # set the default value for whether we need and can adjust pi (ratio of treatment cases)
     # to remove the imaginary part
     # keyimagin <- (4 + 4 * odds_ratio^2 + odds_ratio *
     #                 (-8 + 4 * n_obs * std_err^2 - n_obs * n_treat * std_err^4 + n_treat^2 * std_err^4))
     # minimgain <- 4 + 4 * odds_ratio^2 + odds_ratio * (-8 + n_obs * std_err^2 * (4 - 0.25 * n_obs * std_err^2))
     # keyx1 <- 4 + 4 * odds_ratio^2 + odds_ratio * (-8 + 4 * n_obs * std_err^2)
     # if (keyimagin > 0) {
-    # haveimaginary <- T
+    # haveimaginary <- TRUE
     # if (minimgain <= 0 && keyx1 > 0) {
-    # changepi <- T
+    # changepi <- TRUE
     # n_treat <- n_obs * get_pi(odds_ratio, std_err, n_obs, n_treat)
     # n_cnt <- n_obs - n_treat
     #  } else {
@@ -222,11 +222,11 @@
             change, sprintf("you would need to replace %d", RIR), RIRway, "cases")
 
         if (replace == "control") {
             conclusion1a <- sprintf("with cases for which the probability of 
                                     failure in the control group applies (RIR = %d).", RIR)
         } else {
             conclusion1a <- sprintf("with cases for which the probability of failure 
                                     in the entire sample applies (RIR = %d).", RIR)
         }
 
         conclusion1b <- paste(
@@ -239,14 +239,14 @@
         conclusion1 <- paste(
             change, c("only transferring cases from"), transferway, "is not enough.")
 
         conclusion1b <- paste(sprintf("We also need to transfer %d cases from", 
                                       final_solution$final_extra),
                               transferway_extra, c("as shown, from the User-entered 
                                                    Table to the Transfer Table. "))
 
         conclusion1c <- paste(sprintf("This means we need to replace %d of", RIR), RIRway, 
                               sprintf("with null hypothesis cases; and replace %d", 
                                       RIR_extra), RIRway_extra, 
                               c("with null hypothesis cases to change the inference.")
         )
     }