replace SignedDiff with PairedDifference

qddyy · Jan 6, 2024 · 61b66f4 · 61b66f4
1 parent d1da1b5
commit 61b66f4
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Showing 7 changed files with 72 additions and 113 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -16,6 +16,7 @@ export(MultiCompT)
 export(MultipleComparison)
 export(OneSampleTest)
 export(Page)
+export(PairedDifference)
 export(PermuTest)
 export(Quantile)
 export(RCBD)
@@ -24,7 +25,6 @@ export(RatioMeanDeviance)
 export(ScoreSum)
 export(SiegelTukey)
 export(Sign)
-export(SignedDiff)
 export(TukeyHSD)
 export(TwoSampleAssociationTest)
 export(TwoSamplePairedTest)

diff --git a/R/SignedDiff.R → R/PairedDifference.R b/R/SignedDiff.R → R/PairedDifference.R
@@ -1,30 +1,30 @@
-#' @title `r SignedDiff$private_fields$.name`
+#' @title `r PairedDifference$private_fields$.name`
 #' 
 #' @description Performs two sample signed score test on data vectors. 
 #' 
-#' @aliases paired.signeddiff
+#' @aliases paired.difference
 #' 
 #' @export
 #' 
 #' @importFrom R6 R6Class
 #' @importFrom stats pnorm
 
 
-SignedDiff <- R6Class(
-    classname = "SignedDiff",
+PairedDifference <- R6Class(
+    classname = "PairedDifference",
     inherit = TwoSamplePairedTest,
     cloneable = FALSE,
     public = list(
-        #' @description Create a new `SignedDiff` object. 
+        #' @description Create a new `PairedDifference` object. 
         #' 
         #' @template init_params
         #' @param scoring a character string specifying which scoring system to be used on the absolute differences. 
         #' @param method a character string specifying the method of ranking data in computing adjusted signed ranks for tied data, must be one of `"with_zeros"` (default) or `"ignore"`. Note that the data will be modified when this parameter is set to `"ignore"`. 
         #' @param correct a logical indicating whether to apply continuity correction in the normal approximation for the p-value when `scoring` is set to `"rank"`.
         #' 
-        #' @return A `SignedDiff` object. 
+        #' @return A `PairedDifference` object. 
         initialize = function(
-            type = c("permu", "asymp"), method = c("with_zeros", "ignore"), correct = TRUE,
+            type = c("permu", "asymp"), method = c("with_zeros", "without_zeros"), correct = TRUE,
             alternative = c("two_sided", "less", "greater"), n_permu = 0L, scoring = c("none", "rank", "vw", "expon")
         ) {
             private$.correct <- correct
@@ -35,7 +35,7 @@ SignedDiff <- R6Class(
         }
     ),
     private = list(
-        .name = "Paired Comparison Based on Signed Differences",
+        .name = "Paired Comparison Based on Differences",
 
         .correct = NULL,
 
@@ -44,27 +44,25 @@ SignedDiff <- R6Class(
         .define = function() {
             diff <- private$.data$x - private$.data$y
 
-            if (private$.method == "ignore") {
-                private$.data <- private$.data[diff != 0, ]
-                diff <- diff[diff != 0]
-            }
+            where_zero <- (diff == 0)
 
-            private$.abs_diff <- abs_diff <- abs(diff)
-            if (private$.scoring != "none") {
-                private$.abs_diff <- get_score(
-                    private$.abs_diff, method = private$.scoring
-                )
+            if (private$.method == "without_zeros") {
+                diff <- diff[!where_zero]
+                private$.data <- private$.data[!where_zero, ]
             }
 
-            diff_positive <- (diff > 0)
+            private$.abs_diff <- abs_diff <- if (private$.scoring != "none") {
+                score <- get_score(abs(diff), method = private$.scoring)
+                if (private$.method == "with_zeros") `[<-`(score, where_zero, 0) else score
+            } else abs(diff)
+
+            positive <- (diff > 0)
             private$.statistic_func <- function(swapped) {
-                sum(abs_diff[diff_positive != swapped])
+                sum(abs_diff[positive != swapped])
             }
         },
 
         .calculate_p = function() {
-            n <- nrow(private$.data)
-
             z <- private$.statistic - sum(private$.abs_diff) / 2
             correction <- if (private$.scoring == "rank" & private$.correct) {
                 switch(private$.side, lr = sign(z) * 0.5, r = 0.5, l = -0.5)

diff --git a/R/pmt.R b/R/pmt.R
@@ -61,7 +61,7 @@ tests <- list(
     multicomp.tukey = TukeyHSD,
 
     paired.sign = Sign,
-    paired.signeddiff = SignedDiff,
+    paired.difference = PairedDifference,
 
     rcbd.anova = RCBDANOVA,
     rcbd.friedman = Friedman,

diff --git a/README.Rmd b/README.Rmd
@@ -75,20 +75,10 @@ set.seed(0)
     t$p_value
     ```
 
-There is also support for chaining methods, which means that you can do things like
+All available tests:
 
-```{r, chaining, eval = FALSE}
-t <- pmt(...)$test(...)$print(...)$plot(...)
+```{r}
+pmts()
 ```
 
-## Tips
-
-Check
-
-- `?PermuTest` (all tests' base class) for all available methods and attributes. 
-- `pmts()` for all available tests. 
-    ```{r, pmts}
-    pmts()
-    ```
-
 ## References
diff --git a/README.md b/README.md
@@ -82,53 +82,39 @@ set.seed(0)
   #> [1] 0.0005090729
   ```
 
-There is also support for chaining methods, which means that you can do
-things like
+All available tests:
 
 ``` r
-t <- pmt(...)$test(...)$print(...)$plot(...)
+pmts()
 ```
 
-## Tips
+<div class="kable-table">
+
+| key                  | class              | test                                                 |
+|:---------------------|:-------------------|:-----------------------------------------------------|
+| onesample.quantile   | Quantile           | Quantile Test                                        |
+| onesample.cdf        | CDF                | Cumulative Distribution Function                     |
+| twosample.difference | Difference         | Two Sample Test Based on Mean or Median              |
+| twosample.wilcoxon   | Wilcoxon           | Two Sample Wilcoxon Test                             |
+| twosample.scoresum   | ScoreSum           | Score Sum Test                                       |
+| twosample.ansari     | AnsariBradley      | Ansari-Bradley Test                                  |
+| twosample.siegel     | SiegelTukey        | Siegel-Tukey Test                                    |
+| twosample.rmd        | RatioMeanDeviance  | Ratio Mean Deviance Test                             |
+| twosample.ks         | KolmogorovSmirnov  | Two Sample Kolmogorov-Smirnov Test                   |
+| ksample.anova        | ANOVA              | K Sample Test Based on F Statistic                   |
+| ksample.kw           | KruskalWallis      | Kruskal-Wallis Test                                  |
+| ksample.jt           | JonckheereTerpstra | Jonckheere-Terpstra Test                             |
+| multicomp.t          | MultiCompT         | Multiple Comparison Based on t Statistic             |
+| multicomp.tukey      | TukeyHSD           | Tukey’s HSD                                          |
+| paired.sign          | Sign               | Sign Test                                            |
+| paired.difference    | PairedDifference   | Paired Comparison Based on Differences               |
+| rcbd.anova           | RCBDANOVA          | ANOVA for Randomized Complete Block Design           |
+| rcbd.friedman        | Friedman           | Friedman Test                                        |
+| rcbd.page            | Page               | Page Test                                            |
+| association.corr     | Correlation        | Two Sample Test Based on Correlation Coefficient     |
+| table.chisq          | ChiSquare          | Contingency Table Test Based on Chi-square Statistic |
 
-Check
-
-- `?PermuTest` (all tests’ base class) for all available methods and
-  attributes.
-
-- `pmts()` for all available tests.
-
-  ``` r
-  pmts()
-  ```
-
-  <div class="kable-table">
-
-  | key                  | class              | test                                                 |
-  |:---------------------|:-------------------|:-----------------------------------------------------|
-  | onesample.quantile   | Quantile           | Quantile Test                                        |
-  | onesample.cdf        | CDF                | Cumulative Distribution Function                     |
-  | twosample.difference | Difference         | Two Sample Test Based on Mean or Median              |
-  | twosample.wilcoxon   | Wilcoxon           | Two Sample Wilcoxon Test                             |
-  | twosample.scoresum   | ScoreSum           | Score Sum Test                                       |
-  | twosample.ansari     | AnsariBradley      | Ansari-Bradley Test                                  |
-  | twosample.siegel     | SiegelTukey        | Siegel-Tukey Test                                    |
-  | twosample.rmd        | RatioMeanDeviance  | Ratio Mean Deviance Test                             |
-  | twosample.ks         | KolmogorovSmirnov  | Two Sample Kolmogorov-Smirnov Test                   |
-  | ksample.anova        | ANOVA              | K Sample Test Based on F Statistic                   |
-  | ksample.kw           | KruskalWallis      | Kruskal-Wallis Test                                  |
-  | ksample.jt           | JonckheereTerpstra | Jonckheere-Terpstra Test                             |
-  | multicomp.t          | MultiCompT         | Multiple Comparison Based on t Statistic             |
-  | multicomp.tukey      | TukeyHSD           | Tukey’s HSD                                          |
-  | paired.sign          | Sign               | Sign Test                                            |
-  | paired.signeddiff    | SignedDiff         | Paired Comparison Based on Signed Differences        |
-  | rcbd.anova           | RCBDANOVA          | ANOVA for Randomized Complete Block Design           |
-  | rcbd.friedman        | Friedman           | Friedman Test                                        |
-  | rcbd.page            | Page               | Page Test                                            |
-  | association.corr     | Correlation        | Two Sample Test Based on Correlation Coefficient     |
-  | table.chisq          | ChiSquare          | Contingency Table Test Based on Chi-square Statistic |
-
-  </div>
+</div>
 
 ## References
 

diff --git a/man/SignedDiff.Rd → man/PairedDifference.Rd b/man/SignedDiff.Rd → man/PairedDifference.Rd
diff --git a/vignettes/examples.Rmd b/vignettes/examples.Rmd
@@ -340,9 +340,9 @@ t$p_value
 ## Table 4.1.1
 
 ```{r}
-# See ?SignedDiff or ?paired.signeddiff
+# See ?PairedDifference or ?paired.difference
 t <- pmt(
-    "paired.signeddiff", alternative = "greater",
+    "paired.difference", alternative = "greater",
     scoring = "none"
 )
 
@@ -356,10 +356,10 @@ t$p_value
 ## Example 4.1.1
 
 ```{r}
-# See ?SignedDiff or ?paired.signeddiff
+# See ?PairedDifference or ?paired.difference
 t <- pmt(
-    "paired.signeddiff", alternative = "two_sided",
-    scoring = "none", method = "ignore"
+    "paired.difference", alternative = "two_sided",
+    scoring = "none", method = "without_zeros"
 )
 
 # See ?Table4.1.3
@@ -378,9 +378,9 @@ t$p_value
 ## Example 4.2.1 & 4.2.2
 
 ```{r}
-# See ?SignedDiff or ?paired.signeddiff
+# See ?PairedDifference or ?paired.difference
 t <- pmt(
-    "paired.signeddiff", alternative = "greater",
+    "paired.difference", alternative = "greater",
     scoring = "rank", method = "with_zeros"
 )
 
@@ -394,21 +394,6 @@ t$type <- "asymp"
 t$p_value
 ```
 
-## Table 4.2.3
-
-```{r}
-# See ?SignedDiff or ?paired.signeddiff
-t <- pmt(
-    "paired.signeddiff", alternative = "greater",
-    scoring = "rank", method = "ignore"
-)
-
-t$test(c(-5, -3, -3, 0, 0, 2, 4, 4, 4, 5), 0)
-
-t$statistic
-t$p_value
-```
-
 ## Example 4.3.1
 
 ```{r}