From 7a182540ff98e6e48632a31b07cd69e94bc0caa0 Mon Sep 17 00:00:00 2001
From: Thomas Guillerme <guillert@tcd.ie>
Date: Mon, 21 Oct 2024 16:20:22 +0100
Subject: [PATCH] Works for column bootstrap!

---
 R/dispRity.R                        |  2 +-
 R/dispRity_fun.R                    |  6 +++--
 tests/testthat/test-dispRity.core.R | 34 ++++++++++++++++-------------
 3 files changed, 24 insertions(+), 18 deletions(-)

diff --git a/R/dispRity.R b/R/dispRity.R
index 1930e0e3..0573d467 100755
--- a/R/dispRity.R
+++ b/R/dispRity.R
@@ -331,7 +331,7 @@ dispRity <- function(data, metric, dimensions = NULL, ..., between.groups = FALS
     }
 
     ## Check do_by.col from bootstraps
-    do_by.col <- ifelse(!is.null(data$call$boostrap) && data$call$bootstap[[4]] == "columns", TRUE, FALSE)
+    do_by.col <- ifelse(!is.null(data$call$bootstrap) && data$call$bootstrap[[4]] == "columns", TRUE, FALSE)
 
     ## Serial
     is_between.groups <- FALSE
diff --git a/R/dispRity_fun.R b/R/dispRity_fun.R
index f695063e..b5dc4603 100755
--- a/R/dispRity_fun.R
+++ b/R/dispRity_fun.R
@@ -374,16 +374,16 @@ decompose.matrix <- function(one_subsets_bootstrap, fun, data, nrow, use_tree, d
         dist.data <- TRUE
     } else {
         data_list  <- data$matrix
+    
     }
     ## Select the dimensions
     if(dist.data) {
         bootstrap  <- dimensions <- na.omit(one_subsets_bootstrap)
     } else {
         if(!is.null(by.col)) {
-            stop("DEBUG: dispRity_fun::decompose.matrix")
             ## Dimensions is bootstrap if not elements.
             dimensions <- na.omit(one_subsets_bootstrap)
-            bootstrap <- by.col 
+            bootstrap <- na.omit(by.col) 
         } else {
             ## Base bootstrap use
             dimensions <- data$call$dimensions
@@ -566,6 +566,8 @@ lapply.wrapper <- function(subsets, metrics_list, data, matrix_decomposition, ve
     if(do_by.col) {
         ## Get the elements and pass them on
         by.col <- subsets$elements
+        ## Replace the first subset (elements) by the data dimensions
+        subsets$elements <- matrix(data$call$dimensions, ncol = 1)
     } else {
         ## Don't pass anything
         by.col <- NULL
diff --git a/tests/testthat/test-dispRity.core.R b/tests/testthat/test-dispRity.core.R
index 16b219c4..e2ad8f21 100755
--- a/tests/testthat/test-dispRity.core.R
+++ b/tests/testthat/test-dispRity.core.R
@@ -903,23 +903,27 @@ test_that("dispRity works with boot.by = columns", {
     ## Toggle do_by.col in dispRity
     ## Then pass it to lapply wrapper to change the variable by.col from NULL do subset$elements.
 
+    set.seed(1)
+    data <- matrix(rnorm(50), 10, 5, dimnames = list(letters[1:10]))
+    cust <- custom.subsets(data, group = list(c(1:4), c(5:10)))
 
-    # data <- matrix(rnorm(50), 10, 5, dimnames = list(letters[1:10]))
-    # dist <- as.matrix(dist(matrix(rnorm(45), 9, 5, dimnames = list(letters[1:9]))))
-
-    
-    # ## Simple
-    # test <- boot.matrix(data, bootstraps = 3, boot.by = "rows")
-    # expect_equal(test$subsets[[1]]$elements, matrix(1:10, 10, 1))
-    # expect_equal(dim(test$subsets[[1]][[2]]), c(10, 3))
-    # expect_equal(test$call$bootstrap[[4]], "rows")
-    # # By columns
-    # test <- boot.matrix(data, bootstraps = 3, boot.by = "columns")
-    # expect_equal(test$subsets[[1]]$elements, matrix(1:10, 10, 1))
-    # expect_equal(dim(test$subsets[[1]][[2]]), c(5, 3))
-    # expect_equal(test$call$bootstrap[[4]], "columns")
-    ## By both
+    set.seed(1)
+    boot_test1 <- boot.matrix(cust, bootstraps = 3, boot.by = "rows")
+    expect_equal(boot_test1$subsets[[1]]$elements, matrix(1:4, 4, 1))
+    expect_equal(dim(boot_test1$subsets[[1]][[2]]), c(4, 3))
+    expect_equal(boot_test1$subsets[[2]]$elements, matrix(5:10, 6, 1))
+    expect_equal(dim(boot_test1$subsets[[2]][[2]]), c(6, 3))
+    expect_equal(boot_test1$call$bootstrap[[4]], "rows")
+    expect_equal(summary(dispRity(boot_test1, metric = centroids))$bs.median, c(1.086, 1.156))
 
+    set.seed(1)
+    boot_test2 <- boot.matrix(cust, bootstraps = 3, boot.by = "columns")
+    expect_equal(boot_test2$subsets[[1]]$elements, matrix(1:4, 4, 1))
+    expect_equal(dim(boot_test2$subsets[[1]][[2]]), c(5, 3))
+    expect_equal(boot_test2$subsets[[2]]$elements, matrix(5:10, 6, 1))
+    expect_equal(dim(boot_test2$subsets[[2]][[2]]), c(5, 3))
+    expect_equal(boot_test2$call$bootstrap[[4]], "columns")
+    expect_equal(summary(dispRity(boot_test2, metric = centroids))$bs.median, c(1.919, 1.337))
 })