TRUE, not T

Author: smasongarrison

R/buildComponent.R

@@ -874,7 +874,7 @@ loadOrComputeCheckpoint <- function(file, compute_fn,
   if (config$verbose == TRUE) {
     cat(sprintf(verbose_message, length(idx)))
   }
-# consequence is missing data
+  # consequence is missing data
   if (is.matrix(component) || methods::is(component, "Matrix")) {
     component <- component[idx, , drop = drop]
   } else {

R/buildComponentWrappers.R

@@ -201,6 +201,6 @@ ped2ce <- function(ped, personID = "ID",
     )
     return(mat)
   } else {
-  matrix(1, nrow = nrow(ped), ncol = nrow(ped), dimnames = list(ped[[personID]], ped[[personID]]))
+    matrix(1, nrow = nrow(ped), ncol = nrow(ped), dimnames = list(ped[[personID]], ped[[personID]]))
   }
 }

tests/testthat/test-buildComponent.R

@@ -379,11 +379,11 @@ test_that("keep_ids subset produces correct relatedness values", {
 
 
   r_full <- ped2com(hazard,
-    component = "additive", sparse = T,
+    component = "additive", sparse = TRUE,
     keep_ids = NULL
   )
   r_sub <- ped2com(hazard,
-    component = "additive", sparse = T,
+    component = "additive", sparse = TRUE,
     keep_ids = keep
   )
 
@@ -403,7 +403,7 @@ test_that("keep_ids subset produces correct relatedness values across all famili
   )
 
   r_full_sparse <- ped2com(inbreeding,
-    component = "additive", sparse = T,
+    component = "additive", sparse = TRUE,
     keep_ids = NULL
   )
   for (i in unique(inbreeding$famID)) {
@@ -422,7 +422,7 @@ test_that("keep_ids subset produces correct relatedness values across all famili
 
     r_full <- r_full_sparse
     r_sub <- ped2com(inbreeding,
-      component = "additive", sparse = T,
+      component = "additive", sparse = TRUE,
       keep_ids = keep
     )
 
@@ -438,26 +438,26 @@ test_that("keep_ids subset produces correct relatedness values across all famili
 test_that("keep_ids subset produces correct relatedness values across all families", {
   library(ggpedigree)
   data(ASOIAF)
-df <-ASOIAF |> dplyr::rename(ID = id)
+  df <- ASOIAF |> dplyr::rename(ID = id)
 
   r_full_sparse <- ped2com(df,
-                           component = "additive", sparse = TRUE,
-                           keep_ids = NULL,
-                           mz_twins = FALSE
+    component = "additive", sparse = TRUE,
+    keep_ids = NULL,
+    mz_twins = FALSE
   )
   for (i in unique(df$famID)) {
     n_rows <- sum(df$famID == i)
     if (n_rows < 3) {
       next
     }
-    keep <- as.character(sample(df$ID[df$famID == i], min(15,n_rows)))
+    keep <- as.character(sample(df$ID[df$famID == i], min(15, n_rows)))
 
 
     r_full <- r_full_sparse
     r_sub <- ped2com(df,
-                     component = "additive", sparse = TRUE,
-                     keep_ids = keep,
-                     mz_twins = FALSE
+      component = "additive", sparse = TRUE,
+      keep_ids = keep,
+      mz_twins = FALSE
     )
 
     expect_equal(dim(r_sub), c(length(keep), length(keep)))
@@ -466,15 +466,15 @@ df <-ASOIAF |> dplyr::rename(ID = id)
     # values in the subset must match the corresponding entries of the full matrix
     expect_equal(r_sub, r_full[keep, keep], tolerance = 1e-10, info = paste("Family", i))
 
-    #entirely random subset of IDs across the whole dataset (not just within family)
+    # entirely random subset of IDs across the whole dataset (not just within family)
     keep <- as.character(sample(df$ID, 15))
 
 
     r_full <- r_full_sparse
     r_sub <- ped2com(df,
-                     component = "additive", sparse = TRUE,
-                     keep_ids = keep,
-                     mz_twins = FALSE
+      component = "additive", sparse = TRUE,
+      keep_ids = keep,
+      mz_twins = FALSE
     )
 
     expect_equal(dim(r_sub), c(length(keep), length(keep)))

tests/testthat/test-buildComponent_chunks.R

@@ -32,16 +32,16 @@ test_that("chunked tcrossprod matches standard tcrossprod", {
 
   data(inbreeding)
   r_standard <- ped2com(inbreeding,
-    component = "additive", sparse = T,
+    component = "additive", sparse = TRUE,
     transpose_method = "tcrossprod"
   )
   r_chunked <- ped2com(inbreeding,
-    component = "additive", sparse = T,
+    component = "additive", sparse = TRUE,
     transpose_method = "chunked", chunk_size = 3L, force_symmetric = FALSE
   )
 
   r_chunked_sym <- ped2com(inbreeding,
-    component = "additive", sparse = T,
+    component = "additive", sparse = TRUE,
     transpose_method = "chunked", chunk_size = 3L, force_symmetric = TRUE
   )
 
@@ -86,11 +86,11 @@ test_that("chunked tcrossprod matches standard tcrossprod when also subsetted",
   keep <- as.character(inbreeding$ID[5:10])
 
   r_full <- ped2com(inbreeding,
-    component = "additive", sparse = T,
+    component = "additive", sparse = TRUE,
     keep_ids = NULL
   )
   r_sub <- ped2com(inbreeding,
-    component = "additive", sparse = T,
+    component = "additive", sparse = TRUE,
     keep_ids = keep
   )
 
@@ -101,9 +101,9 @@ test_that("chunked tcrossprod matches standard tcrossprod when also subsetted",
   expect_equal(r_sub, r_full[keep, keep], tolerance = 1e-10)
 
   r_chunked <- ped2com(inbreeding,
-    component = "additive", sparse = T,
+    component = "additive", sparse = TRUE,
     transpose_method = "chunked", chunk_size = 3L,
-    keep_ids = keep, force_symmetric = T
+    keep_ids = keep, force_symmetric = TRUE
   )
 
   expect_equal(as.matrix(r_sub), as.matrix(r_chunked), tolerance = 1e-10)