To-do cleanup

R/tulostaAdmixtureTiedot.R

@@ -1,5 +1,5 @@
 tulostaAdmixtureTiedot <- function(proportions, uskottavuus, alaRaja, niter) {
-    # TODO: discover what this function does. Plotting? Get examples?
+    # ASK: what does this function does. Plotting? Get examples?
     # h0 <- findobj('Tag','filename1_text')
     # inputf = get(h0,'String');
     # h0 = findobj('Tag','filename2_text');

inst/ext/ExamplesDataFormatting/Notes.md

@@ -1 +1 @@
-Most of the data in this directory is in the [Genepop format](https://genepop.curtin.edu.au/help_input.html) format.
+Most of the data in this directory is in the [Genepop format](https://genepop.curtin.edu.au/help_input.html) format.

tests/testthat/test-admix1.R

@@ -148,7 +148,6 @@ test_that("suoritaMuutos works like on Matlab", {
 })
 
 test_that("laskeMuutokset4 works like on Matlab", {
-    # TODO: build these tests based on problems found in etsiParas
     mx1 <- t(c(.4, 7))
     expect_equivalent(
         object = laskeMuutokset4(2, mx1, c(8, 2), 3),

tests/testthat/test-convertedBaseFunctions.R

@@ -223,7 +223,7 @@ test_that("setdiff works as expected", {
 	A <- c(3, 6, 2, 1, 5, 1, 1)
 	B <- c(2, 4, 6)
 	C <- c(1, 3, 5)
-	expect_equal(setdiff_MATLAB(A, B), C) # TODO: export setdiff_MATLAB
+	expect_equal(setdiff_MATLAB(A, B), C)
 	A <- data.frame(
 		Var1 = 1:5,
 		Var2 = LETTERS[1:5],

tests/testthat/test-greedyMix.R

@@ -33,7 +33,7 @@ test_that("handleData works as expected", {
 	expect_equal(data_obs, data_exp)
 })
 
-context("Opening files on greedyMix")
+context("Opening files on greedyMix/load_fasta")
 
 # # TODO: needs #12 to be fixed before this can be done without user intervention
 # greedyMix(
@@ -41,7 +41,7 @@ context("Opening files on greedyMix")
 # 	format = "BAPS",
 # 	savePreProcessed = FALSE
 # ) # Upper bounds 100 100
-# TODO: replace with load_fasta()
+# TODO #16: replace with load_fasta()
 
 context("Linkage")