Commit ⋅ llrs/experDesign

Showing 2 of 2 files from the diff.

@@ -20,10 +20,17 @@

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#' index
design <- function(pheno, size_subset, omit = NULL, iterations = 500,
                   name = "SubSet") {
  stopifnot(is.numeric(size_subset) && is.finite(size_subset))
  stopifnot(length(dim(pheno)) == 2)
  stopifnot(is.numeric(iterations) && is.finite(iterations))
  stopifnot(is.character(name))
  opt <- Inf

  # Calculate batches
  size_data <- nrow(pheno)
  if (size_subset >= size_data) {
    stop("All the data can be done in one batch.", call. = FALSE)
  }
  batches <- optimum_batches(size_data, size_subset)

  if (!valid_sizes(size_data, size_subset, batches)) {

@@ -86,9 +93,14 @@

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#' head(index)
replicates <- function(pheno, size_subset, controls, omit = NULL,
                       iterations = 500){
  stopifnot(is.numeric(size_subset))
  stopifnot(is.numeric(controls))
  stopifnot(is.numeric(size_subset) && is.finite(size_subset))
  stopifnot(length(dim(pheno)) == 2)
  stopifnot(is.numeric(iterations) && is.finite(iterations))

  size_data <- nrow(pheno)
  if (size_subset >= size_data) {
    stop("All the data can be done in one batch.", call. = FALSE)
  }
  if (size_subset < controls) {
    stop("The controls are technical controls for the batches.\n\t",
         "They cannot be above the number of samples per batch.", call. = FALSE)

@@ -19,6 +19,9 @@

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spatial <- function(index, pheno, omit = NULL, remove_positions = NULL, rows = LETTERS[1:5],
         columns = 1:10, iterations = 500) {

  stopifnot(length(dim(pheno)) == 2)
  stopifnot(is.numeric(iterations) && is.finite(iterations))

  nrow <- length(rows)
  ncol <- length(columns)


@@ -33,6 +36,7 @@

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         "\n\tPlease check the rows and columns or how you created the index.",
         call. = FALSE)
  }

  plate <- matrix(nrow = nrow, ncol = ncol, dimnames = list(rows, columns))
  positions <- position_name(rows, columns)
  if (any(!remove_positions %in% positions$name)) {

Files		•	•	•	Coverage
R	374	333	0	41	89.04%
Project Totals (11 files)	374	333	0	41	89.04%

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comment: false

coverage:
  status:
    project:
      default:
        target: auto
        threshold: 1%
    patch:
      default:
        target: auto
        threshold: 1%

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20	20		#' index
21	21		design <- function(pheno, size_subset, omit = NULL, iterations = 500,
22	22		name = "SubSet") {
	23	+	stopifnot(is.numeric(size_subset) && is.finite(size_subset))
	24	+	stopifnot(length(dim(pheno)) == 2)
	25	+	stopifnot(is.numeric(iterations) && is.finite(iterations))
	26	+	stopifnot(is.character(name))
23	27		opt <- Inf
24	28
25	29		# Calculate batches
26	30		size_data <- nrow(pheno)
	31	+	if (size_subset >= size_data) {
	32	+	stop("All the data can be done in one batch.", call. = FALSE)
	33	+	}
27	34		batches <- optimum_batches(size_data, size_subset)
28	35
29	36		if (!valid_sizes(size_data, size_subset, batches)) {

86	93		#' head(index)
87	94		replicates <- function(pheno, size_subset, controls, omit = NULL,
88	95		iterations = 500){
89		-	stopifnot(is.numeric(size_subset))
90		-	stopifnot(is.numeric(controls))
	96	+	stopifnot(is.numeric(size_subset) && is.finite(size_subset))
	97	+	stopifnot(length(dim(pheno)) == 2)
	98	+	stopifnot(is.numeric(iterations) && is.finite(iterations))
91	99
	100	+	size_data <- nrow(pheno)
	101	+	if (size_subset >= size_data) {
	102	+	stop("All the data can be done in one batch.", call. = FALSE)
	103	+	}
92	104		if (size_subset < controls) {
93	105		stop("The controls are technical controls for the batches.\n\t",
94	106		"They cannot be above the number of samples per batch.", call. = FALSE)

19	19		spatial <- function(index, pheno, omit = NULL, remove_positions = NULL, rows = LETTERS[1:5],
20	20		columns = 1:10, iterations = 500) {
21	21
	22	+	stopifnot(length(dim(pheno)) == 2)
	23	+	stopifnot(is.numeric(iterations) && is.finite(iterations))
	24	+
22	25		nrow <- length(rows)
23	26		ncol <- length(columns)
24	27

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33	36		"\n\tPlease check the rows and columns or how you created the index.",
34	37		call. = FALSE)
35	38		}
	39	+
36	40		plate <- matrix(nrow = nrow, ncol = ncol, dimnames = list(rows, columns))
37	41		positions <- position_name(rows, columns)
38	42		if (any(!remove_positions %in% positions$name)) {

1	comment: false
2
3	coverage:
4	status:
5	project:
6	default:
7	target: auto
8	threshold: 1%
9	patch:
10	default:
11	target: auto
12	threshold: 1%

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