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[matrixstats] Contents of /pkg/matrixStats/tests/rowMedians.R
Contents of /pkg/matrixStats/tests/rowMedians.R
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Revision 220 -
(show annotations)
Thu Jun 5 07:33:37 2014 UTC (9 years, 10 months ago) by henrikb
File size: 1316 byte(s)
Thu Jun 5 07:33:37 2014 UTC (9 years, 10 months ago) by henrikb
File size: 1316 byte(s)
CLEANUP: Package tests no longer do benchmarking. BENCHMARK: Made list of alternative methods in reports more explicit.
| 1 | library("matrixStats") |
| 2 | |
| 3 | # - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| 4 | # Consistency checks |
| 5 | # - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| 6 | set.seed(1) |
| 7 | |
| 8 | cat("Consistency checks:\n") |
| 9 | K <- if (Sys.getenv("_R_CHECK_FULL_") == "") 4 else 20 |
| 10 | for (kk in 1:K) { |
| 11 | cat("Random test #", kk, "\n", sep="") |
| 12 | |
| 13 | # Simulate data in a matrix of any shape |
| 14 | dim <- sample(500:2000, size=2) |
| 15 | n <- prod(dim) |
| 16 | x <- rnorm(n, sd=100) |
| 17 | dim(x) <- dim |
| 18 | |
| 19 | # Add NAs? |
| 20 | if ((kk %% 4) %in% c(3,0)) { |
| 21 | cat("Adding NAs\n") |
| 22 | nna <- sample(n, size=1) |
| 23 | naValues <- c(as.double(NA), NaN) |
| 24 | x[sample(length(x), size=nna)] <- sample(naValues, size=nna, replace=TRUE) |
| 25 | } |
| 26 | |
| 27 | # Integer or double? |
| 28 | if ((kk %% 4) %in% c(2,0)) { |
| 29 | cat("Coercing to integers\n") |
| 30 | storage.mode(x) <- "integer" |
| 31 | } |
| 32 | |
| 33 | na.rm <- sample(c(TRUE,FALSE), size=1) |
| 34 | |
| 35 | # rowMedians(): |
| 36 | y1 <- matrixStats::rowMedians(x, na.rm=na.rm) |
| 37 | y2 <- apply(x, MARGIN=1, FUN=median, na.rm=na.rm) |
| 38 | stopifnot(all.equal(y1,y2)) |
| 39 | y3 <- matrixStats::colMedians(t(x), na.rm=na.rm) |
| 40 | stopifnot(all.equal(y1,y3)) |
| 41 | |
| 42 | # colMedians(): |
| 43 | y1 <- matrixStats::colMedians(x, na.rm=na.rm) |
| 44 | y2 <- apply(x, MARGIN=2, FUN=median, na.rm=na.rm) |
| 45 | stopifnot(all.equal(y1,y2)) |
| 46 | y3 <- matrixStats::rowMedians(t(x), na.rm=na.rm) |
| 47 | stopifnot(all.equal(y1,y3)) |
| 48 | } # for (kk ...) |
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