update tests; add NEWS; add documentation (#179)

NEWS

@@ -1,6 +1,32 @@
 poppr 2.8.0
 ===========
 
+BUG FIX
+-------
+
+* `win.ia()` now has more consistent behavior with chromosome structure and will
+  no longer result in an integer overflow 
+  (see https://github.com/grunwaldlab/poppr/issues/179).
+
+ALGORITHMIC CHANGE
+------------------
+
+* `win.ia()` may result in slightly different results because of two changes:
+  1. The windows will now always start at position one on any given chromosome.
+  This will result in some windows at the beginning of chromosomes having a 
+  value of `NA` if the first variant starts beyond the first window. 
+  2. Windows are now calculated for each chromosome independently. The previous
+  version first concatenated chromosomes with at least a window-sized gap 
+  between the chromosomes, but failed to ensure that the window always started
+  at the beginning of the chromosome. This version fixes that issue. 
+  (see https://github.com/grunwaldlab/poppr/issues/179).
+
+DEPRECATION
+-----------
+
+* The `chromosome_buffer` argument for `win.ia()` has been permanently set to
+  `TRUE` and deprecated as it is no longer used. 
+
 NEW FEATURES
 ------------
 

tests/testthat/test-winia.R

@@ -1,41 +1,44 @@
 context("win.ia tests")
-options(poppr.debug = FALSE)
 set.seed(999)
 chrom_pos <- vapply(1:10, function(i) sort(sample(1e3, 100)), integer(100)) %>%
   as.vector()
 chromo    <- rep(1:10, each = 100)
-real_pos  <- chrom_pos + 1000*(chromo - 1) + 1#+ 100*(chromo - 1) + 1  
 set.seed(999)
 x <- glSim(n.ind = 10, n.snp.nonstruc = 5e2, n.snp.struc = 5e2, ploidy = 2, 
            parallel = FALSE)
 
 
 test_that("win.ia will throw an error if duplicate positions are found", {
-  x.naive     <- win.ia(x)
+  options(poppr.debug = TRUE)
+  expect_output(x.naive     <- win.ia(x), "[|=]{2,}")
   position(x) <- chrom_pos
   expect_equal(length(x.naive), 10L)
   expect_error(win.ia(x), "chromosome")
+  options(poppr.debug = FALSE)
 })  
 
+test_that("win.ia will throw a warning if chromosome_buffer is specified", {
+  expect_warning(x.naive <- win.ia(x, quiet = TRUE, chromosome_buffer = FALSE), "deprecated")
+})
+
 test_that("win.ia will use chromosome structure", {
   skip_on_cran()
   position(x)   <- chrom_pos
   chromosome(x) <- chromo
-  x.chrom.bt    <- win.ia(x)
-  expect_equal(sum(is.na(x.chrom.bt) & !is.nan(x.chrom.bt)), 9L)
-  expect_equal(length(x.chrom.bt), 109L)
+  x.chrom.bt    <- win.ia(x, quiet = TRUE)
+  expect_equal(length(x.chrom.bt), 100L)
+  expect_equal(names(x.chrom.bt), as.character(rep(1:10, each = 10)))
 })
 
-test_that("win.ia will take into account chromosome buffer", {
+test_that("win.ia will always start at the beginning of the chromosome", {
   skip_on_cran()
   position(x)   <- chrom_pos
   chromosome(x) <- chromo
-  x.chrom.bf    <- win.ia(x, chromosome_buffer = FALSE)
-  chromosome(x) <- NULL
-  position(x)   <- real_pos
-  x.real        <- win.ia(x)
-  expect_equal(length(x.chrom.bf), 100L)
-  expect_equal(length(x.chrom.bf), length(x.real))
-  expect_equal(x.chrom.bf, x.real, check.attributes = FALSE)
+  x.chrom.bf    <- win.ia(x, window = 300L, quiet = TRUE)
+  x.by.chrom    <- lapply(levels(chromosome(x)), function(i) win.ia(x[, chromosome(x) == i], window = 300L, quiet = TRUE))
+  # There should be 4 windows per chromosome.
+  expect_equal(length(x.chrom.bf), 40L)
+  # Using the function with and without chromosome structure should not matter.
+  expect_equal(x.chrom.bf, unlist(x.by.chrom, use.names = FALSE), check.attributes = FALSE)
+
 })
-