Running 'bar.R' [158s]
  Running 'checksex.R' [0s]
  Comparing 'checksex.Rout' to 'checksex.Rout.save' ... OK
  Running 'foo.R' [174s]
  Running 'gammas.R' [162s]
  Running 'kinship.R' [168s]
  Running 'thompson.R' [0s]
  Comparing 'thompson.Rout' to 'thompson.Rout.save' ... OK
Running the tests in 'tests/bar.R' failed.
Complete output:
  > 
  > # attempt to reproduce some of the numbers from U of Washington Statistics
  > # Tech Report 153 (Geyer, 1988) cited in the help page for R function
  > # descent in this package.
  > 
  > library(sped)
  > data(alberta)
  > 
  > # In alberta pedigree, probability that one gene picked at random
  > # from individuals 1085, 1094, 1180, 1260, and 1272 are each descended
  > # from one gene in founder 52.
  > # TR says 0.0156250, 0.0156250, 0.0078125, 0.0312500, 0.0078125
  > 
  > vescent <- Vectorize(descent, vectorize.args = "individuals")
  > foo <- vescent(c(1085, 1094, 1180, 1260, 1272), alberta, c("52"=1))
  > all(all.equal(foo, c(0.0156250, 0.0156250, 0.0078125, 0.0312500, 0.0078125)))
  [1] TRUE
  > 
  > 
  > proc.time()
     user  system elapsed 
     0.21    0.10    0.29 
Running the tests in 'tests/foo.R' failed.
Complete output:
  > 
  > # attempt to reproduce some of the numbers from U of Washington Statistics
  > # Tech Report 153 (Geyer, 1988) cited in the help page for R function
  > # descent in this package.
  > 
  > # In alberta pedigree, probability that one gene picked at random
  > # from individual 1260 is descended from one gene in founder 52.
  > # TR says 0.03125
  > 
  > library(sped)
  > data(alberta)
  > 
  > foo <- descent(1260, alberta, c("52"=1))
  > all.equal(foo, 0.03125)
  [1] TRUE
  > 
  > # In alberta pedigree, probability that one gene picked at random
  > # from each of the individuals 1085, 1094, 1180, 1260, and 1272
  > # are descended from one gene in founder 52.
  > # TR says 1.91927e-5
  > 
  > foo <- descent(c(1085, 1094, 1180, 1260, 1272), alberta, c("52"=1))
  > all.equal(foo, 1.91927e-5, tol = 1e-4)
  [1] TRUE
  > 
  > 
  > proc.time()
     user  system elapsed 
    12.23    0.35   12.57 
Running the tests in 'tests/gammas.R' failed.
Complete output:
  > # attempt to reproduce some of the numbers from U of Washington Statistics
  > # Tech Report 153 (Geyer, 1988) cited in the help page for R function
  > # descent in this package.
  > 
  > # In alberta pedigree, probability that one gene picked at random
  > # from each of the individuals 1260 and 1272 are descended from either
  > # gene in each founder
  > 
  > library(sped)
  > data(alberta)
  > 
  > foo <- gammas(c(1260, 1272), alberta)
  > 
  > bar <- matrix(c(0.1250000,  0.03125000,
  +                 0.06250000, 0.01562500, 
  +                 0.01562500, 0.0,
  +                 0.00781250, 0.0,
  +                 0.02734375, 0.05078125,
  +                 0.02734375, 0.05078125,
  +                 0.09765625, 0.1210937,
  +                 0.08203125, 0.1054687,
  +                 0.06250000, 0.01562500,
  +                 0.1132812,  0.09765625,
  +                 0.3398437,  0.2929687,
  +                 0.03125000, 0.2187500,
  +                 0.00781250, 0.0),
  +                 ncol = 2, byrow = TRUE)
  > 
  > all(dim(foo) == dim(bar))
  [1] TRUE
  > 
  > dimnames(bar) <- dimnames(foo)
  > 
  > all.equal(foo, bar, tolerance = 1e-6)
  [1] TRUE
  > 
  > 
  > proc.time()
     user  system elapsed 
     0.12    0.14    0.23 
Running the tests in 'tests/kinship.R' failed.
Complete output:
  > 
  > library(sped)
  > library(pooh)
  > data(thompson)
  > 
  > individuals <- sort(unique(thompson))
  > foo <- kinship(individuals, thompson)
  > individuals.too <- rownames(foo)
  > setequal(individuals, individuals.too)
  [1] TRUE
  > 
  > founders <- setdiff(individuals, thompson[ , "ind"])
  > 
  > bar <- foo
  > for (i in 1:nrow(bar))
  +     for (j in 1:ncol(bar)) {
  +         baz <- double(length(founders))
  +         for (k in seq(along = founders)) {
  +             g <- 1
  +             names(g) <- founders[k]
  +             baz[k] <- descent(individuals.too[c(i, j)], thompson, g)
  +         }
  +         bar[i, j] <- bar[j, i] <- 2 * sum(baz)
  +     }
  > 
  > all.equal(foo, bar)
  [1] TRUE
  > 
  > qux <- kinship(c("U", "V", "Q", "R", "W"), thompson)
  > idx <- match(rownames(qux), rownames(foo))
  > all.equal(foo[idx, idx], qux)
  [1] TRUE
  > 
  > 
  > proc.time()
     user  system elapsed 
     0.75    0.15    0.84