PLN RNG

Random generation for the PLN model with latent mean equal to mu, latent covariance matrix equal to Sigma and average depths (sum of counts in a sample) equal to depths

rPLN(
  n = 10,
  mu = rep(0, ncol(Sigma)),
  Sigma = diag(1, 5, 5),
  depths = rep(10000, n)
)

Arguments

n

the sample size

mu

vectors of means of the latent variable

Sigma

covariance matrix of the latent variable

depths

Numeric vector of target depths. The first is recycled if there are not n values

Value

a n * p count matrix, with row-sums close to depths, with an attribute "offsets" corresponding to the true generated offsets (in log-scale).

Details

The default value for mu and Sigma assume equal abundances and no correlation between the different species.

Examples

## 10 samples of 5 species with equal abundances, no covariance and target depths of 10,000
rPLN()
#>       Y1   Y2   Y3   Y4    Y5
#> S1   513  947 2286 5596  9514
#> S2   350 3007 2854 5971    76
#> S3   676 4368  247 1177   445
#> S4  2848 3051  165 1584  2017
#> S5   418 1126 2149 1834  3402
#> S6   159 5210 1035 1525   339
#> S7  3369 2674 2436 1191   421
#> S8   290  659  807  595 11794
#> S9  1249 2402  319  477  2186
#> S10 9480 4030 2043 1148  1935
#> attr(,"offsets")
#>           [,1]     [,2]     [,3]     [,4]     [,5]
#>  [1,] 7.100902 7.100902 7.100902 7.100902 7.100902
#>  [2,] 7.100902 7.100902 7.100902 7.100902 7.100902
#>  [3,] 7.100902 7.100902 7.100902 7.100902 7.100902
#>  [4,] 7.100902 7.100902 7.100902 7.100902 7.100902
#>  [5,] 7.100902 7.100902 7.100902 7.100902 7.100902
#>  [6,] 7.100902 7.100902 7.100902 7.100902 7.100902
#>  [7,] 7.100902 7.100902 7.100902 7.100902 7.100902
#>  [8,] 7.100902 7.100902 7.100902 7.100902 7.100902
#>  [9,] 7.100902 7.100902 7.100902 7.100902 7.100902
#> [10,] 7.100902 7.100902 7.100902 7.100902 7.100902
## 2 samples of 10 highly correlated species with target depths 1,000 and 100,000
## very different abundances
mu <- rep(c(1, -1), each = 5)
Sigma <- matrix(0.8, 10, 10); diag(Sigma) <- 1
rPLN(n=2, mu = mu, Sigma = Sigma, depths = c(1e3, 1e5))
#>      Y1   Y2   Y3   Y4   Y5  Y6  Y7  Y8  Y9 Y10
#> S1   51   72   50  135   60   8  15  16   1  10
#> S2 5018 1832 3759 1615 2299 306 551 563 400 409
#> attr(,"offsets")
#>          [,1]     [,2]     [,3]     [,4]     [,5]     [,6]     [,7]     [,8]
#> [1,] 3.671389 3.671389 3.671389 3.671389 3.671389 3.671389 3.671389 3.671389
#> [2,] 8.276560 8.276560 8.276560 8.276560 8.276560 8.276560 8.276560 8.276560
#>          [,9]    [,10]
#> [1,] 3.671389 3.671389
#> [2,] 8.276560 8.276560