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  1598  1622 4101  374   35
#> S2  1086  1270 1751 2560 1127
#> S3  1031   497 1076 3731 1592
#> S4   449  8035 1300 4238 1044
#> S5  1228  1642  370  761 1782
#> S6   860   747 2003  638 1283
#> S7   581  1690 3943 3269 4859
#> S8  2561  3304 1771 1036 3108
#> S9   223 13983 2157  792 4513
#> S10 1645  2405  471 1459 1760
#> 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    42   71   57    81   30    4    0   5   10    5
#> S2 11183 6657 5511 15542 9003 1146 1066 903 1465 1732
#> 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