nlist

nlist is an R package to create and manipulate numeric list (nlist) objects.

An nlist is an S3 class list of uniquely named numeric atomic (natomic) objects. An natomic object is an integer or double vector, matrix or array. nlist objects are the raw data inputs for analytic engines such as JAGS, STAN and TMB.

An nlists object is a S3 class list of nlist objects with the same names, dimensionalities and typeofs. nlists objects are useful for storing multiple realizations of simulated data sets. They can be converted to coda::mcmc and coda::mcmc.list objects.

Installation

To install the latest release from CRAN

install.packages("nlist")

To install the developmental version from GitHub

# install.packages("remotes")
remotes::install_github("poissonconsulting/nlist")

Demonstration

natomic

An natomic object is an integer or double vector, matrix or array.

library(nlist)
is.natomic(TRUE)
#> [1] FALSE
is.natomic(1L)
#> [1] TRUE
is.natomic(matrix(1:3))
#> [1] TRUE

nlist

An nlist is an S3 class list of uniquely named numeric atomic (natomic) objects.

It is straightforward to create an new nlist object.

library(nlist)

nlist <- nlist(x = 1, y = matrix(1:9, 3))
nlist
#> $x
#> [1] 1
#> 
#> $y
#>      [,1] [,2] [,3]
#> [1,]    1    4    7
#> [2,]    2    5    8
#> [3,]    3    6    9
#> 
#> an nlist object with 2 natomic elements

Or to coerce from a data frame.

data <- data.frame(
  lgl = c(TRUE, NA),
  dte = as.Date(c("2001-01-02", "2001-01-01")),
  fac = factor(c("b", "a"))
)

data
#>    lgl        dte fac
#> 1 TRUE 2001-01-02   b
#> 2   NA 2001-01-01   a
as.nlist(data)
#> $lgl
#> [1]  1 NA
#> 
#> $dte
#> [1] 11324 11323
#> 
#> $fac
#> [1] 2 1
#> 
#> an nlist object with 3 natomic elements

nlists

An nlists object is a S3 class list of nlist objects with the same names, dimensionalities and typeofs. The nchains attribute is used to keep track of the number of chains.

nlists <- nlists(
  nlist(x = 1, y = matrix(1:9, 3)),
  nlist(x = -2, y = matrix(2:10, 3)),
  nlist(x = 10, y = matrix(22:30, 3)),
  nlist(x = -100, y = matrix(-2:-10, 3))
)

print(nlists)
#> $x
#> [1] -22.75
#> 
#> $y
#>      [,1] [,2] [,3]
#> [1,] 5.75 7.25 8.75
#> [2,] 6.25 7.75 9.25
#> [3,] 6.75 8.25 9.75
#> 
#> an nlists object of 4 nlist objects each with 2 natomic elements

Aggregating an nlists object gives an nlist object.

aggregate(nlists, fun = median)
#> $x
#> [1] -0.5
#> 
#> $y
#>      [,1] [,2] [,3]
#> [1,]  1.5  4.5  7.5
#> [2,]  2.5  5.5  8.5
#> [3,]  3.5  6.5  9.5
#> 
#> an nlist object with 2 natomic elements

An nlists object can have its chains split or collapsed.

nlists <- split_chains(nlists)

And can be converted to an mcmc.list object

coda::as.mcmc.list(nlists)
#> $`1`
#> Markov Chain Monte Carlo (MCMC) output:
#> Start = 1 
#> End = 2 
#> Thinning interval = 1 
#>       x y[1,1] y[2,1] y[3,1] y[1,2] y[2,2] y[3,2] y[1,3] y[2,3] y[3,3]
#> [1,]  1      1      2      3      4      5      6      7      8      9
#> [2,] -2      2      3      4      5      6      7      8      9     10
#> 
#> $`2`
#> Markov Chain Monte Carlo (MCMC) output:
#> Start = 1 
#> End = 2 
#> Thinning interval = 1 
#>         x y[1,1] y[2,1] y[3,1] y[1,2] y[2,2] y[3,2] y[1,3] y[2,3] y[3,3]
#> [1,]   10     22     23     24     25     26     27     28     29     30
#> [2,] -100     -2     -3     -4     -5     -6     -7     -8     -9    -10
#> 
#> attr(,"class")
#> [1] "mcmc.list"

Contribution

Please report any issues.

Pull requests are always welcome.

Code of Conduct

Please note that the nlist project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.