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extract \(\Sigma\)

Source: R/extract_sigma.R
extract_sigma.Rd

Extract Bayesian estimates of \(\Sigma\) from data objects created by nicheROVER or SIBER.

Usage

extract_sigma(
  data,
  pkg = NULL,
  isotope_n = NULL,
  isotope_names = NULL,
  data_format = NULL
)

Arguments

data

a list created by the function niw.post() or siberMVN() in the package nicheROVER or SIBER, respectfully.

pkg

a character string that is the name of the package that you're using. Defaults to "nicheROVER". Alternatively the user can supply the argument with "SIBER".

isotope_n

a numeric either 2 or 3 that is the number of isotopes used in the anlsysis. Will default to 2.

isotope_names

is a vector of character string used change the column name of isotopes used in the analysis. Defaults to c("d13c", "d15n").

data_format

a character string that decides whether the returned object is in long or wide format. Default is "wide", with the alternative supplied being "long".

Value

Returns a tibble of extracted estimates of \(\Sigma\) created by the function niw.post() or siberMVN() in the packages nicheROVER. and SIBER.

The returned object will contain five columns in the following order when data_format is set to "wide", metric, id, sample_name, isotope, sample_number, and the posterior sample for \(\Sigma\) (e.g., d13c and d15n).

See also

nicheROVER::niw.post() and SIBER::siberMVN()

Examples

extract_sigma(
data = niw_fish_post
)
#> # A tibble: 8,000 × 6
#>    metric sample_name isotope sample_number  d13c  d15n
#>    <chr>  <chr>       <chr>   <chr>         <dbl> <dbl>
#>  1 sigma  ARCS        d13c    1             1.07  0.305
#>  2 sigma  ARCS        d15n    1             0.305 0.571
#>  3 sigma  ARCS        d13c    2             1.01  0.221
#>  4 sigma  ARCS        d15n    2             0.221 0.657
#>  5 sigma  ARCS        d13c    3             1.21  0.486
#>  6 sigma  ARCS        d15n    3             0.486 0.616
#>  7 sigma  ARCS        d13c    4             1.14  0.352
#>  8 sigma  ARCS        d15n    4             0.352 0.570
#>  9 sigma  ARCS        d13c    5             0.788 0.376
#> 10 sigma  ARCS        d15n    5             0.376 0.849
#> # ℹ 7,990 more rows

extract_sigma(
data = post_sam_siber,
pkg = "SIBER"
)
#> # A tibble: 40,000 × 6
#>    metric sample_name isotope sample_number   d13c   d15n
#>    <chr>  <chr>       <chr>           <int>  <dbl>  <dbl>
#>  1 sigma  1.1         d13c                1  1.58  -0.808
#>  2 sigma  1.1         d15n                1 -0.808  2.22 
#>  3 sigma  1.1         d13c                2  1.49  -0.990
#>  4 sigma  1.1         d15n                2 -0.990  3.64 
#>  5 sigma  1.1         d13c                3  1.60  -1.30 
#>  6 sigma  1.1         d15n                3 -1.30   3.78 
#>  7 sigma  1.1         d13c                4  1.61  -1.48 
#>  8 sigma  1.1         d15n                4 -1.48   3.69 
#>  9 sigma  1.1         d13c                5  1.54  -0.892
#> 10 sigma  1.1         d15n                5 -0.892  2.58 
#> # ℹ 39,990 more rows