bmsma

Goal of package

Installation

‘bmsma’ is under active development, you can install the development version of ‘bmsma’ from GitHub with:

# install.packages("remotes")
remotes::install_github("traitecoevo/bmsma")

library(bmsma)

{bmsma} supported models

Linear model

bmsma_model("ols") |>
  bmsma_assign_data(X = Loblolly$age,
                   Y = Loblolly$height,
                   N = nrow(Loblolly)) |>
  bmsma_run()
#> 
#> SAMPLING FOR MODEL 'ols' NOW (CHAIN 1).
#> Chain 1: 
#> Chain 1: Gradient evaluation took 1.7e-05 seconds
#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.17 seconds.
#> Chain 1: Adjust your expectations accordingly!
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#> Chain 1: 
#> Chain 1:  Elapsed Time: 0.025 seconds (Warm-up)
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#> Chain 1:                0.046 seconds (Total)
#> Chain 1: 
#> 
#> SAMPLING FOR MODEL 'ols' NOW (CHAIN 2).
#> Chain 2: 
#> Chain 2: Gradient evaluation took 3e-06 seconds
#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.03 seconds.
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#> Chain 2: 
#> 
#> SAMPLING FOR MODEL 'ols' NOW (CHAIN 3).
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#> Chain 3: Gradient evaluation took 3e-06 seconds
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#> Chain 3: 
#> 
#> SAMPLING FOR MODEL 'ols' NOW (CHAIN 4).
#> Chain 4: 
#> Chain 4: Gradient evaluation took 3e-06 seconds
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#> Chain 4:  Elapsed Time: 0.026 seconds (Warm-up)
#> Chain 4:                0.022 seconds (Sampling)
#> Chain 4:                0.048 seconds (Total)
#> Chain 4:
#> Inference for Stan model: ols.
#> 4 chains, each with iter=2000; warmup=1000; thin=1; 
#> post-warmup draws per chain=1000, total post-warmup draws=4000.
#> 
#>              mean se_mean   sd    2.5%     25%     50%     75%   97.5% n_eff
#> intercept   -1.34    0.02 0.65   -2.64   -1.77   -1.34   -0.92   -0.08  1632
#> beta         2.59    0.00 0.04    2.51    2.56    2.59    2.62    2.68  1549
#> sigma        3.00    0.01 0.25    2.56    2.83    2.98    3.15    3.54  1846
#> lp__      -132.30    0.04 1.33 -135.80 -132.91 -131.96 -131.34 -130.80  1319
#>           Rhat
#> intercept    1
#> beta         1
#> sigma        1
#> lp__         1
#> 
#> Samples were drawn using NUTS(diag_e) at Thu Mar 13 07:24:11 2025.
#> For each parameter, n_eff is a crude measure of effective sample size,
#> and Rhat is the potential scale reduction factor on split chains (at 
#> convergence, Rhat=1).