Mark and Age-enhanced Genetic Mixture Analysis • magma.gsi

MAGMA is a slowing moving but powerful model that combine mark and age information with genetic mixture analysis. Mainly, MAGMA estimates two sets of parameters: stock and age. A composition of the two, information that is often required for run reconstruction models, is simply the product of these two sets of parameters. After all age/stock compositions in other strata are calculated in the same fashion, they are multiplied by the harvest proportions of their corresponding strata and summed up to get a weighted average age/stock composition.

Installation

You can install the development version of magma.gsi from GitHub with:

# install.packages("devtools")
devtools::install_github("boppingshoe/magma.gsi", build_vignettes = TRUE)

Example

Once you have the data sets up at a designated directory, you can compile the input object:

library(magma.gsi)

wd <- getwd() # path to data folder
magma_data <- magmatize_data(wd = paste0(wd, "/vignettes"), save_data = FALSE)
#> Compiling input data, may take a minute or two...
#> FAKE is the fishery identified in the mixture.RData
#> No missing hatcheries
#> Time difference of 5.265977 secs

Run the model:

magma_out <- magmatize_mdl(magma_data, nreps = 50, nburn = 25, thin = 1, nchains = 3)
#> Running model... and good things come to High Class In A Fur Coat!
#> Time difference of 1.02392 secs
#> 2024-10-08 15:09:24.414875

Summarize the results:

magma_summ <- magmatize_summ(ma_out = magma_out, ma_dat = magma_data, summ_level = "district")
#> Preparing output (patience grasshopper...)
#> Time difference of 0.3430619 secs
#> 2024-10-08 15:09:24.774506

magma_summ$age_summ[1]
#> $D1_Koyukuk
#> # A tibble: 9 × 10
#>   group   age      mean  median     sd      ci.05  ci.95    p0    GR n_eff
#>   <chr>   <fct>   <dbl>   <dbl>  <dbl>      <dbl>  <dbl> <dbl> <dbl> <dbl>
#> 1 Koyukuk 11    0.0161  0.00441 0.0303 0.00000957 0.0747 0.107  1.05  75  
#> 2 Koyukuk 12    0.0165  0.00469 0.0267 0.0000130  0.0700 0.12   1.13  75  
#> 3 Koyukuk 13    0.0189  0.00717 0.0282 0.0000248  0.0679 0.173  1.01  75  
#> 4 Koyukuk 21    0.00993 0.00323 0.0154 0.00000238 0.0446 0.2    1.07  42.2
#> 5 Koyukuk 22    0.0639  0.0471  0.0603 0.00582    0.177  0      1.02  75  
#> 6 Koyukuk 23    0.569   0.585   0.123  0.335      0.714  0      1.02  93.8
#> 7 Koyukuk 31    0.265   0.256   0.0923 0.134      0.431  0      1.02  93.5
#> 8 Koyukuk 32    0.0174  0.00604 0.0286 0.00000185 0.0544 0.133  1.03  75  
#> 9 Koyukuk 33    0.0240  0.00626 0.0406 0.0000675  0.128  0.147  1.03  57.1

There’s a function in the package to make trace plots and inspect mixing of chains.

magmatize_tr_plot(magma_summ$age_prop[[1]])

trace plot render

To see more examples on using magma.gsi, you can call the manual using vignette("magma-vignette", package = "magma.gsi") after you installed magma.gsi.