herring_mixture_sims: Do the mixture simulations and make some nice ggplots of the...

Description Usage Arguments

Description

Quickly threw this together

Usage

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herring_mixture_sims(baseline_path, lat_long_path, locus_columns, rep_unit_path,
  plot_prefix = "herring", bycatch_N = 1000, random_seed = 50,
  num_rando_mix_props = 50, num_simmed_mixtures = 4, point_size = 1.7,
  point_shape = 1)

Arguments

baseline_path

Path to a baseline file that is in the (csv) format that Dan H uses. See alewife-baseline.csv for an example. Importantly, the file must have a column called Drainage.code that has the drainage codes as in DH's file.

lat_long_path

Path to a text file with lats and longs of the pops in the baseline file. See file alewife-lat-long.txt for an example.

locus_columns

integer vector with the columns in the original CSV file that have the loci that you want to use. Should be twice as many columns as loci. In alewife-baseline.csv this is

rep_unit_path

Path to the reporting unit file

plot_prefix

Prefix to put on the plot names

bycatch_N

The number of fish in the simulated bycatch samples.

num_rando_mix_props

the number of random mixing proportiong to simulate num_simmed_mixtures at.

num_simmed_mixtures

the number of mixtures to simulate for each mixing proportion

point_size

Size of the points on the plots.


eriqande/herring documentation built on May 16, 2019, 8:47 a.m.