diff --git a/docs/404.html b/docs/404.html index 0c3bfe5..d448195 100644 --- a/docs/404.html +++ b/docs/404.html @@ -61,16 +61,16 @@ Conducting Multiyear Projections
  • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
  • - Specifying Demographic Rates + Observation Processes
  • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
  • - A Spatial Model Example + Specifying Demographic Rates
    • diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index adeb160..a939499 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -44,16 +44,16 @@ Conducting Multiyear Projections
  • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
  • - Specifying Demographic Rates + Observation Processes
  • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
  • - A Spatial Model Example + Specifying Demographic Rates
    • diff --git a/docs/LICENSE.html b/docs/LICENSE.html index a14ab0c..4d27702 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -44,16 +44,16 @@ Conducting Multiyear Projections
  • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
  • - Specifying Demographic Rates + Observation Processes
  • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
  • - A Spatial Model Example + Specifying Demographic Rates
    • @@ -69,6 +69,7 @@

    MIT License

    +

    Copyright (c) 2024 afscOM authors

    Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

    The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

    diff --git a/docs/articles/index.html b/docs/articles/index.html index 8c286a9..cb999fc 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -44,16 +44,16 @@ Conducting Multiyear Projections
  • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
  • - Specifying Demographic Rates + Observation Processes
  • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
  • - A Spatial Model Example + Specifying Demographic Rates
    • @@ -69,28 +69,25 @@

    Articles

    -

    More

    -

    Vignetttes describing various aspects of afscOM

    +

    All vignettes

    +

    -
    Model Dimensions
    +
    afscOM
    +
    +
    Model Dimensions
    Model Options
    Conducting Multiyear Projections
    -
    Observation Processes
    -
    -
    Specifying Demographic Rates
    +
    Example: Northeast Pacific Transboundary Sablefish Model
    -
    -
    -

    Examples

    -

    A curated listed of fisheries models built using afscOM

    - -
    Example: Northeast Pacific Transboundary Sablefish Model
    +
    Observation Processes
    A Spatial Model Example
    +
    Specifying Demographic Rates
    +
    diff --git a/docs/authors.html b/docs/authors.html index bb601df..002cb93 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -44,16 +44,16 @@ Conducting Multiyear Projections
  • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
  • - Specifying Demographic Rates + Observation Processes
  • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
  • - A Spatial Model Example + Specifying Demographic Rates
    • diff --git a/docs/index.html b/docs/index.html index 3aaf41d..8f44493 100644 --- a/docs/index.html +++ b/docs/index.html @@ -62,16 +62,16 @@ Conducting Multiyear Projections
  • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
  • - Specifying Demographic Rates + Observation Processes
  • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
  • - A Spatial Model Example + Specifying Demographic Rates
    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 4e289b7..55ed560 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 2.16.2 +pandoc: 3.1.11 pkgdown: 2.0.7 pkgdown_sha: ~ articles: @@ -10,5 +10,5 @@ articles: observation_processes: observation_processes.html spatial_om_example: spatial_om_example.html specifying_demographic_parameters: specifying_demographic_parameters.html -last_built: 2024-07-30T09:49Z +last_built: 2024-10-02T16:51Z diff --git a/docs/reference/F_to_mu.html b/docs/reference/F_to_mu.html index 6b18c34..e5d68c9 100644 --- a/docs/reference/F_to_mu.html +++ b/docs/reference/F_to_mu.html @@ -46,16 +46,16 @@ Conducting Multiyear Projections
  • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
  • - Specifying Demographic Rates + Observation Processes
  • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
  • - A Spatial Model Example + Specifying Demographic Rates
    • diff --git a/docs/reference/baranov.html b/docs/reference/baranov.html index 8055693..c70da4f 100644 --- a/docs/reference/baranov.html +++ b/docs/reference/baranov.html @@ -45,16 +45,16 @@ Conducting Multiyear Projections
  • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
  • - Specifying Demographic Rates + Observation Processes
  • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
  • - A Spatial Model Example + Specifying Demographic Rates
    • @@ -119,16 +119,15 @@

    Value

    Examples

    - 
    if (FALSE) {
-naa <- c(100, 50, 25, 10)
-waa <- c(1, 2, 3, 4)
-mort <- c(0.2, 0.2, 0.2, 0.2)
-selex <- c(0.0, 0.5, 1.0, 1.0)
-
-# catch should be 14.35
-catch <- baranov(0.1, naa, waa, mort, selex)
-}
-
    + 
    if (FALSE) {
+naa <- c(100, 50, 25, 10)
+waa <- c(1, 2, 3, 4)
+mort <- c(0.2, 0.2, 0.2, 0.2)
+selex <- c(0.0, 0.5, 1.0, 1.0)
+
+# catch should be 14.35
+catch <- baranov(0.1, naa, waa, mort, selex)
+}
    diff --git a/docs/reference/compute_bio.html b/docs/reference/compute_bio.html new file mode 100644 index 0000000..df43d1c --- /dev/null +++ b/docs/reference/compute_bio.html @@ -0,0 +1,121 @@ + +Compute Total Stock Biomass — compute_bio • afscOM + + +
    +
    + + + +
    +
    +
    +

    Compute Total Stock Biomass

    + + +
    + +
    +

    Compute biomass from a matrix of NAA and a set of demographic +parameters. This computes the sum of male and female biomass +across all age classes. For mature female biomass, see +`compute_ssb`.

    +
    + +
    + 
    compute_bio(naa, dem_params)
    +
    + +
    +

    Arguments

    +
    naa
    +

    numbers-at-age matrix [nyears, nages, nsexes, nregions]

    + + +
    dem_params
    +

    demagraphic parameters list

    + +
    + +
    + +
    + + +
    + + + + + + + + diff --git a/docs/reference/compute_fleet_catch.html b/docs/reference/compute_fleet_catch.html new file mode 100644 index 0000000..3b72d46 --- /dev/null +++ b/docs/reference/compute_fleet_catch.html @@ -0,0 +1,113 @@ + +Compute Catch by Fishing Fleet — compute_fleet_catch • afscOM + + +
    +
    + + + +
    +
    +
    +

    Compute Catch by Fishing Fleet

    + + +
    + +
    +

    Compute total catch volume (in mt) for each fishing +fleet from a matrix of CAA.

    +
    + +
    + 
    compute_fleet_catch(caa)
    +
    + +
    +

    Arguments

    +
    caa
    +

    catch-at-age matrix [nyears, nages, nsexes, nregions, nfleets]

    + +
    + +
    + +
    + + +
    + + + + + + + + diff --git a/docs/reference/compute_ssb.html b/docs/reference/compute_ssb.html index c5d3c55..b79d8b2 100644 --- a/docs/reference/compute_ssb.html +++ b/docs/reference/compute_ssb.html @@ -1,13 +1,5 @@ -Compute Spawning Stock Biomass -#' -Compute SSB from a matrix of NAA and a set of demagraphic -parameters. — compute_ssb • afscOMCompute Spawning Stock Biomass — compute_ssb • afscOM @@ -74,18 +66,13 @@
    -

    Compute Spawning Stock Biomass -#' -Compute SSB from a matrix of NAA and a set of demagraphic -parameters.

    +

    Compute Spawning Stock Biomass

    -

    Compute Spawning Stock Biomass -#' -Compute SSB from a matrix of NAA and a set of demagraphic +

    Compute SSB from a matrix of NAA and a set of demographic parameters.

    @@ -96,7 +83,7 @@

    Compute Spawning Stock Biomass

    Arguments

    naa
    -

    numbers-at-age matrix

    +

    numbers-at-age matrix [nyears, nages, nsexes, nregions]

    dem_params
    diff --git a/docs/reference/compute_total_catch.html b/docs/reference/compute_total_catch.html new file mode 100644 index 0000000..952059a --- /dev/null +++ b/docs/reference/compute_total_catch.html @@ -0,0 +1,111 @@ + +Compute Total Catch — compute_total_catch • afscOM + + +
    +
    + + + +
    +
    +
    +

    Compute Total Catch

    + + +
    + +
    +

    Compute total catch volume (in mt) from a matrix of CAA.

    +
    + +
    + 
    compute_total_catch(caa)
    +
    + +
    +

    Arguments

    +
    caa
    +

    catch-at-age matrix [nyears, nages, nsexes, nregions, nfleets]

    + +
    + +
    + +
    + + +
    +

    Developed by Benjamin Williams, Joshua Zahner, Matt Cheng, Maia Kapur.

    +
    + +
    +

    Site built with pkgdown 2.0.7.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/compute_total_f.html b/docs/reference/compute_total_f.html new file mode 100644 index 0000000..7b607f0 --- /dev/null +++ b/docs/reference/compute_total_f.html @@ -0,0 +1,115 @@ + +Compute Total Fishing Mortality — compute_total_f • afscOM + + +
    +
    + + + +
    +
    +
    +

    Compute Total Fishing Mortality

    + + +
    + +
    +

    Compute total fishing mortality from a matrix of FAA. +Note that this is an approximation of total fishing mortality, +and assumes that selectivity = 1 for some age class.

    +
    + +
    + 
    compute_total_f(faa)
    +
    + +
    +

    Arguments

    +
    faa
    +

    fushing-mortality-at-age matrix [nyears, nages, nsexes, nregions, nfleets]

    + +
    + +
    + +
    + + +
    +

    Developed by Benjamin Williams, Joshua Zahner, Matt Cheng, Maia Kapur.

    +
    + +
    +

    Site built with pkgdown 2.0.7.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/cyclic_recruitment.html b/docs/reference/cyclic_recruitment.html new file mode 100644 index 0000000..42014b4 --- /dev/null +++ b/docs/reference/cyclic_recruitment.html @@ -0,0 +1,138 @@ + +Generate log-recruitment from two defined regimes of a specified length — cyclic_recruitment • afscOM + + +
    +
    + + + +
    +
    +
    +

    Generate log-recruitment from two defined regimes of a specified length

    + + +
    + +
    +

    Description

    +
    + +
    + 
    cyclic_recruitment(n, mu_rec, sd_rec, dur, start = 1, seed = NA)
    +
    + +
    +

    Arguments

    +
    n
    +

    number of recruitment events

    + + +
    mu_rec
    +

    vector of mean log-recruitment levels, one for each regime

    + + +
    sd_rec
    +

    vector of recruitment variation, one for each regime

    + + +
    dur
    +

    duration of regimes

    + + +
    start
    +

    which regime to start in

    + + +
    seed
    +

    a random seed (optional)

    + +
    +
    +

    Value

    + + +

    `n` log-recruitment levels from two different regimes of +length `dur`.

    +
    + +
    + +
    + + +
    +

    Developed by Benjamin Williams, Joshua Zahner, Matt Cheng, Maia Kapur.

    +
    + +
    +

    Site built with pkgdown 2.0.7.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/discard_F.html b/docs/reference/discard_F.html index 42522f2..a3ebbf9 100644 --- a/docs/reference/discard_F.html +++ b/docs/reference/discard_F.html @@ -44,16 +44,16 @@ Conducting Multiyear Projections
  • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
  • - Specifying Demographic Rates + Observation Processes
  • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
  • - A Spatial Model Example + Specifying Demographic Rates
      • diff --git a/docs/reference/extend_years.html b/docs/reference/extend_years.html index 758d92f..aacb370 100644 --- a/docs/reference/extend_years.html +++ b/docs/reference/extend_years.html @@ -44,16 +44,16 @@ Conducting Multiyear Projections
    • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
    • - Specifying Demographic Rates + Observation Processes
    • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
    • - A Spatial Model Example + Specifying Demographic Rates

        • diff --git a/docs/reference/findF_bisection.html b/docs/reference/findF_bisection.html index 7a67891..4fff038 100644 --- a/docs/reference/findF_bisection.html +++ b/docs/reference/findF_bisection.html @@ -46,16 +46,16 @@ Conducting Multiyear Projections
      • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
      • - Specifying Demographic Rates + Observation Processes
      • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
      • - A Spatial Model Example + Specifying Demographic Rates
        • @@ -125,11 +125,10 @@

        Value

        Examples

        - 
        if (FALSE) {
-findF_bisection(f_guess=0.1, naa=naa, waa=waa, mort=mort, selex=selex, prov_catch=12)
-}
-
-
        + 
        if (FALSE) {
+findF_bisection(f_guess=0.1, naa=naa, waa=waa, mort=mort, selex=selex, prov_catch=12)
+}
+
        @@ -125,11 +125,10 @@

        Value

        Examples

        - 
        if (FALSE) {
-find_F(f_guess=0.1, naa=naa, waa=waa, mort=mort, selex=selex, prov_catch=0.12)
-}
-
-
        + 
        if (FALSE) {
+find_F(f_guess=0.1, naa=naa, waa=waa, mort=mort, selex=selex, prov_catch=0.12)
+}
+
        diff --git a/docs/reference/get_model_dimensions.html b/docs/reference/get_model_dimensions.html index fed5746..df06501 100644 --- a/docs/reference/get_model_dimensions.html +++ b/docs/reference/get_model_dimensions.html @@ -47,16 +47,16 @@ Conducting Multiyear Projections
      • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
      • - Specifying Demographic Rates + Observation Processes
      • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
      • - A Spatial Model Example + Specifying Demographic Rates
        • diff --git a/docs/reference/index.html b/docs/reference/index.html index 5d5fd6d..c6fc7f4 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -44,16 +44,16 @@ Conducting Multiyear Projections
      • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
      • - Specifying Demographic Rates + Observation Processes
      • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
      • - A Spatial Model Example + Specifying Demographic Rates
        • @@ -73,10 +73,6 @@

        All functions

        -

        F_to_mu()

        - -

        instantaneous rate to harvest rate

        -

        baranov()

        Baranov Catch Equation

        @@ -84,15 +80,28 @@

        All functions catch_at_age()

        Catch-at-age

        + +

        compute_bio()

        + +

        Compute Total Stock Biomass

        + +

        compute_fleet_catch()

        + +

        Compute Catch by Fishing Fleet

        compute_ssb()

        -

        Compute Spawning Stock Biomass -#' -Compute SSB from a matrix of NAA and a set of demagraphic -parameters.

        +

        Compute Spawning Stock Biomass

        -

        cyclic.recruitment()

        +

        compute_total_catch()

        + +

        Compute Total Catch

        + +

        compute_total_f()

        + +

        Compute Total Fishing Mortality

        + +

        cyclic_recruitment()

        Generate log-recruitment from two defined regimes of a specified length

        @@ -111,6 +120,10 @@

        All functions find_F()

        Find F given a desired level of catch

        + +

        F_to_mu()

        + +

        instantaneous rate to harvest rate

        generate_param_matrix()

        @@ -127,6 +140,26 @@

        All functions mu_to_F()

        harvest rate to instantaneous

        + +

        plot_demographic_parameters()

        + +

        Plot demographic parameters

        + +

        plot_mat()

        + +

        Plot Maturity-at-Age

        + +

        plot_mort()

        + +

        Plot Mortality

        + +

        plot_selret()

        + +

        Plot Selectivity-at-Age and Retention-at-Age

        + +

        plot_waa()

        + +

        Plot Weight-at-Age

        project()

        @@ -151,14 +184,18 @@

        All functions sablefish_dem_params

        Demographic parameter matrices for Alaska Sablefish

        + +

        setup_model_options()

        + +

        Set Default Values for Model Options

        set_model_params()

        Setup model parameters

        -

        setup_model_options()

        +

        simple_om

        -

        Set Default Values for Model Options

        +

        OM Components for a Simple Simulation

        simulate_ac()

        @@ -209,6 +246,10 @@

        All functions simulate_rpw()

        Simulate Relative Population Weight Index

        + +

        spatial_sablefish_assessment_data

        + +

        Spatial Sablefish Assessment

        subset_dem_params()

        diff --git a/docs/reference/listN.html b/docs/reference/listN.html index 027e8ca..cc10cf7 100644 --- a/docs/reference/listN.html +++ b/docs/reference/listN.html @@ -45,16 +45,16 @@ Conducting Multiyear Projections
      • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
      • - Specifying Demographic Rates + Observation Processes
      • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
      • - A Spatial Model Example + Specifying Demographic Rates
        • diff --git a/docs/reference/mu_to_F.html b/docs/reference/mu_to_F.html index ea046d8..2024bd8 100644 --- a/docs/reference/mu_to_F.html +++ b/docs/reference/mu_to_F.html @@ -46,16 +46,16 @@ Conducting Multiyear Projections
      • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
      • - Specifying Demographic Rates + Observation Processes
      • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
      • - A Spatial Model Example + Specifying Demographic Rates
        • diff --git a/docs/reference/plot_demographic_parameters.html b/docs/reference/plot_demographic_parameters.html new file mode 100644 index 0000000..be17146 --- /dev/null +++ b/docs/reference/plot_demographic_parameters.html @@ -0,0 +1,147 @@ + +Plot demographic parameters — plot_demographic_parameters • afscOM + + +
        +
        + + + +
        +
        +
        +

        Plot demographic parameters

        + + +
        + +
        +

        Generate standard plot for all demographic +parameter matrices. Output plots will include: +- weight-at-age +- maturity +- natural mortality +- selectivity +- retention +- discard mortality +Plots will show values of demographic quantities across +time, age, sex, region, and fleet as appropriate.

        +
        + +
        + 
        plot_demographic_parameters(
+  dem_params,
+  params = NA,
+  show_plots = TRUE,
+  out_dir = NA,
+  ...
+)
        +
        + +
        +

        Arguments

        +
        dem_params
        +

        list of demographic parameter matrices

        + + +
        params
        +

        vector of names of parameters to plot (not implemented)

        + + +
        out_dir
        +

        optional directory to save plots to

        + + +
        ...
        +

        additional parameters to be passed to `ggsave`

        + +
        + +
        + +
        + + +
        +

        Developed by Benjamin Williams, Joshua Zahner, Matt Cheng, Maia Kapur.

        +
        + +
        +

        Site built with pkgdown 2.0.7.

        +
        + +
        + + + + + + + + diff --git a/docs/reference/plot_mat.html b/docs/reference/plot_mat.html new file mode 100644 index 0000000..4b0a757 --- /dev/null +++ b/docs/reference/plot_mat.html @@ -0,0 +1,115 @@ + +Plot Maturity-at-Age — plot_mat • afscOM + + +
        +
        + + + +
        +
        +
        +

        Plot Maturity-at-Age

        + + +
        + +
        +

        Generates plot of maturity-at-age across time, age, sex, +and region as appropriate. Only the female maturity ogive +is plotted.

        +
        + +
        + 
        plot_mat(mat)
        +
        + +
        +

        Arguments

        +
        mat
        +

        four-dimensional maturity-at-age matrix

        + +
        + +
        + +
        + + +
        +

        Developed by Benjamin Williams, Joshua Zahner, Matt Cheng, Maia Kapur.

        +
        + +
        +

        Site built with pkgdown 2.0.7.

        +
        + +
        + + + + + + + + diff --git a/docs/reference/plot_mort.html b/docs/reference/plot_mort.html new file mode 100644 index 0000000..71e687e --- /dev/null +++ b/docs/reference/plot_mort.html @@ -0,0 +1,115 @@ + +Plot Mortality — plot_mort • afscOM + + +
        +
        + + + +
        +
        +
        +

        Plot Mortality

        + + +
        + +
        +

        Generates plot of mortality-at-age across time, age, sex, +and region as appropriate. This function can be used for +both natural and discard mortality

        +
        + +
        + 
        plot_mort(mort, is_dmr = FALSE)
        +
        + +
        +

        Arguments

        +
        waa
        +

        four-dimensional mortality-at-age matrix

        + +
        + +
        + +
        + + +
        +

        Developed by Benjamin Williams, Joshua Zahner, Matt Cheng, Maia Kapur.

        +
        + +
        +

        Site built with pkgdown 2.0.7.

        +
        + +
        + + + + + + + + diff --git a/docs/reference/plot_selret.html b/docs/reference/plot_selret.html new file mode 100644 index 0000000..a19e403 --- /dev/null +++ b/docs/reference/plot_selret.html @@ -0,0 +1,114 @@ + +Plot Selectivity-at-Age and Retention-at-Age — plot_selret • afscOM + + +
        +
        + + + +
        +
        +
        +

        Plot Selectivity-at-Age and Retention-at-Age

        + + +
        + +
        +

        Generates plot of selectivity-at-age or retention-at-age +across time, age, sex, region, and fleet as appropriate.

        +
        + +
        + 
        plot_selret(selret, is_selectivity = TRUE)
        +
        + +
        +

        Arguments

        +
        selret
        +

        five-dimensional selectivity-at-age or +retention-at-age matrix

        + +
        + +
        + +
        + + +
        +

        Developed by Benjamin Williams, Joshua Zahner, Matt Cheng, Maia Kapur.

        +
        + +
        +

        Site built with pkgdown 2.0.7.

        +
        + +
        + + + + + + + + diff --git a/docs/reference/plot_waa.html b/docs/reference/plot_waa.html new file mode 100644 index 0000000..e4a7d89 --- /dev/null +++ b/docs/reference/plot_waa.html @@ -0,0 +1,113 @@ + +Plot Weight-at-Age — plot_waa • afscOM + + +
        +
        + + + +
        +
        +
        +

        Plot Weight-at-Age

        + + +
        + +
        +

        Generates plot of weight-at-age across time, age, sex, +and region as appropriate.

        +
        + +
        + 
        plot_waa(waa)
        +
        + +
        +

        Arguments

        +
        waa
        +

        four-dimensional weight-at-age matrix

        + +
        + +
        + +
        + + +
        +

        Developed by Benjamin Williams, Joshua Zahner, Matt Cheng, Maia Kapur.

        +
        + +
        +

        Site built with pkgdown 2.0.7.

        +
        + +
        + + + + + + + + diff --git a/docs/reference/project.html b/docs/reference/project.html index 2c87545..019a0fa 100644 --- a/docs/reference/project.html +++ b/docs/reference/project.html @@ -46,16 +46,16 @@ Conducting Multiyear Projections
      • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
      • - Specifying Demographic Rates + Observation Processes
      • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
      • - A Spatial Model Example + Specifying Demographic Rates
        • @@ -79,7 +79,7 @@

        Project population forward by 1 year

        - 
        project(removals, fleet.props, dem_params, prev_naa, recruitment, options = NA)
        + 
        project(removals, dem_params, prev_naa, recruitment, options = NA)
        @@ -88,10 +88,6 @@

        Arguments

        population removals (either in catch or F units)

        -
        fleet.props
        -

        the proportion of the TAC allocated to each fleet

        - -
        dem_params

        list of demographic parameter matrices

        @@ -104,6 +100,10 @@

        Arguments

        total recruiment to occurin this year

        +
        fleet.props
        +

        the proportion of the TAC allocated to each fleet

        + +
        option

        additional model options

        diff --git a/docs/reference/project_multi.html b/docs/reference/project_multi.html index e33d681..28ee646 100644 --- a/docs/reference/project_multi.html +++ b/docs/reference/project_multi.html @@ -1,6 +1,6 @@ Project Population Forward Multiple Years — project_multi • afscOM @@ -74,7 +74,7 @@

        Project Population Forward Multiple Years

        A wrapper function around the base `project` function that handles -projecting forward multiple years given a removals timeseries and a +projecting forward multiple years given a removals timeseries and a recruitment timeseries.

        diff --git a/docs/reference/resample_recruitment.html b/docs/reference/resample_recruitment.html index 7709f1f..93d32c2 100644 --- a/docs/reference/resample_recruitment.html +++ b/docs/reference/resample_recruitment.html @@ -1,5 +1,5 @@ -Resample from historical recruitment timeseries — resample_recruitment • afscOMResample from historical recruitment timeseries — resample_recruitment • afscOM @@ -72,7 +72,7 @@

        Resample from historical recruitment timeseries

        -

        Draw `n` random samples, with replacement, from the +

        Draw `n` random samples, with replacement, from the historical recruitment timeseries.

        @@ -102,6 +102,14 @@

        Value

        recruitment timeseries.

        +
        +

        Examples

        + 
        set.seed(1120)
+n <- 100
+hist.rec <- c(100, 200, 50, 100, 120)
+resample.recruitment(n, hist.rec)
+
        +
        diff --git a/docs/reference/sablefish_assessment_data.html b/docs/reference/sablefish_assessment_data.html index a9b130f..fb78f96 100644 --- a/docs/reference/sablefish_assessment_data.html +++ b/docs/reference/sablefish_assessment_data.html @@ -44,16 +44,16 @@ Conducting Multiyear Projections
      • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
      • - Specifying Demographic Rates + Observation Processes
      • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
      • - A Spatial Model Example + Specifying Demographic Rates
        • @@ -80,7 +80,7 @@

        Sablefish assessment

        Format

        -

        A list containing assessment data:

        +

        A list containing assessment data

        diff --git a/docs/reference/sablefish_dem_params.html b/docs/reference/sablefish_dem_params.html index 74198a2..83d574b 100644 --- a/docs/reference/sablefish_dem_params.html +++ b/docs/reference/sablefish_dem_params.html @@ -46,16 +46,16 @@ Conducting Multiyear Projections
      • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
      • - Specifying Demographic Rates + Observation Processes
      • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
      • - A Spatial Model Example + Specifying Demographic Rates
        • @@ -84,7 +84,7 @@

        Demographic parameter matrices for Alaska Sablefish

        Format

        -

        A list containing demographic matrices:

        +

        A list containing demographic matrices

        diff --git a/docs/reference/set_model_params.html b/docs/reference/set_model_params.html index 3127194..a93d1cd 100644 --- a/docs/reference/set_model_params.html +++ b/docs/reference/set_model_params.html @@ -44,16 +44,16 @@ Conducting Multiyear Projections
      • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
      • - Specifying Demographic Rates + Observation Processes
      • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
      • - A Spatial Model Example + Specifying Demographic Rates
        • diff --git a/docs/reference/setup_model_options.html b/docs/reference/setup_model_options.html index 7ed613c..e190cab 100644 --- a/docs/reference/setup_model_options.html +++ b/docs/reference/setup_model_options.html @@ -45,16 +45,16 @@ Conducting Multiyear Projections
      • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
      • - Specifying Demographic Rates + Observation Processes
      • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
      • - A Spatial Model Example + Specifying Demographic Rates
        • @@ -87,6 +87,14 @@

        Arguments

        +
        +

        Examples

        + 
        if (FALSE) {
+     dimensions = list(nyears=60, nages=50, nsexes=2, nregions=1, nfleets=1)
+     model_options = setup_model_options(dimensions)
+}
+
        +
        diff --git a/docs/reference/simulate_caa.html b/docs/reference/simulate_caa.html index e025b26..1a560b0 100644 --- a/docs/reference/simulate_caa.html +++ b/docs/reference/simulate_caa.html @@ -45,16 +45,16 @@ Conducting Multiyear Projections
      • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
      • - Specifying Demographic Rates + Observation Processes
      • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
      • - A Spatial Model Example + Specifying Demographic Rates
        • diff --git a/docs/reference/simulate_catch.html b/docs/reference/simulate_catch.html index af09e78..7c88d0f 100644 --- a/docs/reference/simulate_catch.html +++ b/docs/reference/simulate_catch.html @@ -44,16 +44,16 @@ Conducting Multiyear Projections
      • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
      • - Specifying Demographic Rates + Observation Processes
      • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
      • - A Spatial Model Example + Specifying Demographic Rates
        • @@ -75,7 +75,7 @@

        Simulate catches in one region during on year

        - 
        simulate_catch(removals, fleet.props, dem_params, naa, options)
        + 
        simulate_catch(removals, dem_params, naa, options)
        @@ -84,10 +84,6 @@

        Arguments

        desired removals either in catch or F units

        -
        fleet.props
        -

        the proportion of the TAC that should be taken by each fleet

        - -
        dem_params

        demographic parameter matrices for population

        @@ -96,6 +92,10 @@

        Arguments

        the current numbers-at-age in the population

        +
        fleet.props
        +

        the proportion of the TAC that should be taken by each fleet

        + +
        option

        list of model options

        diff --git a/docs/reference/simulate_lognormal_obs.html b/docs/reference/simulate_lognormal_obs.html index d98f413..4974ccf 100644 --- a/docs/reference/simulate_lognormal_obs.html +++ b/docs/reference/simulate_lognormal_obs.html @@ -59,16 +59,16 @@ Conducting Multiyear Projections
      • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
      • - Specifying Demographic Rates + Observation Processes
      • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
      • - A Spatial Model Example + Specifying Demographic Rates
        • @@ -117,11 +117,10 @@

        Arguments

        Examples

        - 
        if (FALSE) {
-simulate_lognormal_obs(10, 0.20)
-}
-
-
        + 
        if (FALSE) {
+simulate_lognormal_obs(10, 0.20)
+}
+
        @@ -136,11 +136,10 @@

        Arguments

        Examples

        - 
        if (FALSE) {
-simulate_multinomial_obs(c(0.25, 0.50, 0.25), 100)
-}
-
-
        + 
        if (FALSE) {
+simulate_multinomial_obs(c(0.25, 0.50, 0.25), 100)
+}
+
        diff --git a/docs/reference/simulate_population.html b/docs/reference/simulate_population.html index 116dd9a..3ace857 100644 --- a/docs/reference/simulate_population.html +++ b/docs/reference/simulate_population.html @@ -50,16 +50,16 @@ Conducting Multiyear Projections
      • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
      • - Specifying Demographic Rates + Observation Processes
      • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
      • - A Spatial Model Example + Specifying Demographic Rates
        • @@ -113,10 +113,9 @@

        Arguments

        Examples

        - 
        if (FALSE) {
-simulate_population(prev_naa, faa, recruitment, dem_params, options)}
-
-
        + 
        if (FALSE) {
+simulate_population(prev_naa, faa, recruitment, dem_params, options)}
+
        diff --git a/docs/reference/simulate_rpw.html b/docs/reference/simulate_rpw.html index 735fbe0..297780b 100644 --- a/docs/reference/simulate_rpw.html +++ b/docs/reference/simulate_rpw.html @@ -45,16 +45,16 @@ Conducting Multiyear Projections
      • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
      • - Specifying Demographic Rates + Observation Processes
      • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
      • - A Spatial Model Example + Specifying Demographic Rates
        • diff --git a/docs/reference/spatial_sablefish_assessment_data.html b/docs/reference/spatial_sablefish_assessment_data.html new file mode 100644 index 0000000..eceb984 --- /dev/null +++ b/docs/reference/spatial_sablefish_assessment_data.html @@ -0,0 +1,117 @@ + +Spatial Sablefish Assessment — spatial_sablefish_assessment_data • afscOM + + +
        +
        + + + +
        +
        +
        +

        Spatial Sablefish Assessment

        + + +
        + +
        +

        Demographic parameter inputs and estimated +derived quantities (selectivity, spawning biomass timeseries, +fishing mortality, etc.) from a run of the SpatialSablefishAssessment +model (https://craig44.github.io/SpatialSablefishAssessment/index.html). +Model developed by Craig Marsh. Data are considered preliminary.

        +
        + +
        + 
        spatial_sablefish_assessment_data
        +
        + +
        +

        Format

        +

        A list of data inputs and model outputs

        +
        + +
        + +
        + + +
        + + + + + + + + diff --git a/docs/reference/subset_dem_params.html b/docs/reference/subset_dem_params.html index d079a8e..59133bf 100644 --- a/docs/reference/subset_dem_params.html +++ b/docs/reference/subset_dem_params.html @@ -45,16 +45,16 @@ Conducting Multiyear Projections
      • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
      • - Specifying Demographic Rates + Observation Processes
      • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
      • - A Spatial Model Example + Specifying Demographic Rates
        • diff --git a/docs/reference/subset_matrix.html b/docs/reference/subset_matrix.html index f651643..59f65eb 100644 --- a/docs/reference/subset_matrix.html +++ b/docs/reference/subset_matrix.html @@ -46,16 +46,16 @@ Conducting Multiyear Projections
      • - Observation Processes + Example: Northeast Pacific Transboundary Sablefish Model
      • - Specifying Demographic Rates + Observation Processes
      • - Example: Northeast Pacific Transboundary Sablefish Model + A Spatial Model Example
      • - A Spatial Model Example + Specifying Demographic Rates
        • diff --git a/docs/reference/validate_dem_params.html b/docs/reference/validate_dem_params.html index 8eeeb0f..a96d64b 100644 --- a/docs/reference/validate_dem_params.html +++ b/docs/reference/validate_dem_params.html @@ -1,6 +1,6 @@ Validate Demographic Parameter Matrices — validate_dem_params • afscOM @@ -74,7 +74,7 @@

        Validate Demographic Parameter Matrices

        Helper function for validating that all required demographic -parameter matrices have been defined and that they are all of +parameter matrices have been defined and that they are all of the correct dimension.

        @@ -103,11 +103,15 @@

        Value

        Details

        -

        Required demographic parameters are: mort, waa, sexrat, sel, +

        Required demographic parameters are: mort, waa, sexrat, sel, ret, dmr, and surv_sel

        Expected dimensions are: [nyears, nages, nsexes, nregions, nfleets]

        +
        +

        Examples

        + +