# Density Dependent IPMs

# Density dependent models

Density dependent model classes are now implemented. This vignette will get more details shortly. For now, see the example below:

## Example of a simple, stochastic, kernel-resampled model with density dependence

This example assumes that density dependence is modeled as a fixed effect in survival and recruit production models, and assumes there is no density dependence in growth or probability of reproducing models. The survival (\(s(z, N)\)/`s_yr`), growth (\(G_{yr}(z',z)\)/ `g_yr`), and number of recruit models (\(r_{s,yr}(z, N)\)/`r_s_yr`) have year-specific intercepts as well.

The mathematical form for the IPM is below:

1. \(n(z', t+1) = K_{yr}(z', z, N)n(z, t)dz\)

2. \(N = \int_L^Un(z,t)dz\)

3. \(K_{yr}(z', z, N) = P_{yr}(z', z, N) + F_{yr}(z', z, N)\)

Here, \(N\) represents the total population size. The kernel values fluctuate as a function of \(N\) at each iteration of the model.

The \(P_{yr}(z', z, N)\) kernel is comprised of a density independent function for growth (Eq 6-7) and a density dependent function for survival (Eq 5). \(f_G\) denotes a Gaussian probability density function:

4. \(P(z', z, N) = s(z, N) * G(z', z)\)

5. \(Logit(s(z, N)) = \alpha_s + \alpha_{s,yr} + \beta_s^z * z + \beta_s^{N} * N\)

6. \(G(z', z, \theta) = f_G(z', \mu_{G,yr}(z), \sigma_G)\)

7. \(\mu_{G,yr}(z) = \alpha_G + \alpha_{G,yr} + \beta_G^z * z\)

The \(F_{yr}(z',z, N)\) kernel is comprised of a density independent function for recruit size (Eq 10) and probability of reproducing (Eq 9), and a density dependent function for number of recruits produced by parents (Eq 11). \(f_{r_d}\) denotes a Gaussian probability density function:

8. \(F_{yr}(z', z, N) = r_r(z) * r_{s,yr}(z, N) + r_d(z')\)

9. \(Logit(r_r(z)) = \alpha_{r_r} + \beta_{r_r}^z * z\)

10. \(r_d(z') = f_{r_d}(z', \mu_{r_d}, \sigma_{r_d})\)

11. \(Log(r_{s,yr}(z, N)) = \alpha_{r_s} + \alpha_{{r_s},yr} + \beta_{r_s}^z * z + \beta_{r_s}^N * N\)

We’ll simulate a 50 year time series using hypothetical parameter values. The fixed parameter values are created as with a density independent model. The difference is that we now have two more parameters: `s_dd`, and `r_s_dd`. These are the coefficients that correspond to \(\beta_s^N\) and \(\beta_{r_s}^N\), respectively. The chunk below initializes the data list object, which we name `params`.

    library(ipmr)

    data_list = list(
      s_int     = 1.03,
      s_slope   = 2.2,
      s_dd      = -0.7,
      g_int     = 8,
      g_slope   = 0.92,
      sd_g      = 0.9,
      r_r_int   = 0.09,
      r_r_slope = 0.05,
      r_s_int   = 0.1,
      r_s_slope = 0.005,
      r_s_dd    = -0.03,
      mu_rd     = 9,
      sd_rd     = 2
    )

    # Now, simulate some random intercepts for growth, survival, and offspring production

    g_r_int   <- rnorm(5, 0, 0.3)
    s_r_int   <- rnorm(5, 0, 0.7)
    r_s_r_int <- rnorm(5, 0, 0.2)

    nms <- paste("r_", 1:5, sep = "")

    names(g_r_int) <- paste("g_", nms, sep = "")
    names(s_r_int) <- paste("s_", nms, sep = "")
    names(r_s_r_int) <- paste("r_s_", nms, sep = "")

    params     <- c(data_list, g_r_int, s_r_int, r_s_r_int)

Next, we initialize the model using `init_ipm`. The difference is that the second argument is now changed to `"dd"` to denote that this is a density dependent model.

    dd_ipm <- init_ipm(sim_gen = "simple",
                       di_dd = "dd",
                       det_stoch = "stoch",
                       kern_param = "kern")

Once we’ve done that, we’re ready to begin specifying the kernel forms. One previously not mentioned aspect of `define_pop_state()` is that, in addition to defining initial conditions, 2 additional helper variables are generated: `n_stateVariable_t` and `n_stateVariable_t_1`. These can be used to reference the population states in vital rate and/or kernel expressions.

These will look very similar to the ones we specified for density-independent models, except that we now include the term `s_dd * sum(n_size_t)` in the survival expression. `sum(n_size_t)` is the syntax `ipmr` uses to denote total population size. Further down, there is an example of how to use subsets of the trait distribution.

    dd_ipm <- define_kernel(
      proto_ipm        = dd_ipm,
      name             = "P_yr",
      formula          = s_yr * g_yr,
      family           = "CC",
      s_yr             = plogis(s_int + s_r_yr + s_slope * size_1 + s_dd * sum(n_size_t)),
      g_yr             = dnorm(size_2, g_mu_yr, sd_g),
      g_mu_yr          = g_int + g_r_yr + g_slope * size_1,
      data_list        = params,
      states           = list(c("size")),
      uses_par_sets    = TRUE,
      par_set_indices = list(yr = 1:5),
      evict_cor        = TRUE,
      evict_fun        = truncated_distributions("norm", "g_yr")
    )

Other than the inclusion of the density dependent term in the survival expression, this should look quite similar to the density-independent kernel-resampled models from the Introduction vignette. We are now ready to continue defining the \(F_{yr}(z',z,N)\) kernel.

    dd_ipm <- define_kernel(
      proto_ipm        = dd_ipm,
      name             = "F_yr",
      formula          = r_r * r_s_yr * r_d,
      family           = "CC",
      r_r              = plogis(r_r_int + r_r_slope * size_1),
      r_s_yr           = exp(r_s_int + r_s_r_yr + r_s_slope * size_1 + r_s_dd * sum(n_size_t)),
      r_d              = dnorm(size_2, mu_rd, sd_rd),
      data_list        = params,
      states           = list(c("size")),
      uses_par_sets    = TRUE,
      par_set_indices = list(yr = 1:5),
      evict_cor        = TRUE,
      evict_fun        = truncated_distributions("norm", "r_d")
      )

Again, we’ve add the `f_s_dd * sum(n_size_t)` to the expression for `f_s_yr`, but otherwise, not much is different from how we’ve defined density independent models. The rest of the model definition process is unchanged.

     dd_ipm <-  dd_ipm %>%
      define_impl(
        make_impl_args_list(
          kernel_names = c("P_yr", "F_yr"),
          int_rule     = rep("midpoint", 2),
          state_start    = rep("size", 2),
          state_end      = rep("size", 2)
        )
      ) %>%
      define_domains(
        size = c(0, 50, 200)
      ) %>%
      define_pop_state(
        n_size = runif(200)
      ) %>%
      make_ipm(
        iterate = TRUE,
        iterations = 50,
        kernel_seq = sample(1:5, 50, replace = TRUE)
      )

`lambda` methods are defined for all density-dependent models as well. It is fairly straightforward to plot population sizes for these models by extracting the column sums of the arrays in `pop_state`.

    time_step_lams <- lambda(dd_ipm, type_lambda = "all")
    stoch_lam      <- lambda(dd_ipm, type_lambda = "stochastic", burn_in = 0.15)

    pop_sizes <- colSums(dd_ipm$pop_state$n_size)

    plot(pop_sizes, type = "l")