bizicount: Bizicount: Maximum likelihood estimation of copula-based...
In bizicount: Bivariate Zero-Inflated Count Models Using Copulas

bizicount

R Documentation

Bizicount: Maximum likelihood estimation of copula-based bivariate zero-inflated (and non-inflated) count models

Description

The main bivariate regression function of the bizicount-package Estimates copula-based bivariate zero-inflated (and non-inflated) count models via maximum likelihood. Supports the Frank and Gaussian copulas, as well as zero-inflated Poisson and negative binomial margins (and their non-inflated counterparts). It's class has associated simulate methods for post-estimation diagnostics using the DHARMa package, as well as an extract method for printing professional tables using texreg, and a test for zero-modification using zi_test. See the 'See Also' section for links to these methods.

Usage

bizicount(
  fmla1,
  fmla2,
  data,
  cop = "gaus",
  margins = c("pois", "pois"),
  link.ct = c("log", "log"),
  link.zi = c("logit", "logit"),
  scaling = "none",
  starts = NULL,
  keep = TRUE,
  subset,
  na.action,
  weights,
  frech.min = 1e-07,
  pmf.min = 1e-07,
  ...
)

Arguments

`fmla1`, `fmla2`	`formula`s for the first margin and second margins, respectively. If non-inflated, of the form `y ~ x_1 + x_2 + ... + x_k`; if inflated, of the form `y ~ x1 + x2 + ... + x_k\| z1 + z2 + ... + z_p`, where `y` is the outcome for the first margin, `x` are covariates for count parameters, and `z` are covariates for zero-inflated parameters in each margin. All covariates can be the same.
`data`	A `data.frame` containing the response variables, covariates, and offsets for the model. If `NULL`, these quantities are searched for in the parent environment.
`cop`	Character string specifying the copula to be used. One of `c("gaus", "frank")`. Partial matching supported.
`margins`	Length 2 character vector specifying the marginal distributions for each outcome. Each of the two elements must be one of `c("pois", "nbinom", "zip", "zinb")`, and must be consistent with its corresponding formula (i.e., zero-inflated margins with zero-inflated formulas).
`link.ct`	Length 2 character string specifying the link function used for the count portion of each margin. One of `c("log", "identity", "sqrt")`.
`link.zi`	Length 2 character string specifying the link function used for the zero-inflation portion of each margin. One of `c("logit", "probit", "cauchit", "log", "cloglog")`. Ignored if corresponding `margins` entry is not zero-inflated.
`scaling`	Deprecated. It is recommended that users scale their covariates if they encounter convergence issues, which can be accomplished using the `scale()` function on their data before putting it into the `bizicount()` function.
`starts`	Numeric vector of starting values for parameter estimates. See 'Details' section regarding the correct order for the values in this vector. If `NULL`, starting values are obtained automatically by a univariate regression fit.
`keep`	Logical indicating whether to keep the model matrix in the returned model object. Defaults to `TRUE`, but can be set to `FALSE` to conserve memory. NOTE: Must be `TRUE` to use any post-estimation functions in this package, including `zi_test`.
`subset`	A vector indicating the subset of observations to use in estimation.
`na.action`	Deprecated.
`weights`	An optional numeric vector of weights for each observation.
`frech.min`	Lower boundary for Frechet-Hoeffding bounds on copula CDF. Used for computational purposes to prevent over/underflow in likelihood search. Must be in `[0, 1e-5]`, with `0` imposing the original FH bounds without computational consideration. See 'Details.'
`pmf.min`	Lower boundary on copula PMF evaluations. Used for computational purposes to prevent over/underflow in likelihood search. Must be in `[0, 1e-5]`, with `0` imposing no bound. See ‘Details.’
`...`	Additional arguments to be passed on to the quasi-newton fitting function, `nlm`. See 'Details' for some parameters that may be useful to alter.

Details

starts – Starting values should be organized as follows:
1. count parameters for margin 1
2. count parameters for margin 2
3. zero-inflated parameters for margin 1 (if applicable),
4. zero-inflated parameters for margin 2 (if applicable),
5. inverse dispersion parameter for margin 1 (if applicable),
6. inverse dispersion parameter for margin 2 (if applicable)
Thus, in general count parameters should come first, followed by zero-inflation parameters, and finally inverse dispersion parameters.
frech.min – Changing this argument should almost never be necessary. Frechet (1951) and Hoeffding (1940) showed that copula CDFs have bounds of the form max\{u + v - 1, 0\} \le C(u, v) \le min\{u, v\}, where u and v are uniform realizations derived from the probability integral transform. Due to numerical underflow, very small values of u and v can be rounded to zero. Particularly when evaluating the Gaussian copula CDF this is problematic, ultimately leading to infinite-valued likelihood evaluations. Therefore, we impose Frechet-Hoeffding bounds numerically as max\{u + v - 1, frech.min\} \le C(u, v) \le min\{u, v, 1 - frech.min\}. NOTE: Setting this to 0 imposes the original Frechet bounds mentioned above.
pmf.min – Changing this argument should almost never be necessary. Observations can have likelihoods that are extremely close to 0. Numerically, these get rounded to 0 due to underflow. Then, taking logarithms results in an infinite likelihood. To avoid this, we bound PMF evaluations from below at pmf.min.
... – Sometimes it may be useful to alter nlm's default parameters. This can be done by simply passing those arguments into bizicount(). The two that seem to benefit the fitting process the most are stepmax and steptol. Readers are referred to the documentation on nlm for more details on these parameters. It can be useful to lower stepmax particularly when the Hessian is not negative definite at convergence, sometimes to a value between 0 and 1. It can also be beneficial to increase steptol.

Value

An S3 bizicount-class object, which is a list containing:

coef – Coefficients of the model
coef.nid – Coefficients without margin IDs
coef.orig – Coefficients prior to transformations, for Gaussian dependence and negative binomial dispersion.
coef.orig.nid – Coefficients prior to transforms, no margin IDs.
se – Asymptotic normal-theory standard errors based on observed Fisher Information
se.nid – Standard errors without margin IDs
z – z-scores for parameter estimates
z.nid – z-scores without margin IDs
p – p-values for parameter estimates
p.nid – p-values without margin IDs
coefmats – A list containing coeficient matrices for each margin
loglik – Scalar log-likelihood at convergence
grad – Numerical gradient vector at convergence
n.iter – Number of quasi-newton fitting iterations.
covmat – Covariance matrix of parameter estimates based on observed Fisher Information
aic – Model's Akaike information
bic – Model's Bayesian information criterion
nobs – Number of observations
margins – Marginal distributions used in fitting
⁠link.zi, link.ct⁠ – Names of link functions used in fitting
⁠invlink.ct, invlink.zi⁠ – Inverse link functions used in fitting (the actual function, not their names)
outcomes – Name of the response vector
conv – Integer telling convergence status in nlm. See ?nlm.
cop – The copula used in fitting
starts – list of starting values used
call – The model's call
model – List containing model matrices, or NULL if keep = F.

Author(s)

John Niehaus

References

doi:10.18637/jss.v109.i01

Genest C, Nešlehová J (2007). “A primer on copulas for count data.” ASTIN Bulletin: The Journal of the IAA, 37(2), 475–515.

Inouye DI, Yang E, Allen GI, Ravikumar P (2017). “A review of multivariate distributions for count data derived from the Poisson distribution.” Wiley Interdisciplinary Reviews: Computational Statistics, 9(3).

Joe H (1997). Multivariate models and multivariate dependence concepts. CRC Press.

Nikoloulopoulos A (2013). “Copula-Based Models for Multivariate Discrete Response Data.” In P Jaworski, F Durante, WK Härdle (eds.), Copulae in Mathematical and Quantitative Finance, chapter 11, pp. 231–250. Springer.

Nelsen RB (2007). An Introduction to Copulas. Springer Science & Business Media.

Trivedi P, Zimmer D (2017). “A note on identification of bivariate copulas for discrete countdata.” Econometrics, 5(1), 10.

Trivedi PK, Zimmer DM (2007). Copula modeling: an introduction for practitioners. NowPublishers Inc.

Examples

### bizicount example

## SETUP
set.seed(123)
n = 300

# define a function to simulate from a gaussian copula
# first margin is zero-inflated negative binomial (zinb)
# second margin is zero-inflated poisson (zip)
# Note: marginal distributions are hard-coded in function, including
# inverse dispersion parameter for zinb.
gen = function(n,
               b1,
               b2,
               g1,
               g2,
               dep) {

     k1 = length(b1)
     k2 = length(b2)

     X1 = cbind(1, matrix(rbinom(n * (k1 - 1), 1, .5), ncol = k1 - 1))
     X2 = cbind(1, matrix(rexp(n * (k2 - 1), 3), ncol = k2 - 1))

     lam1 = exp(X1 %*% b1)
     lam2 = exp(X2 %*% b2)

     Z1 = cbind(1, matrix(runif(n * (k1 - 1), -1, 1), ncol = k1 - 1))
     Z2 = cbind(1, matrix(rnorm(n * (k2 - 1)), ncol = k2 - 1))

     psi1 = plogis(Z1 %*% g1)
     psi2 = plogis(Z2 %*% g2)

     norm_vars = MASS::mvrnorm(
          n,
          mu = c(0, 0),
          Sigma = matrix(c(1, dep, dep, 1), ncol =2)
          )

     U = pnorm(norm_vars)

     y1 =  qzinb(U[, 1],
                 mu = lam1,
                 psi = psi1,
                 size = .3)
     y2 =  qzip(U[, 2],
                lambda = lam2,
                psi = psi2)

     dat = data.frame(
          X1 = X1[, -1],
          X2 = X2[, -1],
          Z1 = Z1[, -1],
          Z2 = Z2[, -1],
          y1,
          y2,
          lam1,
          lam2,
          psi1,
          psi2
     )
     return(dat)
}


# define parameters
b1 = c(1, -2, 3)
b2 = c(-1, 3, 1)
g1 = c(2, -1.5, 2)
g2 = c(-1, -3.75, 1.25)
rho = .5


# generate data
dat = gen(n, b1, b2, g1, g2, rho)
f1 = y1 ~ X1.1 + X1.2 | Z1.1 + Z1.2
f2 = y2 ~ X2.1 + X2.2 | Z2.1 + Z2.2

## END SETUP

# estimate model

mod = bizicount(f1, f2, dat, cop = "g", margins = c("zinb", "zip"), keep = TRUE)

print(mod)
summary(mod)

bizicount documentation built on May 29, 2024, 9:10 a.m.