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dBerLGG): the alternating sum over s was taken over all
observed zeros, including those with k_j = 1, which produced biased
estimates whenever clusters contained zeros. The sum now runs only over
positions with y_j = 0 and k_j = 0, matching the expansion of pi^(z - k)
in Theorem 1.rhzip() examples are now wrapped
in \donttest{}.rhzip() where the Bernoulli draw used to
generate structural zeros had its probability inverted
(rbinom(m[i], 1, p) instead of
rbinom(m[i], 1, 1 - p)), which produced
P(Y=0) = (1-pi) + pi*exp(-mu) instead of the correct
P(Y=0) = pi + (1-pi)*exp(-mu).simulate.hzip(), which implemented a
hurdle-Poisson generative mechanism (rejection/retry sampling to avoid
zero counts) instead of the correct ZIP/HZIP mixture mechanism (an
ordinary, non-truncated Poisson draw that can itself be zero). This
affected the parametric bootstrap used by testZI() and
testDisp().rhzip() to no longer silently drop the first
column of x1 and/or x2. Previously the first
column of each matrix was always removed, assuming it was an intercept;
this discarded a real covariate whenever x1/x2
did not include an intercept as their first column. All supplied columns
are now kept and renamed (x1 ->
x1, ..., xp1; x2 ->
w1, ..., wp2).hzip() documentation, which described the
two-part formula as y ~ w_zero + ... | x_count + ...; the
actual (and now documented) convention is
y ~ x_zero + ... | w_count + ..., matching
rhzip()’s column-naming convention.AICz, BICz, AIC_HZIP and
BIC_HZIP are temporarily disabled (commented out) in
hzip(), summary.hzip() and
print.summary.hzip() and are no longer computed, returned,
or printed.print.summary.hzip(), Convergence is
now shown as an additional column in the main summary table (alongside
logLik, AIC, BIC,
Iter) instead of on a separate line.HZIP to
hzip; all S3 methods (print,
summary, residuals, simulate,
testDisp, testZI) were updated
accordingly.rHZIP() was renamed to rhzip().envelope.HZIP() was renamed to
envelope().testDisp() and testZI() are now S3
generics with explicit arguments (nsim,
alternative, alpha, seed,
plot).salamanders dataset now includes the variable
sample; examples were updated to use it.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.