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New function clusterpci() for CI and test for a single binomial proportion
from clustered data.
Example datasets are now included.
Improved documentation with pkgdown website & vignettes.
In pairbinci():
skew for skewness correction.
bcf for variance bias correction.
Default paired RD and RR method changed to new SCAS method
(i.e. including skewness correction - manuscript under review).
method_RD, method_RR and method_OR are replaced with method.
Bonett-Price methods for RD and RR (including proposed Jeffreys variant
option for RR).
TDAS method is deprecated.
Default for MOVER method changed to Jeffreys.
MOVER calculations now use x/N as point estimate instead of median from the
Beta distribution.
cc uses a new form of correction for RR giving equivariant intervals. Also
allows consistency with the continuity-corrected McNemar test (or an
intermediate correction of the user's choosing). cctype is deprecated.
Default conditional odds ratio method changed to SCASp (with closed-form
calculation).
Output object now includes estimates of p1, p2, phi (correlation)
and psi (odds ratio used by Fagerland et al).
Output object now includes function call.
In scaspci():
bcf option now implemented for contrast = "p" (default = FALSE).
bign allows a different sample size to be used in the bias correction
(used within transformed SCASp method for paired OR in pairbinci, for
consistency with 'N-1' test).
In scoreci():
bcf option now implemented for contrast = "p" (default = FALSE).
(Note adjusted sample size for bias correction can be achieved by including a
non-zero value for n2.)
ORbias, RRtang, and MNtol arguments renamed as or_bias, rr_tang and mn_tol.
Implementation of precis argument is improved for RR and OR contrasts.
For contrast = "RD", weighting = "Tang" provides optimal test if RR is
constant across strata.
Bug fixes
In exactci():
Corrected duplicate point estimate reported for vector inputs.
Derive point estimates to match LCL and UCL with level = 0.
Corrected LCL for Poisson mid-p method.
Other
Output object column names are updated (lower, est, upper) for consistency
and style conformity.
Tests added to confirm consistency of score methods vs McNemar test.