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.
Dependence on polynom package removed.
Edition 3 of testthat implemented.
ratesci 0.5.0 (2025-01-10)
New features
In pairbinci():
cc continuity correction is now available for all
methods for all contrasts.
cctype controls the type of correction to apply for
contrast = “RR”.
New default method_RD = “Score_closed” for
non-iterative calculation of the Tango score interval for
contrast = “RD”. Thanks to Tony Yang for permission to use
the code in his 2013 paper.
New default method_RR = “Score_closed” for
non-iterative calculation of the Tang score interval for
contrast = “RR”. Thanks to Guogen Shan for contributing
code via email.
Added paired MOVER methods with method_RD = “MOVER” and
method_RR = “MOVER”. Also “MOVER_newc” incorporates
Newcombe’s correlation correction.
Added moverbase, for specifying different versions of
the MOVER methods (Wilson, Jeffreys, midp or SCAS).
Added “jeff” and “wilson” method_OR options for
transformed binomial methods for OR.
Confirmed and documented that the 2-sided significance test is
equivalent to the McNemar test (with or without continuity
correction).
In scoreci():
Confirmed that continuity corrections for all stratified
(fixed-effects) binomial contrasts are consistent with the
Mantel-Haenszel correction.
Updated heterogeneity test to consistently omit non-informative (but
non-empty) strata, and output the degrees of freedom.
In moverci():
Added continuity correction for type = “wilson”.
Added options for type = “SCAS” and “midp”
intervals.
Standardised output to include lower CL, midpoint, upper CL, in that
order.
Bug fixes
In scoreci():
Improved handling of special cases for MN weighting (#25, thanks to
Vincent Jaquet for reporting the issue and proposed solution. Also #27
for RR, thanks to @lovestat.) As a result, double-zero strata
need not be excluded when weighting = “MN”.
In moverci():
Corrected calculation of score intervals for single Poisson rate,
using Rao score interval.
Same correction affects MOVER method for comparison of Poisson rates
[i.e. moverci() with distrib = “poi” and
type = “wilson”]
Other
Improved documentation of hypothesis tests and continuity
corrections, clarifying links to Chi-squared tests and CMH test with
selected weights.
Correction to documentation of default weights for OR.
Added tests confirming equivalence of iterative and closed-form
methods in pairbinci.
ratesci 0.4-0 (2021-12-04)
New features
In scoreci():
MN weighting now iterates to convergence (@jonjvallejo, #20).
Added optional prediction interval for random effects method (also
in tdasci()).
Added xlim and ylim arguments to control plot output.
Added sda & fda arguments for optional sparse/full data
adjustment when x1 + x2 = 0 or x1 + x2 = n1 + n2 in a stratum.
Added INV option for weights that omit the variance bias
correction.
Added RRtang argument to apply Tang’s alternative score for RR
(recommended for stratified analysis with INV/IVS weights. Experimental
for Poisson RR). Stheta = (p1hat - p2hat * theta) / p2d
(see Tang 2020)
Added simplified skewness correction option (causes p-values to be
omitted, see Tang 2021 & Laud 2021).
Introduced warning and plot features for very rare occasions when
quadratic skewness correction cannot be calculated due to a negative
discriminant.
p-value suppressed where affected by negative discriminants.
Changed ORbias default to TRUE (see Laud 2018).
Changed weighting default to MH for RD & RR, INV for OR (for
consistency with CMH test).
Added hetplot argument to separate heterogeneity plots from score
function plot.
Uninformative strata are now retained in the analysis except if:
contrast = OR with MH weighting;
contrast = RR with IVS/INV weighting if RRtang = FALSE;
random = TRUE (needs further evaluation);
excluded using new option dropzeros = TRUE.
In tdasci():
Default uses skew = TRUE for stratum CIs.
Bug fixes
MN weighting in scoreci() corrected for
distrib=“poi”.
Fixed bug in scoreci() for calculation of stratum CIs
with random=TRUE.
Fixed bug in scoreci() for distrib = “poi” and contrast
= “p” (#7).
Fixed finite precision bug in scaspci().
Fixed bug in rateci() for closed-form calculation of
continuity-corrected SCAS.
Fixed bug in scoreci() for stratified zero scores
calculated as NA, resulting in UL = 0. (Thanks to Lidia Mukina for
reporting the bug.)
Fixed variable plot ranges for vectorised inputs.
Other
Renamed tdas argument to ‘random’.
Removed redundant t2 variable.
ratesci 0.3-0 (2018-02-15)
New features
Added bias correction in scoreci() for OR SCAS method
(derived from Gart 1985).
Added score methods (Tango & Tang) as default for paired
binomial RD and RR in pairbinci().
Added transformed mid-p method for paired OR for comparison with
transformed SCAS.
Added scaspci() for non-iterative SCAS methods for
single binomial or Poisson rate.
Added rateci() for selected methods for single binomial
or Poisson rate.
Bug fixes
Fixed bug in pairbinci() for contrast=“OR”.
Fixed bug in moverci() for contrast=“p” and
type=“wilson”.
Corrected error in cc for stratified SCAS method for OR.