sen {fugue} | R Documentation |
Sensitivity Analysis for a Matched Comparison in an Observational Study.
Description
Each matched set contains one treated
individual and one or more controls.
Uses Huber's M-statistic as the basis for
the test, for instance, a mean. Matched sets of different sizes
use different \psi
-functions, creating what is called a fugue statistic.
Performs either a randomization
test (Gamma=1) or an analysis of sensitivity to departures from random
assignment (Gamma>1). For confidence intervals, use function senCI().
The method is described in Li and Rosenbaum (2019); see also Rosenbaum (2007,2013).
Usage
sen(y, z, mset, gamma = 1, inner = NULL, trim = NULL, lambda = 1/2,
tau = 0, alternative = "greater")
Arguments
y |
A vector of responses with no missing data. |
z |
Treatment indicator, z=1 for treated, z=0 for control with length(z)==length(y). |
mset |
Matched set indicator, 1, 2, ..., sum(z) with length(mset)==length(y). Matched set indicators should be either integers or a factor. |
gamma |
gamma is the sensitivity parameter |
inner |
inner and trim together define the |
trim |
inner and trim together define the |
lambda |
Before applying the An error will result unless 0 < lambda < 1. |
tau |
The null hypothesis asserts that the treatment has an additive effect, tau. By default, tau=0, so by default the null hypothesis is Fisher's sharp null hypothesis of no treatment effect. |
alternative |
If alternative="greater", the null hypothesis of a treatment effect of tau is tested against the alternative of a treatment effect larger than tau. If alternative="less", the null hypothesis of a treatment effect of tau is tested against the alternative of a treatment effect smaller than tau. In particular, alternative="less" is equivalent to: (i) alternative="greater", (ii) y replaced by -y, and (iii) tau replaced by -tau. See the note for discussion of two-sided sensitivity analyses. |
Details
The novel element in the fugue package is the automatic use of different
\psi
-functions for matched sets of different sizes. These
\psi
-functions have been selected to approximately equate the
design sensitivities in sets of unequal sizes when the errors are
Normal and the additive effect is half the standard deviation of
a matched pair difference; see Li and Rosenbaum (2019). If you
disable this automatic feature by manually setting a single value for inner
and trim, then the results will agree with senm() in the R
package sensitivitymult. For instance, using both sen() in the
fugue package and senm() in the sensitivitymult package will
yield the same deviate and P-value in:
data(nh1and3)
attach(nh1and3)
sen(homocysteine,z,mset,inner=0,gamma=1.9)
senm(homocysteine,z,mset,inner=0,trim=3,gamma=1.9)
Note that the sensitivitymult package is intended to
implement methods from Rosenbaum (2016,2019) that are
not implemented in the fugue package.
For the given \Gamma
, sen() computes the upper bound on the 1-sided
P-value testing the null hypothesis
of an additive treatment effect tau against the alternative hypothesis of
a treatment effect larger than tau. By default, sen() tests the null hypothesis of
no treatment effect against the alternative of a positive treatment effect.
The P-value is an approximate P-value
based on a Normal approximation to the null distribution; see Rosenbaum (2007).
Matched sets of unequal size are weighted using weights that would be efficient in a randomization test under a simple model with additive set and treatment effects and errors with constant variance; see Rosenbaum (2007).
The upper bound on the P-value is based on the separable approximation described in Gastwirth, Krieger and Rosenbaum (2000); see also Rosenbaum (2007, 2018).
Value
pval |
The upper bound on the 1-sided P-value. |
deviate |
The deviate that was compared to the Normal distribution to produce pval. |
statistic |
The value of the M-statistic. |
expectation |
The maximum expectation of the
M-statistic for the given |
variance |
The maximum variance of the M-statistic among treatment assignments that achieve the maximum expectation. Part of the separable approximation. |
Note
The function sen() performs 1-sided tests. One approach
to a 2-sided, \alpha
-level test does both 1-sided tests
at level \alpha/2
, and rejects the null hypothesis if either
1-sided
test rejects. Equivalently, a bound on the two sided
P-value is the smaller of 1 and twice the smaller of the two 1-sided
P-values. This approach views a 2-sided test as two 1-sided tests
with a Bonferroni correction; see Cox (1977, Section 4.2). In all
cases, this approach is a valid large sample test: a true
null hypothesis is falsely
rejected with probability at most \alpha
if the bias in
treatment assignment is at most \Gamma
; so, this procedure
is entirely safe to use. For a randomization test, \Gamma=1
, this
Bonferroni procedure is not typically conservative. For large \Gamma
,
this Bonferroni procedure tends to be somewhat conservative.
The examples reproduce some results from Li and Rosenbaum (2019).
Author(s)
Xinran Li and Paul R. Rosenbaum.
References
Cox, D. R. (1977). The role of signficance tests (with Discussion). Scand. J. Statist. 4, 49-70.
Huber, P. (1981) Robust Statistics. New York: John Wiley. (M-estimates based on M-statistics.)
Li, X. and Rosenbaum, P. R. (2019) Maintaining high constant design sensitivity in observational studies with matched sets of varying sizes. Manuscript.
Maritz, J. S. (1979). A note on exact robust confidence intervals for location. Biometrika 66 163–166. (Introduces exact permutation tests based on M-statistics by redefining the scaling parameter.)
Rosenbaum, P. R. (2007). Sensitivity analysis for m-estimates, tests and confidence intervals in matched observational studies. Biometrics 63 456-64. (R package sensitivitymv) <doi:10.1111/j.1541-0420.2006.00717.x>
Rosenbaum, P. R. (2013). Impact of multiple matched controls on design sensitivity in observational studies. Biometrics 69 118-127. (Introduces inner trimming.) <doi:10.1111/j.1541-0420.2012.01821.x>
Rosenbaum, P. R. (2014). Weighted M-statistics with superior design sensitivity in matched observational studies with multiple controls. J. Am. Statist. Assoc. 109 1145-1158. (R package sensitivitymw) <doi:10.1080/01621459.2013.879261>
Rosenbaum, P. R. (2015). Two R packages for sensitivity analysis in observational studies. Observational Studies, v. 1. (Free on-line.)
Rosenbaum, P. R. (2016) Using Scheffe projections for multiple outcomes in an observational study of smoking and periondontal disease. Annals of Applied Statistics, 10, 1447-1471. <doi:10.1214/16-AOAS942>
Rosenbaum, P. R. (2018). Sensitivity analysis for stratified comparisons in an observational study of the effect of smoking on homocysteine levels. The Annals of Applied Statistics, 12(4), 2312-2334. <doi:10.1214/18-AOAS1153>
Rosenbaum, P. R. (2019). Combining planned and discovered comparisons in observational studies. Biostatistics, to appear. <doi.org/10.1093/biostatistics/kxy055>
Examples
# Reproduces results from Table 3 of Li and Rosenbaum (2019)
data(nh1and3)
attach(nh1and3)
sen(homocysteine,z,mset,gamma=1)
sen(homocysteine,z,mset,gamma=1.9)
sen(homocysteine,z,mset,inner=0,gamma=1.9)
amplify(1.9,c(3,3.5,4))
detach(nh1and3)