R: Simultaneous Inference for Multiple Marginal Models
mmm
R Documentation
Simultaneous Inference for Multiple Marginal Models
Description
Calculation of correlation between test statistics from multiple marginal models
using the score decomposition
Usage
mmm(...)
mlf(...)
Arguments
...
A names argument list containing fitted models (mmm) or
definitions of linear functions (mlf). If
only one linear function is defined for mlf,
it will be applied to all models in mmm by
glht.mlf.
Details
Estimated correlations of the estimated parameters of interest from the
multiple marginal models are obtained using a stacked version of the
i.i.d. decomposition of parameter estimates by means of score components
(first derivatives of the log likelihood). The method is less
conservative than the Bonferroni correction. The details are provided by
Pipper and Ritz (2012).
The implementation assumes that the model were fitted to the same data,
i.e., the rows of the matrices returned by estfun belong to the
same observations for each model.
The reference distribution is always multivariate normal, if you want
to use the multivariate t, please specify the corresponding degrees of
freedom as an additional df argument to glht.
Observations with missing values contribute zero to the score function.
Models have to be fitted using na.exclude as na.action
argument.
Value
An object of class mmm or mlf, basically a named list of the
arguments with a special method for glht being available for
the latter. vcov, estfun, and
bread methods are available for objects of class
mmm.
Author(s)
Code for the computation of the joint covariance and
sandwich matrices was contributed by Christian Ritz and
Christian B. Pipper.
References
Christian Bressen Pipper, Christian Ritz and Hans Bisgaard (2012),
A Versatile Method for Confirmatory Evaluation of the Effects
of a Covariate in Multiple Models,
Journal of the Royal Statistical Society,
Series C (Applied Statistics), 61, 315–326.
Examples
### replicate analysis of Hasler & Hothorn (2011),
### A Dunnett-Type Procedure for Multiple Endpoints,
### The International Journal of Biostatistics: Vol. 7: Iss. 1, Article 3.
### DOI: 10.2202/1557-4679.1258
### see ?coagulation
if (require("SimComp")) {
data("coagulation", package = "SimComp")
### level "S" is the standard, "H" and "B" are novel procedures
coagulation$Group <- relevel(coagulation$Group, ref = "S")
### fit marginal models
(m1 <- lm(Thromb.count ~ Group, data = coagulation))
(m2 <- lm(ADP ~ Group, data = coagulation))
(m3 <- lm(TRAP ~ Group, data = coagulation))
### set-up Dunnett comparisons for H - S and B - S
### for all three models
g <- glht(mmm(Thromb = m1, ADP = m2, TRAP = m3),
mlf(mcp(Group = "Dunnett")), alternative = "greater")
### joint correlation
cov2cor(vcov(g))
### simultaneous p-values adjusted by taking the correlation
### between the score contributions into account
summary(g)
### simultaneous confidence intervals
confint(g)
### compare with
## Not run:
library("SimComp")
SimCiDiff(data = coagulation, grp = "Group",
resp = c("Thromb.count","ADP","TRAP"),
type = "Dunnett", alternative = "greater",
covar.equal = TRUE)
## End(Not run)
### use sandwich variance matrix
library("sandwich")
g <- glht(mmm(Thromb = m1, ADP = m2, TRAP = m3),
mlf(mcp(Group = "Dunnett")),
alternative = "greater", vcov = sandwich)
summary(g)
confint(g)
}
### attitude towards science data
data("mn6.9", package = "TH.data")
### one model for each item
mn6.9.y1 <- glm(y1 ~ group, family = binomial(),
na.action = na.omit, data = mn6.9)
mn6.9.y2 <- glm(y2 ~ group, family = binomial(),
na.action = na.omit, data = mn6.9)
mn6.9.y3 <- glm(y3 ~ group, family = binomial(),
na.action = na.omit, data = mn6.9)
mn6.9.y4 <- glm(y4 ~ group, family = binomial(),
na.action = na.omit, data = mn6.9)
### test all parameters simulaneously
summary(glht(mmm(mn6.9.y1, mn6.9.y2, mn6.9.y3, mn6.9.y4),
mlf(diag(2))))
### group differences
summary(glht(mmm(mn6.9.y1, mn6.9.y2, mn6.9.y3, mn6.9.y4),
mlf("group2 = 0")))
### alternative analysis of Klingenberg & Satopaa (2013),
### Simultaneous Confidence Intervals for Comparing Margins of
### Multivariate Binary Data, CSDA, 64, 87-98
### http://dx.doi.org/10.1016/j.csda.2013.02.016
### see supplementary material for data description
### NOTE: this is not the real data but only a subsample
influenza <- structure(list(
HEADACHE = c(1L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 1L,
0L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L,
1L, 1L), MALAISE = c(0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 1L,
0L, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 0L, 1L,
0L), PYREXIA = c(0L, 0L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 0L, 1L,
1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 1L
), ARTHRALGIA = c(0L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 0L,
0L, 1L, 1L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L
), group = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L), .Label = c("pla", "trt"), class = "factor"), Freq = c(32L,
165L, 10L, 23L, 3L, 1L, 4L, 2L, 4L, 2L, 1L, 1L, 1L, 1L, 167L,
1L, 11L, 37L, 7L, 7L, 5L, 3L, 3L, 1L, 2L, 4L, 2L)), .Names = c("HEADACHE",
"MALAISE", "PYREXIA", "ARTHRALGIA", "group", "Freq"), row.names = c(1L,
2L, 3L, 5L, 9L, 36L, 43L, 50L, 74L, 83L, 139L, 175L, 183L, 205L,
251L, 254L, 255L, 259L, 279L, 281L, 282L, 286L, 302L, 322L, 323L,
366L, 382L), class = "data.frame")
influenza <- influenza[rep(1:nrow(influenza), influenza$Freq), 1:5]
### Fitting marginal logistic regression models
(head_logreg <- glm(HEADACHE ~ group, data = influenza,
family = binomial()))
(mala_logreg <- glm(MALAISE ~ group, data = influenza,
family = binomial()))
(pyre_logreg <- glm(PYREXIA ~ group, data = influenza,
family = binomial()))
(arth_logreg <- glm(ARTHRALGIA ~ group, data = influenza,
family = binomial()))
### Simultaneous inference for log-odds
xy.sim <- glht(mmm(head = head_logreg,
mala = mala_logreg,
pyre = pyre_logreg,
arth = arth_logreg),
mlf("grouptrt = 0"))
summary(xy.sim)
confint(xy.sim)
### Artificial examples
### Combining linear regression and logistic regression
set.seed(29)
y1 <- rnorm(100)
y2 <- factor(y1 + rnorm(100, sd = .1) > 0)
x1 <- gl(4, 25)
x2 <- runif(100, 0, 10)
m1 <- lm(y1 ~ x1 + x2)
m2 <- glm(y2 ~ x1 + x2, family = binomial())
### Note that the same explanatory variables are considered in both models
### but the resulting parameter estimates are on 2 different scales
### (original and log-odds scales)
### Simultaneous inference for the same parameter in the 2 model fits
summary(glht(mmm(m1 = m1, m2 = m2), mlf("x12 = 0")))
### Simultaneous inference for different parameters in the 2 model fits
summary(glht(mmm(m1 = m1, m2 = m2),
mlf(m1 = "x12 = 0", m2 = "x13 = 0")))
### Simultaneous inference for different and identical parameters in the 2
### model fits
summary(glht(mmm(m1 = m1, m2 = m2),
mlf(m1 = c("x12 = 0", "x13 = 0"), m2 = "x13 = 0")))
### Examples for binomial data
### Two independent outcomes
y1.1 <- rbinom(100, 1, 0.5)
y1.2 <- rbinom(100, 1, 0.5)
group <- factor(rep(c("A", "B"), 50))
m1 <- glm(y1.1 ~ group, family = binomial)
m2 <- glm(y1.2 ~ group, family = binomial)
summary(glht(mmm(m1 = m1, m2 = m2),
mlf("groupB = 0")))
### Two perfectly correlated outcomes
y2.1 <- rbinom(100, 1, 0.5)
y2.2 <- y2.1
group <- factor(rep(c("A", "B"), 50))
m1 <- glm(y2.1 ~ group, family = binomial)
m2 <- glm(y2.2 ~ group, family = binomial)
summary(glht(mmm(m1 = m1, m2 = m2),
mlf("groupB = 0")))
### use sandwich covariance matrix
summary(glht(mmm(m1 = m1, m2 = m2),
mlf("groupB = 0"), vcov = sandwich))