Meta-analysis of incidence rates
Calculation of fixed effect and random effects estimates (incidence
rate ratio or incidence rate difference) for meta-analyses with
event counts. Mantel-Haenszel, Cochran, inverse variance method,
and generalised linear mixed model (GLMM) are available for
pooling. For GLMMs, the rma.glmm
function
from R package metafor (Viechtbauer 2010) is called
internally.
metainc( event.e, time.e, event.c, time.c, studlab, data = NULL, subset = NULL, exclude = NULL, method = if (sm == "IRSD") "Inverse" else "MH", sm = gs("sminc"), incr = gs("incr"), allincr = gs("allincr"), addincr = gs("addincr"), model.glmm = "UM.FS", level = gs("level"), level.comb = gs("level.comb"), comb.fixed = gs("comb.fixed"), comb.random = gs("comb.random"), overall = comb.fixed | comb.random, overall.hetstat = comb.fixed | comb.random, hakn = gs("hakn"), adhoc.hakn = gs("adhoc.hakn"), method.tau = ifelse(!is.na(charmatch(tolower(method), "glmm", nomatch = NA)), "ML", gs("method.tau")), method.tau.ci = gs("method.tau.ci"), tau.preset = NULL, TE.tau = NULL, tau.common = gs("tau.common"), prediction = gs("prediction"), level.predict = gs("level.predict"), method.bias = gs("method.bias"), n.e = NULL, n.c = NULL, backtransf = if (sm == "IRSD") FALSE else gs("backtransf"), irscale = 1, irunit = "person-years", text.fixed = gs("text.fixed"), text.random = gs("text.random"), text.predict = gs("text.predict"), text.w.fixed = gs("text.w.fixed"), text.w.random = gs("text.w.random"), title = gs("title"), complab = gs("complab"), outclab = "", label.e = gs("label.e"), label.c = gs("label.c"), label.left = gs("label.left"), label.right = gs("label.right"), byvar, bylab, print.byvar = gs("print.byvar"), byseparator = gs("byseparator"), keepdata = gs("keepdata"), warn = gs("warn"), control = NULL, ... )
event.e |
Number of events in experimental group. |
time.e |
Person time at risk in experimental group. |
event.c |
Number of events in control group. |
time.c |
Person time at risk in control group. |
studlab |
An optional vector with study labels. |
data |
An optional data frame containing the study information, i.e., event.e, time.e, event.c, and time.c. |
subset |
An optional vector specifying a subset of studies to be used. |
exclude |
An optional vector specifying studies to exclude from meta-analysis, however, to include in printouts and forest plots. |
method |
A character string indicating which method is to be
used for pooling of studies. One of |
sm |
A character string indicating which summary measure
( |
incr |
A numerical value which is added to each cell frequency for studies with a zero cell count, see Details. |
allincr |
A logical indicating if |
addincr |
A logical indicating if |
model.glmm |
A character string indicating which GLMM should
be used. One of |
level |
The level used to calculate confidence intervals for individual studies. |
level.comb |
The level used to calculate confidence intervals for pooled estimates. |
comb.fixed |
A logical indicating whether a fixed effect meta-analysis should be conducted. |
comb.random |
A logical indicating whether a random effects meta-analysis should be conducted. |
overall |
A logical indicating whether overall summaries should be reported. This argument is useful in a meta-analysis with subgroups if overall results should not be reported. |
overall.hetstat |
A logical value indicating whether to print heterogeneity measures for overall treatment comparisons. This argument is useful in a meta-analysis with subgroups if heterogeneity statistics should only be printed on subgroup level. |
hakn |
A logical indicating whether the method by Hartung and Knapp should be used to adjust test statistics and confidence intervals. |
adhoc.hakn |
A character string indicating whether an ad hoc variance correction should be applied in the case of an arbitrarily small Hartung-Knapp variance estimate, see Details. |
method.tau |
A character string indicating which method is
used to estimate the between-study variance τ^2 and its
square root τ. Either |
method.tau.ci |
A character string indicating which method is
used to estimate the confidence interval of τ^2 and
τ. Either |
tau.preset |
Prespecified value for the square root of the between-study variance τ^2. |
TE.tau |
Overall treatment effect used to estimate the between-study variance τ^2. |
tau.common |
A logical indicating whether tau-squared should be the same across subgroups. |
prediction |
A logical indicating whether a prediction interval should be printed. |
level.predict |
The level used to calculate prediction interval for a new study. |
method.bias |
A character string indicating which test is to
be used. Either |
n.e |
Number of observations in experimental group (optional). |
n.c |
Number of observations in control group (optional). |
backtransf |
A logical indicating whether results for
incidence rate ratio ( |
irscale |
A numeric defining a scaling factor for printing of incidence rate differences. |
irunit |
A character string specifying the time unit used to calculate rates, e.g. person-years. |
text.fixed |
A character string used in printouts and forest plot to label the pooled fixed effect estimate. |
text.random |
A character string used in printouts and forest plot to label the pooled random effects estimate. |
text.predict |
A character string used in printouts and forest plot to label the prediction interval. |
text.w.fixed |
A character string used to label weights of fixed effect model. |
text.w.random |
A character string used to label weights of random effects model. |
title |
Title of meta-analysis / systematic review. |
complab |
Comparison label. |
outclab |
Outcome label. |
label.e |
Label for experimental group. |
label.c |
Label for control group. |
label.left |
Graph label on left side of forest plot. |
label.right |
Graph label on right side of forest plot. |
byvar |
An optional vector containing grouping information
(must be of same length as |
bylab |
A character string with a label for the grouping variable. |
print.byvar |
A logical indicating whether the name of the grouping variable should be printed in front of the group labels. |
byseparator |
A character string defining the separator between label and levels of grouping variable. |
keepdata |
A logical indicating whether original data (set) should be kept in meta object. |
warn |
A logical indicating whether warnings should be printed
(e.g., if |
control |
An optional list to control the iterative process to
estimate the between-study variance τ^2. This argument
is passed on to |
... |
Additional arguments passed on to
|
Calculation of fixed and random effects estimates for meta-analyses comparing two incidence rates.
The following measures of treatment effect are available:
Incidence Rate Ratio (sm = "IRR"
)
Incidence Rate Difference (sm = "IRD"
)
Square root transformed Incidence Rate Difference (sm =
"IRSD"
)
Default settings are utilised for several arguments (assignments
using gs
function). These defaults can be changed for
the current R session using the settings.meta
function.
Furthermore, R function update.meta
can be used to
rerun a meta-analysis with different settings.
By default, both fixed effect and random effects models are
considered (see arguments comb.fixed
and
comb.random
). If method
is "MH"
(default), the
Mantel-Haenszel method is used to calculate the fixed effect
estimate (Greenland & Robbins, 1985); if method
is
"Inverse"
, inverse variance weighting is used for pooling;
if method
is "Cochran"
, the Cochran method is used
for pooling (Bayne-Jones, 1964, Chapter 8).
A distinctive and frequently overlooked advantage of incidence
rates is that individual patient data (IPD) can be extracted from
count data. Accordingly, statistical methods for IPD, i.e.,
generalised linear mixed models, can be utilised in a meta-analysis
of incidence rate ratios (Stijnen et al., 2010). These methods are
available (argument method = "GLMM"
) by calling the
rma.glmm
function from R package
metafor internally.
Three different GLMMs are available for meta-analysis of incidence
rate ratios using argument model.glmm
(which corresponds to
argument model
in the rma.glmm
function):
1. | Poisson regression model with fixed study effects (default) |
(model.glmm = "UM.FS" , i.e., Unconditional
Model - Fixed Study effects) |
|
2. | Mixed-effects Poisson regression model with random study effects |
(model.glmm = "UM.RS" , i.e., Unconditional
Model - Random Study effects) |
|
3. | Generalised linear mixed model (conditional Poisson-Normal) |
(model.glmm = "CM.EL" , i.e., Conditional
Model - Exact Likelihood)
|
Details on these three GLMMs as well as additional arguments which
can be provided using argument '...
' in metainc
are described in rma.glmm
where you can also
find information on the iterative algorithms used for estimation.
Note, regardless of which value is used for argument
model.glmm
, results for two different GLMMs are calculated:
fixed effect model (with fixed treatment effect) and random effects
model (with random treatment effects).
For studies with a zero cell count, by default, 0.5 is added to all
cell frequencies of these studies (argument incr
). This
continuity correction is used both to calculate individual study
results with confidence limits and to conduct meta-analysis based
on the inverse variance method. For Mantel-Haenszel method, Cochran
method, and GLMMs, nothing is added to zero cell counts.
Accordingly, estimates for these methods are not defined if the
number of events is zero in all studies either in the experimental
or control group.
The following methods to estimate the between-study variance τ^2 are available for the inverse variance method:
DerSimonian-Laird estimator (method.tau = "DL"
)
Paule-Mandel estimator (method.tau = "PM"
)
Restricted maximum-likelihood estimator (method.tau =
"REML"
)
Maximum-likelihood estimator (method.tau = "ML"
)
Hunter-Schmidt estimator (method.tau = "HS"
)
Sidik-Jonkman estimator (method.tau = "SJ"
)
Hedges estimator (method.tau = "HE"
)
Empirical Bayes estimator (method.tau = "EB"
)
See metagen
for more information on these
estimators. Note, the maximum-likelihood method is utilized for
GLMMs.
The following methods to calculate a confidence interval for τ^2 and τ are available.
Argument | Method |
method.tau.ci = "J"
|
Method by Jackson |
method.tau.ci = "BJ"
|
Method by Biggerstaff and Jackson |
method.tau.ci = "QP"
|
Q-Profile method |
See metagen
for more information on these
methods. For GLMMs, no confidence intervals for τ^2 and
τ are calculated. Likewise, no confidence intervals for
τ^2 and τ are calculated if method.tau.ci =
""
.
Hartung and Knapp (2001a,b) proposed an alternative method for random effects meta-analysis based on a refined variance estimator for the treatment estimate. Simulation studies (Hartung and Knapp, 2001a,b; IntHout et al., 2014; Langan et al., 2019) show improved coverage probabilities compared to the classic random effects method.
In rare settings with very homogeneous treatment estimates, the Hartung-Knapp variance estimate can be arbitrarily small resulting in a very narrow confidence interval (Knapp and Hartung, 2003; Wiksten et al., 2016). In such cases, an ad hoc variance correction has been proposed by utilising the variance estimate from the classic random effects model with the HK method (Knapp and Hartung, 2003; IQWiQ, 2020). An alternative approach is to use the wider confidence interval of classic fixed or random effects meta-analysis and the HK method (Wiksten et al., 2016; Jackson et al., 2017).
Argument adhoc.hakn
can be used to choose the ad hoc
method:
Argument | Ad hoc method |
adhoc.hakn = ""
|
not used |
adhoc.hakn = "se"
|
use variance correction if HK standard error is smaller |
than standard error from classic random effects | |
meta-analysis (Knapp and Hartung, 2003) | |
adhoc.hakn = "iqwig6"
|
use variance correction if HK confidence interval |
is narrower than CI from classic random effects model | |
with DerSimonian-Laird estimator (IQWiG, 2020) | |
adhoc.hakn = "ci"
|
use wider confidence interval of classic random effects |
and HK meta-analysis | |
(Hybrid method 2 in Jackson et al., 2017) |
For GLMMs, a method similar to Knapp and Hartung (2003) is
implemented, see description of argument tdist
in
rma.glmm
, and the ad hoc variance
correction is not available.
A prediction interval for the proportion in a new study (Higgins et
al., 2009) is calculated if arguments prediction
and
comb.random
are TRUE
. Note, the definition of
prediction intervals varies in the literature. This function
implements equation (12) of Higgins et al., (2009) which proposed a
t distribution with K-2 degrees of freedom where
K corresponds to the number of studies in the meta-analysis.
Argument byvar
can be used to conduct subgroup analysis for
a categorical covariate. The metareg
function can be
used instead for more than one categorical covariate or continuous
covariates.
Arguments subset
and exclude
can be used to exclude
studies from the meta-analysis. Studies are removed completely from
the meta-analysis using argument subset
, while excluded
studies are shown in printouts and forest plots using argument
exclude
(see Examples in metagen
).
Meta-analysis results are the same for both arguments.
Internally, both fixed effect and random effects models are
calculated regardless of values choosen for arguments
comb.fixed
and comb.random
. Accordingly, the estimate
for the random effects model can be extracted from component
TE.random
of an object of class "meta"
even if
argument comb.random = FALSE
. However, all functions in R
package meta will adequately consider the values for
comb.fixed
and comb.random
. E.g. function
print.meta
will not print results for the random
effects model if comb.random = FALSE
.
An object of class c("metainc", "meta")
with corresponding
print
, summary
, and forest
functions. The
object is a list containing the following components:
event.e, time.e, event.c, time.c, studlab, exclude, |
As defined above. |
sm, method, incr, allincr, addincr, model.glmm, warn, |
As defined above. |
level, level.comb, comb.fixed, comb.random, |
As defined above. |
overall, overall.hetstat, |
As defined above. |
hakn, adhoc.hakn, method.tau, method.tau.ci, |
As defined above. |
tau.preset, TE.tau, method.bias, |
As defined above. |
tau.common, title, complab, outclab, |
As defined above. |
label.e, label.c, label.left, label.right, |
As defined above. |
byvar, bylab, print.byvar, byseparator |
As defined above. |
TE, seTE |
Estimated treatment effect and standard error of individual studies. |
lower, upper |
Lower and upper confidence interval limits for individual studies. |
zval, pval |
z-value and p-value for test of treatment effect for individual studies. |
w.fixed, w.random |
Weight of individual studies (in fixed and random effects model). |
TE.fixed, seTE.fixed |
Estimated overall treatment effect and standard error (fixed effect model). |
lower.fixed, upper.fixed |
Lower and upper confidence interval limits (fixed effect model). |
statistic.fixed, pval.fixed |
z-value and p-value for test of overall treatment effect (fixed effect model). |
TE.random, seTE.random |
Estimated overall treatment effect and standard error (random effects model). |
lower.random, upper.random |
Lower and upper confidence interval limits (random effects model). |
statistic.random, pval.random |
z-value or t-value and corresponding p-value for test of overall treatment effect (random effects model). |
prediction, level.predict |
As defined above. |
seTE.predict |
Standard error utilised for prediction interval. |
lower.predict, upper.predict |
Lower and upper limits of prediction interval. |
k |
Number of studies combined in meta-analysis. |
Q |
Heterogeneity statistic Q. |
df.Q |
Degrees of freedom for heterogeneity statistic. |
pval.Q |
P-value of heterogeneity test. |
Q.LRT |
Heterogeneity statistic for likelihood-ratio test
(only if |
df.Q.LRT |
Degrees of freedom for likelihood-ratio test |
pval.Q.LRT |
P-value of likelihood-ratio test. |
tau2 |
Between-study variance τ^2. |
se.tau2 |
Standard error of τ^2. |
lower.tau2, upper.tau2 |
Lower and upper limit of confidence interval for τ^2. |
tau |
Square-root of between-study variance τ. |
lower.tau, upper.tau |
Lower and upper limit of confidence interval for τ. |
H |
Heterogeneity statistic H. |
lower.H, upper.H |
Lower and upper confidence limit for heterogeneity statistic H. |
I2 |
Heterogeneity statistic I^2. |
lower.I2, upper.I2 |
Lower and upper confidence limit for heterogeneity statistic I^2. |
Rb |
Heterogeneity statistic R_b. |
lower.Rb, upper.Rb |
Lower and upper confidence limit for heterogeneity statistic R_b. |
sparse |
Logical flag indicating if any study included in meta-analysis has any zero cell frequencies. |
incr.event |
Increment added to number of events. |
df.hakn |
Degrees of freedom for test of treatment effect for
Hartung-Knapp method (only if |
k.MH |
Number of studies combined in meta-analysis using Mantel-Haenszel method. |
bylevs |
Levels of grouping variable - if |
TE.fixed.w, seTE.fixed.w |
Estimated treatment effect and
standard error in subgroups (fixed effect model) - if
|
lower.fixed.w, upper.fixed.w |
Lower and upper confidence
interval limits in subgroups (fixed effect model) - if
|
statistic.fixed.w, pval.fixed.w |
z-value and p-value for test of
treatment effect in subgroups (fixed effect model) - if
|
TE.random.w, seTE.random.w |
Estimated treatment effect and
standard error in subgroups (random effects model) - if
|
lower.random.w, upper.random.w |
Lower and upper confidence
interval limits in subgroups (random effects model) - if
|
statistic.random.w, pval.random.w |
z-value or t-value and
corresponding p-value for test of treatment effect in subgroups
(random effects model) - if |
w.fixed.w, w.random.w |
Weight of subgroups (in fixed and
random effects model) - if |
df.hakn.w |
Degrees of freedom for test of treatment effect
for Hartung-Knapp method in subgroups - if |
event.e.w |
Number of events in experimental group in
subgroups - if |
time.e.w |
Total person time in subgroups (experimental
group) - if |
n.e.w |
Number of observations in experimental group in
subgroups - if |
event.c.w |
Number of events in control group in subgroups -
if |
time.c.w |
Total person time in subgroups (control group) - if
|
n.c.w |
Number of observations in control group in subgroups -
if |
k.w |
Number of studies combined within subgroups - if
|
k.all.w |
Number of all studies in subgroups - if |
Q.w.fixed |
Overall within subgroups heterogeneity statistic Q
(based on fixed effect model) - if |
Q.w.random |
Overall within subgroups heterogeneity statistic
Q (based on random effects model) - if |
df.Q.w |
Degrees of freedom for test of overall within
subgroups heterogeneity - if |
pval.Q.w.fixed |
P-value of within subgroups heterogeneity
statistic Q (based on fixed effect model) - if |
pval.Q.w.random |
P-value of within subgroups heterogeneity
statistic Q (based on random effects model) - if |
Q.b.fixed |
Overall between subgroups heterogeneity statistic
Q (based on fixed effect model) - if |
Q.b.random |
Overall between subgroups heterogeneity statistic
Q (based on random effects model) - if |
df.Q.b |
Degrees of freedom for test of overall between
subgroups heterogeneity - if |
pval.Q.b.fixed |
P-value of between subgroups heterogeneity
statistic Q (based on fixed effect model) - if |
pval.Q.b.random |
P-value of between subgroups heterogeneity
statistic Q (based on random effects model) - if |
tau.w |
Square-root of between-study variance within subgroups
- if |
H.w |
Heterogeneity statistic H within subgroups - if
|
lower.H.w, upper.H.w |
Lower and upper confidence limit for
heterogeneity statistic H within subgroups - if |
I2.w |
Heterogeneity statistic I^2 within subgroups - if
|
lower.I2.w, upper.I2.w |
Lower and upper confidence limit for
heterogeneity statistic I^2 within subgroups - if |
keepdata |
As defined above. |
data |
Original data (set) used in function call (if
|
subset |
Information on subset of original data used in
meta-analysis (if |
.glmm.fixed |
GLMM object generated by call of
|
.glmm.random |
GLMM object generated by call of
|
call |
Function call. |
version |
Version of R package meta used to create object. |
version.metafor |
Version of R package metafor used for GLMMs. |
Guido Schwarzer sc@imbi.uni-freiburg.de
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data(smoking) m1 <- metainc(d.smokers, py.smokers, d.nonsmokers, py.nonsmokers, data = smoking, studlab = study) print(m1, digits = 2) m2 <- update(m1, method = "Cochran") print(m2, digits = 2) data(lungcancer) m3 <- metainc(d.smokers, py.smokers, d.nonsmokers, py.nonsmokers, data = lungcancer, studlab = study) print(m3, digits = 2) # Redo Cochran meta-analysis with inflated standard errors # # All cause mortality # TEa <- log((smoking$d.smokers/smoking$py.smokers) / (smoking$d.nonsmokers/smoking$py.nonsmokers)) seTEa <- sqrt(1 / smoking$d.smokers + 1 / smoking$d.nonsmokers + 2.5 / smoking$d.nonsmokers) metagen(TEa, seTEa, sm = "IRR", studlab = smoking$study) # Lung cancer mortality # TEl <- log((lungcancer$d.smokers/lungcancer$py.smokers) / (lungcancer$d.nonsmokers/lungcancer$py.nonsmokers)) seTEl <- sqrt(1 / lungcancer$d.smokers + 1 / lungcancer$d.nonsmokers + 2.25 / lungcancer$d.nonsmokers) metagen(TEl, seTEl, sm = "IRR", studlab = lungcancer$study) ## Not run: # Meta-analysis using generalised linear mixed models # (only if R packages 'metafor' and 'lme4' are available) # Poisson regression model (fixed study effects) # m4 <- metainc(d.smokers, py.smokers, d.nonsmokers, py.nonsmokers, data = smoking, studlab = study, method = "GLMM") m4 # Mixed-effects Poisson regression model (random study effects) # update(m4, model.glmm = "UM.RS", nAGQ = 1) # # Generalised linear mixed model (conditional Poisson-Normal) # update(m4, model.glmm = "CM.EL") ## End(Not run)
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