metainc: Meta-analysis of incidence rates

View source: R/metainc.R

metaincR Documentation

Meta-analysis of incidence rates

Description

Calculation of common 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.

Usage

metainc(
  event.e,
  time.e,
  event.c,
  time.c,
  studlab,
  data = NULL,
  subset = NULL,
  exclude = NULL,
  cluster = NULL,
  method = if (sm == "IRSD") "Inverse" else "MH",
  sm = gs("sminc"),
  incr = gs("incr"),
  method.incr = gs("method.incr"),
  model.glmm = "UM.FS",
  level = gs("level"),
  common = gs("common"),
  random = gs("random") | !is.null(tau.preset),
  overall = common | random,
  overall.hetstat = common | random,
  prediction = gs("prediction"),
  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"),
  level.ma = gs("level.ma"),
  method.random.ci = gs("method.random.ci"),
  adhoc.hakn.ci = gs("adhoc.hakn.ci"),
  level.predict = gs("level.predict"),
  method.predict = gs("method.predict"),
  adhoc.hakn.pi = gs("adhoc.hakn.pi"),
  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.common = gs("text.common"),
  text.random = gs("text.random"),
  text.predict = gs("text.predict"),
  text.w.common = gs("text.w.common"),
  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"),
  subgroup,
  subgroup.name = NULL,
  print.subgroup.name = gs("print.subgroup.name"),
  sep.subgroup = gs("sep.subgroup"),
  test.subgroup = gs("test.subgroup"),
  prediction.subgroup = gs("prediction.subgroup"),
  byvar,
  hakn,
  adhoc.hakn,
  keepdata = gs("keepdata"),
  warn = gs("warn"),
  warn.deprecated = gs("warn.deprecated"),
  control = NULL,
  ...
)

Arguments

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.

cluster

An optional vector specifying which estimates come from the same cluster resulting in the use of a three-level meta-analysis model.

method

A character string indicating which method is to be used for pooling of studies. One of "MH", "Inverse", "Cochran", or "GLMM" can be abbreviated.

sm

A character string indicating which summary measure ("IRR", "IRD" or "IRSD") is to be used for pooling of studies, see Details.

incr

A numerical value which is added to cell frequencies for studies with a zero cell count, see Details.

method.incr

A character string indicating which continuity correction method should be used ("only0", "if0all", or "all"), see Details.

model.glmm

A character string indicating which GLMM should be used. One of "UM.FS", "UM.RS", and "CM.EL", see Details.

level

The level used to calculate confidence intervals for individual studies.

common

A logical indicating whether a common effect meta-analysis should be conducted.

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.

prediction

A logical indicating whether a prediction interval should be printed.

method.tau

A character string indicating which method is used to estimate the between-study variance τ^2 and its square root τ (see meta-package).

method.tau.ci

A character string indicating which method is used to estimate the confidence interval of τ^2 and τ (see meta-package).

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 tau-squared.

tau.common

A logical indicating whether tau-squared should be the same across subgroups.

level.ma

The level used to calculate confidence intervals for meta-analysis estimates.

method.random.ci

A character string indicating which method is used to calculate confidence interval and test statistic for random effects estimate (see meta-package).

adhoc.hakn.ci

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 meta-package).

level.predict

The level used to calculate prediction interval for a new study.

method.predict

A character string indicating which method is used to calculate a prediction interval (see meta-package).

adhoc.hakn.pi

A character string indicating whether an ad hoc variance correction should be applied for prediction interval (see meta-package).

method.bias

A character string indicating which test is to be used. Either "Begg", "Egger", or "Thompson", can be abbreviated. See function metabias.

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 (sm = "IRR") should be back transformed in printouts and plots. If TRUE (default), results will be presented as incidence rate ratios; otherwise log incidence rate ratios will be shown.

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.common

A character string used in printouts and forest plot to label the pooled common 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.common

A character string used to label weights of common 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.

subgroup

An optional vector to conduct a meta-analysis with subgroups.

subgroup.name

A character string with a name for the subgroup variable.

print.subgroup.name

A logical indicating whether the name of the subgroup variable should be printed in front of the group labels.

sep.subgroup

A character string defining the separator between name of subgroup variable and subgroup label.

test.subgroup

A logical value indicating whether to print results of test for subgroup differences.

prediction.subgroup

A logical indicating whether prediction intervals should be printed for subgroups.

byvar

Deprecated argument (replaced by 'subgroup').

hakn

Deprecated argument (replaced by 'method.random.ci').

adhoc.hakn

Deprecated argument (replaced by 'adhoc.hakn.ci').

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 incr is added to studies with zero cell frequencies).

warn.deprecated

A logical indicating whether warnings should be printed if deprecated arguments are used.

control

An optional list to control the iterative process to estimate the between-study variance τ^2. This argument is passed on to rma.uni or rma.glmm, respectively.

...

Additional arguments passed on to rma.glmm function and to catch deprecated arguments.

Details

Calculation of common 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")

A three-level random effects meta-analysis model (Van den Noortgate et al., 2013) is utilized if argument cluster is used and at least one cluster provides more than one estimate. Internally, rma.mv is called to conduct the analysis and weights.rma.mv with argument type = "rowsum" is used to calculate random effects weights.

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.

Meta-analysis method

By default, both common effect and random effects models are considered (see arguments common and random). If method is "MH" (default), the Mantel-Haenszel method is used to calculate the common 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: common effect model (with fixed treatment effect) and random effects model (with random treatment effects).

Continuity correction

Three approaches are available to apply a continuity correction:

  • Only studies with a zero cell count (method.incr = "only0", default)

  • All studies if at least one study has a zero cell count (method.incr = "if0all")

  • All studies irrespective of zero cell counts (method.incr = "all")

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.

Subgroup analysis

Argument subgroup 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.

Exclusion of studies from meta-analysis

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.

Presentation of meta-analysis results

Internally, both common effect and random effects models are calculated regardless of values choosen for arguments common and 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 random = FALSE. However, all functions in R package meta will adequately consider the values for common and random. E.g. function print.meta will not print results for the random effects model if random = FALSE.

A prediction interval will only be shown if prediction = TRUE.

Value

An object of class c("metainc", "meta") with corresponding generic functions (see meta-object).

Author(s)

Guido Schwarzer sc@imbi.uni-freiburg.de

References

Bayne-Jones S et al. (1964): Smoking and Health: Report of the Advisory Committee to the Surgeon General of the United States. U-23 Department of Health, Education, and Welfare. Public Health Service Publication No. 1103.

Greenland S & Robins JM (1985): Estimation of a common effect parameter from sparse follow-up data. Biometrics, 41, 55–68

Stijnen T, Hamza TH, Ozdemir P (2010): Random effects meta-analysis of event outcome in the framework of the generalized linear mixed model with applications in sparse data. Statistics in Medicine, 29, 3046–67

Van den Noortgate W, López-López JA, Marín-Martínez F, Sánchez-Meca J (2013): Three-level meta-analysis of dependent effect sizes. Behavior Research Methods, 45, 576–94

Viechtbauer W (2010): Conducting Meta-Analyses in R with the Metafor Package. Journal of Statistical Software, 36, 1–48

See Also

meta-package, metabin, update.meta, print.meta

Examples

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)


meta documentation built on Sept. 18, 2022, 1:06 a.m.