metamean: Meta-analysis of single means

View source: R/metamean.R

metameanR Documentation

Meta-analysis of single means

Description

Calculation of an overall mean from studies reporting a single mean using the inverse variance method for pooling; inverse variance weighting is used for pooling.

Usage

metamean(
  n,
  mean,
  sd,
  studlab,
  data = NULL,
  subset = NULL,
  exclude = NULL,
  cluster = NULL,
  median,
  q1,
  q3,
  min,
  max,
  method.mean = "Luo",
  method.sd = "Shi",
  approx.mean,
  approx.sd,
  sm = gs("smmean"),
  method.ci = gs("method.ci.cont"),
  level = gs("level"),
  common = gs("common"),
  random = gs("random") | !is.null(tau.preset),
  overall = common | random,
  overall.hetstat = common | random,
  prediction = gs("prediction") | !missing(method.predict),
  method.tau = 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"),
  null.effect = NA,
  method.bias = gs("method.bias"),
  backtransf = gs("backtransf"),
  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 = "",
  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,
  adhoc.hakn,
  keepdata = gs("keepdata"),
  warn = gs("warn"),
  warn.deprecated = gs("warn.deprecated"),
  control = NULL,
  ...
)

Arguments

n

Number of observations.

mean

Estimated mean.

sd

Standard deviation.

studlab

An optional vector with study labels.

data

An optional data frame containing the study information.

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.

median

Median (used to estimate the mean and standard deviation).

q1

First quartile (used to estimate the mean and standard deviation).

q3

Third quartile (used to estimate the mean and standard deviation).

min

Minimum (used to estimate the mean and standard deviation).

max

Maximum (used to estimate the mean and standard deviation).

method.mean

A character string indicating which method to use to approximate the mean from the median and other statistics (see Details).

method.sd

A character string indicating which method to use to approximate the standard deviation from sample size, median, interquartile range and range (see Details).

approx.mean

Approximation method to estimate means (see Details).

approx.sd

Approximation method to estimate standard deviations (see Details).

sm

A character string indicating which summary measure ("MRAW" or "MLN") is to be used for pooling of studies.

method.ci

A character string indicating which method is used to calculate confidence intervals for individual studies, 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).

null.effect

A numeric value specifying the effect under the null hypothesis.

method.bias

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

backtransf

A logical indicating whether results should be back transformed in printouts and plots for sm = "MLN". If TRUE (default), results will be presented as means; otherwise logarithm of means will be shown.

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.

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').

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 studies are excluded from meta-analysis due to zero standard deviations).

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.

...

Additional arguments (to catch deprecated arguments).

Details

Common effect and random effects meta-analysis of single means to calculate an overall mean; inverse variance weighting is used for pooling. Note, you should use R function metacont to compare means of pairwise comparisons instead of using metamean for each treatment arm separately which will break randomisation in randomised controlled trials.

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.

The following transformations of means are implemented to calculate an overall mean:

  • Raw, i.e. untransformed, means (sm = "MRAW", default)

  • Log transformed means (sm = "MLN")

Calculations are conducted on the log scale if sm = "ROM". Accordingly, list elements TE, TE.common, and TE.random contain the logarithm of means. In printouts and plots these values are back transformed if argument backtransf = TRUE.

Approximate means from sample sizes, medians and other statistics

Missing means can be derived from

  1. sample size, median, interquartile range and range (arguments n, median, q1, q3, min, and max),

  2. sample size, median and interquartile range (arguments n, median, q1, and q3), or

  3. sample size, median and range (arguments n, median, min, and max).

By default, methods described in Luo et al. (2018) are utilized (argument method.mean = "Luo"):

  • equation (15) if sample size, median, interquartile range and range are available,

  • equation (11) if sample size, median and interquartile range are available,

  • equation (7) if sample size, median and range are available.

Instead the methods described in Wan et al. (2014) are used if argument method.mean = "Wan":

  • equation (10) if sample size, median, interquartile range and range are available,

  • equation (14) if sample size, median and interquartile range are available,

  • equation (2) if sample size, median and range are available.

By default, missing means are replaced successively using interquartile ranges and ranges (if available), interquartile ranges (if available) and finally ranges. Argument approx.mean can be used to overwrite this behaviour for each individual study and treatment arm:

  • use means directly (entry "" in argument approx.mean);

  • median, interquartile range and range ("iqr.range");

  • median and interquartile range ("iqr");

  • median and range ("range").

Approximate standard deviations from sample sizes, medians and other statistics

Missing standard deviations can be derived from

  1. sample size, median, interquartile range and range (arguments n, median, q1, q3, min, and max),

  2. sample size, median and interquartile range (arguments n, median, q1 and q3), or

  3. sample size, median and range (arguments n, median, min and max).

Wan et al. (2014) describe methods to estimate the standard deviation from the sample size, median and additional statistics. Shi et al. (2020) provide an improved estimate of the standard deviation if the interquartile range and range are available in addition to the sample size and median. Accordingly, equation (11) in Shi et al. (2020) is the default (argument method.sd = "Shi"), if the median, interquartile range and range are provided. The method by Wan et al. (2014) is used if argument method.sd = "Wan" and, depending on the sample size, either equation (12) or (13) is used. If only the interquartile range or range is available, equations (15) / (16) and (7) / (9) in Wan et al. (2014) are used, respectively.

By default, missing standard deviations are replaced successively using these method, i.e., interquartile ranges and ranges are used before interquartile ranges before ranges. Argument approx.sd can be used to overwrite this default for each individual study and treatment arms:

  • sample size, median, interquartile range and range ("iqr.range");

  • sample size, median and interquartile range ("iqr");

  • sample size, median and range ("range").

Confidence intervals for individual studies

For untransformed means (argument sm = "MRAW"), the confidence interval for individual studies can be based on the

  • standard normal distribution (method.ci = "z", default), or

  • t-distribution (method.ci = "t").

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. functions print.meta and forest.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("metamean", "meta") with corresponding generic functions (see meta-object).

Note

The function metagen is called internally to calculate individual and overall treatment estimates and standard errors.

Author(s)

Guido Schwarzer sc@imbi.uni-freiburg.de

References

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

See Also

meta-package, update.meta, metamean, metagen

Examples

m1 <- metamean(rep(100, 3), 1:3, rep(1, 3))
m1

m2 <- update(m1, sm = "MLN")
m2

# With test for overall mean equal to 2
#
update(m1, null.effect = 2)
update(m2, null.effect = 2)

# Print results without back-transformation
#
update(m1, backtransf = FALSE)
update(m2, backtransf = FALSE)
update(m1, null.effect = 2, backtransf = FALSE)
update(m2, null.effect = 2, backtransf = FALSE)


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