escalc(measure, formula, ...)
"escalc"(measure, formula, ai, bi, ci, di, n1i, n2i, x1i, x2i, t1i, t2i, m1i, m2i, sd1i, sd2i, xi, mi, ri, ti, sdi, ni, yi, vi, sei, data, slab, subset, add=1/2, to="only0", drop00=FALSE, vtype="LS", var.names=c("yi","vi"), add.measure=FALSE, append=TRUE, replace=TRUE, digits=4, ...)
"escalc"(measure, formula, weights, data, add=1/2, to="only0", drop00=FALSE, vtype="LS", var.names=c("yi","vi"), digits=4, ...)add should be added (either "all", "only0", "if0all", or "none"). See ‘Details’."LS", "UB", "HO", "ST", or vtype="CS"). See ‘Details’."yi" and "vi")."measure") that indicates the type of outcome measure computed. When using this option, var.names can have a third element to change this variable name.data argument (if one has been specified) should be returned together with the observed outcomes and corresponding sampling variances (the default is TRUE).yi and vi in the data frame should be replaced or not. Only relevant when append=TRUE and the data frame already contains the yi and vi variables. If replace=TRUE (the default), all of the existing values will be overwritten. If replace=FALSE, only NA values will be replaced. See ‘Value’ section below for more details.c("escalc","data.frame"). The object is a data frame containing the following components:If append=TRUE and a data frame was specified via the data argument, then yi and vi are append to this data frame. Note that the var.names argument actually specifies the names of these two variables.If the data frame already contains two variables with names as specified by the var.names argument, the values for these two variables will be overwritten when replace=TRUE (which is the default). By setting replace=FALSE, only values that are NA will be replaced.The object is formated and printed with the print.escalc function. The summary.escalc function can be used to obtain confidence intervals for the individual outcomes.
escalc function. The measure argument is a character string specifying which outcome measure should be calculated (see below for the various options), arguments ai through ni are then used to specify the information needed to calculate the various measures (depending on the chosen outcome measure, different arguments need to be specified), and data can be used to specify a data frame containing the variables given to the previous arguments. The add, to, and drop00 arguments may be needed when dealing with frequency or count data that may need special handling when some of the frequencies or counts are equal to zero (see below for details). Finally, the vtype argument is used to specify how to estimate the sampling variances (again, see below for details).
To provide a structure to the various effect size or outcome measures that can be calculated with the escalc function, we can distinguish between measures that are used to:
Outcome Measures for Two-Group Comparisons
In many meta-analyses, the goal is to synthesize the results from studies that compare or contrast two groups. The groups may be experimentally defined (e.g., a treatment and a control group created via random assignment) or may naturally occur (e.g., men and women, employees working under high- versus low-stress conditions, people exposed to some environmental risk factor versus those not exposed).
Measures for Dichotomous Variables
In various fields (such as the health and medical sciences), the response or outcome variable measured is often dichotomous (binary), so that the data from a study comparing two different groups can be expressed in terms of a $2x2$ table, such as:
| outcome 1 | outcome 2 | |
| total | group 1 | ai |
bi |
n1i |
ai, bi, ci, and di denote the cell frequencies (i.e., the number of people falling into a particular category) and n1i and n2i the row totals (i.e., the group sizes).For example, in a set of randomized clinical trials, group 1 and group 2 may refer to the treatment and placebo/control group, respectively, with outcome 1 denoting some event of interest (e.g., death, complications, failure to improve under the treatment) and outcome 2 its complement. Similarly, in a set of cohort studies, group 1 and group 2 may denote those who engage in and those who do not engage in a potentially harmful behavior (e.g., smoking), with outcome 1 denoting the development of a particular disease (e.g., lung cancer) during the follow-up period. Finally, in a set of case-control studies, group 1 and group 2 may refer to those with the disease (i.e., cases) and those free of the disease (i.e., controls), with outcome 1 denoting, for example, exposure to some risk environmental risk factor in the past and outcome 2 non-exposure. Note that in all of these examples, the stratified sampling scheme fixes the row totals (i.e., the group sizes) by design.
A meta-analysis of studies reporting results in terms of $2x2$ tables can be based on one of several different outcome measures, including the relative risk (risk ratio), the odds ratio, the risk difference, and the arcsine square-root transformed risk difference (e.g., Fleiss & Berlin, 2009, Rücker et al., 2009). For any of these outcome measures, one needs to specify the cell frequencies via the ai, bi, ci, and di arguments (or alternatively, one can use the ai, ci, n1i, and n2i arguments).
The options for the measure argument are then:
"RR" for the log relative risk.
"OR" for the log odds ratio.
"RD" for the risk difference.
"AS" for the arcsine square-root transformed risk difference (Rücker et al., 2009).
"PETO" for the log odds ratio estimated with Peto's method (Yusuf et al., 1985).
Cell entries with a zero count can be problematic, especially for the relative risk and the odds ratio. Adding a small constant to the cells of the $2x2$ tables is a common solution to this problem. When to="only0" (the default), the value of add (the default is 1/2) is added to each cell of those $2x2$ tables with at least one cell equal to 0. When to="all", the value of add is added to each cell of all $2x2$ tables. When to="if0all", the value of add is added to each cell of all $2x2$ tables, but only when there is at least one $2x2$ table with a zero cell. Setting to="none" or add=0 has the same effect: No adjustment to the observed table frequencies is made. Depending on the outcome measure and the data, this may lead to division by zero inside of the function (when this occurs, the resulting value is recoded to NA). Also, studies where ai=ci=0 or bi=di=0 may be considered to be uninformative about the size of the effect and dropping such studies has sometimes been recommended (Higgins & Green, 2008). This can be done by setting drop00=TRUE. The values for such studies will then be set to NA.
A dataset corresponding to data of this type is provided in dat.bcg.
Assuming that the dichotomous outcome is actually a dichotomized version of the responses on an underlying quantitative scale, it is also possible to estimate the standardized mean difference based on $2x2$ table data, using either the probit transformed risk difference or a transformation of the odds ratio (e.g., Cox & Snell, 1989; Chinn, 2000; Hasselblad & Hedges, 1995; Sanchez-Meca et al., 2003). The options for the measure argument are then:
"PBIT" for the probit transformed risk difference as an estimate of the standardized mean difference.
"OR2DN" for the transformed odds ratio as an estimate of the standardized mean difference (normal distributions).
"OR2DL" for the transformed odds ratio as an estimate of the standardized mean difference (logistic distributions).
A dataset corresponding to data of this type is provided in dat.gibson2002.
Measures for Event Counts
In medical and epidemiological studies comparing two different groups (e.g., treated versus untreated patients, exposed versus unexposed individuals), results are sometimes reported in terms of event counts (i.e., the number of events, such as strokes or myocardial infarctions) over a certain period of time. Data of this type are also referred to as ‘person-time data’. In particular, assume that the studies report data in the form:
| number of events | |
| total person-time | group 1 |
x1i |
t1i |
x1i and x2i denote the total number of events in the first and the second group, respectively, and t1i and t2i the corresponding total person-times at risk. Often, the person-time is measured in years, so that t1i and t2i denote the total number of follow-up years in the two groups. This form of data is fundamentally different from what was described in the previous section, since the total follow-up time may differ even for groups of the same size and the individuals studied may experience the event of interest multiple times. Hence, different outcome measures than the ones described in the previous section must be considered when data are reported in this format. These inlude the incidence rate ratio, the incidence rate difference, and the square-root transformed incidence rate difference (Bagos & Nikolopoulos, 2009; Rothman et al., 2008). For any of these outcome measures, one needs to specify the total number of events via the x1i and x2i arguments and the corresponding total person-time values via the t1i and t2i arguments.
The options for the measure argument are then:
"IRR" for the log incidence rate ratio.
"IRD" for the incidence rate difference.
"IRSD" for the square-root transformed incidence rate difference.
Studies with zero events in one or both groups can be problematic, especially for the incidence rate ratio. Adding a small constant to the number of events is a common solution to this problem. When to="only0" (the default), the value of add (the default is 1/2) is added to x1i and x2i only in the studies that have zero events in one or both groups. When to="all", the value of add is added to x1i and x2i in all studies. When to="if0all", the value of add is added to x1i and x2i in all studies, but only when there is at least one study with zero events in one or both groups. Setting to="none" or add=0 has the same effect: No adjustment to the observed number of events is made. Depending on the outcome measure and the data, this may lead to division by zero inside of the function (when this occurs, the resulting value is recoded to NA). Like for $2x2$ table data, studies where x1i=x2i=0 may be considered to be uninformative about the size of the effect and dropping such studies has sometimes been recommended. This can be done by setting drop00=TRUE. The values for such studies will then be set to NA.
A dataset corresponding to data of this type is provided in dat.hart1999.
Measures for Quantitative Variables
When the response or dependent variable assessed in the individual studies is measured on some quantitative scale, it is customary to report certain summary statistics, such as the mean and standard deviation of the scores. The data layout for a study comparing two groups with respect to such a variable is then of the form:
| mean | standard deviation | |
| group size | group 1 | m1i |
sd1i |
n1i |
m1i and m2i are the observed means of the two groups, sd1i and sd2i the observed standard deviations, and n1i and n2i the number of individuals in each group. Again, the two groups may be experimentally created (e.g., a treatment and control group based on random assignment) or naturally occurring (e.g., men and women). In either case, the raw mean difference, the standardized mean difference, and the (log transformed) ratio of means (also called log response ratio) are useful outcome measures when meta-analyzing studies of this type (e.g., Borenstein, 2009). The options for the measure argument are then:
"MD" for the raw mean difference.
"SMD" for the standardized mean difference.
"SMDH" for the standardized mean difference with heteroscedastic population variances in the two groups (Bonett, 2008, 2009).
"ROM" for the log transformed ratio of means (Hedges et al., 1999; Lajeunesse, 2011).
m1i and m2i have opposite signs, this outcome measure cannot be computed. The positive bias in the standardized mean difference is automatically corrected for within the function, yielding Hedges' g for measure="SMD" (Hedges, 1981). Similarly, the same bias correction is applied for measure="SMDH" (Bonett, 2009). For measure="SMD", one can choose between vtype="LS" (the default) and vtype="UB". The former uses a large-sample approximation to compute the sampling variances. The latter provides unbiased estimates of the sampling variances. Finally, for measure="MD" and measure="ROM", one can choose between vtype="LS" (the default) and vtype="HO". The former computes the sampling variances without assuming homoscedasticity (i.e., that the true variances of the measurements are the same in group 1 and group 2 within each study), while the latter assumes homoscedasticity.
A dataset corresponding to data of this type is provided in dat.normand1999 (for mean differences and standardized mean differences). A dataset showing the use of the ratio of means measure is provided in dat.curtis1998.
It is also possible to transform standardized mean differences into log odds ratios (e.g., Cox & Snell, 1989; Chinn, 2000; Hasselblad & Hedges, 1995; Sanchez-Meca et al., 2003). The options for the measure argument are then:
"D2ORN" for the transformed standardized mean difference as an estimate of the log odds ratio (normal distributions).
"D2ORL" for the transformed standardized mean difference as an estimate of the log odds ratio (logistic distributions).
A dataset illustrating the combined analysis of standardized mean differences and probit transformed risk differences is provided in dat.gibson2002.
Outcome Measures for Variable Association
Meta-analyses are often used to synthesize studies that examine the direction and strength of the association between two variables measured concurrently and/or without manipulation by experimenters. In this section, a variety of outcome measures will be discussed that may be suitable for a meta-analyses with this purpose. We can distinguish between measures that are applicable when both variables are measured on quantitative scales, when both variables measured are dichotomous, and when the two variables are of mixed types.
Measures for Two Quantitative Variables
The (Pearson or product moment) correlation coefficient quantifies the direction and strength of the (linear) relationship between two quantitative variables and is therefore frequently used as the outcome measure for meta-analyses (e.g., Borenstein, 2009). Two alternative measures are a bias-corrected version of the correlation coefficient and Fisher's r-to-z transformed coefficient.
For these measures, one needs to specify ri, the vector with the raw correlation coefficients, and ni, the corresponding sample sizes. The options for the measure argument are then:
"COR" for the raw correlation coefficient.
"UCOR" for the raw correlation coefficient corrected for its slight negative bias (based on equation 2.3 in Olkin & Pratt, 1958).
"ZCOR" for the Fisher's r-to-z transformed correlation coefficient (Fisher, 1921).
measure="UCOR", one can choose between vtype="LS" (the default) and vtype="UB". The former uses the standard large-sample approximation to compute the sampling variances. The latter provides unbiased estimates of the sampling variances (see Hedges, 1989, but using the exact equation instead of the approximation). Datasets corresponding to data of this type are provided in dat.mcdaniel1994 and dat.molloy2014.
Measures for Two Dichotomous Variables
When the goal of a meta-analysis is to examine the relationship between two dichotomous variables, the data for each study can again be presented in the form of a $2x2$ table, except that there may not be a clear distinction between the group (i.e., the row) and the outcome (i.e., the column) variable. Moreover, the table may be a result of cross-sectional (i.e., multinomial) sampling, where none of the table margins (except the total sample size) is fixed by the study design.
The phi coefficient and the odds ratio are commonly used measures of association for $2x2$ table data (e.g., Fleiss & Berlin, 2009). The latter is particularly advantageous, as it is directly comparable to values obtained from stratified sampling (as described earlier). Yule's Q and Yule's Y (Yule, 1912) are additional measures of association for $2x2$ table data (although they are not typically used in meta-analyses). Finally, assuming that the two dichotomous variables are actually dichotomized versions of the responses on two underlying quantitative scales (and assuming that the two variables follow a bivariate normal distribution), it is also possible to estimate the correlation between the two variables using the tetrachoric correlation coefficient (Pearson, 1900; Kirk, 1973).
For any of these outcome measures, one needs to specify the cell frequencies via the ai, bi, ci, and di arguments. The options for the measure argument are then:
"OR" for the log odds ratio.
"PHI" for the phi coefficient.
"YUQ" for Yule's Q (Yule, 1912).
"YUY" for Yule's Y (Yule, 1912).
"RTET" for the tetrachoric correlation.
Measures for Mixed Variable Types
Finally, we will consider outcome measures that can be used to describe the relationship between two variables, where one variable is dichotomous and the other variable measures some quantitative characteristic. In that case, it is likely that study authors again report summary statistics, such as the mean and standard deviation of the scores within the two groups (defined by the dichotomous variable). In that case, one can compute the point-biserial (Tate, 1954) as a measure of association between the two variables. If the dichotomous variable is actually a dichotomized version of the responses on an underlying quantitative scale (and assuming that the two variables follow a bivariate normal distribution), it is also possible to estimate the correlation between the two variables using the biserial correlation coefficient (Pearson, 1909; Soper, 1914).
Here, one again needs to specify m1i and m2i for the observed means of the two groups, sd1i and sd2i for the observed standard deviations, and n1i and n2i for the number of individuals in each group. The options for the measure argument are then:
"RPB" for the point-biserial correlation.
"RBIS" for the biserial correlation.
measure="RPB", one must indicate via vtype="ST" or vtype="CS" whether the data for the studies were obtained using stratified or cross-sectional (i.e., multinomial) sampling, respectively (it is also possible to specify an entire vector for the vtype argument in case the sampling schemes differed for the various studies).
Outcome Measures for Individual Groups
In this section, outcome measures will be described which may be useful when the goal of a meta-analysis is to synthesize studies that characterize some property of individual groups. We will again distinguish between measures that are applicable when the characteristic of interest is a dichotomous variable, when the characteristic represents an event count, or when the characteristic assessed is a quantiative variable.
Measures for Dichotomous Variables
A meta-analysis may be conducted to aggregate studies that provide data for individual groups with respect to a dichotomous dependent variable. Here, one needs to specify xi and ni, denoting the number of individuals experiencing the event of interest and the total number of individuals, respectively. Instead of specifying ni, one can use mi to specify the number of individuals that do not experience the event of interest. The options for the measure argument are then:
"PR" for the raw proportion.
"PLN" for the log transformed proportion.
"PLO" for the logit transformed proportion (i.e., log odds).
"PAS" for the arcsine square-root transformed proportion (i.e., the angular transformation).
"PFT" for the Freeman-Tukey double arcsine transformed proportion (Freeman & Tukey, 1950).
to="only0" (the default), the value of add (the default is 1/2) is added to xi and mi only for studies where xi or mi is equal to 0. When to="all", the value of add is added to xi and mi in all studies. When to="if0all", the value of add is added in all studies, but only when there is at least one study with a zero value for xi or mi. Setting to="none" or add=0 has the same effect: No adjustment to the observed values is made. Depending on the outcome measure and the data, this may lead to division by zero inside of the function (when this occurs, the resulting value is recoded to NA). Datasets corresponding to data of this type are provided in dat.pritz1997 and dat.debruin2009.
Measures for Event Counts
Various measures can be used to characterize individual groups when the dependent variable assessed is an event count. Here, one needs to specify xi and ti, denoting the total number of events that occurred and the total person-times at risk, respectively. The options for the measure argument are then:
"IR" for the raw incidence rate.
"IRLN" for the log transformed incidence rate.
"IRS" for the square-root transformed incidence rate.
"IRFT" for the Freeman-Tukey transformed incidence rate (Freeman & Tukey, 1950).
to="only0" (the default), the value of add (the default is 1/2) is added to xi only in the studies that have zero events. When to="all", the value of add is added to xi in all studies. When to="if0all", the value of add is added to xi in all studies, but only when there is at least one study with zero events. Setting to="none" or add=0 has the same effect: No adjustment to the observed number of events is made. Depending on the outcome measure and the data, this may lead to division by zero inside of the function (when this occurs, the resulting value is recoded to NA).
Measures for Quantitative Variables
The goal of a meta-analysis may also be to characterize individual groups, where the response, characteristic, or dependent variable assessed in the individual studies is measured on some quantitative scale. In the simplest case, the raw mean for the quantitative variable is reported for each group, which then becomes the observed outcome for the meta-analysis. Here, one needs to specify mi, sdi, and ni for the observed means, the observed standard deviations, and the sample sizes, respectively. The only option for the measure argument is then:
"MN" for the raw mean.
sdi is used to specify the standard deviations of the observed values of the response, characteristic, or dependent variable and not the standard errors of the means. A more complicated situation arises when the purpose of the meta-analysis is to assess the amount of change within individual groups. In that case, either the raw mean change, standardized versions thereof, or the (log transformed) ratio of means (log response ratio) can be used as outcome measures (Becker, 1988; Gibbons et al., 1993; Lajeunesse, 2011; Morris, 2000). Here, one needs to specify m1i and m2i, the observed means at the two measurement occasions, sd1i and sd2i for the corresponding observed standard deviations, ri for the correlation between the scores observed at the two measurement occasions, and ni for the sample size. The options for the measure argument are then:
"MC" for the raw mean change.
"SMCC" for the standardized mean change using change score standardization.
"SMCR" for the standardized mean change using raw score standardization.
"SMCRH" for the standardized mean change using raw score standardization with heteroscedastic population variances at the two measurement occasions (Bonett, 2008).
"ROMC" for the log transformed ratio of means (Lajeunesse, 2011).
A few notes about the change score measures. In practice, one often has a mix of information available from the individual studies to compute these measures. In particular, if m1i and m2i are unknown, but the raw mean change is directly reported in a particular study, then you can set m1i to that value and m2i to 0 (making sure that the raw mean change was computed as m1i-m2i within that study and not the other way around). Note that this does not work for ratios of means ("ROMC"). Also, for the raw mean change ("MC") or the standardized mean change using change score standardization ("SMCC"), if sd1i, sd2i, and ri are unknown, but the standard deviation of the change scores is directly reported, then you can set sd1i to that value and both sd2i and ri to 0. Finally, for the standardized mean change using raw score standardization ("SMCR"), argument sd2i is actually not needed, as the standardization is only based on sd1i (Becker, 1988; Morris, 2000), which is usually the pre-test standard deviation (if the post-test standard deviation should be used, then set sd1i to that). Finally, all of these measures are also applicable for matched-pairs designs (subscripts 1 and 2 then simply denote the first and second group that are formed by the matching).
Other Outcome Measures for Meta-Analyses
Other outcome measures are sometimes used for meta-analyses that do not directly fall into the categories above. These are described in this section.
Cronbach's alpha and Transformations Thereof
Meta-analytic methods can also be used to aggregate Cronbach's alpha values. This is usually referred to as a ‘reliability generalization meta-analysis’ (Vacha-Haase, 1998). Here, one needs to specify ai, mi, and ni for the observed alpha values, the number of items/replications/parts of the measurement instrument, and the sample sizes, respectively. One can either directly analyze the raw Cronbach's alpha values or transformations thereof (Bonett, 2002, 2010; Hakstian & Whalen, 1976). The options for the measure argument are then:
"ARAW" for raw alpha values.
"AHW" for transformed alpha values (Hakstian & Whalen, 1976).
"ABT" for transformed alpha values (Bonett, 2002).
"AHW", the transformation $1-(1-\alpha)^(1/3)$ is used, while for "ABT", the transformation $-ln(1-\alpha)$ is used. This ensures that the transformed values are monotonically increasing functions of $\alpha$. A dataset corresponding to data of this type is provided in dat.bonett2010.
Formula Interface
There are two general ways of specifying the data for computing the various effect size or outcome measures when using the escalc function, the default and a formula interface. When using the default interface, which is described above, the information needed to compute the various outcome measures is passed to the function via the various arguments outlined above (i.e., arguments ai through ni).
The formula interface works as follows. As above, the argument measure is a character string specifying which outcome measure should be calculated. The formula argument is then used to specify the data structure as a multipart formula. The data argument can be used to specify a data frame containing the variables in the formula. The add, to, and vtype arguments work as described above.
Outcome Measures for Two-Group Comparisons
Measures for Dichotomous Variables
For $2x2$ table data, the formula argument takes the form outcome ~ group | study, where group is a two-level factor specifying the rows of the tables, outcome is a two-level factor specifying the columns of the tables (the two possible outcomes), and study is a factor specifying the study factor. The weights argument is used to specify the frequencies in the various cells.
Measures for Event Counts
For two-group comparisons with event counts, the formula argument takes the form events/times ~ group | study, where group is a two-level factor specifying the group factor and study is a factor specifying the study factor. The left-hand side of the formula is composed of two parts, with the first variable for the number of events and the second variable for the person-times at risk.
Measures for Quantitative Variables
For two-group comparisons with quantitative variables, the formula argument takes the form means/sds ~ group | study, where group is a two-level factor specifying the group factor and study is a factor specifying the study factor. The left-hand side of the formula is composed of two parts, with the first variable for the means and the second variable for the standard deviations. The weights argument is used to specify the sample sizes in the groups.
Outcome Measures for Variable Association
Measures for Two Quantitative Variables
For these outcome measures, the formula argument takes the form outcome ~ 1 | study, where outcome is used to specify the observed correlations and study is a factor specifying the study factor. The weights argument is used to specify the sample sizes.
Measures for Two Dichotomous Variables
Here, the data layout is assumed to be the same as for two-group comparisons with dichotomous variables. Hence, the formula argument is specified in the same manner.
Measures for Mixed Variable Types
Here, the data layout is assumed to be the same as for two-group comparisons with quantitative variables. Hence, the formula argument is specified in the same manner.
Outcome Measures for Individual Groups
Measures for Dichotomous Variables
For these outcome measures, the formula argument takes the form outcome ~ 1 | study, where outcome is a two-level factor specifying the columns of the tables (the two possible outcomes) and study is a factor specifying the study factor. The weights argument is used to specify the frequencies in the various cells.
Measures for Event Counts
For these outcome measures, the formula argument takes the form events/times ~ 1 | study, where study is a factor specifying the study factor. The left-hand side of the formula is composed of two parts, with the first variable for the number of events and the second variable for the person-times at risk.
Measures for Quantitative Variables
For this outcome measures, the formula argument takes the form means/sds ~ 1 | study, where study is a factor specifying the study factor. The left-hand side of the formula is composed of two parts, with the first variable for the means and the second variable for the standard deviations. The weights argument is used to specify the sample sizes.
Note: The formula interface is (currently) not implemented for the raw mean change and the standardized mean change measures.
Other Outcome Measures for Meta-Analyses
Cronbach's alpha and Transformations Thereof
For these outcome measures, the formula argument takes the form alpha/items ~ 1 | study, where study is a factor specifying the study factor. The left-hand side of the formula is composed of two parts, with the first variable for the Cronbach's alpha values and the second variable for the number of items.
Converting a Data Frame to an 'escalc' Object
The function can also be used to convert a regular data frame to an 'escalc' object. One simply sets the measure argument to one of the options described above (or to measure="GEN" for a generic outcome measure not further specified) and passes the observed effect sizes or outcomes via the yi argument and the corresponding sampling variances via the vi argument (or the standard errors via the sei argument).
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print.escalc, summary.escalc, rma.uni, rma.mh, rma.peto, rma.glmm
### load BCG vaccine data
dat <- get(data(dat.bcg))
### calculate log relative risks and corresponding sampling variances
dat <- escalc(measure="RR", ai=tpos, bi=tneg, ci=cpos, di=cneg, data=dat)
dat
### suppose that for a particular study, yi and vi are known (i.e., have
### already been calculated) but the 2x2 table counts are not known; with
### replace=FALSE, the yi and vi values for that study are not replaced
dat[1:12,10:11] <- NA
dat[13,4:7] <- NA
dat <- escalc(measure="RR", ai=tpos, bi=tneg, ci=cpos, di=cneg, data=dat, replace=FALSE)
dat
### using formula interface (first rearrange data into long format)
dat.long <- to.long(measure="RR", ai=tpos, bi=tneg, ci=cpos, di=cneg,
data=dat, append=FALSE, vlong=TRUE)
escalc(measure="RR", outcome ~ group | study, weights=freq, data=dat.long)
### convert a regular data frame to an 'escalc' object
### dataset from Lipsey & Wilson (2001), Table 7.1, page 130
dat <- data.frame(id = c(100, 308, 1596, 2479, 9021, 9028, 161, 172, 537, 7049),
yi = c(-0.33, 0.32, 0.39, 0.31, 0.17, 0.64, -0.33, 0.15, -0.02, 0.00),
vi = c(0.084, 0.035, 0.017, 0.034, 0.072, 0.117, 0.102, 0.093, 0.012, 0.067),
random = c(0, 0, 0, 0, 0, 0, 1, 1, 1, 1),
intensity = c(7, 3, 7, 5, 7, 7, 4, 4, 5, 6))
dat <- escalc(measure="SMD", yi=yi, vi=vi, data=dat, slab=paste("Study ID:", id), digits=3)
dat
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