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```r library(metaumbrella) library(DT)
The metaumbrella package offers several facilities to assist in data analysis when performing an umbrella review. More precisely, this package is built around three core functions which aim to facilitate (i) the completion of the statistical analyses required for an umbrella review, (ii) the stratification of the evidence and (iii) the graphical presentation of the results of an umbrella review. An associated app is also available to conduct umbrella reviews with a graphical user interface, [directly on your web browser](https://www.metaumbrella.org/).
In this document, we present a very brief description of the core functions available in the metaumbrella package. Then, we give several concrete examples of umbrella reviews conducted in R using this package.
The package includes 3 core functions:
1. umbrella() The umbrella()
function allows to perform the calculations required to stratify the evidence. The main argument required by this function is a well-formatted dataset. How properly formatting your dataset is beyond the scope of this vignette but general guidance can be found in the manual of this package and another vignette is specifically dedicated to this issue.
Once your dataset has been correctly formatted, it is used as an argument of the umbrella function, which automatically:
For example, using `df.SMD` as a well-formatted dataset, you can automatically perform all the calculations required for an umbrella review using this R code: wzxhzdk:1
2. add.evidence() The `add.evidence()` function uses the calculations performed by the `umbrella()` function to perform a stratification of evidence according to algorithmic criteria:
Ioannidis criteria
To obtain a stratification of evidence according to the Ioannidis criteria, it only requires to specify criteria = "Ioannidis"
in the add.evidence()
function.
umb <- umbrella(df.SMD) strat.io <- add.evidence(umb.SMD, criteria = "Ioannidis")
GRADE criteria
To obtain a stratification of evidence according to the GRADE criteria, it only requires to specify criteria = "GRADE"
in the add.evidence()
function.
umb <- umbrella(df.SMD) strat.grd <- add.evidence(umb.SMD, criteria = "GRADE")
Personalized criteria
Up to 13 criteria can be used to stratify evidence in this Personalized classification.
3. forest() The `forest()` function allows to have a visualization of the results of the umbrella review
umb <- umbrella(df.SMD) strat.io <- add.evidence(umb.SMD, criteria = "Ioannidis") forest(strat.io)
This example uses the dataset named `df.OR` distributed along with the metaumbrella package. You can access and visualize the dataset in R with the following command
df.OR
wzxhzdk:7
Because the dataset includes four factors (ASD, ADHD, ID and dyslexia), the calculations and the stratification of evidence will be performed independently for each of these factors.
To perform the calculations, simply apply the umbrella function on this well-formatted dataset.
umb.OR <- umbrella(df.OR) summary(umb.OR)
umb.OR <- metaumbrella:::.quiet(umbrella(df.OR)) DT::datatable(summary(umb.OR), options = list( scrollX = TRUE, dom = c('t'), ordering = FALSE, pageLength = 5, columnDefs = list( list(width = '110px', targets = "_all"), list(className = 'dt-center', targets = "_all"))))
This output shows the results of the calculations conducted by the `umbrella()` function. Results are presented independently for each factor included in the dataset.
Once calculations have been performed via the umbrella function, you can stratify the evidence with the `add.evidence()` function. Here, we present an example of stratification according to the "Ioannidis" criteria.
strat.io <- add.evidence(umb.OR, criteria = "Ioannidis") summary(strat.io)
strat.io <- metaumbrella:::.quiet(add.evidence(umb.OR, criteria = "Ioannidis")) DT::datatable(summary(strat.io), options = list( scrollX = TRUE, dom = c('t'), ordering = FALSE, pageLength = 5, columnDefs = list( list(width = '110px', targets = "_all"), list(className = 'dt-center', targets = "_all"))))
A visual description of the results can be obtained using the `forest()` function. More information on how generating nice plots using the `forest()` function can be found in another vignette dedicated to this function.
forest(strat.io, measure = "eOR", smlab = "umbrella review of risk \nfactors for NDD")
metaumbrella:::.quiet(forest(strat.io, measure = "eOR", smlab = "umbrella review of risk \nfactors for NDD"))
This example uses the dataset named `df.RR` distributed along with the metaumbrella package. You can access and visualize the dataset in R with the following command
df.RR
wzxhzdk:15
The dataset includes only one factor. To perform the calculations required for the stratification of evidence, simply apply the umbrella function on the `df.RR` well-formatted dataset.
umb.RR <- umbrella(df.RR) summary(umb.RR)
umb.RR <- metaumbrella:::.quiet(umbrella(df.RR)) DT::datatable(summary(umb.RR), options = list( scrollX = TRUE, dom = c('t'), ordering = FALSE, pageLength = 2, columnDefs = list( list(width = '110px', targets = "_all"), list(className = 'dt-center', targets = "_all"))))
This output shows the results of the calculations for the factor included in the dataset.
Once the calculations have been performed via the umbrella function, you can stratify the evidence with the `add.evidence()` function. Here, we present an example of stratification according to the "GRADE" criteria.
strat.grade <- add.evidence(umb.RR, criteria = "GRADE") summary(strat.grade)
strat.grade <- metaumbrella:::.quiet(add.evidence(umb.RR, criteria = "GRADE")) DT::datatable(summary(strat.grade), options = list( scrollX = TRUE, dom = c('t'), ordering = FALSE, pageLength = 5, columnDefs = list( list(width = '110px', targets = "_all"), list(className = 'dt-center', targets = "_all"))))
A visual description of the results can be obtained using the `forest()` function. More information on how generating nice plots using the `forest()` function can be found in another vignette dedicated to this function.
forest(strat.grade, measure = "eOR", smlab = "umbrella review of adverse events\n of SSRI treatment.")
metaumbrella:::.quiet(forest(strat.grade, measure = "eOR", smlab = "umbrella review of adverse events\n of SSRI treatment."))
This example uses the dataset named `df.SMD` distributed along with the metaumbrella package. You can access and visualize the dataset in R with the following command
df.SMD
wzxhzdk:23
Because the dataset includes two factors, the umbrella review will consider these factors as independent. The calculations and the stratification of evidence will be performed independently for these two factors.
To perform these calculations, simply apply the umbrella function on the `df.SMD` well-formatted dataset.
umb.SMD <- umbrella(df.SMD) summary(umb.SMD)
umb.SMD <- metaumbrella:::.quiet(umbrella(df.SMD)) DT::datatable(summary(umb.SMD), options = list( scrollX = TRUE, dom = c('t'), ordering = FALSE, pageLength = 5, columnDefs = list( list(width = '110px', targets = "_all"), list(className = 'dt-center', targets = "_all"))))
This output shows the results of the calculations for the two factors included in the dataset.
In this example, we stratify evidence according to `Personalized` criteria. We take into account the number of cases, the excess significance bias and the proportion of participants in studies at low risk of bias.
For the number of cases (n_cases), we set the following criteria:
This translates into this R code
wzxhzdk:26
For the excess significance bias (esb_p), we set the following criteria:
This translates into this R code
wzxhzdk:27
For the proportion of participants included in studies at low risk of bias (rob), we set the following criteria:
This translates into this R code
wzxhzdk:28
You can obtain the stratification of evidence via the standard `summary` command
wzxhzdk:29
wzxhzdk:30
A visual description of the results can be obtained using the `forest()` function. More information on how generating nice plots using the `forest()` function can be found in another vignette dedicated to this function.
forest(strat.pers1, measure = "eG", smlab = "Umbrella review of interventions\n on a numeric outcome.")
metaumbrella:::.quiet(forest(strat.pers1, measure = "eG", smlab = "Umbrella review of interventions\n on a numeric outcome."))
This example uses the dataset named `df.OR.multi` distributed along with the metaumbrella package. You can access and visualize the dataset in R with the following command
df.OR.multi
wzxhzdk:34
The dataset describes an umbrella review of meta-analyses of RCTs assessing the efficacy of several nutritional interventions on binary outcomes.
To perform the calculations required to stratify evidence, simply apply the umbrella function on the well-formatted dataset. Because multiple studies have several effect sizes, you have to indicate to the umbrella function that the data have a multilevel structure by specifying the `mult.level = TRUE` argument. Moreover, to apply the Borenstein method for the multiple outcomes, the correlation between outcomes had to be specified with the `r` argument of the umbrella function (by default, the umbrella function assumes an unique r = 0.5) or the `r` column of the dataset.
Here, we assume that the study of Godebu has a mean correlation between outcomes of .30 while all other studies have a mean correlation between outcomes of .60. The `r` argument of the umbrella function accepts only one value. To have varying within-study correlations across multivariate studies, you have to use the `r` column of the dataset. If a multivariate study has no `r` value in the dataset, the correlation indicated in the `r` argument of the umbrella function is used.
df.OR.multi$r <- NA # we initialize the r column in the dataset df.OR.multi[df.OR.multi$author == "Godebu", ]$r <- .30 # we indicate a mean correlation of .30 for the study of Godebu # option 1: we specify - via the r argument of the umbrella function - that all studies with multiple outcomes # but no r values in the dataset are assigned with a correlation of .60. umb.OR.multi_1 <- umbrella(df.OR.multi, mult.level = TRUE, r = 0.6) # option 2: we manually specify - via the r argument of the dataset - the correlation for other studies df.OR.multi[df.OR.multi$multiple_es == "outcomes" & !is.na(df.OR.multi$multiple_es) & !df.OR.multi$author %in% c("Godebu"), ]$r <- .60 # you no longer have to specify the r value in the umbrella function as it is already specified for all studies in the dataset umb.OR.multi_2 <- umbrella(df.OR.multi, mult.level = TRUE) # as usual, you can obtain results of the calculations using the summary command summary(umb.OR.multi_2) # check: you can check results are equal regardless of the method used all(summary(umb.OR.multi_1) == summary(umb.OR.multi_2), na.rm = TRUE)
df.OR.multi$r <- NA # we initialize the r column in the dataset df.OR.multi[df.OR.multi$author == "Godebu", ]$r <- .30 # we indicate a mean correlation of .30 for the study of Godebu # option 1: we specify - via the r argument of the umbrella function - that all studies with multiple outcomes # but no r values in the dataset are assigned with a correlation of .60. umb.OR.multi_1 <- metaumbrella:::.quiet(umbrella(df.OR.multi, mult.level = TRUE, r = 0.6)) # option 2: we manually specify - via the r argument of the dataset - the correlation for other studies df.OR.multi[df.OR.multi$multiple_es == "outcomes" & !is.na(df.OR.multi$multiple_es) & !df.OR.multi$author %in% c("Godebu"), ]$r <- .60 # you no longer have to specify the r value in the umbrella function as it is already specified for all studies in the dataset # you no longer have to specify the r value in the umbrella function as it is already specified for all studies in the dataset umb.OR.multi_2 <- metaumbrella:::.quiet(umbrella(df.OR.multi, mult.level = TRUE)) DT::datatable(summary(umb.OR.multi_2), options = list( scrollX = TRUE, dom = c('t'), ordering = FALSE, pageLength = 5, columnDefs = list( list(width = '110px', targets = "_all"), list(className = 'dt-center', targets = "_all")))) paste0("all(summary(umb.OR.multi_1) == summary(umb.OR.multi_2), na.rm = TRUE) returns " , all(summary(umb.OR.multi_1) == summary(umb.OR.multi_2), na.rm = TRUE))
Once the multivariate structure of the data has been indicated in the umbrella function, the stratification of evidence is performed as for regular data.
In this example, we stratify evidence according Personalized criteria. We take into account the inconsistency, the small-study effects, the statistical significance of the largest study and the imprecision.
For the inconsistency, we set the following criteria:
This translates into this R code
wzxhzdk:37For the small-study effects, we set the following criteria:
This translates into this R code
wzxhzdk:38For the significance of the largest study, we set the following criteria:
This translates into this R code
wzxhzdk:39For the imprecision, we set the following criteria:
This translates into this R code
wzxhzdk:40
Once these criteria have been indicated, you can obtain the stratification of evidence via the standard `summary` command
wzxhzdk:41
wzxhzdk:42
A visual description of the results can be obtained using the `forest()` function. More information on how generating nice plots using the `forest()` function can be found in another vignette dedicated to this function.
forest(strat.pers2, measure = "eOR")
metaumbrella:::.quiet(forest(strat.pers2))
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