Package ‘EvidenceSynthesis’ March 19, 2018 Type Package Title An R Package for Combining Evidence from Multiple Sources Version 0.0.3 Date 2018-03-19 Author Martijn Schuemie, Marc Suchard Maintainer Martijn Schuemie Description Routines for combining evidence and diagnostics across multiple sources, such as multiple data sites in a distributed study. This includes functions for performing meta-analysis and forest plots. Imports ggplot2 (>= 2.0.0), gridExtra, meta, EmpiricalCalibration License Apache License 2.0 URL https://github.com/OHDSI/EvidenceSynthesis BugReports https://github.com/OHDSI/EvidenceSynthesis/issues RoxygenNote 6.0.1

R topics documented: EvidenceSynthesis . . plotCovariateBalances plotEmpiricalNulls . . plotMetaAnalysisForest plotPreparedPs . . . . preparePsPlot . . . . .

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EvidenceSynthesis

Description EvidenceSynthesis

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plotCovariateBalances

plotCovariateBalances Plot covariate balances

Description plotCovariateBalances plots the covariate balance before and after matching for multiple data sources. Usage plotCovariateBalances(balances, labels, threshold = 0, beforeLabel = "Before matching", afterLabel = "After matching", fileName = NULL) Arguments balances

A list of covariate balance objects as created using the computeCovariateBalance function in the CohortMethod package. Each balance object is expected to be a data.frame with at least these two columns: beforeMatchingStdDiff and afterMatchingStdDiff.

labels

A vector containing the labels for the various sources.

threshold

Show a threshold value for the standardized difference.

beforeLabel

Label for before matching / stratification / trimming.

afterLabel

Label for after matching / stratification / trimming.

fileName

Name of the file where the plot should be saved, for example ’plot.png’. See the function ggsave in the ggplot2 package for supported file formats.

Details Creates a plot showing the covariate balance before and after matching. Balance distributions are displayed as box plots combined with scatterplots. Value A Ggplot object. Use the ggsave function to save to file. Examples # Some example data: balance1 <- data.frame(beforeMatchingStdDiff = rnorm(1000, 0.1, 0.1), afterMatchingStdDiff = rnorm(1000, 0.0, 0.01)) balance2 <- data.frame(beforeMatchingStdDiff = rnorm(1000, 0.2, 0.1), afterMatchingStdDiff = rnorm(1000, 0.0, 0.05)) balance3 <- data.frame(beforeMatchingStdDiff = rnorm(1000, 0.0, 0.1), afterMatchingStdDiff = rnorm(1000, 0.0, 0.03)) plotCovariateBalances(balances = list(balance1, balance2, balance3), labels = c("Site A", "Site B", "Site C"))

plotEmpiricalNulls

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plotEmpiricalNulls

Plot empirical null distributions

Description plotEmpiricalNulls plots the empirical null distribution for multiple data sources. Usage plotEmpiricalNulls(logRr, seLogRr, labels, xLabel = "Relative risk", limits = c(0.1, 10), showCis = TRUE, fileName = NULL) Arguments logRr

A numeric vector of effect estimates for the negative controls on the log scale.

seLogRr

The standard error of the log of the effect estimates. Hint: often the standard error = (log() - l og())/qnorm(0.025).

labels

A vector containing the labels for the various sources. Should be of equal length as logRr and seLogRr.

xLabel

The label on the x-axis: the name of the effect estimate.

limits

The limits of the effect size axis.

showCis

Show the 95 percent confidence intervals on the null distribution and distribution parameter estimates?

fileName

Name of the file where the plot should be saved, for example ’plot.png’. See the function ggsave in the ggplot2 package for supported file formats.

Details Creates a plot showing the empirical null distributions. Distributions are shown as mean plus minus one standard deviation, as well as a distribution plot. Value A Ggplot object. Use the ggsave function to save to file. Examples # Some example data: site1 <- EmpiricalCalibration::simulateControls(n = 50, mean = 0, sd = 0.1, trueLogRr = 0) site1$label <- "Site 1" site2 <- EmpiricalCalibration::simulateControls(n = 50, mean = 0.1, sd = 0.2, trueLogRr = 0) site2$label <- "Site 2" site3 <- EmpiricalCalibration::simulateControls(n = 50, mean = 0.15, sd = 0.25, trueLogRr = 0) site3$label <- "Site 3" sites <- rbind(site1, site2, site3) plotEmpiricalNulls(logRr = sites$logRr, seLogRr = sites$seLogRr, labels = sites$label)

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plotMetaAnalysisForest

plotMetaAnalysisForest Perform a meta-analysis and create a forest plot

Description plotMetaAnalysisForest performs a meta-analysis and creates a forest plot of effect size estimates. Usage plotMetaAnalysisForest(logRr, logLb95Ci, logUb95Ci, labels, xLabel = "Relative risk", limits = c(0.1, 10), hakn = TRUE, fileName = NULL) Arguments logRr

A numeric vector of effect estimates on the log scale.

logLb95Ci

The lower bound of the 95 percent confidence interval on the log scale.

logUb95Ci

The upper bound of the 95 percent confidence interval on the log scale.

labels

A vector containing the labels for the various estimates.

xLabel

The label on the x-axis: the name of the effect estimate.

limits

The limits of the effect size axis.

hakn

A logical indicating whether method by Hartung and Knapp should be used to adjust test statistics and confidence intervals.

fileName

Name of the file where the plot should be saved, for example ’plot.png’. See the function ggsave in the ggplot2 package for supported file formats.

Details Creates a forest plot of effect size estimates, and includes a meta-analysis estimate using a random effects model. The DerSimonian-Laird estimate (1986) is used. Value A Ggplot object. Use the ggsave function to save to file. References DerSimonian R, Laird N (1986), Meta-analysis in clinical trials. Controlled Clinical Trials, 7, 177188. Examples plotMetaAnalysisForest(logRr = c(0, 0.2, -0.2, 0, 0.2, -0.2), logLb95Ci = c(-0.2, -0.2, -0.6, -0.2, -0.2, -0.6), logUb95Ci = c(0.2, 0.6, 0.2, 0.2, 0.6, 0.2), labels = c("Site A", "Site B", "Site C", "Site D", "Site E", "Site F"))

plotPreparedPs

plotPreparedPs

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Plot the propensity score distribution

Description Plot the propensity score distribution Usage plotPreparedPs(preparedPsPlots, labels, treatmentLabel = "Target", comparatorLabel = "Comparator", fileName = NULL) Arguments preparedPsPlots

labels

A list of prepared propensity score data as created by the preparePsPlot function. A vector containing the labels for the various sources.

treatmentLabel A label to us for the treated cohort. comparatorLabel A label to us for the comparator cohort. fileName

Name of the file where the plot should be saved, for example ’plot.png’. See the function ggsave in the ggplot2 package for supported file formats.

Value A ggplot object. Use the ggsave function to save to file in a different format. Examples treatment <- rep(0:1, each = 100) propensityScore <- c(rnorm(100, mean = 0.4, sd = 0.25), rnorm(100, mean = 0.6, sd = 0.25)) data <- data.frame(treatment = treatment, propensityScore = propensityScore) data <- data[data$propensityScore > 0 & data$propensityScore < 1, ] preparedPlot <- preparePsPlot(data) # Just reusing the same data three times for demonstration purposes: preparedPsPlots <- list(preparedPlot, preparedPlot, preparedPlot) labels <- c("Data site A", "Data site B", "Data site C")

preparePsPlot

Prepare to plot the propensity score distribution

Description preparePsPlot prepares to plot the propensity (or preference) score distribution. It computes the distribution, so the output does not contain person-level data.

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preparePsPlot

Usage preparePsPlot(data, unfilteredData = NULL, scale = "preference") Arguments data

A data frame with at least the two columns described below

unfilteredData To be used when computing preference scores on data from which subjects have already been removed, e.g. through trimming and/or matching. This data frame should have the same structure as data. scale

The scale of the graph. Two scales are supported: scale = 'propensity' or scale = 'preference'. The preference score scale is defined by Walker et al (2013).

Details The data frame should have a least the following two columns: treatment

(integer)

propensityScore

(numeric)

Column indicating whether the person is in the treated (1) or comparator (0) group Propensity score

Value A data frame describing the propensity score (or preference score) distribution at 100 equallyspaced points. References Walker AM, Patrick AR, Lauer MS, Hornbrook MC, Marin MG, Platt R, Roger VL, Stang P, and Schneeweiss S. (2013) A tool for assessing the feasibility of comparative effectiveness research, Comparative Effective Research, 3, 11-20 Examples treatment <- rep(0:1, each = 100) propensityScore <- c(rnorm(100, mean = 0.4, sd = 0.25), rnorm(100, mean = 0.6, sd = 0.25)) data <- data.frame(treatment = treatment, propensityScore = propensityScore) data <- data[data$propensityScore > 0 & data$propensityScore < 1, ] preparedPlot <- preparePsPlot(data)

Index EvidenceSynthesis, 1 EvidenceSynthesis-package (EvidenceSynthesis), 1 ggsave, 5 plotCovariateBalances, 2 plotEmpiricalNulls, 3 plotMetaAnalysisForest, 4 plotPreparedPs, 5 preparePsPlot, 5, 5

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Package 'EvidenceSynthesis' - GitHub

Mar 19, 2018 - This includes functions for performing meta-analysis and forest plots. Imports ggplot2 (>= 2.0.0),. gridExtra, meta,. EmpiricalCalibration. License Apache License 2.0. URL https://github.com/OHDSI/EvidenceSynthesis. BugReports https://github.com/OHDSI/EvidenceSynthesis/issues. RoxygenNote 6.0.1.

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