aides

    Additive Information & Details of Evidence Synthesis

      Enoch Kang

CRAN Date Lifecycle: stable Licence
Dependencis Functions Monthly Downloads metacran downloads



About aides

aides is an R package which is planned to support users to do additional analysis or graphics of evidence synthesis. Essentially, package aides serves as an aiding toolkit for pooled analysis of aggregated data, crafted with a vision to support a more inclusive and informed approach to evidence-based decision-making; and it is developed with values of flexibility, ease of use, and comprehensibility. Package aides will be updated with advances of methodology of data synthesis and evidence evaluation.

The initial goals of package aides are to simplify analysis process for both professionals and public users, and to support them in navigating the complexities of synthesized evidence. Long-term goals of package aides are to support knowledge translation and decision-making based on the obtained information with comprehensive understanding of the evidence.


Features

Briefly, aides currently consists of three tasks as follows:


Dependencies and installation

Package aides depends on various packages, and is developed using R (version 4.2.2). Therefore, those packages are concurrently installed with package aides. The dependencies are listed as follows:

Formal released package aides can be installed from CRAN via R with following syntax:

install.packages("aides")


Flow and functions

Users can import their data and do relevant tests or graphics using functions in package aides. The present package consists of seven functions listed as follows.

Disparity:

Discordance:

Sequential analysis:


Examples

1. Disparity test

The following steps and syntax demonstrate how user can carry out disparity test.

STEP 1. Import data (example of the study by Olkin 1995)

library(meta)
data("Olkin1995")
data <- Olkin1995

STEP 2. Process data

data$n  <- data$n.exp + data$n.cont

STEP 3. Test assumption of discordance in study size

output <- output <- aides::TestDisparity(n = n, 
                                         data = data, 
                                         study = author, 
                                         time = year,
                                         outlier = "MAD", 
                                         rblty = "MAD", 
                                         plot = TRUE)

STEP 4. Illustrate discordance plot

TestDisparity(n = n, 
              data = data, 
              study = author, 
              time = year, 
              outlier = "MAD", 
              plot = TRUE)


PlotDisparity(object = output, 
              which = "CV")


2. Discordance test

The following steps and syntax demonstrate how user can carry out discordance test.

STEP 1. Import data (example of the study by Fleiss 1993)

library(meta)
data("Fleiss1993bin")
data <- Fleiss1993bin

STEP 2. Process data

data$n  <- data$n.asp + data$n.plac
data$se <- sqrt((1 / data$d.asp) - (1 / data$n.asp) + (1 / data$d.plac) - (1 / data$n.plac))

STEP 3. Test assumption of discordance in study size

output <- TestDiscordance(n = n, 
                          se = se, 
                          study = study,
                          data = data)

STEP 4. Illustrate discordance plot

TestDiscordance(n = n, 
                se = se, 
                study = study, 
                data = data, 
                plot = TRUE)


3. Sequential analysis

The following steps and syntax demonstrate how user can carry out sequential analysis.

STEP 1. Import data (example of the study by Fleiss 1993)

library(meta)
data("Fleiss1993bin")
data <- Fleiss1993bin

STEP 2. Perform sequentail analysis

DoSA(Fleiss1993cont, study, year,
     r1 = d.asp, n1 = n.asp,
     r2 = d.plac, n2 = n.plac,
     measure = "RR", PES = 0.5,
     group = c("Aspirin", "Control"), 
     plot = TRUE)



Coding conventions

There are some rules for version numbering in package aides (June 20, 2023). Basically, version number consists of three integers with a period between them (eg. version 1.0.0).

  1. Updating the first integer refers to package update(s) with new methodological impact.

  2. Changing the second integer refers to package update(s) with new function(s) without new methodological impact.

  3. Updating the third integer refers to formal modification(s) of existed function(s).


This package is mainly written according to Google’s R style. For readers, details of naming rules are listed as follows:

  1. .R file is named using lower case with underscore "_" between words (e.g. test_disparity.R).

  2. function is named using verb or verb with noun, and the first character of each word is written in capital letter (e.g. TestDiscordance()).

  3. object is named using noun with the first word in lower case, but the first character of rest words is written using capital letter (e.g. dataCases).

  4. variable is named using noun written in lower case. Words of variable name are separated by “.” if a variable name consists of more than two words (e.g. dataDiSS$w.normality).


Common-used prefix in package aides are listed as follows:

  1. angl... refers angle of text.

  2. clr... refers to color.

  3. lgc... refers to logic value.

  4. szFnt... refers to font size.

  5. szLn... refers to line width.

  6. szPnt... refers to point size.

  7. txt... refers text (string).

  8. typLn... refers type of line.

  9. typPnt... refers type of point.


License

This package is licensed under the GPL-3 License.


To do list

Task force will keep update package aides for relevant issues.