sumComposite: Score Data Using a simple sum In pscore: Standardizing Physiological Composite Risk Endpoints

Description

Create a composite using summation

Usage

 ```1 2``` ```sumComposite(object, transform = c("square", "abs", "none"), type = c("sum", "mean"), systems) ```

Arguments

 `object` An object ready for use `transform` A character string indicating the type of transformation to use. One of “square”, “abs”, or “none”, which either sums the raw data, sums the squared data and then takes the square root, or sums the absolute values of the data. `type` A character string indicating the type of aggregation to use. One of “sum” or “mean”. `systems` An optional list where each element is a character vector of the variable names within a particular system. If given, scores are first averaged within a system, before being aggregated across systems.

Value

A list of results.

See Also

Other composite: `distanceScores`; `factorComposite`; `mahalanobisComposite`; `prepareComposite`

Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64``` ```# this example creates distances for the built in mtcars data # see ?mtcars for more details # The distances are calculated from the "best" in the dataset # defined by these thresholds thresholds <- with(mtcars, c( mpg = max(mpg), hp = max(hp), wt = min(wt), qsec = min(qsec))) # higher mpg and hp are better, # whereas lower wt and qsec are better dres <- distanceScores(mtcars[, c("mpg", "hp", "wt", "qsec")], thresholds = list(thresholds), higherisbetter = c(TRUE, TRUE, FALSE, FALSE), saveall = TRUE) # see a density plot of the distance scores dres\$Density # now prepare to create the composite # covariance matrix will be calculated from the data # and data will be standardized to unit variance by default cprep <- prepareComposite(dres) # now we can create the composite based on summing the (standardized) # distances from our defined thresholds # by default, distances are squared, then summed, and then square rooted # to be back on the original scale scomp <- sumComposite(cprep, "square", "sum") # view a histogram and summary of the composite scores scomp\$ScoreHistogram summary(scomp\$Scores) # calculate average (mean) instead of sum scomp2 <- sumComposite(cprep, "square", "mean") # view a histogram and summary of the composite scores scomp2\$ScoreHistogram summary(scomp2\$Scores) # scores are still the same plot(scomp\$Scores, scomp2\$Scores) # first average scores within a system, then sum # note that within a system, scores are always averaged, # never summed. scomp3 <- sumComposite(cprep, "square", "sum", systems = list( environment = c("mpg"), performance = c("hp", "qsec", "wt"))) # view a histogram and summary of the composite scores scomp3\$ScoreHistogram summary(scomp3\$Scores) # compare all three scores # because of the different number of indicators within each system # there is a re-weighting for S3 plot(data.frame(S1 = scomp\$Scores, S2 = scomp2\$Scores, S3 = scomp3\$Scores)) # cleanup rm(thresholds, dres, cprep, scomp, scomp2, scomp3) ```

pscore documentation built on May 29, 2017, 9:02 a.m.