estimateIGTProjection {EHRtemporalVariability}

Estimates an Information Geometric Temporal plot projection

Description

Estimates an IGTProjection object from a DataTemporalMap object.

Usage

estimateIGTProjection(
  dataTemporalMap,
  dimensions = 3,
  startDate = NULL,
  endDate = NULL,
  embeddingType = "classicalmds"
)

## S4 method for signature 'DataTemporalMap'
estimateIGTProjection(
  dataTemporalMap,
  dimensions = 3,
  startDate = NULL,
  endDate = NULL,
  embeddingType = "classicalmds"
)

Arguments

dataTemporalMap

of class DataTemporalMap object.

dimensions

numeric integer value indicating the number of dimensions for the projection.

startDate

a Date object indicating the date at which to start the analysis, in case of being different from the first chronological date in the date column (the default).

endDate

a Date object indicating the date at which to end the analysis, in case of being different from the last chronological date in the date column (the default).

embeddingType

the type of embedding to apply to the dissimilarity matrix of time batches in order to obtain the non-parametric Statistical Manifold, from "classicalmds" and "nonmetricmds", with "classicalmds" as default. "classicalmds" uses the base R stats::cmdscale function, while "nonmetricmds" uses the MASS:isoMDS function. The returned stress format will depend on the selected embedding type: "classicalmds" returns 1-GOF as returned by stats::cmdscale function, "nonmetricmds" returns the final stress in percent, as returned by the MASS::isoMDS function

Value

An IGTProjection object containing the projected coordinates of each temporal batch in the embedded non-parametric Statistical Manifold, as well as the embedding stress according to the embeddingType.

Examples

load(system.file("extdata",
                 "variabilityDemoNHDSdiagcode1-phewascode.RData",
                  package="EHRtemporalVariability"))
igtProj <- estimateIGTProjection( dataTemporalMap = probMaps$`diagcode1-phewascode`, 
dimensions      = 3, 
startDate       = "2000-01-01", 
endDate         = "2010-12-31")

## Not run: 

# For additional and larger examples download the following .Rdata file:

gitHubUrl  <- 'http://github.com/'
gitHubPath <- 'hms-dbmi/EHRtemporalVariability-DataExamples/'
gitHubFile <- 'raw/master/variabilityDemoNHDS.RData'
inputFile  <-  paste0(gitHubUrl, gitHubPath, gitHubFile)

load(url(inputFile))
igtProj <- estimateIGTProjection( dataTemporalMap = probMaps[[1]], 
dimensions      = 3, 
startDate       = "2000-01-01", 
endDate         = "2010-12-31")

## End(Not run)