SurveySankey: #' Determine the patient metric of choice over time WORK IN...

In sebastiz/EndoMineR_devlop: Functions to mine endoscopic and associated pathology datasets

Description

#' Determine the patient metric of choice over time WORK IN PROGRESS #' #' This function aims to show what is happening over time to a metric #' of choice on a per patient basis. #' An example might be to demonstrate the worst grade of histopathology #' on repeated endoscopic biopsies eg for Barrett's oesophagus #' @param theframe the dataframe, #' @param EndoReportColumn the column of interest, #' @param myNotableWords list of words you are interested in #' @import ggplot2 #' @import stringr #' @import ggplus #' @keywords patient flow #' @export #' @examples #The function relies on defined a list of #' # words you are interested in and then choosing the column you are #' # interested in looking in for these words. This can be for histopathology #' # free text columns or endoscopic. In this example it is for endoscopic #' # columns #' v<-HistolAll(Mypath) #' v<-Endomerge2(Myendo,'Dateofprocedure','HospitalNumber',v,'Dateofprocedure','HospitalNumber') #' b<-Barretts_PathStage(v,'Histology') #' aa<-Barretts_PragueScore(b,'Findings') #' aa<-SurveilTimeByRow(aa,'pHospitalNum','Date.y') #' myNotableWords<-c("No_IM","IM","LGD","HGD","T1a) #' PatientFlowBasic(aa,"IMorNoIM",myNotableWords)

Usage

SurveySankey(dfw, ProcPerformedColumn, PatientID)

Arguments

dfw	the dataframe extracted using the standard cleanup scripts
ProcPerformedColumn	the column containing the test like P rocPerformed for example
PatientID	the column containing the patients unique identifier eg hostpital number

Details

PatientFlowBasic <- function(theframe, EndoReportColumn, myNotableWords)

theframe["RecodedColumn"] <- as.integer(factor(theframe[,EndoReportColumn], myNotableWords, ordered = TRUE))

#Now develop the patient specific journey with faceted plot in ggplot2 f<-ggplot(theframe) + geom_point(aes(Date.x,type),shape=16,size=1) + xlab("Date") + ylab("Histopathological State") + theme(axis.text.x=element_text(angle=-90))

t<-facet_multiple(plot = f, facets = 'pHospitalNum', ncol = 2, nrow = 2) mylist<-as.list(aa,t)

return(mylist) Create a Sankey plot for patient flow

This creates a Sankey plot to see the order of tests for all patients: dfw is the dataframe, y is the value of in this case the procedure type (eg EMR, radiofrequency ablation for Barrett's but can be any description of a procedure you desire) Note the Hospital Number column MUST be called PatientID.

Examples

# The purpose of the function is to
# provide a Sankey plot which allows the analyst to see the proportion
# of patients moving from one state (in this case type of Procedure) to
# another. This allows us to see for example how many EMRs are done after
#RFA. For further patient flow examples see PatientFlow_CircosPlots
names(Myendo)[names(Myendo) == 'HospitalNumber'] <- 'PatientID'
gg<-SurveySankey(Myendo,"ProcedurePerformed","PatientID")

sebastiz/EndoMineR_devlop documentation built on May 29, 2019, 7:33 a.m.