case.series {rSPARCS}

Generate the Case Series

Description

Estimates the daily number of cases reported by multiple grouping factors.

Usage

case.series(data,ICD,diagnosis,date,start,end,by1,by2,by3,by4,by5)

Arguments

data

a data.frame containing with each row representing a case, and each column representing the patient characteristics such as gender, age, admission date, and discharge date, etc.

ICD

a vector of ICD 9, or 10 codes, or a mix of them, which users are willing to calculate the daily numbers for; can be of length 3-6.

diagnosis

the name of the variable in the data containing the diagnostic code upon admission.

date

the name of the variable in the data showing the admission date, either in the format like "20181129" or "2018/11/29".

start, end

the start and end date for the case series to be generated.

by1, by2, by3, by4, by5

the name of the variable in the data used as grouping variables.

Details

Not limited to hospital data, but also applicable to other surveillance data.

Value

dataset

A case series will be generated for time series analysis, trend analysis and displaying, with following variables:

date

from the start date to the end date as user specified, with 1 day bin.

case

the daily number of cases diagnosed with diseases of user specified ICD codes.

others

grouping variables.

Note

When applied to other medical data without ICD code, users may arbitrarily set a ICD code, meanwhile, define the diagnosis variable in the data to the same ICD code.

Examples

set.seed(2018)

data=data.frame(
  patient=1:10000,
  primdiag=sample(390:398,10000,replace=TRUE),
  onset=sample(seq.Date(as.Date("2015/2/1"),
    as.Date("2016/2/1"),"1 day"),10000,replace=TRUE),
  sex=sample(c("M","F"),10000,replace=TRUE),
  county=sample(c("Albany","New York"),10000,replace=TRUE)
)

output.series=case.series(
  data,ICD=392:396,diagnosis="primdiag",
  date="onset",start="2015/1/1",end="2016/12/31",by1="sex")
  
head(output.series)