common_DxArg: Common argument of diagnostic functions

common_DxArgR Documentation

Common argument of diagnostic functions

Description

Common argument of diagnostic functions

Arguments

dxDataFile

A data frame object of clinical diagnostic data with at least 3 columns: ID, ICD, and Date. As for date column, the data format should be YYYY/MM/DD or YYYY-MM-DD.

idColName

Column name of ID column in dxDataFile. Data type of this argumant should be string without quotation marks.

icdColName

Column name of ICD column in dxDataFile. Data type of this argumant should be string without quotation marks.

dateColName

Column name of date column in dxDataFile, and the type of date column should be a date format in R or a string format with date information in YYYY/MM/DD or YYYY-MM-DD. Data type of this argumant should be string without quotation marks.

icdVerColName

(Optional) Column name if there is a columns to record ICD-9/10 version used in dxDataFile. In this column, data format should be numeric 9L or 10L to indicate which ICD version is used for each cell. See examples below to get more information.

icd10usingDate

The date that ICD-10 was started to be used in dxDataFile dataset. The data format should be YYYY/MM/DD or YYYY-MM-DD. Necessary if icdVerColName is null.

isDescription

Binary. If true, category description of classification methods will be used in the group column. If false, category name will be used. By default, it is set to be True (standard category description).

groupDataType

Five Stratified methods can be chosen: CCS (ccs), multiple-level CCS (ccslvl1, ccslvl2, CCSR (ccsr),ccslvl3, ccslvl4), PheWAS (PheWAS), comorbidities (ahrq,charlson, elix), precise or fuzzy customized method (customGrepIcdGroup, customIcdGroup). The value should be string stated above without quotation mark. Default value is ccs. When conducting cases selection by un-grouped ICD codes, then use the method: ICD (ICD).

customGroupingTable

Used-defined grouping categories. icdDxToCustom needs a dataset with two columns called "Group" and "ICD", respectively; User can define one or more disease categories in "Group" column, and define a list of corresponding category-related ICD codes in "ICD" column. icdDxToCustomGrep needs a dataset with two columns: "Group", "grepIcd"; "Group" defines one or more disease categories and "grepICD" defines disease-related ICD code character strings containing regular expressions.

selectedCaseFile

A data frame with the label of case selected or not. Can be generated by selectCases function or a self-defined data frame (as long as the column names and data type are the same as the output of selectCases function, but not recommended). Default is 'NULL'

Details

Common argument of diagnostic functions


DHLab-CGU/emr documentation built on Sept. 2, 2023, 9:16 p.m.