recode.check {BCRA}

Recode and check the relative risk covariate values

Description

A function to recode the relative risk covariates and check errors.

Usage

recode.check(data, Raw_Ind=1)

Arguments

data

A data set containing all the required input data needed to perform risk projections, such as initial age, projection age, BrCa relative risk covariates and race. See exampledata for details.

Raw_Ind

The raw file indicator with default value 1. Raw_Ind=1 means RR covariates are in raw/original format. Raw_Ind=0 means RR covariates have already been re-coded to 0, 1, 2 or 3.

Details

This function is to recode the following relative risk covariates. Recoded RR covariates are named as NB_Cat, AM_Cat, AF_Cat and NR_Cat for N_Biop, AgeMen, Age1st and N_Rels, respectively.

N_Biop:	The number of biopsies.
AgeMen:	Age at menarchy.
Age1st:	Age at first live birth.
N_Rels:	The number of first degree relatives with BrCa.

See the following table for recoding details.

Covariate	Raw Value	Recoded to
N_Biop	0 or 99 (unk or not applicable)	0
	1	1
	2,3,4 ... and not 99	2
AgeMen	14,15,16 ... or 99 (unk)	0
	12,13	1
	11 and younger	2
Age1st	19 and younger or 99 (unk)	0
	20,21,22,23,24	1
	25,26,27,28,29 or 98 (nulliparous)	2
	30,31,32 ... and not 98 and not 99	3
N_Rels	0 or 99 (unk)	0
	1	1
	2,3,4 ... and not 99	2

This function is also used to check consistency and errors of input data. Let set_T1_missing and set_T2_missing be the checking variables for T1 and T2. The constraint on T1 and T2 is 20<=T1<T2<=90. If it is violated, set_T1_missing and set_T2_missing and the absolute risk will be set to the missing value NA.

Let RacCat be the checking variable for Race. If the Race value is not included in the 11 races defined, the absolute risk will be set to the missing value NA and RacCat will be set to "U" (undefined). The corresponding character of Race CharRace will be set to "??".

Let set_HyperP_missing and set_R_Hyp_missing be the checking variables for
HypPlas and R_Hyp. Consistency patterns for the number of Biopsies and Hyperplasia are:

Requirment (A)	N_Biops=0 or 99, then HypPlas MUST = 99 (not applicable).
Requirment (B)	N_Biops>0 and <99, then HypPlas = 0, 1 or 99.

If ANY of the above 2 REQUIREMENTS is violated, NB_Cat, set_HyperP_missing and set_R_Hyp_missing will be set to the corresponding character "A" or "B" and the absolute risk will be set to the missing value NA. The consequences to the relative risk (RR) for the above two requirements are:

(A) N_Biops=0 or 99, HypPlas=99 (not applicable) inflates RR by 1.00.

(B) N_Biops>0 and <99, HypPlas=0 (no) inflates RR by 0.93;
N_Biops>0 and <99, HypPlas=1 (yes) inflates RR by 1.82;
N_Biops>0 and <99, HypPlas=99 (unk) inflates RR by 1.00.

For remaining relative risk covariates, AgeMen, Age1st and N_Rels:

AgeMen	Age at menarchy must be postive integer less than or equal to initial age T1.
	NOTE: (1) For African-American women AgeMen<=11 are grouped with AgeMen=12
	or 13. (2) For US Born Hispanic women AgeMen is not included in the RR model
	and all values for this variable are recoded to 0.
Age1st	Age at 1st live birth must be postive integer greater than equal to AgeMen
	and less than or equal to initial age T1.
	NOTE: (1) For African-American women, Age1st is not included in the RR model
	and all values for this variable are recoded to 0. (2) For US Born and Foreign
	Born Hispanic women, the recoding for this variable follows:

Age1st	19 and younger or 99 (unk)	0
	20 - 29	1
	30+ or 98 (nulliparous) and not 99	2

N_Rels	The number of 1st degree relatives with BrCa must be 0,1,2....
	NOTE: For Asian-Americans Race=6-11 and Hispanic-Americans (US and foreign born),
	the number of 1st degree relative coded value of 2 gets grouped with 1.

Value

A data frame containing the error indictors, recoded covariates as well as other checking variables defined for checking the consistency of the input data.

See Also

error.table.all, error.table

Examples

data(exampledata)
recode.check(exampledata)