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Adds a Parameter for Framingham Heart Study Cardiovascular Disease 10-Year Risk Score

Source: R/derive_param_framingham.R
derive_param_framingham.Rd

Adds a record for framingham score (FCVD101) for each by group (e.g., subject and visit) where the source parameters are available.

Usage 

derive_param_framingham(
  dataset,
  by_vars,
  set_values_to = exprs(PARAMCD = "FCVD101"),
  sysbp_code = "SYSBP",
  chol_code = "CHOL",
  cholhdl_code = "CHOLHDL",
  age = AGE,
  sex = SEX,
  smokefl = SMOKEFL,
  diabetfl = DIABETFL,
  trthypfl = TRTHYPFL,
  get_unit_expr,
  filter = NULL
)

Arguments

dataset

Input dataset

The variables specified by the by_vars argument are expected to be in the dataset. PARAMCD, and AVAL are expected as well.

The variable specified by by_vars and PARAMCD must be a unique key of the input dataset after restricting it by the filter condition (filter parameter) and to the parameters specified by sysbp_code, chol_code and hdl_code.

Default value

none

by_vars

Grouping variables

Only variables specified in by_vars will be populated in the newly created records.

Permitted values

list of variables created by exprs(), e.g., exprs(USUBJID, VISIT)

Default value

none

set_values_to

Variables to be set

The specified variables are set to the specified values for the new observations. For example exprs(PARAMCD = "MAP") defines the parameter code for the new parameter.

Permitted values

List of variable-value pairs

Default value

exprs(PARAMCD = "MAP")

sysbp_code

Systolic blood pressure parameter code

The observations where PARAMCD equals the specified value are considered as the systolic blood pressure assessments.

Permitted values

a character scalar, i.e., a character vector of length one

Default value

"SYSBP"

chol_code

Total serum cholesterol code

The observations where PARAMCD equals the specified value are considered as the total cholesterol assessments. This must be measured in mg/dL.

Permitted values

a character scalar, i.e., a character vector of length one

Default value

"CHOL"

cholhdl_code

HDL serum cholesterol code

The observations where PARAMCD equals the specified value are considered as the HDL cholesterol assessments. This must be measured in mg/dL.

Permitted values

a character scalar, i.e., a character vector of length one

Default value

"CHOLHDL"

age

Subject age

A variable containing the subject's age.

Permitted values

A numeric variable name that refers to a subject age column of the input dataset

Default value

AGE

sex

Subject sex

A variable containing the subject's sex.

Permitted values

A character variable name that refers to a subject sex column of the input dataset

Default value

SEX

smokefl

Smoking status flag

A flag indicating smoking status.

Permitted values

A character variable name that refers to a smoking status column of the input dataset.

Default value

SMOKEFL

diabetfl

Diabetic flag

A flag indicating diabetic status.

Permitted values

A character variable name that refers to a diabetic status column of the input dataset

Default value

DIABETFL

trthypfl

Treated with hypertension medication flag

A flag indicating if a subject was treated with hypertension medication.

Permitted values

A character variable name that refers to a column that indicates whether a subject is treated for high blood pressure

Default value

TRTHYPFL

get_unit_expr

An expression providing the unit of the parameter

The result is used to check the units of the input parameters.

Permitted values

An expression which is evaluable in the input dataset and results in a character value

Default value

none

filter

Filter condition

The specified condition is applied to the input dataset before deriving the new parameter, i.e., only observations fulfilling the condition are taken into account.

Comparing derived numeric variables to fixed values, e.g., PCHG <= -90, may give unexpected results due to floating point representation. For details and solutions see the "Floating Point Comparisons" section in vignette("concepts_conventions").

Permitted values

an unquoted condition, e.g., AVISIT == "BASELINE"

Default value

NULL

Value

The input dataset with the new parameter added

Details

The values of age, sex, smokefl, diabetfl and trthypfl will be added to the by_vars list. The predicted probability of having cardiovascular disease (CVD) within 10-years according to Framingham formula. See AHA Journal article General Cardiovascular Risk Profile for Use in Primary Care for reference.

For Women:

Factor Amount
Age 2.32888
Total Chol 1.20904
HDL Chol -0.70833
Sys BP 2.76157
Sys BP + Hypertension Meds 2.82263
Smoker 0.52873
Non-Smoker 0
Diabetic 0.69154
Not Diabetic 0
Average Risk 26.1931
Risk Period 0.95012

For Men:

Factor Amount
Age 3.06117
Total Chol 1.12370
HDL Chol -0.93263
Sys BP 1.93303
Sys BP + Hypertension Meds 2.99881
Smoker .65451
Non-Smoker 0
Diabetic 0.57367
Not Diabetic 0
Average Risk 23.9802
Risk Period 0.88936

The equation for calculating risk:

$$RiskFactors = (log(Age) * AgeFactor) + (log(TotalChol) * TotalCholFactor) + (log(CholHDL) * CholHDLFactor) \\ + (log(SysBP) * SysBPFactor) + Smoker + Diabetes Present - AvgRisk$$

$$Risk = 100 * (1 - RiskPeriodFactor^{RiskFactors})$$

See also

compute_framingham()

BDS-Findings Functions for adding Parameters/Records: default_qtc_paramcd(), derive_basetype_records(), derive_expected_records(), derive_extreme_event(), derive_extreme_records(), derive_locf_records(), derive_param_bmi(), derive_param_bsa(), derive_param_computed(), derive_param_doseint(), derive_param_exist_flag(), derive_param_exposure(), derive_param_map(), derive_param_qtc(), derive_param_rr(), derive_param_wbc_abs(), derive_summary_records()

Examples 

library(tibble)

adcvrisk <- tribble(
  ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU,
  ~VISIT, ~AGE, ~SEX, ~SMOKEFL, ~DIABETFL, ~TRTHYPFL,
  "01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 121,
  "mmHg", "BASELINE", 44, "F", "N", "N", "N",
  "01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 115,
  "mmHg", "WEEK 2", 44, "F", "N", "N", "Y",
  "01-701-1015", "CHOL", "Total Cholesterol (mg/dL)", 216.16,
  "mg/dL", "BASELINE", 44, "F", "N", "N", "N",
  "01-701-1015", "CHOL", "Total Cholesterol (mg/dL)", 210.78,
  "mg/dL", "WEEK 2", 44, "F", "N", "N", "Y",
  "01-701-1015", "CHOLHDL", "Cholesterol/HDL-Cholesterol (mg/dL)", 54.91,
  "mg/dL", "BASELINE", 44, "F", "N", "N", "N",
  "01-701-1015", "CHOLHDL", "Cholesterol/HDL-Cholesterol (mg/dL)", 26.72,
  "mg/dL", "WEEK 2", 44, "F", "N", "N", "Y",
  "01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", 119,
  "mmHg", "BASELINE", 55, "M", "Y", "Y", "Y",
  "01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", 101,
  "mmHg", "WEEK 2", 55, "M", "Y", "Y", "Y",
  "01-701-1028", "CHOL", "Total Cholesterol (mg/dL)", 292.01,
  "mg/dL", "BASELINE", 55, "M", "Y", "Y", "Y",
  "01-701-1028", "CHOL", "Total Cholesterol (mg/dL)", 246.73,
  "mg/dL", "WEEK 2", 55, "M", "Y", "Y", "Y",
  "01-701-1028", "CHOLHDL", "Cholesterol/HDL-Cholesterol (mg/dL)", 65.55,
  "mg/dL", "BASELINE", 55, "M", "Y", "Y", "Y",
  "01-701-1028", "CHOLHDL", "Cholesterol/HDL-Cholesterol (mg/dL)", 44.62,
  "mg/dL", "WEEK 2", 55, "M", "Y", "Y", "Y"
)


adcvrisk %>%
  derive_param_framingham(
    by_vars = exprs(USUBJID, VISIT),
    set_values_to = exprs(
      PARAMCD = "FCVD101",
      PARAM = "FCVD1-Framingham CVD 10-Year Risk Score (%)"
    ),
    get_unit_expr = AVALU
  )
#> # A tibble: 16 × 11
#>    USUBJID     PARAMCD PARAM       AVAL AVALU VISIT   AGE SEX   SMOKEFL DIABETFL
#>    <chr>       <chr>   <chr>      <dbl> <chr> <chr> <dbl> <chr> <chr>   <chr>   
#>  1 01-701-1015 SYSBP   Systolic… 121    mmHg  BASE…    44 F     N       N       
#>  2 01-701-1015 SYSBP   Systolic… 115    mmHg  WEEK…    44 F     N       N       
#>  3 01-701-1015 CHOL    Total Ch… 216.   mg/dL BASE…    44 F     N       N       
#>  4 01-701-1015 CHOL    Total Ch… 211.   mg/dL WEEK…    44 F     N       N       
#>  5 01-701-1015 CHOLHDL Choleste…  54.9  mg/dL BASE…    44 F     N       N       
#>  6 01-701-1015 CHOLHDL Choleste…  26.7  mg/dL WEEK…    44 F     N       N       
#>  7 01-701-1028 SYSBP   Systolic… 119    mmHg  BASE…    55 M     Y       Y       
#>  8 01-701-1028 SYSBP   Systolic… 101    mmHg  WEEK…    55 M     Y       Y       
#>  9 01-701-1028 CHOL    Total Ch… 292.   mg/dL BASE…    55 M     Y       Y       
#> 10 01-701-1028 CHOL    Total Ch… 247.   mg/dL WEEK…    55 M     Y       Y       
#> 11 01-701-1028 CHOLHDL Choleste…  65.6  mg/dL BASE…    55 M     Y       Y       
#> 12 01-701-1028 CHOLHDL Choleste…  44.6  mg/dL WEEK…    55 M     Y       Y       
#> 13 01-701-1015 FCVD101 FCVD1-Fr…   3.14 NA    BASE…    44 F     N       N       
#> 14 01-701-1015 FCVD101 FCVD1-Fr…   5.80 NA    WEEK…    44 F     N       N       
#> 15 01-701-1028 FCVD101 FCVD1-Fr…  42.3  NA    BASE…    55 M     Y       Y       
#> 16 01-701-1028 FCVD101 FCVD1-Fr…  37.5  NA    WEEK…    55 M     Y       Y       
#> # ℹ 1 more variable: TRTHYPFL <chr>

derive_param_framingham(
  adcvrisk,
  by_vars = exprs(USUBJID, VISIT),
  set_values_to = exprs(
    PARAMCD = "FCVD101",
    PARAM = "FCVD1-Framingham CVD 10-Year Risk Score (%)"
  ),
  get_unit_expr = extract_unit(PARAM)
)
#> # A tibble: 16 × 11
#>    USUBJID     PARAMCD PARAM       AVAL AVALU VISIT   AGE SEX   SMOKEFL DIABETFL
#>    <chr>       <chr>   <chr>      <dbl> <chr> <chr> <dbl> <chr> <chr>   <chr>   
#>  1 01-701-1015 SYSBP   Systolic… 121    mmHg  BASE…    44 F     N       N       
#>  2 01-701-1015 SYSBP   Systolic… 115    mmHg  WEEK…    44 F     N       N       
#>  3 01-701-1015 CHOL    Total Ch… 216.   mg/dL BASE…    44 F     N       N       
#>  4 01-701-1015 CHOL    Total Ch… 211.   mg/dL WEEK…    44 F     N       N       
#>  5 01-701-1015 CHOLHDL Choleste…  54.9  mg/dL BASE…    44 F     N       N       
#>  6 01-701-1015 CHOLHDL Choleste…  26.7  mg/dL WEEK…    44 F     N       N       
#>  7 01-701-1028 SYSBP   Systolic… 119    mmHg  BASE…    55 M     Y       Y       
#>  8 01-701-1028 SYSBP   Systolic… 101    mmHg  WEEK…    55 M     Y       Y       
#>  9 01-701-1028 CHOL    Total Ch… 292.   mg/dL BASE…    55 M     Y       Y       
#> 10 01-701-1028 CHOL    Total Ch… 247.   mg/dL WEEK…    55 M     Y       Y       
#> 11 01-701-1028 CHOLHDL Choleste…  65.6  mg/dL BASE…    55 M     Y       Y       
#> 12 01-701-1028 CHOLHDL Choleste…  44.6  mg/dL WEEK…    55 M     Y       Y       
#> 13 01-701-1015 FCVD101 FCVD1-Fr…   3.14 NA    BASE…    44 F     N       N       
#> 14 01-701-1015 FCVD101 FCVD1-Fr…   5.80 NA    WEEK…    44 F     N       N       
#> 15 01-701-1028 FCVD101 FCVD1-Fr…  42.3  NA    BASE…    55 M     Y       Y       
#> 16 01-701-1028 FCVD101 FCVD1-Fr…  37.5  NA    WEEK…    55 M     Y       Y       
#> # ℹ 1 more variable: TRTHYPFL <chr>