rfs.predict {nhs.predict}

rfs.predict

Description

Calculates 'NHS Predict' v2.1 Recurrence-free survival and therapy benefits

Usage

rfs.predict(
  data,
  year = 10,
  age.start,
  screen,
  size,
  grade,
  nodes,
  er,
  her2,
  ki67,
  generation,
  horm,
  traz,
  bis
)

Arguments

data

A dataframe containing patient data with the necessary variables.

year

Numeric, Specify the year since surgery for which the predictions are calculated, ranges between 1 and 15. Default at 10.

age.start

Numeric, Age at diagnosis of the patient. Range between 25 and 85.

screen

Numeric, Clinically detected = 0, Screen detected = 1, Unknown = 2.

size

Numeric, Tumor size in millimeters.

grade

Numeric, Tumor grade. Values: 1,2,3. Missing=9.

nodes

Numeric, Number of positive nodes.

er

Numeric, ER status, ER+ = 1, ER- = 0.

her2

Numeric, HER2 status, HER2+ = 1, HER2- = 0. Unknown = 9.

ki67

Numeric, ki67 status, KI67+ = 1, KI67- = 0, Unknown = 9.

generation

Numeric, Chemotherapy generation. Values: 0,2,3. If value is missing, default=3.

horm

Numeric, Hormone therapy, Yes = 1, No = 0. If value is missing, default= er status.

traz

Numeric, Trastuzumab therapy, Yes = 1, No = 0. If value is missing, default= her2 status.

bis

Numeric, Bisphosphonate therapy, Yes = 1, No = 0. if value is missing, default=1.

Value

The function attaches additional columns to the dataframe, matched for patient observation, containing recurrence-free survival at the specified year, plus the additional benefit for each type of therapy.

Examples

data(example_data)

example_data <- rfs.predict(example_data,age.start = age,screen = detection,size = t.size,
                     grade = t.grade, nodes = nodes, er = er.status, her2 = her2.status,
                     ki67 = ki67.status, generation = chemo.gen, horm = horm.t,
                     traz = trastuzumab, bis = bis.t)

data(example_data)

example_data <- rfs.predict(example_data,year = 15, age,detection,t.size,t.grade,
                           nodes,er.status,her2.status,ki67.status,chemo.gen,horm.t,
                           trastuzumab,bis.t)