os.predict {nhs.predict}

os.predict

Description

Calculates 'NHS Predict' v2.1 Overall survival and therapy benefits

Usage

os.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..

horm

Numeric, Hormone therapy, Yes = 1, No = 0.

traz

Numeric, Trastuzumab therapy, Yes = 1, No = 0.

bis

Numeric, Bisphosphonate therapy, Yes = 1, No = 0..

Value

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

Examples

data(example_data)

example_data <- os.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 <- os.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)