mylongevity_method2: mylongevity_method2

In mylongevityapp/mylongevity: Calculation of life expectancy (Calculation of life expectancy)

Description

This function loads a file as a data frame of clients. Using the argument 'indexes_of_variables', this function selects the columns of factors Then using the argument 'list_of_variables' this functions selects the columns of interest to be matched with coefficients (i.e log-hazard ratios) estimated in analysis

Usage

mylongevity_method2(
  data,
  indexes_of_variables,
  list_of_variables,
  age,
  a,
  b,
  working_directory
)

Arguments

data	given data frame of clients,
indexes_of_variables	indices for columns of interest
list_of_variables	columns of interest to be matched to coefficients (i.e log-hazard ratios)
age	age of clients
a	intercept from Gompertz baseline hazards
b	slope from Gompertz baseline hazards
working_directory	the working directory for any data that is produced from the functions to be saved in a folder

Details

This method calculates life expectancies using the log-hazard ratio estimates from the landmark analysis Kulinskaya et al. (2020c) and the weights of the risk groups estimated from the given dataset. These weights correspond to frequencies of risk profiles in the dataset.

mylongevity_method2 uses log-hazard ratio coefficients from website mylongevity.org with inputted data. mylongevity_method2 takes the log-hazard ratio coefficients and calculates the weights from data.

For mylongevity_method2 user should specify the directory where all the temporary files will be stored. The directory should be specified as working_directory=' E:/myproject'. A folder called 'temp' will be created in the specified directory. This is the folder where all necessary/temporary files will be stored. Also for method 2 and method 3 we need a function - function_for_table_of_combination() and a function calculate_life_expectancy() which are separate functions within this R package. For mylongevity_method2, user has to input the data with columns of interest using the argument 'indexes_of_variables'. Also, user has to specify the particular age of interest for a given data to select the corresponding log-hazard ratio coefficients from landmark model for a particular age. User also has to specify values for a and b for Gompertz distribution. User has to specify the names of variables which will be used in calculation with the same names as in inputted data using the variable list_of_variables For mylongevity_method2, user can only input columns for variables ('statins','cvd_risk','diabetes','HTN_diag_treat','hypercholesterolaemia','BMI','Smoking') User has to specify the variables of interest using the argument 'list_of_variables'. The order of specified columns using the argument 'indexes_of_variables' should match the variables of interest 'list_of_variables' by names.

Value

data frame with life expectancies for given data frame of clients

Examples

set.seed(1234)
n<-1000
gender <- c(rep('M',times=n/2),rep('F',times=n/2))
townsend <- round(runif(n, min = 1, max = 5))
smokerCategory <- round(runif(n, min = 1, max = 3))
HTN_diag_treat  <- round(runif(n, min = 1, max = 3))
diabetes  <- round(runif(n, min = 0, max = 1))
hypercholesterolaemia <- round(runif(n, min = 0, max = 1))
bmiCategory <- round(runif(n, min = 1, max = 3))
cvd_risk <- round(runif(n, min = 0, max = 2))
statins <- round(runif(n, min = 0, max = 1))
age <-61
a=-12.459132
b=0.11764571
list_of_variables<-c("statins","cvd_risk","diabetes","HTN_diag_treat","hypercholesterolaemia")
data<-data.frame(statins,cvd_risk,diabetes,HTN_diag_treat,hypercholesterolaemia)
indexes_of_variables <- c(1,2,3,4,5)
working_directory<-"E:/Documentation for R package/" #please edit this to your working directory
mylongevity_method2(data=data,indexes_of_variables=indexes_of_variables,list_of_variables,age,a,b,working_directory)

mylongevityapp/mylongevity documentation built on Dec. 21, 2021, 11:07 p.m.