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Performs poisson regression with strata effect

Source: R/Poisson_Regression.R
RunPoissonRegression_STRATA.Rd

RunPoissonRegression_STRATA uses user provided data, time/event columns, vectors specifying the model, and options to control the convergence and starting positions

Usage

RunPoissonRegression_STRATA(
  df,
  pyr0 = "pyr",
  event0 = "event",
  names = c("CONST"),
  term_n = c(0),
  tform = "loglin",
  keep_constant = c(0),
  a_n = c(0),
  modelform = "M",
  fir = 0,
  der_iden = 0,
  control = list(),
  strat_col = "null"
)

Arguments

df

a data.table containing the columns of interest

pyr0

column used for person-years per row

event0

column used for event status

names

columns for elements of the model, used to identify data columns

term_n

term numbers for each element of the model

tform

list of string function identifiers, used for linear/step

keep_constant

binary values to denote which parameters to change

a_n

list of initial parameter values, used to determine number of parameters. May be either a list of vectors or a single vector.

modelform

string specifying the model type: M, ME, A, PA, PAE, GMIX, GMIX-R, GMIX-E

fir

term number for the initial term, used for models of the form T0*f(Ti) in which the order matters

der_iden

number for the subterm to test derivative at, only used for testing runs with a single varying parameter, should be smaller than total number of parameters. indexed starting at 0

control

list of parameters controlling the convergence, see Def_Control() for options or vignette("Control_Options")

strat_col

column to stratify by if needed

Value

returns a list of the final results

See also

Other Poisson Wrapper Functions: RunPoissonEventAssignment(), RunPoissonEventAssignment_bound(), RunPoissonRegression(), RunPoissonRegression_Guesses_CPP(), RunPoissonRegression_Joint_Omnibus(), RunPoissonRegression_Omnibus(), RunPoissonRegression_Residual(), RunPoissonRegression_Single(), RunPoissonRegression_Tier_Guesses()

Examples

library(data.table)
## basic example code reproduced from the starting-description vignette
df <- data.table::data.table(
  "UserID" = c(112, 114, 213, 214, 115, 116, 117),
  "Starting_Age" = c(18, 20, 18, 19, 21, 20, 18),
  "Ending_Age" = c(30, 45, 57, 47, 36, 60, 55),
  "Cancer_Status" = c(0, 0, 1, 0, 1, 0, 0),
  "a" = c(0, 1, 1, 0, 1, 0, 1),
  "b" = c(1, 1.1, 2.1, 2, 0.1, 1, 0.2),
  "c" = c(10, 11, 10, 11, 12, 9, 11),
  "d" = c(0, 0, 0, 1, 1, 1, 1),
  "e" = c(0, 0, 0, 0, 1, 0, 1)
)
# For the interval case
df$pyr <- df$Ending_Age - df$Starting_Age
pyr <- "pyr"
event <- "Cancer_Status"
names <- c("a", "b", "c", "d")
term_n <- c(0, 1, 1, 2)
tform <- c("loglin", "lin", "lin", "plin")
modelform <- "M"
fir <- 0
a_n <- c(0.1, 0.1, 0.1, 0.1)
keep_constant <- c(0, 0, 0, 0)
der_iden <- 0
control <- list(
  "ncores" = 2, "lr" = 0.75, "maxiter" = 5, "halfmax" = 5,
  "epsilon" = 1e-3, "deriv_epsilon" = 1e-3,
  "abs_max" = 1.0, "change_all" = TRUE, "dose_abs_max" = 100.0,
  "verbose" = FALSE, "double_step" = 1
)
strat_col <- c("e")
e <- RunPoissonRegression_STRATA(
  df, pyr, event, names,
  term_n, tform, keep_constant,
  a_n, modelform, fir, der_iden, control, strat_col
)