Performs basic Logistic regression using the omnibus function

RunLogisticRegression_Omnibus uses user provided data, time/event columns, vectors specifying the model, and options to control the convergence and starting positions. Has additional options to starting with several initial guesses

Usage

RunLogisticRegression_Omnibus(
  df,
  trial0 = "CONST",
  event0 = "event",
  names = c("CONST"),
  term_n = c(0),
  tform = "loglin",
  keep_constant = c(0),
  a_n = c(0),
  modelform = "M",
  control = list(),
  model_control = list(),
  cons_mat = as.matrix(c(0)),
  cons_vec = c(0)
)

Arguments

df

a data.table containing the columns of interest

trial0

column with the number of trials per row, assumed to be 1 if a column not provided

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 the 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

control

list of parameters controlling the convergence, see the Control_Options vignette for details

model_control

controls which alternative model options are used, see the Control_Options vignette for further details

cons_mat

Matrix containing coefficients for a system of linear constraints, formatted as matrix

cons_vec

Vector containing constants for a system of linear constraints, formatted as vector

Value

returns a list of the final results

See also

Other Logistic Wrapper Functions: LogisticRun()

Examples

library(data.table)
## basic example code reproduced from the starting-description vignette
df <- data.table::data.table(
  "Trials" = 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, 1, 0, 0, 0, 1)
)
# For the interval case
trial <- "Trials"
event <- "Cancer_Status"
names <- c("a", "b", "c", "d")
a_n <- c(1.1, -0.1, 0.2, 0.5) # used to test at a specific point
term_n <- c(0, 1, 1, 2)
tform <- c("loglin", "lin", "lin", "plin")
modelform <- "M"
keep_constant <- c(0, 0, 0, 0)
control <- list(
  "ncores" = 2, "lr" = 0.75, "maxiter" = 5,
  "halfmax" = 5, "epsilon" = 1e-3,
  "deriv_epsilon" = 1e-3, "step_max" = 1.0,
  "thres_step_max" = 100.0, "verbose" = FALSE, "ties" = "breslow",
  "double_step" = 1
)
guesses_control <- list(
  "maxiter" = 10, "guesses" = 10, "lin_min" = 0.001,
  "lin_max" = 1, "loglin_min" = -1, "loglin_max" = 1, "lin_method" = "uniform",
  "loglin_method" = "uniform", strata = FALSE
)
strat_col <- "e"
e <- RunLogisticRegression_Omnibus(
  df, trial, event, names, term_n,
  tform, keep_constant,
  a_n, modelform,
  control
)