RunPoissonRegression_Joint_Omnibus {Colossus} | R Documentation |
Performs basic Poisson regression using the omnibus function
Description
RunPoissonRegression_Joint_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, uses joint competing risks equation
Usage
RunPoissonRegression_Joint_Omnibus(
df,
pyr0,
events,
name_list,
Term_n_list = list(),
tform_list = list(),
keep_constant_list = list(),
a_n_list = list(),
modelform = "M",
fir = 0,
der_iden = 0,
control = list(),
Strat_Col = "null",
model_control = list(),
Cons_Mat = as.matrix(c(0)),
Cons_Vec = c(0)
)
Arguments
df |
a data.table containing the columns of interest |
pyr0 |
column used for person-years per row |
events |
vector of event column names |
name_list |
list of vectors for columns for event specific or shared model elements, required |
Term_n_list |
list of vectors for term numbers for event specific or shared model elements, defaults to term 0 |
tform_list |
list of vectors for subterm types for event specific or shared model elements, defaults to loglinear |
keep_constant_list |
list of vectors for constant elements for event specific or shared model elements, defaults to free (0) |
a_n_list |
list of vectors for parameter values for event specific or shared model elements, defaults to term 0 |
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 |
control |
list of parameters controlling the convergence, see Def_Control() for options or vignette("starting_description") |
Strat_Col |
column to stratify by if needed |
model_control |
controls which alternative model options are used, see Def_model_control() for options and vignette("Alt_Run_opt") for further details |
Cons_Mat |
Matrix containing coefficients for system of linear constraints, formatted as matrix |
Cons_Vec |
Vector containing constants for system of linear constraints, formatted as vector |
Value
returns a list of the final results
See Also
Other Poisson Wrapper Functions:
RunPoissonEventAssignment()
,
RunPoissonRegression()
,
RunPoissonRegression_Guesses_CPP()
,
RunPoissonRegression_Omnibus()
,
RunPoissonRegression_STRATA()
,
RunPoissonRegression_Single()
,
RunPoissonRegression_Tier_Guesses()
Examples
library(data.table)
## basic example code reproduced from the starting-description vignette
a <- c(0,0,0,1,1,1)
b <- c(1,1,1,2,2,2)
c <- c(0,1,2,2,1,0)
d <- c(1,1,0,0,1,1)
e <- c(0,1,1,1,0,0)
f <- c(0,1,0,0,1,1)
df <- data.table('t0'=a,'t1'=b,'e0'=c,'e1'=d,'fac'=e)
time1 <- "t0"
time2 <- "t1"
df$pyr <- df$t1 - df$t0
pyr <- "pyr"
events <- c('e0','e1')
names_e0 <- c('fac')
names_e1 <- c('fac')
names_shared <- c('t0','t0')
Term_n_e0 <- c(0)
Term_n_e1 <- c(0)
Term_n_shared <- c(0,0)
tform_e0 <- c("loglin")
tform_e1 <- c("loglin")
tform_shared <- c("quad_slope","loglin_top")
keep_constant_e0 <- c(0)
keep_constant_e1 <- c(0)
keep_constant_shared <- c(0,0)
a_n_e0 <- c(-0.1)
a_n_e1 <- c(0.1)
a_n_shared <- c(0.001, -0.02)
name_list <- list('shared'=names_shared,'e0'=names_e0,'e1'=names_e1)
Term_n_list <- list('shared'=Term_n_shared,'e0'=Term_n_e0,'e1'=Term_n_e1)
tform_list <- list('shared'=tform_shared,'e0'=tform_e0,'e1'=tform_e1)
keep_constant_list <- list('shared'=keep_constant_shared,
'e0'=keep_constant_e0,'e1'=keep_constant_e1)
a_n_list <- list('shared'=a_n_shared,'e0'=a_n_e0,'e1'=a_n_e1)
der_iden <- 0
modelform <- "M"
fir <- 0
control <- list("Ncores"=2,'lr' = 0.75,'maxiter' = 5,'halfmax' = 5,'epsilon' = 1e-3,
'dbeta_max' = 0.5,'deriv_epsilon' = 1e-3, 'abs_max'=1.0,'change_all'=TRUE,
'dose_abs_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 <- 'f'
e <- RunPoissonRegression_Joint_Omnibus(df, pyr, events, name_list, Term_n_list,
tform_list, keep_constant_list, a_n_list,
modelform, fir, der_iden, control,Strat_Col)