RunPoissonRegression_Joint_Omnibus {Colossus} | R Documentation |
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
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)
)
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. 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 |
model_control |
controls which alternative model options are used, see Def_model_control() for options and vignette("Control_Options") 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 |
returns a list of the final results
Other Poisson Wrapper Functions:
RunPoissonEventAssignment()
,
RunPoissonEventAssignment_bound()
,
RunPoissonRegression()
,
RunPoissonRegression_Guesses_CPP()
,
RunPoissonRegression_Omnibus()
,
RunPoissonRegression_Residual()
,
RunPoissonRegression_STRATA()
,
RunPoissonRegression_Single()
,
RunPoissonRegression_Tier_Guesses()
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,
'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)