This function runs multiple Longitudinal Modified Treatment Policy (LMTP) models for specified outcome variables, calculates contrasts, creates evaluation tables, and optionally saves the complete output.
Usage
margot_lmtp(
data,
outcome_vars,
trt,
shift_functions = list(),
include_null_shift = TRUE,
lmtp_model_type = lmtp::lmtp_tmle,
contrast_type = c("pairwise", "null"),
contrast_scale = c("additive", "rr", "or"),
lmtp_defaults = list(),
n_cores = parallel::detectCores() - 1,
save_output = FALSE,
save_path = here::here("push_mods"),
base_filename = "lmtp_output",
use_timestamp = FALSE,
prefix = NULL
)Arguments
- data
A data frame containing all necessary variables.
- outcome_vars
A character vector of outcome variable names to be modeled.
- trt
A character string specifying the treatment variable.
- shift_functions
A list of shift functions to be applied. Each function should take `data` and `trt` as arguments.
- include_null_shift
Logical, whether to include a null shift. Default is TRUE.
- lmtp_model_type
The LMTP model function to use. Default is lmtp_tmle.
- contrast_type
Type of contrasts to compute: "pairwise" or "null". Default is "pairwise".
- contrast_scale
Scale for contrasts: "additive", "rr", or "or". Default is "additive".
- lmtp_defaults
A list of default parameters for the LMTP models.
- n_cores
Number of cores to use for parallel processing. Default is detectCores() - 1.
- save_output
Logical, whether to save the complete output. Default is FALSE.
- save_path
The directory path to save the output. Default is "push_mods" in the current working directory.
- base_filename
The base filename for saving the output. Default is "lmtp_output".
- use_timestamp
Logical, whether to include a timestamp in the filename. Default is FALSE.
- prefix
Optional prefix to add to the saved output filename. Default is NULL.
Value
A list containing:
- models
A list of all LMTP models for each outcome and shift function.
- contrasts
A list of contrasts computed for each outcome.
- individual_tables
A list of individual tables for each contrast and outcome.
- combined_tables
A list of combined tables for each contrast type across all outcomes.
Examples
if (FALSE) { # \dontrun{
# Assume we have a dataset 'my_data' with variables 'outcome', 'treatment', and some confounders
# Define shift functions
gain_function <- function(data, trt) {
data[[trt]] + 1
}
loss_function <- function(data, trt) {
pmax(data[[trt]] - 1, 0)
}
# Run LMTP analysis
result <- margot_lmtp(
data = my_data,
outcome_vars = c("outcome1", "outcome2"),
trt = "treatment",
shift_functions = list(gain = gain_function, loss = loss_function),
lmtp_defaults = list(baseline = c("confounder1", "confounder2"),
time_vary = c("time_var1", "time_var2"),
outcome_type = "continuous"),
save_output = TRUE,
save_path = here::here("output", "lmtp_results"),
prefix = "my_study"
)
} # }