covariate_step_tibble: Prepare forward covariate step

View source: R/stepwise-covariate.R

covariate_step_tibbleR Documentation

Prepare forward covariate step



Takes a base nm object and a set of relationships to test (from test_relations()) and prepares a tibble of NONMEM runs.

The goal of NMproject's covariate modelling functions is to provide a stepwise covariate method with manual decision making. This important to ensure that the full model selection/evaluation criteria (should be defined in statistical analysis plans) can be applied at every step rather than just log likelihood ratio testing, where the most significant model may be unstable, may worsen model predictions or may only be slightly more significant than a more physiologically plausible covariate relationship.

The functions test_relations(), covariate_step_tibble(), bind_covariate_results() together comprise NMproject stepwise covariate method with manual decision. The goal is to be part way between PsN's SCM and completely manual process at each forward and backward elimination step. The syntax of how covariates are included is the same as PsN's SCM routine - See PsN documentation for more information.


  run_in = nm_dir("models"),
  direction = c("forward", "backward"),



An nm object.


Base run_id to construct run_ids of covariate runs.


Character. See run_in().


dplyr::tibble with testing relations (from test_relations()).


Character. "forward" (default) or "backward".


Additional arguments passed to add_cov().


Will return dtest a dplyr::tibble with appended columns.

See Also

test_relations(), bind_covariate_results(), add_cov()


dtest <- test_relations(param = c("KA", "K", "V"),
                        cov = c("LIN1", "LIN2", "LIN3", "RND1", "RND2", "RND3"),
                        state = c("linear", "power"),
                        continuous = TRUE) %>%
         test_relations(param = c("KA", "K", "V"),
                        cov = "BN1",
                        state = "linear",
                        continuous = FALSE)
# create example object m1 from package demo files
exdir <- system.file("extdata", "examples", "theopp", package = "NMproject")
m1 <- new_nm(run_id = "m1", 
             based_on = file.path(exdir, "Models", "ADVAN2.mod"),
             data_path = file.path(exdir, "SourceData", "THEOPP.csv"))

temp_data_file <- paste0(tempfile(), ".csv")

## dataset has missing WTs so create a new one and assign this to the run
input_data(m1) %>% 
  dplyr::group_by(ID) %>%
  dplyr::mutate(WT = na.omit(WT)) %>%
m1 <- m1 %>% data_path(temp_data_file)
dtest <- test_relations(param = c("K", "V"),
                        cov = c("WT"),
                        state = c("linear", "power"),
                        continuous = TRUE)

## requires NONMEM to be installed
## Not run: 
## create tibble of covariate step with model objects as column m
dsm1 <- m1 %>% covariate_step_tibble(run_id = "m1_f1",
                                     dtest = dtest,
                                     direction = "forward")

## run all models greedily
dsm1$m <- dsm1$m %>% run_nm()

## extract results and put into tibble
dsm1 <- dsm1 %>% bind_covariate_results()

## sort by BIC (for example) and view
dsm1 <- dsm1 %>% arrange(BIC)

## check condition number, covariance,...
## run any diagnostics here

## when happy with selection, select run for subsequent step

m1_f1 <- dsm1$m[1] ## select most signifcant BIC
# alternative select by relationship
m1_f1 <- dsm1 %>%
  filter(param = "CL", cov = "BWT", state = "power") %$%

## do next forward step

dsm2 <- m1_f1 %>% covariate_step_tibble(run_id = "m1_f2",
                                        dtest = dtest,
                                        direction = "forward")

## continue ...

## End(Not run)

NMproject documentation built on Sept. 30, 2022, 1:06 a.m.