add docs

seroanalytics · Oct 17, 2024 · e7b129e · e7b129e
1 parent 75c60f5
commit e7b129e
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Showing 3 changed files with 29 additions and 3 deletions.
diff --git a/R/biokinetics.R b/R/biokinetics.R
@@ -56,7 +56,7 @@ biokinetics <- R6::R6Class(
     },
     construct_design_matrix = function() {
       var <- pid <- NULL
-      dt_design_matrix <- as.character(private$data[, .SD, .SDcols = private$all_formula_vars, by = pid]) |>
+      dt_design_matrix <- private$data[, .SD, .SDcols = private$all_formula_vars, by = pid] |>
         unique()
 
       # Build the full design matrix using model.matrix

diff --git a/man/biokinetics.Rd b/man/biokinetics.Rd
diff --git a/tests/testthat/test-data.R b/tests/testthat/test-data.R
@@ -47,3 +47,17 @@ test_that("Can handle non-numeric pids", {
   stan_data <- mod$get_stan_data()
   expect_equivalent(stan_data$id, ids)
 })
+
+test_that("Natural scale data is converted to log scale for stan", {
+  dat <- data.table::fread(system.file("delta_full.rds", package = "epikinetics"))
+  mod <- biokinetics$new(data = dat)
+  stan_data <- mod$get_stan_data()
+  expect_equivalent(stan_data$value, convert_log_scale(dat, "value")$value)
+})
+
+test_that("Log scale data is passed directly to stan", {
+  dat <- data.table::fread(system.file("delta_full.rds", package = "epikinetics"))
+  mod <- biokinetics$new(data = dat, scale = "log")
+  stan_data <- mod$get_stan_data()
+  expect_equivalent(stan_data$value, dat$value)
+})