Fix/block occ

.Rbuildignore

@@ -20,3 +20,5 @@
 ^dev$
 ^\.posit$
 ^temp$
+^codecov\.yml$
+^vignettes/\.quarto$

.gitignore

@@ -48,6 +48,7 @@ inst/rust/template/*
 
 # Example runs
 data-raw/Runs/
+data-raw/errors.xlsx
 inst/Examples/
 
 

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: Pmetrics
 Title: Pmetrics for Population Modeling and Simulation
-Version: 3.2.6
+Version: 3.2.7
 Authors@R: c(
     person("Michael", "Neely", , "mneely@usc.edu", role = c("aut", "cre")),
     person("Julián", "Otálvaro", , "juliandavid347@gmail.com", role = "aut"),

NAMESPACE

@@ -69,6 +69,7 @@ export(PM_sim)
 export(PM_step)
 export(PM_tree)
 export(PM_tutorial)
+export(PM_upgrade)
 export(PM_valid)
 export(PMbuild)
 export(PMcheck)
@@ -157,6 +158,7 @@ export(two_comp_bolus_cl)
 export(two_comp_iv)
 export(two_comp_iv_cl)
 export(zBMI)
+importFrom(DT,datatable)
 importFrom(R6,R6Class)
 importFrom(bslib,
   accordion,
@@ -264,6 +266,7 @@ importFrom(graphics,
   segments,
   text
 )
+importFrom(magrittr,not)
 importFrom(parallel,
   clusterExport,
   makeCluster,
@@ -304,6 +307,7 @@ importFrom(readr,
 importFrom(rlang,
   ":=",
   .data,
+  .env,
   set_names
 )
 importFrom(shiny,

R/PM_cov.R

@@ -97,8 +97,9 @@ PM_cov <- R6::R6Class(
       if (file.exists(file.path(path, "posterior.csv"))) {
         posts <- readr::read_csv(file = file.path(path, "posterior.csv"), show_col_types = FALSE)
       } else if (inherits(data, "PM_cov") & !is.null(data$data)) { # file not there, and already PM_cov
-        class(data$data) <- c("PM_cov_data", "data.frame")
-        return(data$data)
+        upgraded_data <- PM_upgrade(data$data)
+        class(upgraded_data) <- c("PM_cov_data", "data.frame")
+        return(upgraded_data)
       } else {
         cli::cli_warn(c(
           "!" = "Unable to generate covariate-posterior information.",
@@ -110,8 +111,9 @@ PM_cov <- R6::R6Class(
       if (file.exists(file.path(path, "covs.csv"))) {
         covs <- readr::read_csv(file = file.path(path, "covs.csv"), show_col_types = FALSE)
       } else if (inherits(data, "PM_cov")) { # file not there, and already PM_cov
-        class(data$data) <- c("PM_cov_data", "data.frame")
-        return(data$data)
+        upgraded_data <- PM_upgrade(data$data)
+        class(upgraded_data) <- c("PM_cov_data", "data.frame")
+        return(upgraded_data)
       } else {
         cli::cli_warn(c(
           "!" = "Unable to generate covariate-posterior information.",
@@ -120,7 +122,9 @@ PM_cov <- R6::R6Class(
         return(NULL)
       }
 
-      covs <- covs |> mutate(block = block + 1)
+      covs <- covs |>
+        mutate(occasion = block + 1) |>
+        select(-block)
 
 
       post_mean <- posts |>
@@ -140,10 +144,10 @@ PM_cov <- R6::R6Class(
         dplyr::left_join(post_mean, covs, by = "id"),
         dplyr::left_join(post_med, covs, by = "id")
       ) |>
-        select(id, time, block, icen, everything())
+        select(id, time, occasion, icen, everything())
 
       class(res) <- c("PM_cov_data", "data.frame")
-      attr(res, "ncov") <- ncol(covs) - 3 # subtract id, time, block
+      attr(res, "ncov") <- ncol(covs) - 3 # subtract id, time, occasion
 
       return(res)
     }
@@ -564,7 +568,7 @@ summary.PM_cov <- function(object, icen = "median", ...) {
 
   sumCov <- data |>
     group_by(id) |>
-    dplyr::summarize(across(c(-time, -block), ~ purrr::exec(icen, x = .x, na.rm = TRUE))) |>
+    dplyr::summarize(across(c(-time, -occasion), ~ purrr::exec(icen, x = .x, na.rm = TRUE))) |>
     mutate(icen = !!icen)
 
   return(sumCov)

R/PM_cycle.R

@@ -126,8 +126,9 @@ PM_cycle <- R6::R6Class(
           write.csv(raw, file.path(path, "cycles.csv"), row.names = FALSE)
         }
       } else if (inherits(data, "PM_cycle") & !is.null(data$data)) { # file not there, and already PM_cycle
-        class(data$data) <- c("PM_cycle_data", "list")
-        return(data$data)
+        upgraded_data <- PM_upgrade(data$data)
+        class(upgraded_data) <- c("PM_cycle_data", "list")
+        return(upgraded_data)
       } else {
         cli::cli_warn(c(
           "!" = "Unable to generate cycle information.",
@@ -153,8 +154,9 @@ PM_cycle <- R6::R6Class(
           ), show_col_types = FALSE
         ) |> filter(!is.na(obs))
       } else if (inherits(data, "PM_cycle")) { # file not there, and already PM_op
-        class(data$data) <- c("PM_cycle_data", "list")
-        return(data$data)
+        upgraded_data <- PM_upgrade(data$data)
+        class(upgraded_data) <- c("PM_cycle_data", "list")
+        return(upgraded_data)
       } else {
         cli::cli_warn(c(
           "!" = "Unable to generate cycle information.",
@@ -167,8 +169,9 @@ PM_cycle <- R6::R6Class(
       if (file.exists(file.path(path, "settings.json"))) {
         config <- jsonlite::fromJSON(file.path(path, "settings.json"))
       } else if (inherits(data, "PM_cycle") & !is.null(data$data)) { # file not there, and already PM_op
-        class(data$data) <- c("PM_cycle_data", "list")
-        return(data$data)
+        upgraded_data <- PM_upgrade(data$data)
+        class(upgraded_data) <- c("PM_cycle_data", "list")
+        return(upgraded_data)
       } else {
         cli::cli_warn(c(
           "!" = "Unable to generate cycle information.",