Using xpose sets • xpose.xtras

Introduction

A powerful new object building upon the xpose framework is the xpose_set. Much like how xpose_data is in essence a list of information and data about the fitted model, xpose_set is a list of xpose_data (or xp_xtras) objects with information about how these models relate to one another.

Creating a set is easy. An important point to remember about usage is that each set item must have a label. Depending on how the set is created, the default is to use the name of the xpose_data object, but if an unnamed list is spliced or any objects share the same label, an error will occur. Note, however, that duplicate xpose_data objects can be used, as long as they have different labels. In the xpose_set() example below, three example models fitting the same dataset are made into a set, and alternative labels are used for one version of the set.

xpose_set(pheno_base, pheno_final, pheno_saem)
#> 
#> ── xpose_set object ────────────────────────────────────────────────────────────
#> • Number of models: 3
#> • Model labels: pheno_base, pheno_final, and pheno_saem
#> • Number of relationships: 0
#> • Focused xpdb objects: none
#> • Exposed properties: none
#> • Base model: none
xpose_set(base=pheno_base, reparam=pheno_final, reparam_saem=pheno_saem)
#> 
#> ── xpose_set object ────────────────────────────────────────────────────────────
#> • Number of models: 3
#> • Model labels: base, reparam, and reparam_saem
#> • Number of relationships: 0
#> • Focused xpdb objects: none
#> • Exposed properties: none
#> • Base model: none

The print output hints at features that will be explored in this vignette. A few example sets are in the package that can be used to test some of the elements discussed here. A relatively complex example explores typical model-building steps for the common phenobarbital in neonates dataset, called pheno_set, diagrammed below.

diagram_lineage(pheno_set) %>%
  DiagrammeR::render_graph(layout="tree")

Relationships

Relationships between models in a set can be declared with formula notation, where one or more child models is dependent on one or more parents (child1+... ~ parent1+...). To demonstrate, parts of pheno_set can be reproduced.

phrun3 <- pheno_set$run3$xpdb
phrun5 <- pheno_set$run5$xpdb
phrun6 <- pheno_set$run6$xpdb
phrun7 <- pheno_set$run7$xpdb
phrun8 <- pheno_set$run8$xpdb
phrun9 <- pheno_set$run9$xpdb
pheno_stem <- xpose_set(phrun3,phrun5,phrun6, .as_ordered = TRUE)
pheno_stem
#> 
#> ── xpose_set object ────────────────────────────────────────────────────────────
#> • Number of models: 3
#> • Model labels: phrun3, phrun5, and phrun6
#> • Number of relationships: 2
#> • Focused xpdb objects: none
#> • Exposed properties: none
#> • Base model: none
diagram_lineage(pheno_stem) %>%
  DiagrammeR::render_graph(layout="tree")

pheno_branch <- xpose_set(phrun6,phrun7,phrun8,phrun9, .relationships = c(phrun7+phrun8+phrun9~phrun6))
pheno_branch
#> 
#> ── xpose_set object ────────────────────────────────────────────────────────────
#> • Number of models: 4
#> • Model labels: phrun6, phrun7, phrun8, and phrun9
#> • Number of relationships: 3
#> • Focused xpdb objects: none
#> • Exposed properties: none
#> • Base model: none
diagram_lineage(pheno_branch) %>%
  DiagrammeR::render_graph(layout="tree")

Trees can also be concatenated, using typical R/tidyverse syntax.

pheno_tree <- pheno_stem %>% 
  # drop phrun6 from stem
  select(-phrun6) %>%
  c(
    pheno_branch,
    .relationships = c(phrun6~phrun5)
  )
pheno_tree
#> 
#> ── xpose_set object ────────────────────────────────────────────────────────────
#> • Number of models: 6
#> • Model labels (truncated): phrun3, phrun5, phrun6, phrun7, and phrun8 (...)
#> • Number of relationships: 5
#> • Focused xpdb objects: none
#> • Exposed properties: none
#> • Base model: none
#> # ℹ 1 more xpdbs
#> # ℹ Use `print(n = ...)` to see more than n = 5
diagram_lineage(pheno_tree) %>%
  DiagrammeR::render_graph(layout="tree")

The documentation for ?add_relationship contains more information about declaring and removing relationships. Users should be aware that model lineage is actually used by some functions that process xpose_set objects to generate output, so declaring parentage should be done only when it is valid. This does not mean necessarily that the child should be nested in the parent(s), but lineage is considered relevant in functions that compare models.

Comparing models in sets

Models in a set can be compared with a few functions and plots. The functions for comparison include a diff() method.

diff(pheno_set)
#> [1] -148.723  -37.080  -60.163  -43.281   35.133

The method above limits the comparison to the longest lineage in the provided set, starting at a base model if one is declared. The models included can be examined by probing with the xset_lineage() function.

tbl_diff <- function(set) tibble(
  models = xset_lineage(set),
  diff = c(0,diff(set))
)
tbl_diff(pheno_set)
#> # A tibble: 6 × 2
#>   models   diff
#>   <chr>   <dbl>
#> 1 run3      0  
#> 2 run5   -149. 
#> 3 run6    -37.1
#> 4 run9    -60.2
#> 5 run14   -43.3
#> 6 run15    35.1
pheno_set %>%
  remove_relationship(run9~run6) %>%
  tbl_diff()
#> # A tibble: 5 × 2
#>   models      diff
#>   <chr>      <dbl>
#> 1 run3      0     
#> 2 run5   -149.    
#> 3 run6    -37.1   
#> 4 run10    -0.0230
#> 5 run12    -0.181
pheno_set %>%
  set_base_model(run6) %>%
  tbl_diff()
#> # A tibble: 4 × 2
#>   models  diff
#>   <chr>  <dbl>
#> 1 run6     0  
#> 2 run9   -60.2
#> 3 run14  -43.3
#> 4 run15   35.1
tibble(
  models = xset_lineage(pheno_set,run6),
  diff = c(0,diff(pheno_set,run6))
)
#> # A tibble: 4 × 2
#>   models  diff
#>   <chr>  <dbl>
#> 1 run6     0  
#> 2 run9   -60.2
#> 3 run14  -43.3
#> 4 run15   35.1

xset_lineage() and diff() can also generate lists if multiple models are passed to ..., which treats those as base models.

diff(pheno_set, run10,run9)
#> $run10
#> [1] -0.181
#> 
#> $run9
#> [1] -43.281  35.133
xset_lineage(pheno_set, run10,run9)
#> $run10
#> [1] "run10" "run12"
#> 
#> $run9
#> [1] "run9"  "run14" "run15"

Models can also be compared through various plots. Many that use individual objective function values (iOFVs) require these values to be in the xpdb data. If these are missing and the xpose_data object is generated based on a NONMEM run, these can be added with the backfill_iofv() function. We discuss focusing in another section, but it is useful here,

Two models can be compared one way using an updated version of a xpose4 function; this is referred to in some places as a “shark plot”, and it is called xpose4::dOFV.vs.id() in xpose4. As such, it is called shark_plot() or dofv_vs_id() in xpose.xtras.

pheno_set %>%
  focus_qapply(backfill_iofv) %>%
  shark_plot(run6, run9, quiet = TRUE)

There are also functions to use an xpose_set for model-averaging and other ways to visually explore the impact of model changes on individual fits which are all documented within the package. Many of these are considered experimental, but all facilitate further improvements.

Manipulating a set

We have already explored a few ways to manipulate a set. These manipulations are distinctly designed so that a user can change the overall set or xpose_data elements within the set using fairly intuitive functionality.

Information from xpose_data summary or parameter values can be “exposed”, which means they become associated with the set item on the top level. To view these as a table, the function reshape_set() can be used. Note the exposed data are denoted by the prefix .. (two dots) in their column names.

pheno_set %>%
  expose_property(ofv) %>%
  expose_param(ome1) %>%
  reshape_set() %>%
  head()
#> # A tibble: 6 × 7
#>   xpdb         label parent       base  focus ..ofv ..ome1
#>   <named list> <chr> <named list> <lgl> <lgl> <dbl>  <dbl>
#> 1 <xp_xtras>   run3  <chr [1]>    FALSE FALSE  874.  1.69 
#> 2 <xp_xtras>   run4  <chr [1]>    FALSE FALSE  834.  0.608
#> 3 <xp_xtras>   run5  <chr [1]>    FALSE FALSE  726.  0.198
#> 4 <xp_xtras>   run6  <chr [1]>    FALSE FALSE  689.  0.239
#> 5 <xp_xtras>   run10 <chr [1]>    FALSE FALSE  688.  0.243
#> 6 <xp_xtras>   run12 <chr [1]>    FALSE FALSE  688.  0.232

There are methods for the popular dplyr verbs which attempt to produce the expected results despite the underlying structure of an xpose_set not being tabular.

pheno_set %>%
  select(run3,run15) %>%
  names()
#> [1] "run3"  "run15"
pheno_set %>%
  # Note renaming can affect parentage.
  # For simplicity, this method does not change 
  # parent automatically in child
  rename(NewName = run3) %>%
  names()
#>  [1] "NewName" "run4"    "run5"    "run6"    "run10"   "run12"   "run11"  
#>  [8] "run13"   "run7"    "run8"    "run9"    "run14"   "run15"   "run16"
pheno_set %>%
  expose_property(ofv) %>%
  filter(..ofv < 700) %>%
  names()
#>  [1] "run6"  "run10" "run12" "run11" "run13" "run7"  "run8"  "run9"  "run14"
#> [10] "run15" "run16"
pheno_set %>%
  expose_param(ome1) %>%
  pull(..ome1)
#>  [1] 1.69000 0.60800 0.19800 0.23900 0.24270 0.23200 0.23700 0.22800 0.25400
#> [10] 0.03432 0.17600 0.03870 0.03470 0.04037

These verbs are also defined for xpose_data objects, and it may be desired to “forward” the function to the xpose_data objects in a set instead of applying them to the set object. That functionality is available through focusing. Focused elements in the set automatically forward functions to the xpose_data objects in the element, and do nothing to unfocused elements.

focus_test <- pheno_set %>%
  focus_xpdb(run3,run15) %>%
  mutate(test_col = 1) %>%
  unfocus_xpdb()
tail(names(get_data(focus_test$run6$xpdb, quiet=TRUE)))
#> [1] "CWRES" "NPDE"  "DV"    "PRED"  "RES"   "WRES"
tail(names(get_data(focus_test$run3$xpdb, quiet=TRUE)))
#> [1] "NPDE"     "DV"       "PRED"     "RES"      "WRES"     "test_col"

Any function can be passed to focused xpose_data objects with focus_function(). A shortcut for focusing everything, applying a function and unfocusing everything is available in the form of focus_qapply().