osp.snapshots

osp.snapshots provides an R interface for working with PK-Sim project snapshots: import, navigate, modify, and export the nested JSON structure as R objects and data frames.

Installation

Released version, as a prebuilt binary on Windows and macOS. osp.snapshots comes from the esqLABS universe and its ospsuite dependency from the Open Systems Pharmacology universe, so both go on repos:

install.packages(
  "osp.snapshots",
  repos = c(
    esqLABS = "https://esqlabs.r-universe.dev",
    OSP = "https://open-systems-pharmacology.r-universe.dev",
    getOption("repos")
  )
)

Development version from GitHub. pak takes osp.snapshots from GitHub, so only the OSP universe is needed, for ospsuite:

# install.packages("pak")
options(repos = c(
  OSP = "https://open-systems-pharmacology.r-universe.dev",
  getOption("repos")
))

pak::pak("esqLABS/osp.snapshots")

Usage

library(osp.snapshots)

# Load a snapshot from a template name, a local .json path, or a URL
snapshot <- load_snapshot("Midazolam")
snapshot
#> 
#> ── PKSIM Snapshot ──────────────────────────────────────────────────────────────
#> ℹ Version: 80 (PKSIM 12.0)
#> • Compounds: 1
#> • Events: 1
#> • ExpressionProfiles: 8
#> • Formulations: 2
#> • Individuals: 2
#> • ObservedData: 115
#> • ObservedDataClassifications: 47
#> • ParameterIdentifications: 3
#> • Protocols: 33
#> • SimulationClassifications: 4
#> • Simulations: 37

# Navigate the building blocks
snapshot$individuals$`European (P-gp modified, CYP3A4 36 h)`
#> 
#> ── Individual: European (P-gp modified, CYP3A4 36 h) | Seed: 17189110 ──────────
#> 
#> ── Characteristics ──
#> 
#> • Species: Human
#> • Population: European_ICRP_2002
#> • Gender: MALE
#> • Age: 30 year(s)
#> • Calculation Methods:
#>   • SurfaceAreaPlsInt_VAR1
#>   • Body surface area - Mosteller
#> 
#> ── Parameters ──
#> 
#> • Organism|Liver|EHC continuous fraction: 1
#> 
#> ── Expression Profiles ──
#> 
#> • CYP3A4|Human|European (P-gp modified, CYP3A4 36 h)
#> • AADAC|Human|European (P-gp modified, CYP3A4 36 h)
#> • P-gp|Human|European (P-gp modified, CYP3A4 36 h)
#> • OATP1B1|Human|European (P-gp modified, CYP3A4 36 h)
#> • ATP1A2|Human|European (P-gp modified, CYP3A4 36 h)
#> • UGT1A4|Human|European (P-gp modified, CYP3A4 36 h)
#> • GABRG2|Human|European (P-gp modified, CYP3A4 36 h)

# Convert a collection to tibbles for analysis
as_tibbles(snapshot, "individuals")
#> $individuals
#> # A tibble: 2 × 18
#>   individual_id         name  description   seed species population gender   age
#>   <chr>                 <chr> <chr>        <int> <chr>   <chr>      <chr>  <dbl>
#> 1 European (P-gp modif… Euro… <NA>        1.72e7 Human   European_… MALE    30  
#> 2 Korean (Yu 2004 stud… Kore… <NA>        5.30e7 Human   Asian_Tan… MALE    23.3
#> # ℹ 10 more variables: age_unit <chr>, gestational_age <dbl>,
#> #   gestational_age_unit <chr>, weight <dbl>, weight_unit <chr>, height <dbl>,
#> #   height_unit <chr>, disease_state <chr>, calculation_methods <glue>,
#> #   disease_state_parameters <chr>
#> 
#> $individuals_parameters
#> # A tibble: 2 × 7
#>   individual_id                   path  value unit  source description source_id
#>   <chr>                           <chr> <dbl> <chr> <chr>  <chr>           <int>
#> 1 European (P-gp modified, CYP3A… Orga…     1 <NA>  Unkno… <NA>               NA
#> 2 Korean (Yu 2004 study)          Orga…     1 <NA>  Unkno… <NA>               NA
#> 
#> $individuals_expressions
#> # A tibble: 14 × 2
#>    individual_id                         profile                                
#>    <chr>                                 <chr>                                  
#>  1 European (P-gp modified, CYP3A4 36 h) CYP3A4|Human|European (P-gp modified, …
#>  2 European (P-gp modified, CYP3A4 36 h) AADAC|Human|European (P-gp modified, C…
#>  3 European (P-gp modified, CYP3A4 36 h) P-gp|Human|European (P-gp modified, CY…
#>  4 European (P-gp modified, CYP3A4 36 h) OATP1B1|Human|European (P-gp modified,…
#>  5 European (P-gp modified, CYP3A4 36 h) ATP1A2|Human|European (P-gp modified, …
#>  6 European (P-gp modified, CYP3A4 36 h) UGT1A4|Human|European (P-gp modified, …
#>  7 European (P-gp modified, CYP3A4 36 h) GABRG2|Human|European (P-gp modified, …
#>  8 Korean (Yu 2004 study)                CYP3A4|Human|Korean (Yu 2004 study)    
#>  9 Korean (Yu 2004 study)                AADAC|Human|European (P-gp modified, C…
#> 10 Korean (Yu 2004 study)                P-gp|Human|European (P-gp modified, CY…
#> 11 Korean (Yu 2004 study)                OATP1B1|Human|European (P-gp modified,…
#> 12 Korean (Yu 2004 study)                ATP1A2|Human|European (P-gp modified, …
#> 13 Korean (Yu 2004 study)                UGT1A4|Human|European (P-gp modified, …
#> 14 Korean (Yu 2004 study)                GABRG2|Human|European (P-gp modified, …

Key features

• Import and export: Load snapshots from JSON files, URLs, or templates, and export the modified snapshot back to JSON.
• Navigate: Reach every building block (individuals, compounds, formulations, and the rest) with R syntax.
• Modify: Change parameters and add or remove building blocks in place.
• Convert: Turn any building block collection into structured tibbles with as_tibbles().
• Integrate: Bridge PK-Sim observed data to ospsuite::DataSet objects.

Learn more

• vignette("osp-snapshots"): getting started
• vignette("creating-building-blocks"): creating and managing building blocks
• vignette("exporting-snapshots-to-dataframes"): exporting snapshots to data frames
• vignette("simulations"): building simulations from scratch

Getting help

• Function reference
• Report bugs