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artoo is a lightweight, lossless, CDISC-native reader and writer for clinical-trial datasets. It moves data between SAS XPORT (XPT), CDISC Dataset-JSON v1.1, NDJSON, Apache Parquet, and RDS through one canonical metadata model, so converting between any two is lossless by construction — not by best effort. It also reads and writes the specification itself: Define-XML 2.1 and 2.0, Pinnacle 21 workbooks, and a native lossless JSON.
Install the released version from CRAN:
install.packages("artoo")Or the development version from GitHub:
# install.packages("pak")
pak::pak("vthanik/artoo")
# or
remotes::install_github("vthanik/artoo")A spec describes the dataset; apply_spec() conforms a
raw frame to it; the writers carry every piece of metadata to disk — one
pipeable chain:
library(artoo)
# Coerce, order, sort, stamp metadata, then write. The writers return their
# input invisibly, so one conformed frame fans out to every deliverable.
path <- tempfile(fileext = ".xpt")
adsl <- cdisc_adsl |>
apply_spec(adam_spec, "ADSL") |>
write_xpt(path)
#> 6 variables the spec declares are absent from the data (not added): `TRTDURD`,
#> `DISONDT`, `EOSSTT`, `DCSREAS`, `EOSDISP`, and `MMS1TSBL`.
#> ℹ See `conformance(x)` for the findings.
# Read it back — labels, formats, types, and record count intact.
get_meta(read_xpt(path))@dataset$records
#> [1] 60The same spec is the submission’s define.xml.
write_spec() dispatches on the extension, schema-validates
the document before it reaches its destination, and
lint_define() checks the references the schema cannot
see:
define <- tempfile(fileext = ".xml")
write_spec(adam_spec, define)
# 227 definitions, 248 references, nothing dangling and nothing orphaned.
lint_define(define)
#> artoo Define-XML Reference Check
#> ================================
#>
#> Summary
#> -------
#> Document: file8588416783eb.xml
#> Definitions: 227 References: 248
#>
#> Findings Summary
#> ----------------
#> error 0
#> warning 32
#> note 0
#>
#> Warnings
#> --------
#> [define_orphan_codelist] Codelist CL.AVISIT is defined but nothing references it.
#> [define_orphan_codelist] Codelist CL.AVISITN is defined but nothing references it.
#> [define_orphan_codelist] Codelist CL.AWU is defined but nothing references it.
#> [define_orphan_codelist] Codelist CL.DTYPE is defined but nothing references it.
#> [define_orphan_codelist] Codelist CL.PARAMCD_ADQSADAS is defined but nothing references it.
#> [define_orphan_codelist] Codelist CL.PARAMN_ADQSADAS is defined but nothing references it.
#> [define_orphan_codelist] Codelist CL.PARAM_ADQSADAS is defined but nothing references it.
#> [define_orphan_codelist] Codelist CL.AWRANGE_ADQSADAS is defined but nothing references it.
#> [define_orphan_codelist] Codelist CL.VISIT is defined but nothing references it.
#> [define_orphan_codelist] Codelist CL.VISITNUM is defined but nothing references it.
#> [define_orphan_method] Method MT.ADQSADAS.AVISIT is defined but nothing references it.
#> [define_orphan_method] Method MT.ADQSADAS.ADY is defined but nothing references it.
#> [define_orphan_method] Method MT.ADQSADAS.ADT is defined but nothing references it.
#> [define_orphan_method] Method MT.ADQSADAS.BASE is defined but nothing references it.
#> [define_orphan_method] Method MT.ADQSADAS.CHG is defined but nothing references it.
#> ... and 17 more (see x@findings)columns() is the quick look a SAS programmer expects
from PROC CONTENTS, on a conformed frame or straight off a
file:
columns(adsl)
#> <artoo_columns> ADSL -- 48 variables, 60 obs
#> # Variable Type Len Format Label Key
#> 1 STUDYID Char 12 Study Identifier 1
#> 2 USUBJID Char 11 Unique Subject Identifier 2
#> 3 SUBJID Char 4 Subject Identifier for the Study
#> 4 SITEID Char 3 Study Site Identifier
#> 5 SITEGR1 Char 3 Pooled Site Group 1
#> 6 ARM Char 20 Description of Planned Arm
#> 7 TRT01P Char 20 Planned Treatment for Period 01
#> 8 TRT01PN Num Planned Treatment for Period 01 (N)
#> 9 TRT01A Char 20 Actual Treatment for Period 01
#> 10 TRT01AN Num Actual Treatment for Period 01 (N)
#> 11 TRTSDT Num DATE9. Date of First Exposure to Treatment
#> 12 TRTEDT Num DATE9. Date of Last Exposure to Treatment
#> 13 AVGDD Num 5.1 Avg Daily Dose (as planned)
#> 14 CUMDOSE Num 8.1 Cumulative Dose (as planned)
#> 15 AGE Num Age
#> 16 AGEGR1 Char 5 Pooled Age Group 1
#> 17 AGEGR1N Num Pooled Age Group 1 (N)
#> 18 AGEU Char 5 Age Units
#> 19 RACE Char 32 Race
#> 20 RACEN Num Race (N)
#> 21 SEX Char 1 Sex
#> 22 ETHNIC Char 22 Ethnicity
#> 23 SAFFL Char 1 Safety Population Flag
#> 24 ITTFL Char 1 Intent-To-Treat Population Flag
#> 25 EFFFL Char 1 Efficacy Population Flag
#> 26 COMP8FL Char 1 Completers of Week 8 Population Flag
#> 27 COMP16FL Char 1 Completers of Week 16 Population Flag
#> 28 COMP24FL Char 1 Completers of Week 24 Population Flag
#> 29 DISCONFL Char 1 Subject Discontinued Study Flag
#> 30 DSRAEFL Char 1 Subject Discontinued due to AE Flag
#> 31 DTHFL Char 1 Subject Death Flag
#> 32 BMIBL Num 5.1 Baseline BMI (kg/m^2)
#> 33 BMIBLGR1 Char 6 Pooled Baseline BMI Group 1
#> 34 HEIGHTBL Num 6.1 Baseline Height (cm)
#> 35 WEIGHTBL Num 6.1 Baseline Weight (kg)
#> 36 EDUCLVL Num Years of Education
#> 37 DURDIS Num 6.1 Duration of Disease (Months)
#> 38 DURDSGR1 Char 4 Pooled Disease Duration Group 1
#> 39 VISIT1DT Num DATE9. Date of Visit 1
#> 40 RFSTDTC Char 10 Subject Reference Start Date/Time
#> 41 RFENDTC Char 10 Subject Reference End Date/Time
#> 42 VISNUMEN Num End of Trt Visit (Vis 12 or Early Term.)
#> 43 RFENDT Num Date of Discontinuation/Completion
#> 44 TRTDUR Num
#> 45 DISONSDT Num DATE9.
#> 46 DCDECOD Char 27
#> 47 DCREASCD Char 18
#> 48 MMSETOT Num--DTC
text, and codelists follow the Dataset-JSON v1.1 vocabulary. Specs read
from and write back to Define-XML 2.1 and 2.0, Pinnacle 21 workbooks,
and a native lossless JSON — so a workbook becomes a submission-grade
define.xml in one line.artoo is the carrier between the formats a clinical-trial dataset travels in: the XPORT a regulator expects, the Dataset-JSON modern CDISC exchange uses, the Parquet an analytics stack reads, and an R-native checkpoint. Reach for it whenever a dataset must change formats without losing the metadata that makes it submission-ready — labels, types, lengths, display formats, codelists, and keys — and you want that guarantee enforced rather than hoped for. It is a focused reader/writer, not a validation suite or a table renderer.
| Format | Reader | Writer | Use |
|---|---|---|---|
| SAS XPORT (XPT) | read_xpt() |
write_xpt() |
FDA / PMDA submission |
| CDISC Dataset-JSON | read_json() |
write_json() |
Modern CDISC interchange |
| NDJSON | read_ndjson() |
write_ndjson() |
Streaming Dataset-JSON |
| Apache Parquet | read_parquet() |
write_parquet() |
Analytics, columnar store |
| RDS | read_rds() |
write_rds() |
Fast R-native storage |
The generic read_dataset() /
write_dataset() dispatch on the file extension; every
reader supports partial reads via col_select and
n_max.
Specifications travel the same way, through read_spec()
and write_spec():
| Format | Extension | Use |
|---|---|---|
| Define-XML | .xml |
The submission deliverable, 2.1 or 2.0 |
| Pinnacle 21 | .xlsx |
The workbook a spec is authored in |
| Native JSON | .json |
Lossless checkpoint, nothing dropped |
write_spec() schema-validates a define.xml before the
file reaches its destination, so an invalid one never overwrites a good
file. validate_define() checks any vendor’s document
against the bundled CDISC schemas offline; lint_define()
walks the OID graph the schema cannot see; write_template()
writes a blank workbook shaped exactly like the reader.
Partial ISO 8601 dates are first-class: a character
--DTC column typed date writes to XPT as ISO
text — "1951-12" survives byte for byte — while
targetDataType = "integer" drives the ADaM numeric-date
convention. SAS TIME values arrive as hms
(seconds since midnight), and >24h, negative, and
fractional times round-trip every format.
apply_spec() and every conformance
finding.MIT © Vignesh Thanikachalam
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.