| Title: | VeloMetrix R Client |
|---|---|
| Description: | A native R client for the VeloMetrix REST API (vmx-api). Wraps the treatment-to-simulation analysis workflow in ergonomic, pipe-friendly verbs that block-and-poll for asynchronous server jobs and return native R objects (tibbles and typed S3 objects). The package orchestrates server-side jobs; it holds no business logic of its own. Targets API 0.2.x / CLI 0.6.x. |
| Authors: | Eric Novik [aut, cre], Juho Timonen [ctb], Generable [cph, fnd] |
| Maintainer: | Eric Novik <[email protected]> |
| License: | Apache License (>= 2) |
| Version: | 0.1.1 |
| Built: | 2026-07-02 15:18:36 UTC |
| Source: | https://github.com/generable/vmxr |
GET /studies/{std_id}/analysis-log — the unified newest-first event feed,
auto-paginated into a tibble with a kind discriminator per row.
vmx_analysis_log( study, kind = NULL, event_type = NULL, outcome = NULL, severity = NULL, since = NULL, resource = NULL, client = vmx_client() )vmx_analysis_log( study, kind = NULL, event_type = NULL, outcome = NULL, severity = NULL, since = NULL, resource = NULL, client = vmx_client() )
study |
A study id ( |
kind |
Optional kind filter. |
event_type |
Optional event-type filter. |
outcome |
Optional outcome filter. |
severity |
Optional severity filter. |
since |
Optional lower time bound: a |
resource |
Optional resource id (or object) to scope to. |
client |
A |
A tibble.
Resolves connection config with the precedence: explicit args ->
VMX_API_BASE_URL / VMX_API_TOKEN environment variables -> ~/.Renviron
-> a classed error. The token is stored on the object but redacted in
print() and never logged.
vmx_client(base_url = NULL, token = NULL, ...)vmx_client(base_url = NULL, token = NULL, ...)
base_url |
API base URL. Defaults to |
token |
Authentik personal access token (PAT). Defaults to
|
... |
Reserved for future options (timeouts, retries, user agent). |
An object of class vmx_client.
Fetch one data version
vmx_data_version(id, client = vmx_client())vmx_data_version(id, client = vmx_client())
id |
A data-version id ( |
client |
A |
A vmx_data_version.
Archive a data version
vmx_data_version_archive(dv, reason = NULL, client = vmx_client())vmx_data_version_archive(dv, reason = NULL, client = vmx_client())
dv |
A data-version id or |
reason |
Optional free-text reason. |
client |
A |
The updated vmx_data_version.
Starts a format job over an explicit upload composition
(POST /datasets/{ds_id}/data-versions). Returns the in-flight prep-status;
poll it with vmx_wait().
vmx_data_version_create( dataset, uploads, prior_config = NULL, client = vmx_client() )vmx_data_version_create( dataset, uploads, prior_config = NULL, client = vmx_client() )
dataset |
A dataset id ( |
uploads |
Character vector of upload ids ( |
prior_config |
Optional prior data-version ( |
client |
A |
A vmx_prep_status for the new job.
Fetches the signed-URL export envelope (GET /data-versions/{id}/export).
When dest is supplied the bundle is streamed to that path; otherwise the
parsed envelope (including the signed download_url) is returned.
vmx_data_version_export(dv, dest = NULL, client = vmx_client())vmx_data_version_export(dv, dest = NULL, client = vmx_client())
dv |
A data-version id or |
dest |
Optional local file path to stream the bundle to. |
client |
A |
The export envelope (list), or, when dest is set, dest invisibly.
GET /data-versions/{id}/tables/{domain} — returns the formatter's prepared
domain table as a tibble (columns typed per the server's column metadata,
which is attached as the "columns" attribute). gen_subject_uuid is the
canonical subject join key.
vmx_data_version_table( dv, domain = c("subjects", "pk", "dosing", "pd", "labs", "covariates"), client = vmx_client() )vmx_data_version_table( dv, domain = c("subjects", "pk", "dosing", "pd", "labs", "covariates"), client = vmx_client() )
dv |
A data-version id ( |
domain |
One of |
client |
A |
A tibble.
Unarchive a data version
vmx_data_version_unarchive(dv, client = vmx_client())vmx_data_version_unarchive(dv, client = vmx_client())
dv |
A data-version id or |
client |
A |
The updated vmx_data_version.
List data versions
vmx_data_versions( treatment = NULL, study = NULL, include_archived = FALSE, eligible_for_modeling = NULL, client = vmx_client() )vmx_data_versions( treatment = NULL, study = NULL, include_archived = FALSE, eligible_for_modeling = NULL, client = vmx_client() )
treatment |
Optional treatment filter. |
study |
Optional study filter. |
include_archived |
Include archived versions. |
eligible_for_modeling |
Optional modeling-eligibility filter. |
client |
A |
A tibble.
Fetch one dataset
vmx_dataset(id, client = vmx_client())vmx_dataset(id, client = vmx_client())
id |
A dataset id ( |
client |
A |
A vmx_dataset.
POST /datasets/{ds_id}/cancel — terminates the format job and mints a
cancelled DataVersion.
vmx_dataset_cancel(dataset, client = vmx_client())vmx_dataset_cancel(dataset, client = vmx_client())
dataset |
A dataset id or |
client |
A |
The updated vmx_prep_status.
Not implemented: the API's dataset-files listing does not expose per-file
download URLs. Use vmx_data_version_export() to pull a curated bundle.
vmx_dataset_download(dataset, dest = ".", client = vmx_client())vmx_dataset_download(dataset, dest = ".", client = vmx_client())
dataset |
A dataset id or |
dest |
Destination directory. |
client |
A |
Not yet implemented.
List the files in a dataset
vmx_dataset_files(dataset, client = vmx_client())vmx_dataset_files(dataset, client = vmx_client())
dataset |
A dataset id or |
client |
A |
A tibble.
Returns the dataset's allowlisted tag map as a two-column (key, value)
tibble. Reads the tags off a vmx_dataset object when given one, else
fetches the dataset.
vmx_dataset_tags(dataset, client = vmx_client())vmx_dataset_tags(dataset, client = vmx_client())
dataset |
A dataset id or |
client |
A |
A tibble with key and value columns.
List datasets
vmx_datasets(study = NULL, treatment = NULL, client = vmx_client())vmx_datasets(study = NULL, treatment = NULL, client = vmx_client())
study |
Optional study filter. |
treatment |
Optional treatment filter. |
client |
A |
A tibble.
POST /model-fits/{mf_id}/simulation-dosing-inputs.
vmx_dosing_input(fit, dosing_text, scenario_name, client = vmx_client())vmx_dosing_input(fit, dosing_text, scenario_name, client = vmx_client())
fit |
A fit id ( |
dosing_text |
The dosing regimen text. |
scenario_name |
One or more scenario names. |
client |
A |
A vmx_dosing_input (carries dosing_input_id).
Dosing-input status
vmx_dosing_input_status(dosing_input, client = vmx_client())vmx_dosing_input_status(dosing_input, client = vmx_client())
dosing_input |
A dosing-input id or |
client |
A |
A vmx_dosing_input.
One row per parameter, with the point estimate and credible interval.
vmx_fit_global_estimates(fit, client = vmx_client())vmx_fit_global_estimates(fit, client = vmx_client())
fit |
A fit id or |
client |
A |
A tibble.
Reshapes the pk block's parallel observation arrays (subject ids, time,
observed concentration, BLQ/ALOQ flags, LLOQ, …) into a one-row-per-
observation tibble. Non-columnar members — notably the predicted-
concentration quantile bands — are kept on the "extra" attribute; the PD
block is on "pd" and the fit id on "model_fit_id".
vmx_fit_obs_vs_pred(fit, client = vmx_client())vmx_fit_obs_vs_pred(fit, client = vmx_client())
fit |
A fit id or |
client |
A |
A tibble (one row per PK observation).
One row per subject x parameter, with the posterior point estimate (value)
and credible interval (ci_lower/ci_upper).
vmx_fit_subject_estimates(fit, client = vmx_client())vmx_fit_subject_estimates(fit, client = vmx_client())
fit |
A fit id or |
client |
A |
A tibble.
Returns the parsed VPC artifact (per dose-group and per-subject quantile bands over time grids). Tibble reshaping is deferred; see the package NEWS.
vmx_fit_vpc(fit, client = vmx_client())vmx_fit_vpc(fit, client = vmx_client())
fit |
A fit id or |
client |
A |
A list (the parsed artifact).
Calls GET /health.
vmx_health(client = vmx_client())vmx_health(client = vmx_client())
client |
A |
Invisibly, a vmx_health object (status, version,
api_contract_version, engine, engine_version); raises a classed error
if the API is unreachable or unhealthy.
pd_marker uses the design's "GEN_uuid:increasing" / ":decreasing"
shorthand; it is parsed into the API's {gen_uuid, direction} form.
vmx_model_build( data_version, time_basis, pd_marker = NULL, covariate = NULL, idempotency_key = NULL, retried_from = NULL, wait = FALSE, ..., client = vmx_client() )vmx_model_build( data_version, time_basis, pd_marker = NULL, covariate = NULL, idempotency_key = NULL, retried_from = NULL, wait = FALSE, ..., client = vmx_client() )
data_version |
A data-version id or |
time_basis |
Time basis. |
pd_marker |
Optional |
covariate |
Optional covariate name(s). |
idempotency_key |
Optional idempotency key. |
retried_from |
Optional prior run to retry from. |
wait |
If |
... |
Polling controls forwarded to |
client |
A |
A vmx_model_build_run.
Download build-run artifacts
vmx_model_build_artifacts(run, dest = ".", client = vmx_client())vmx_model_build_artifacts(run, dest = ".", client = vmx_client())
run |
A build-run id or object. |
dest |
Destination directory. |
client |
A |
Not yet implemented.
Cancel a build run
vmx_model_build_cancel(run, client = vmx_client())vmx_model_build_cancel(run, client = vmx_client())
run |
A build-run id or object. |
client |
A |
A vmx_model_build_run.
Build-run events (SSE stream)
vmx_model_build_events(run, client = vmx_client())vmx_model_build_events(run, client = vmx_client())
run |
A build-run id or object. |
client |
A |
Not yet implemented.
Markdown export of a build run
vmx_model_build_export(run, client = vmx_client())vmx_model_build_export(run, client = vmx_client())
run |
A build-run id or object. |
client |
A |
The export markdown as a length-1 character vector.
Build-run logs
vmx_model_build_logs(run, client = vmx_client())vmx_model_build_logs(run, client = vmx_client())
run |
A build-run id or object. |
client |
A |
A tibble of log lines.
Build-run report status (signed HTML report URL when ready)
vmx_model_build_report(run, client = vmx_client())vmx_model_build_report(run, client = vmx_client())
run |
A build-run id or object. |
client |
A |
A list with status and, when ready, url.
POST /model-build-runs/{run_id}/report queues HTML report generation.
vmx_model_build_report_create( run, subject_plot_mode = c("all", "none"), client = vmx_client() )vmx_model_build_report_create( run, subject_plot_mode = c("all", "none"), client = vmx_client() )
run |
A build-run id or object. |
subject_plot_mode |
One of |
client |
A |
A list with report status.
Build-run results
vmx_model_build_results(run, client = vmx_client())vmx_model_build_results(run, client = vmx_client())
run |
A build-run id or object. |
client |
A |
A list (fits summary, modeling population, PK structure selection).
List model build runs
vmx_model_build_runs( data_version = NULL, study = NULL, treatment = NULL, status = NULL, client = vmx_client() )vmx_model_build_runs( data_version = NULL, study = NULL, treatment = NULL, status = NULL, client = vmx_client() )
data_version, study, treatment, status
|
Optional filters. |
client |
A |
A tibble.
Build-run status
vmx_model_build_status(run, client = vmx_client())vmx_model_build_status(run, client = vmx_client())
run |
A build-run id ( |
client |
A |
A vmx_model_build_run.
GET /model-catalog returns categories of models; this flattens them into
one tibble with a category column.
vmx_model_catalog(data_version = NULL, client = vmx_client())vmx_model_catalog(data_version = NULL, client = vmx_client())
data_version |
Optional data-version to tailor the catalog to. |
client |
A |
A tibble.
Returns a vmx_model_data bundle with $subjects, $pk, $pd (each a
tibble, or NULL when the DataVersion has no such prepared table), and
$meta (units, time bases, PD-marker manifest, subject count) read from the
DataVersion. Only domains flagged in the DV's table_availability are
fetched, so absent optional tables don't 404.
vmx_model_data(dv, client = vmx_client())vmx_model_data(dv, client = vmx_client())
dv |
A data-version id or |
client |
A |
A vmx_model_data object.
Describe a model
vmx_model_describe(model_name, client = vmx_client())vmx_model_describe(model_name, client = vmx_client())
model_name |
Catalog model name. |
client |
A |
A named list.
Fetch one model fit's details
vmx_model_fit(id, client = vmx_client())vmx_model_fit(id, client = vmx_client())
id |
A fit id ( |
client |
A |
A vmx_model_fit (metadata / model / inference).
Model-fit postprocessor status
vmx_model_fit_postprocessor_status(fit, client = vmx_client())vmx_model_fit_postprocessor_status(fit, client = vmx_client())
fit |
A fit id or |
client |
A |
A list with postprocessor status.
List model fits
vmx_model_fits( run = NULL, data_version = NULL, model_type = NULL, marker_name = NULL, status = NULL, client = vmx_client() )vmx_model_fits( run = NULL, data_version = NULL, model_type = NULL, marker_name = NULL, status = NULL, client = vmx_client() )
run, data_version, model_type, marker_name, status
|
Optional filters. |
client |
A |
A tibble.
Preview modeling options for a data version
vmx_modeling_options( data_version, time_basis, pd_marker = NULL, covariate = NULL, client = vmx_client() )vmx_modeling_options( data_version, time_basis, pd_marker = NULL, covariate = NULL, client = vmx_client() )
data_version |
A data-version id or |
time_basis |
Time basis. |
pd_marker |
Optional PD marker gen_uuid(s) (character vector). |
covariate |
Optional covariate name(s). |
client |
A |
A list (the selection preview).
Creates the analysis (POST /nca-analyses) and, by default, blocks until it
settles. time_basis is one of "observed", "nominal", or
"nominal_from_observed_dose" (validated server-side against the
DataVersion's available bases).
vmx_nca( data_version, time_basis, idempotency_key = NULL, retried_from = NULL, wait = TRUE, ..., client = vmx_client() )vmx_nca( data_version, time_basis, idempotency_key = NULL, retried_from = NULL, wait = TRUE, ..., client = vmx_client() )
data_version |
A data-version id ( |
time_basis |
The time basis to compute on. |
idempotency_key, retried_from
|
Optional create fields. |
wait |
If |
... |
Polling controls forwarded to |
client |
A |
A vmx_nca_analysis.
List NCA analyses
vmx_nca_analyses( data_version = NULL, study = NULL, treatment = NULL, status = NULL, time_basis = NULL, client = vmx_client() )vmx_nca_analyses( data_version = NULL, study = NULL, treatment = NULL, status = NULL, time_basis = NULL, client = vmx_client() )
data_version |
Optional data-version ( |
study |
Optional study ( |
treatment |
Optional treatment ( |
status |
Optional status filter ( |
time_basis |
Optional time-basis filter. |
client |
A |
A tibble, one row per analysis.
Fetch one NCA analysis
vmx_nca_get(id, client = vmx_client())vmx_nca_get(id, client = vmx_client())
id |
An NCA id ( |
client |
A |
A vmx_nca_analysis.
Reshapes the point_estimates payload (metric -> per-subject values, parallel
to the subject arrays) into a tidy tibble: subject_id, gen_subject_uuid,
and one column per PK quantity. The quantity metadata (display names, units,
explanations) is attached as the "quantities" attribute.
vmx_nca_result(nca, client = vmx_client())vmx_nca_result(nca, client = vmx_client())
nca |
An NCA id or |
client |
A |
A tibble.
Not yet implemented. Assembling the NONMEM/nlmixr2 layout
(ID/TIME/DV/AMT/EVID/CMT/MDV/RATE/II/ADDL/SS + covariates) from the pk and
dosing domain tables requires the DataVersion column/manifest contract to
be pinned and validated against real data; see the package NEWS. Use
vmx_pk() / vmx_data_version_table() for the tidy tables today.
vmx_nlmixr_data(dv, analyte = NULL, client = vmx_client())vmx_nlmixr_data(dv, analyte = NULL, client = vmx_client())
dv |
A data-version id or |
analyte |
Analyte to assemble. |
client |
A |
Not yet implemented.
PD observations table
vmx_pd(dv, client = vmx_client())vmx_pd(dv, client = vmx_client())
dv |
A data-version id or |
client |
A |
A tibble.
PK observations + events table
vmx_pk(dv, client = vmx_client())vmx_pk(dv, client = vmx_client())
dv |
A data-version id or |
client |
A |
A tibble.
Answer prep questions and resume formatting
vmx_prep_answer(dataset, answers, client = vmx_client())vmx_prep_answer(dataset, answers, client = vmx_client())
dataset |
A dataset id or |
answers |
A named list mapping each prompt |
client |
A |
Questions raised by prep (when awaiting input)
vmx_prep_questions(dataset, client = vmx_client())vmx_prep_questions(dataset, client = vmx_client())
dataset |
A dataset id or |
client |
A |
A tibble of pending questions.
Calls GET /datasets/{ds_id}/prep-status.
vmx_prep_status(dataset, client = vmx_client())vmx_prep_status(dataset, client = vmx_client())
dataset |
A dataset id ( |
client |
A |
A vmx_prep_status (status, and data_version_id once settled).
Cancel a simulation job
vmx_sim_cancel(job, client = vmx_client())vmx_sim_cancel(job, client = vmx_client())
job |
A job id or |
client |
A |
A vmx_simulation_job.
POST /model-fits/{mf_id}/existing-subject-simulation-jobs.
vmx_sim_existing_subject( fit, dosing_input, subjects, idempotency_key = NULL, retried_from = NULL, min_timepoints = NULL, wait = FALSE, ..., client = vmx_client() )vmx_sim_existing_subject( fit, dosing_input, subjects, idempotency_key = NULL, retried_from = NULL, min_timepoints = NULL, wait = FALSE, ..., client = vmx_client() )
fit |
A fit id or |
dosing_input |
A dosing-input id or |
subjects |
Subjects to simulate: a data.frame/tibble with
|
idempotency_key, retried_from
|
Optional create fields. |
min_timepoints |
Optional minimum number of simulated timepoints. |
wait |
If |
... |
Polling controls forwarded to |
client |
A |
A vmx_simulation_job.
POST /model-fits/{mf_id}/existing-subject-simulation-jobs/from-text.
vmx_sim_existing_subject_from_text( fit, dosing_text, subjects, idempotency_key = NULL, retried_from = NULL, min_timepoints = NULL, wait = FALSE, ..., client = vmx_client() )vmx_sim_existing_subject_from_text( fit, dosing_text, subjects, idempotency_key = NULL, retried_from = NULL, min_timepoints = NULL, wait = FALSE, ..., client = vmx_client() )
fit |
A fit id or |
dosing_text |
The dosing regimen text. |
subjects |
Subjects to simulate: a data.frame/tibble with
|
idempotency_key, retried_from
|
Optional create fields. |
min_timepoints |
Optional minimum number of simulated timepoints. |
wait |
If |
... |
Polling controls forwarded to |
client |
A |
A vmx_simulation_job.
POST /model-fits/{mf_id}/hypothetical-subject-simulation-jobs.
vmx_sim_hypothetical_subject( fit, dosing_input, subjects, idempotency_key = NULL, retried_from = NULL, min_timepoints = NULL, wait = FALSE, ..., client = vmx_client() )vmx_sim_hypothetical_subject( fit, dosing_input, subjects, idempotency_key = NULL, retried_from = NULL, min_timepoints = NULL, wait = FALSE, ..., client = vmx_client() )
fit |
A fit id or |
dosing_input |
A dosing-input id or |
subjects |
A data.frame/tibble with a |
idempotency_key, retried_from
|
Optional create fields. |
min_timepoints |
Optional minimum number of simulated timepoints. |
wait |
If |
... |
Polling controls forwarded to |
client |
A |
A vmx_simulation_job.
POST /model-fits/{mf_id}/hypothetical-subject-simulation-jobs/from-text.
vmx_sim_hypothetical_subject_from_text( fit, dosing_text, subjects, idempotency_key = NULL, retried_from = NULL, min_timepoints = NULL, wait = FALSE, ..., client = vmx_client() )vmx_sim_hypothetical_subject_from_text( fit, dosing_text, subjects, idempotency_key = NULL, retried_from = NULL, min_timepoints = NULL, wait = FALSE, ..., client = vmx_client() )
fit |
A fit id or |
dosing_text |
The dosing regimen text. |
subjects |
A data.frame/tibble with a |
idempotency_key, retried_from
|
Optional create fields. |
min_timepoints |
Optional minimum number of simulated timepoints. |
wait |
If |
... |
Polling controls forwarded to |
client |
A |
A vmx_simulation_job.
List simulation jobs for a model fit
vmx_sim_jobs(fit, client = vmx_client())vmx_sim_jobs(fit, client = vmx_client())
fit |
A fit id or |
client |
A |
A tibble.
POST /model-fits/{mf_id}/population-simulation-jobs.
vmx_sim_population( fit, dosing_input, scenario_name, idempotency_key = NULL, retried_from = NULL, min_timepoints = NULL, wait = FALSE, ..., client = vmx_client() )vmx_sim_population( fit, dosing_input, scenario_name, idempotency_key = NULL, retried_from = NULL, min_timepoints = NULL, wait = FALSE, ..., client = vmx_client() )
fit |
A fit id or |
dosing_input |
A dosing-input id or |
scenario_name |
The population scenario name. |
idempotency_key, retried_from
|
Optional create fields. |
min_timepoints |
Optional minimum number of simulated timepoints. |
wait |
If |
... |
Polling controls forwarded to |
client |
A |
A vmx_simulation_job.
POST /model-fits/{mf_id}/population-simulation-jobs/from-text.
vmx_sim_population_from_text( fit, dosing_text, scenario_name, idempotency_key = NULL, retried_from = NULL, min_timepoints = NULL, wait = FALSE, ..., client = vmx_client() )vmx_sim_population_from_text( fit, dosing_text, scenario_name, idempotency_key = NULL, retried_from = NULL, min_timepoints = NULL, wait = FALSE, ..., client = vmx_client() )
fit |
A fit id or |
dosing_text |
The dosing regimen text. |
scenario_name |
The population scenario name. |
idempotency_key, retried_from
|
Optional create fields. |
min_timepoints |
Optional minimum number of simulated timepoints. |
wait |
If |
... |
Polling controls forwarded to |
client |
A |
A vmx_simulation_job.
GET /simulation-jobs/{id}/result. Returns the parsed result payload
(subject/time series with prediction bands). Tibble reshaping is deferred
pending confirmation of the artifact shape; see the package NEWS.
vmx_sim_result(job, grouping_variable = NULL, client = vmx_client())vmx_sim_result(job, grouping_variable = NULL, client = vmx_client())
job |
A job id or |
grouping_variable |
Optional server-side grouping. |
client |
A |
A list (the parsed result).
Simulation job status
vmx_sim_status(job, client = vmx_client())vmx_sim_status(job, client = vmx_client())
job |
A job id ( |
client |
A |
A vmx_simulation_job.
List studies for a treatment
vmx_studies(treatment = NULL, status = NULL, client = vmx_client())vmx_studies(treatment = NULL, status = NULL, client = vmx_client())
treatment |
A treatment id ( |
status |
Optional status filter. |
client |
A |
A tibble, one row per study.
Fetch one study
vmx_study(id, client = vmx_client())vmx_study(id, client = vmx_client())
id |
A study id ( |
client |
A |
A vmx_study.
Create a study
vmx_study_create( treatment, name, study_type = "clinical", phase = NULL, ..., client = vmx_client() )vmx_study_create( treatment, name, study_type = "clinical", phase = NULL, ..., client = vmx_client() )
treatment |
A treatment id or |
name |
Study name. |
study_type |
Study type; defaults to |
phase |
Optional clinical phase. |
... |
Additional fields ( |
client |
A |
A vmx_study.
Only the fields you pass are changed (the server applies exclude_unset).
vmx_study_update(id, ..., client = vmx_client())vmx_study_update(id, ..., client = vmx_client())
id |
A study id or |
... |
Fields to update. |
client |
A |
A vmx_study.
Subjects table (one row per subject)
vmx_subjects(dv, client = vmx_client())vmx_subjects(dv, client = vmx_client())
dv |
A data-version id or |
client |
A |
A tibble.
Not yet implemented. The per-subject start[i]/end[i] index ranges and
iObs observation index must be derived and verified against real data
before shipping (this is the error-prone derivation the design flags); see
the package NEWS.
vmx_torsten_data(dv, analyte = NULL, client = vmx_client())vmx_torsten_data(dv, analyte = NULL, client = vmx_client())
dv |
A data-version id or |
analyte |
Analyte to assemble. |
client |
A |
Not yet implemented.
Fetch one treatment
vmx_treatment(id, client = vmx_client())vmx_treatment(id, client = vmx_client())
id |
A treatment id ( |
client |
A |
A vmx_treatment.
Create a treatment
vmx_treatment_create( name, indication = NULL, description = NULL, client = vmx_client() )vmx_treatment_create( name, indication = NULL, description = NULL, client = vmx_client() )
name |
Treatment name. |
indication |
Optional indication. |
description |
Optional free-text description. |
client |
A |
A vmx_treatment.
Only the fields you pass are changed (the server applies exclude_unset).
vmx_treatment_update(id, ..., client = vmx_client())vmx_treatment_update(id, ..., client = vmx_client())
id |
A treatment id or |
... |
Fields to update ( |
client |
A |
A vmx_treatment.
List treatments
vmx_treatments(status = NULL, client = vmx_client())vmx_treatments(status = NULL, client = vmx_client())
status |
Optional status filter. |
client |
A |
A tibble, one row per treatment.
Streamed multipart upload. With wait = TRUE, blocks through the prep
pipeline (see vmx_wait()).
vmx_upload( study, files, mode = c("initial", "incremental", "replacement"), treatment = NULL, config = NULL, wait = FALSE, client = vmx_client() )vmx_upload( study, files, mode = c("initial", "incremental", "replacement"), treatment = NULL, config = NULL, wait = FALSE, client = vmx_client() )
study |
A study id or |
files |
Character vector of local file paths. |
mode |
One of |
treatment |
Optional treatment; inferred from |
config |
Optional gecodata v2 |
wait |
If |
client |
A |
A vmx_dataset (status "uploaded").
POST /datasets/{ds_id}/ignore-upload. Soft-ignores one delivery.
vmx_upload_ignore(dataset, upload, client = vmx_client())vmx_upload_ignore(dataset, upload, client = vmx_client())
dataset |
A dataset id or |
upload |
The upload id ( |
client |
A |
The updated vmx_prep_status.
POST /datasets/{ds_id}/unignore-upload.
vmx_upload_unignore(dataset, upload, client = vmx_client())vmx_upload_unignore(dataset, upload, client = vmx_client())
dataset |
A dataset id or |
upload |
The upload id ( |
client |
A |
The updated vmx_prep_status.
An S3 generic dispatching on the handle type. Each method has a sensible default terminal state. Terminal-but-unsuccessful states raise a classed error so scripts fail loudly rather than hang.
vmx_wait( x, until = NULL, timeout = 900, interval = 5, progress = interactive(), client = vmx_client(), ... )vmx_wait( x, until = NULL, timeout = 900, interval = 5, progress = interactive(), client = vmx_client(), ... )
x |
A pollable handle: a dataset / prep-status or an NCA analysis (more types as the API surface lands: model-build-run, simulation-job). |
until |
Target terminal state(s); a sensible default per type when
|
timeout |
Timeout in seconds. |
interval |
Poll interval in seconds (exponential backoff up to 30s). |
progress |
Show a progress message each poll; defaults to
|
client |
A |
... |
Passed to methods. |
The updated object, or a vmx_timeout_error.
Calls GET /me.
vmx_whoami(client = vmx_client())vmx_whoami(client = vmx_client())
client |
A |
A vmx_me object: user_id, email, name, workspace_id,
roles, and counts.