workspace

The runtime context generate, compute, associate, evaluate and visualize all resolve against: configuration, resource catalogs, external-tool setup and execution internals. Created by .onLoad.

An environment of class PolyGeniusWorkspace with members config, catalogs, setup and .internal.

Four members, each read-only — assigning to one aborts.

• workspace$config — runtime settings, listed below; change them with workspace$config$update(...).
• workspace$catalogs — GenomeBuilds, ReferencePanels, VariantSpaces, LiftoverChains, LDblocks and LDs.
• workspace$setup — external tool management: install(), check(), status() and get() for PLINK2, GCTB, the PRS-CS Python environment and the bigsnpr R stack.
• workspace$.internal — store, resolver, executor and rules, for extension authors.

Each field is read-only and changed only through workspace$config$update(). Many functions resolve a NULL argument from one of them.

• root — character scalar path, default tools::R_user_dir("PolyGenius", "cache"). Cache and output root; every cached resource lives beneath it.
• log.dir — character scalar path, derived as file.path(root, "logs"). General log directory; not settable on its own.
• execution.dir — character scalar path, derived as file.path(root, "execution"). Execution-engine log and state directory; not settable on its own.
• max.cores — positive integer, Inf, or NULL; default NULL. Engine worker cap; NULL and Inf both resolve to detected cores minus one.
• max.memory — positive numeric scalar in GiB, or Inf; default Inf. Engine memory budget. A value strictly between 0 and 1 is rejected as a unit error.
• max.model.column.bytes — positive numeric scalar in bytes, or Inf; default 4294967296 (4 GiB). Byte budget on the column(s) a single mutate.variants() call materializes.
• max.absorb.batch.models — positive integer, or Inf; default 50. How many models generate$models() folds into one PolyGeniusBackbone$absorb() call while collecting results.
• oversubscribe — logical scalar, default FALSE. When TRUE, an explicit finite max.cores is honored above the detected-core cap.
• verbosity — one of "fatal", "error", "warn", "info", "debug", "trace", "all", "off"; default "info". Console logger threshold.
• execution.status — one of "auto", "yes", "no"; default "yes". Execution status display mode.
• execution.log.propagate — one of "yes", "no"; default "no". Whether execution logs propagate to the parent logger.
• palette — one of "polygenius", "nature-npg"; default "polygenius". Plot palette system applied by default across every visualize function; a per-plot palette argument overrides it.
• dashboard.live — one of "auto", "yes", "no"; default "auto". Whether to auto-host a live execution dashboard.

workspace_config, workspace_setup, workspace_catalogs, ResourceStore