library("tima")
# Run full workflow with defaults (INFO level)
run_tima()
# Run with debug logging for troubleshooting
run_tima(log_level = "debug")
# Run with minimal logging (warnings and errors only)
run_tima(log_level = "warn")
# Run with custom target pattern
run_tima(target_pattern = "^prepare_")
# Preserve existing logs
run_tima(clean_old_logs = FALSE)
# Combine multiple options
run_tima(
target_pattern = "^ann_",
log_level = "debug",
clean_old_logs = FALSE
)Run Complete TIMA Workflow
Description
Executes the full Taxonomically Informed Metabolite Annotation (TIMA) workflow from start to finish. This includes data preparation, library loading, annotation, weighting, and output generation. The function runs the targets pipeline and archives logs with timestamps for reproducibility.
Usage
run_tima(
target_pattern = "^ann_wei\$",
log_file = "tima.log",
clean_old_logs = TRUE,
log_level = "info"
)
Arguments
target_pattern
|
Character. Regex pattern for target selection. Default: "^ann_wei$" (annotation preparation target) |
log_file
|
Character. Path to log file. Default: "tima.log" |
clean_old_logs
|
Logical. Remove old log file before starting. Default: TRUE |
log_level
|
Character or numeric. Logging verbosity level. Can be one of: "trace", "debug", "info", "warn", "error", "fatal" or numeric values: TRACE=600, DEBUG=500, INFO=400, WARN=300, ERROR=200, FATAL=100. Default: "info" (400). Use "debug" for detailed troubleshooting. |
Details
The workflow performs the following steps:
-
Initializes logging and timing
-
Navigates to cache directory
-
Executes the targets pipeline (annotation preparation)
-
Archives timestamped logs to data/processed/
Value
Invisible NULL. Executes workflow as side effect and creates timestamped log files in data/processed/