Man pages for iAM-AMR/sawmill
Process Queries from the CEDAR Database
| add_CI | Fill in the confidence interval (CI) column |
| add_HTMLink | Generate HTML links using a document identifier |
| add_ident | Generate a suggested Analytica identifier |
| add_URL | Generate URLs using document identifiers |
| append_scraps | Append the scrap pile to the processed timber (planks) |
| build_chairs | Calculate the odds ratio (OR) and the SE(log(OR)) |
| build_horse | Calculate the significance of a resistance outcome |
| build_table | Complete contingency tables for count and prevalence-based... |
| check_grain | Determine the grain of each resistance outcome in timber and... |
| check_version | Check that the CEDAR version specified is valid |
| create_status_cols | Initializes the 'sawmill_status' and 'sawmill_pass' columns... |
| debark | Standardize column names and screen for data entry errors, or... |
| dedupe_MA | Remove Duplicate Rows for Meta-Analysis |
| do_MA | Perform meta-analyses on specified factors in timber |
| expect_snapshot_csv | Helper function to perform snapshot testing for whole .CSV... |
| format_ma_results | Format all meta-analyses results |
| get_col_types | Get the Expected Column Types for an Input CEDAR Query |
| handle_col_warnings | Handles Warnings Generated by Unexpected Data Types in Input... |
| hello | Hello, World! |
| local_timber | A CEDAR timber |
| log_warnings | Log Warning Messages in the Console |
| mill | The sawmill Pipeline |
| read_timber | Read timber |
| reorder_fields | Reorder the processed timber's fields |
| risk_ratio_to_odds_ratio | Calculate an odds ratio (OR) from a risk ratio (RR) |
| save_csv | Saves the passed tibble to a csv file |
| sawmill | sawmill: A Package to Process CEDAR Queries |
| set_blade_depth | Generate a mapping of timber column names to their... |
| start_mill | Start the interactive sawmill pipeline |
| sub_mill | Run a Substep of the sawmill Pipeline, with Error Handling |
| sweep_scraps | Write Unusable Factors to a CSV |
| trim_scraps | Trim unusable factors from timber |
| update_sawmill | Update sawmill |
| validate_contingency_table | Check if contingency table parameters are sufficient and... |
| validate_odds_ratio | Check if the odds ratio parameters are sufficient |
| validate_prevalence_table | Check if the prevalence table parameters are sufficient and... |
| validate_ratio | Validate ratio parameters |
| validate_risk_ratio | Check if the risk ratio parameters are sufficient |
| write_tibble_to_csv | Helper function to write tibble to a .CSV file |
