Man pages for jesse-smith/coviData
COVID-19 Data Munging Tools for the Shelby County Health Department
| add_axis_labels | Add Axis Labels to a Plot |
| add_collection_date | Add Specimen Collection Date to a Report Date Tibble |
| add_covid_events | Add a Set of Events From the Shelby County COVID Response to... |
| add_event | Add an Event Marker on a Plot |
| add_scale_month | Add a Monthly X-Axis Scale to a Time-Based Plot |
| add_title_caption | Add a Title, Subtitle, and/or Caption to a Plot |
| add_today | Add a Marker for Today's Date to a Plot |
| archive_report_date | Archive 'fst' Files of NBS Report Dates Based on Date of... |
| assert | Flexible Error Assertion |
| assert_bool | Assert that an Object is Boolean |
| assert_cols | Assert That a Data Frame Selection Matches the Specified Type... |
| assert_dataframe | Assert that an Object Is a Data Frame |
| check_date_updated | Check Update Date in Data for Regions REDcap Project |
| check_deaths | Compare Linelists from NBS and Surveillance Team and Report... |
| check_linelist_dates | Check and Clean Dates in a Linelist |
| chr_to_dttm | Parse Dates in Character Format to Datetime Format |
| coalesce_across | Coalesce with *tidyselect* Semantics |
| coalesce_by_column | Coalesce Rows by Columns in Data Frame |
| coalesce_dupes | Coalesce Information in Duplicate Rows |
| coalesce_report_date | Coalesce Report Dates from Archived 'fst' Files |
| cols_exist | Do One or More Columns Actually Exist? |
| convert_snapshot_to_xlsx | Find a Snapshot File and Convert to XLSX Format |
| convert_to_xlsx | Convert a File to XLSX Format Natively in Excel |
| coviData-package | coviData: COVID-19 Data Munging Tools for the Shelby County... |
| create_path | Create a Tidy Path from Directory + File + Extension |
| data-for-regions-snapshots | Download a File from the Data for Regions REDcap Project |
| date-data | Get Dates for Data files |
| decimal_time | Extract Time as a Decimal of Hours |
| distinct_inv | Get Distinct Investigations |
| download-case-projects | Download New Interview Tool Data |
| download_data_for_regions | Download a File from the Data for Regions REDcap Project |
| download_integrated_data | Download Data from the Integrated Data Tool REDcap Project |
| download_interview_report | Download a Report from the Integrated Data Tool REDcap... |
| download_redcap_records | Download New Interview Tool Data |
| download_servu | Download Lab File from Serv-U |
| download_state_contacts | Download "Automated Contacts for State Monitoring" Report |
| dttm_to_dt | Coerce Datetimes to Dates if No Information is Lost |
| ennotify | 'entrace()' + 'notify()' |
| env_vars | How to Access Sensitive Information Non-Interactively with... |
| fill_dates | Fill Implicitly Missing Dates in a Time-Indexed Data Frame |
| find_file | Find a File with the Specified Date + Pattern in the File... |
| gg_var | Extract an Axis Variable Name |
| guess_filetype | Guess the Filetype of a Data File |
| is_open | Test Whether a File is Open |
| is_windows | Check Whether *R* is Running in Windows |
| load-case-projects | Load Last Downloaded Data for a REDcap Project |
| load_data | Load a Data File Using the Directory, Date, and Extension |
| load_integrated_data | Load Data from the Integrated Data Tool REDcap Project |
| load_nbs | Load NBS Data from Disk |
| load_pcr | Load AEL Data from Disk |
| load_report_date | Load Report Dates from 'fst' File |
| load_sas | Load Cleaned Data from SAS Program |
| log_dir | Set/Get Logging Directory |
| log_end | End a Logging Session |
| log_start | Start a Logging Session |
| magrittr-helpers | Magrittr Pipe Helpers |
| notify | Send an Email Notification with Outlook |
| path_by_date | Return the Path to a NBS Investigations File |
| path_by_pattern | Get Path(s) to Recent Files Matching a Pattern |
| path_clean | Clean a Path with the fs Package |
| path_create | Create a Path from Components |
| path_deaths | Most Recent Deaths File |
| path_inv_id | Path to Processed Investigation Local IDs |
| preprocess | Standardize Variables, Handle Dates, and Remove Bad Columns |
| process-nbs | Run the Cases Workflow for Daily Report |
| randomize | Create Column-Wise Randomized Test Data for Non-Statistical... |
| read_file | Read a Tabular Data File |
| read_file_delim | Efficently Read Delimited Files |
| read_file_excel | Read Excel Files |
| read_inv_id | Read Investigation ID by Status |
| read-nbs | Read NBS Files |
| read_vac | Read Vaccination Data |
| reduce_fst_report_dates | Join Report Dates from 'fst' Files |
| reexports | Objects exported from other packages |
| replace_deaths_id | Replace NBS ID in Surveillance Deaths Linelist with... |
| sample_unique | Sample from Unique Values of Data |
| save_plot | Save a 'ggplot' Object |
| save_report_date | Save Report Dates to 'fst' File |
| select_colnames | Select Column Names Using Tidyselect Specifications |
| set_axis_limits | Set Viewing Limits on a Plot |
| set_covid_theme | Set a Standard Theme for SCHD COVID Plots |
| sftp_changedir | Move to another directory in an SFTP account |
| sftp_connect | Create a List Object with SFTP Connection Details |
| sftp_delete | Delete files in an SFTP account |
| sftp_dir_info | Query File Metadata from SFTP Connection |
| sftp_download | Download files from an SFTP account |
| sftp_list | List Files and/or Folders in an SFTP Directory |
| sftp_listdirs | List folders in an SFTP directory |
| sftp_listfiles | List files in an SFTP directory |
| sftp_makedir | Create a new directory in an SFTP account |
| sftp_removedir | Remove a new directory in an SFTP account |
| sftp_rename | Rename a single file or single directory in an SFTP account |
| sftp_upload | Upload files to an SFTP account |
| shelby_zip | Vector of Shelby County ZIP Codes |
| standardize_string | Standardize String Formatting |
| std_dates | Parse Dates to Standard Format |
| std_names | Parse Investigator Names and Remove (Most) Non-Alphabetical... |
| str_invert_na | Invert 'NA' String Replacement |
| str_remove_numeric | Remove Numeric Symbols from String |
| str_remove_ordinal | Remove Mixed Ordinal Numbers with Text Representation |
| str_remove_parenthetic | Remove Text Surrounded by Parentheses |
| str_remove_symbols | Remove Symbols from String |
| str_replace_brackets | Replace Square Brackets and Curly Braces with Parentheses |
| str_to_ascii | Convert a String to ASCII Representation |
| str_to_vb_html | Convert String to HTML Suitable for Inclusion in VB Script |
| team_schedules | Team Schedules Used for Case Assignment |
| to_report_date_fst | Convert NBS Data to 'fst' Files Containing Report Dates |
| trim_backups | Remove Files from Directory Based on Date Created |
| utils-tidyeval-symbols | Symbols Used in Tidy Evaluation |
| vac_distinct | Deduplicate Vaccination Data |
| vac_filter_doses | Filter to Valid Doses in Vaccination Data |
| vac_filter_residents | Filter to Possible Shelby Residents in Vaccination Data |
| vac_load | Deprecated - Use 'read_vac()' (now the backend of this... |
| vac_mutate | Create and Transform Variables in Vaccination Data |
| vac_parse_zip | Parse Zip Codes from Vaccination Data |
| vac_prep | Prepare Vaccine Data for Analysis |
| var_load | Load Variant Cases from NIT Project |
| var_parse | Parse Variant Data from NIT Project |
| vctr-helpers | vctrs: Vector Helpers |
| vec_sample | Re-implementation of 'base::sample()' Using the vctrs Package |
| write_file_delim | Efficiently Write Delimited Files |
| write_sas_nbs | Separate +/- Investigation/PCR Data Files for SAS |
| write_sas_neg | Write Negative Investigation and PCR Data to CSV for SAS |
| write_sas_pos | Write Positive Investigation and PCR Data to CSV for SAS |
