| add_id_date_repeated | Returns a dataframe with the Id, Date, and Repeated column... |
| add_sqlmed_codes | Returns df dataframe with the SqlMed procedure_name,... |
| apply_divisor | Returns mfi_df with each value divided by the appropriate... |
| blank_fill_ids | Returns the Ids in right blank filled and upper case animal... |
| combine_lines | Returns character vector of length 1 made up of text found in... |
| create_luminex_screen_results_tbl | Returns TRUE if the creation of the pdl_result table was... |
| create_pdl_results_tbl | Returns TRUE if the creation of the pdl_results table was... |
| create_spf_samples_tbl | Returns TRUE if the creation of the spf_samples table was... |
| divisors_match | Returns a logical value indicating whether or not the list of... |
| fix_pdl_csv_columns | Returns pdl_df with columns renamed, added and ordered to... |
| fmt_luminex_results | Conditionally formats a worksheet based on data within the... |
| get_agents_and_antigen_pairs | Returns dataframe of possible antigen pairs and agents |
| get_all_combined | Returns dataframe with multiple combined results from antigen... |
| get_all_df | Returns a dataframe with all bead or all summary results... |
| get_all_files | Returns the list of pathology report files with an extension... |
| get_all_regions | Returns a dataframe with the files, order, and Region[@name]s... |
| get_all_summary_df | Returns a dataframe with all summary results combined. |
| get_antigen_pairs | Returns a dataframe with the agent and two antigens used to... |
| get_assay_pairs | Returns a dataframe, with sets of assays with an antibody... |
| get_bad_date_ids_and_id_ids | Returns a list with two character vectors containing the... |
| get_bead_df | Get bead call multipliers from results section of Excel SPF... |
| get_bead_headers | Returns a dataframe with all headers found in the bead... |
| get_col_boundaries | Returns an integer vector with the the positions in the line... |
| get_col_names | Returns character vector of column names base on type... |
| get_combined | Returns dataframe with combined results from antigen results |
| get_date_from_sample | Returns the date from a sample column if it exist else NA. |
| get_divisor_mismatch | Returns a charcter vector with the file names of files that... |
| get_divisors | Returns a named numeric vector with the divisors originally... |
| get_empty_pdl_df | Returns empty pdl_df |
| get_excel_divisors | Returns a named numeric vector with the divisors originally... |
| get_file_ids | Returns integer vector with plate numbers |
| get_followup | Returns "followup" assay results, which are groups of assay... |
| get_followup_pool_samples | Returns assay results for individual animals based on assay... |
| get_id_date_repeated | Returns dataframe with true animal Ids (Id) and date strings... |
| get_id_from_sample | Returns the first integer value from a sample column if it... |
| get_low_positive_controls | Finds any wells with low positive controls |
| get_luminex_species | Returns species desination of "CYNO", "MACAQUE" or "PAPIO" at... |
| get_Machine_info | Returns Machine serialNumber, name, sftwareVersion,... |
| get_mean_raw_mfi | Returns dataframe with means of replicated samples |
| get_mean_raw_mfi_from_lxd | Returns the mean_raw_mfi_df from an XML file (.lxd extension)... |
| get_mean_raw_mfi_from_xlsx | Returns the mean_raw_mfi_df from an Excel file (.xlsx... |
| get_melted_bead_2_wide | Returns bead based wide dataframe from bead based melted... |
| get_most_recent_file | Returns the most recent assay file name for each plate number |
| get_most_recent_files | Returns the most recent assay file name for each plate number |
| get_one_record_df | Returns a one record dataframe with the data from one assay... |
| get_pdl_csv_data | Returns pdl data from their CSV files given a list of... |
| get_pdl_meta_data_from_content | Returns specified value from a pdl_report$content object |
| get_pdl_nonnegative_reports | Returns non-negative results from PDL reports results |
| get_pdl_report_date | Returns report date from a pdl_report object |
| get_pdl_report_file_name | Returns report file name from a pdl_report object |
| get_pdl_reports | Returns a list of lists of length two containing $content and... |
| get_pdl_results | Get PDL results |
| get_pdl_results_test_comment | Returns a character vector of length 2 with the result and... |
| get_plateID | Returns Plate[@plateID] (plateID attribute of the Plate... |
| get_pooled_sample_df | Returns dataframe with animal Ids, cage location, bleed date,... |
| get_positive_antigens | Returns positive antigens based on low control value and a... |
| get_possible_ids_dates | Returns a list of length 2 with possible$ids and... |
| get_raw_mfi | Returns dataframe of original values |
| get_raw_mfi_df | Returns dataframe with raw mfi values from the raw section of... |
| get_raw_mfi_tables | Returns character vector with the raw data (raw mfi) table |
| get_region_df | Returns a dataframe with region order, region name, and... |
| get_repeated_from_sample | Returns a character vector of 'Y' if the sample indicates it... |
| get_report_date_from_filename | Returns report date in yyyy-mm-dd format as derived from the... |
| get_result_tables | Returns character vector with the result tables |
| getRunPropertyValue | Returns value of run property if one is available else NA is... |
| get_sample_df | Returns dataframe with animal Ids, cage location, bleed date,... |
| get_sample_type_trans | Returns the corrected sample type given slightly malformed or... |
| get_session_date_tm | Returns date and time of assay based on '//Plate[@name]. |
| get_setup_name | Returns the Setup[@name]s for a lum |
| get_snprc_id | Returns an SNPRC animal Id of the pdl_animal_id represents an... |
| get_start_end_dates | Returns data frame with file and start_date as the two... |
| get_still_pos | Get dataframe of animals where the most recent assay was not... |
| get_summary_df | Returns dataframe with summary results from the results... |
| get_test_antigens | Returns the list of test antigens |
| getTransformedOutputFile | Returns full name with path of transformed output file. |
| get_usable_files | Returns a character vector of names of usable files. |
| get_version | getVersion Get the version number of snprcspf |
| get_wide_df | Returns a list of dataframes that have been converted to wide... |
| get_workset_desc | Returns /WorkSet/Description from XML |
| get_yyyymmdd_from_possible_dates | Returns yyyymmdd in with optional separator between date... |
| handleErrorsAndWarnings | Returns NULL: does not return - writes the maximumSeverity... |
| insert_combined_assay_results | Returns the number of saved records |
| insert_missing_lines | Returns character vector representing the contents of the... |
| insert_pdl_results | Returns the number of records inserted into pdl_results |
| insert_spf_samples | Returns the number of records inserted into spf_samples |
| is_column_labels | Returns TRUE if a line is an expected set of column labels |
| luminex_agent_to_sqlmed_test_id | Returns a numeric vector of SqlMed test_id given a character... |
| luminex_agent_to_sqlmed_test_name | Returns a character vector of SqlMed test_name given a... |
| luminex_to_sqlmed_procedure_id | Returns a numeric vector of SqlMed procedure_id given a... |
| luminex_to_sqlmed_procedure_name | Returns a character vector of SqlMed procedure_names given a... |
| make_excel_wkbk | Form an Excel workbook and worksheet similar in format to... |
| mdy_to_yyyymmdd | Returns character vector of dates where entities of mm/dd/yy... |
| merge_pooled_and_pdl | Returns a dataframe with pooled_df merged with pdl_df by... |
| na_to_char | Replaces an NA value with a character string |
| pdl_assay_to_sqlmed_procedure_id | Returns a character vector of SqlMed procedure_id given a... |
| pdl_assay_to_sqlmed_procedure_name | Returns a character vector of SqlMed procedure_names given a... |
| pdl_assay_to_sqlmed_test_id | Returns a character vector of SqlMed test_id given a... |
| pdl_assay_to_sqlmed_test_name | Returns a character vector of SqlMed test_name given a... |
| pdl_reports_to_df | Returns dataframe with results from all report files in... |
| pdl_report_to_df | Returns dataframe with parsed content of pdl_report |
| plate165_dfs | plate165_dfs is a loadable version of the dfs list of... |
| plate165_mean_raw_mfi_df | plate165_mean_raw_mfi_df is a loadable version of the... |
| plate166_combined_df | combined_df is a loadable version of the combined_df... |
| plate166_dfs | plate166_dfs is a loadable version of the dfs list of... |
| plate166_mean_raw_mfi_df | plate166_mean_raw_mfi_df is a loadable version of the... |
| plate166_r_mfi_df | plate166_r_mfi_df is a loadable version of the r_mfi_df... |
| pooled_bleed_date_to_sample_date | Returns pooled_df dataframe with bleed_date replaced by... |
| pooled_Y_or_N | Returns "Y" if a sample is pooled and "N" if it is an... |
| print_bad_animal_ids | Returns a dataframe of file names, sample, snprc_id, and... |
| print_bad_sample_dates | Returns a dataframe of file names, LocName, animal Id, and... |
| readRunPropertiesFile | Returns a dataframe with four columns ("name", "value",... |
| read_sample_file | Read blood or dna sample file |
| remove_bad_animal_ids | Returns only good SNPRC animal Ids given a character vector... |
| remove_bn_and_dash_R | Returns samples with "Bn" and "-R" trimmed off of each end |
| remove_pdl_report_headers | Returns content for PDL reports without introductory material... |
| replace_bad_csv_files | Returns a dataframe with a row for each bad CSV file with the... |
| report_missing_samples | Creates an Excel file with a list of samples that were... |
| report_unexpected_samples | Returns a list of samples that were expected but not... |
| save_excel_sheet | Returns the file name of the Excel file created which... |
| setMaxSeverity | Returns integer value of error level (0:NONE, 1:WARN,... |
| sort_occurances | Returns a sorted dataframe with First occurrances appearing... |
| spf_odbcConnect | Returns database connection object |
| strip_column_labels | Returns content minus column labels. Fails with a call to... |
| subtract_background | Returns mfi_df dataframe values with wBAC column subtracted... |
| test_for_bleed_date | Throws and error on one or more provided bleed dates occur on... |
| test_for_cage | Throws and error on one or more bad cage numbers are... |
| test_for_snprc_id | Throws and error on one or more bad animal Ids. It terminates... |
| test_for_yes_no | Throws and error on bad input for the 'expected_blood' or... |
| triggerError | Returns NULL: does not return - triggers error and stops... |
| triggerWarning | Returns 'run_error', after setting 'run_error$level' to 1 if... |
