Files in rmsharp/snprcspf

SNPRC SPF Colony Screening Data Software Tool Package

.Rbuildignore

.gitignore

.travis.yml

DESCRIPTION

LICENSE

NAMESPACE

NEWS.Rmd NEWS.md R/add_id_date_repeated.R R/add_sqlmed_codes.R R/apply_divisor.R R/blank_fill_ids.R R/combine_lines.R R/create_luminex_screen_results_tbl.R R/create_pdl_results_tbl.R R/create_spf_samples_tbl.R R/data.R R/depricated_format_luminex_results.R R/divisors_match.R R/fix_pdl_csv_columns.R R/fmt_luminex_results.R R/getRunPropertyValue.R R/getTransformedOutputFile.R R/get_Machine_info.R R/get_agents_and_antigen_pairs.R R/get_all_combined.R R/get_all_df.R R/get_all_files.R R/get_all_regions.R R/get_all_summary_df.R R/get_antigen_pairs.R R/get_assay_pairs.R R/get_bad_date_ids_and_id_ids.R R/get_bead_df.R R/get_bead_headers.R R/get_col_boundaries.R R/get_col_names.R R/get_combined.R R/get_date_from_sample.R R/get_divisor_mismatch.R R/get_divisors.R R/get_empty_pdl_df.R R/get_excel_divisors.R R/get_file_ids.R R/get_followup.R R/get_followup_pool_samples.R R/get_id_date_repeated.R R/get_id_from_sample.R R/get_low_positive_controls.R R/get_luminex_species.R R/get_mean_raw_mfi.R R/get_mean_raw_mfi_from_lxd.R R/get_mean_raw_mfi_from_xlsx.R R/get_melted_bead_2_wide.R R/get_most_recent_file.R R/get_most_recent_files.R R/get_one_record_df.R R/get_pdl_csv_data.R R/get_pdl_meta_data_from_content.R R/get_pdl_nonnegative_reports.R R/get_pdl_report_date.R R/get_pdl_report_file_name.R R/get_pdl_reports.R R/get_pdl_results.R R/get_pdl_results_test_comment.R R/get_plateID.R R/get_pooled_sample_df.R R/get_positive_antigens.R R/get_possible_ids_dates.R R/get_raw_mfi.R R/get_raw_mfi_df.R R/get_raw_mfi_tables.R R/get_region_df.R R/get_repeated_from_sample.R R/get_report_date_from_filename.R R/get_result_tables.R R/get_sample_df.R R/get_sample_type_trans.R R/get_session_data_tm.R R/get_setup_name.R R/get_spnrc_id.R R/get_start_end_dates.R R/get_still_pos.R R/get_summary_df.R R/get_test_antigens.R R/get_usable_files.R R/get_version.R R/get_wide_df.R R/get_workset_desc.R R/get_yyyymmdd_from_possible_dates.R R/handleErrorsAndWarnings.R R/insert_combined_assay_results.R R/insert_missing_lines.R R/insert_pdl_results.R R/insert_spf_samples.R R/is_column_labels.R R/luminex_agent_to_sqlmed_test_id.R R/luminex_agent_to_sqlmed_test_name.R R/luminex_sqlmed_procedure_id.R R/luminex_to_sqlmed_procedure_name.R R/make_excel_wkbk.R R/make_get_agents_and_antigen_pairs.R R/mdy_to_yyyymmdd.R R/merge_pooled_and_pdl.R R/na_to_char.R R/pdl_assay_to_sqlmed_procedure_id.R R/pdl_assay_to_sqlmed_procedure_name.R R/pdl_assay_to_sqlmed_test_id.R R/pdl_assay_to_sqlmed_test_name.R R/pdl_report_td_df.R R/pdl_reports_to_df.R R/pooled_Y_or_N.R R/pooled_bleed_date_to_sample_date.R R/print_bad_animal_ids.R R/print_bad_sample_dates.R R/readRunPropertiesFile.R R/read_sample_file.R R/remove_bad_animal_ids.R R/remove_bn_and_dash_R.R R/remove_pdl_report_headers.R R/replace_bad_csv_files.R R/report_missing_samples.R R/report_unexpected_samples.R R/save_excel_sheet.R R/setMaxSeverity.R R/sort_occurances.R R/spf_odbcConnect.R R/strip_column_labels.R R/subtract_background.R R/test_for_bleed_date.R R/test_for_cage.R R/test_for_snprc_id.R R/test_for_yes_no.R R/triggerError.R R/triggerWarning.R README.Rmd README.md

data/plate165_dfs.RData

data/plate165_mean_raw_mfi_df.RData

data/plate166_combined_df.RData

data/plate166_dfs.RData

data/plate166_mean_raw_mfi_df.RData

data/plate166_r_mfi_df.RData

docs/404.html

docs/LICENSE-text.html

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/news/index.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/add_id_date_repeated.html

docs/reference/add_sqlmed_codes.html

docs/reference/apply_divisor.html

docs/reference/blank_fill_ids.html

docs/reference/combine_lines.html

docs/reference/combined_df.html

docs/reference/create_luminex_screen_results_tbl.html

docs/reference/create_pdl_results_tbl.html

docs/reference/create_spf_samples_tbl.html

docs/reference/dfs.html

docs/reference/divisors_match.html

docs/reference/fix_pdl_csv_columns.html

docs/reference/fmt_luminex_results.html

docs/reference/getRunPropertyValue.html

docs/reference/getTransformedOutputFile.html

docs/reference/getVersion.html

docs/reference/get_Machine_info.html

docs/reference/get_agents_and_antigen_pairs.html

docs/reference/get_all_combined.html

docs/reference/get_all_df.html

docs/reference/get_all_files.html

docs/reference/get_all_regions.html

docs/reference/get_all_summary_df.html

docs/reference/get_antigen_pairs.html

docs/reference/get_assay_pairs.html

docs/reference/get_bad_date_ids_and_id_ids.html

docs/reference/get_bead_df.html

docs/reference/get_bead_headers.html

docs/reference/get_col_boundaries.html

docs/reference/get_col_names.html

docs/reference/get_combined.html

docs/reference/get_date_from_sample.html

docs/reference/get_divisor_mismatch.html

docs/reference/get_divisors.html

docs/reference/get_empty_pdl_df.html

docs/reference/get_excel_divisors.html

docs/reference/get_file_ids.html

docs/reference/get_followup.html

docs/reference/get_followup_pool_samples.html

docs/reference/get_id_date_repeated.html

docs/reference/get_id_from_sample.html

docs/reference/get_low_positive_controls.html

docs/reference/get_luminex_species.html

docs/reference/get_mean_raw_mfi.html

docs/reference/get_mean_raw_mfi_from_lxd.html

docs/reference/get_mean_raw_mfi_from_xlsx.html

docs/reference/get_melted_bead_2_wide.html

docs/reference/get_most_recent_file.html

docs/reference/get_most_recent_files.html

docs/reference/get_one_record_df.html

docs/reference/get_pdl_csv_data.html

docs/reference/get_pdl_meta_data_from_content.html

docs/reference/get_pdl_nonnegative_reports.html

docs/reference/get_pdl_report_date.html

docs/reference/get_pdl_report_file_name.html

docs/reference/get_pdl_reports.html

docs/reference/get_pdl_results.html

docs/reference/get_pdl_results_test_comment.html

docs/reference/get_plateID.html

docs/reference/get_pooled_sample_df.html

docs/reference/get_positive_antigens.html

docs/reference/get_possible_ids_dates.html

docs/reference/get_raw_mfi.html

docs/reference/get_raw_mfi_df.html

docs/reference/get_raw_mfi_tables.html

docs/reference/get_region_df.html

docs/reference/get_repeated_from_sample.html

docs/reference/get_report_date_from_filename.html

docs/reference/get_result_tables.html

docs/reference/get_sample_df.html

docs/reference/get_sample_type_trans.html

docs/reference/get_session_date_tm.html

docs/reference/get_setup_name.html

docs/reference/get_snprc_id.html

docs/reference/get_start_end_dates.html

docs/reference/get_still_pos.html

docs/reference/get_summary_df.html

docs/reference/get_test_antigens.html

docs/reference/get_usable_files.html

docs/reference/get_version.html

docs/reference/get_wide_df.html

docs/reference/get_workset_desc.html

docs/reference/get_yyyymmdd_from_possible_dates.html

docs/reference/handleErrorsAndWarnings.html

docs/reference/index.html

docs/reference/insert_combined_assay_results.html

docs/reference/insert_missing_lines.html

docs/reference/insert_pdl_results.html

docs/reference/insert_spf_samples.html

docs/reference/is_column_labels.html

docs/reference/luminex_agent_to_sqlmed_test_id.html

docs/reference/luminex_agent_to_sqlmed_test_name.html

docs/reference/luminex_to_sqlmed_procedure_id.html

docs/reference/luminex_to_sqlmed_procedure_name.html

docs/reference/make_excel_wkbk.html

docs/reference/mdy_to_yyyymmdd.html

docs/reference/mean_raw_mfi_df.html

docs/reference/merge_pooled_and_pdl.html

docs/reference/na_to_char.html

docs/reference/pdl_assay_to_sqlmed_procedure_id.html

docs/reference/pdl_assay_to_sqlmed_procedure_name.html

docs/reference/pdl_assay_to_sqlmed_test_id.html

docs/reference/pdl_assay_to_sqlmed_test_name.html

docs/reference/pdl_report_to_df.html

docs/reference/pdl_reports_to_df.html

docs/reference/plate165_dfs.html

docs/reference/plate165_mean_raw_mfi_df.html

docs/reference/plate166_combined_df.html

docs/reference/plate166_dfs.html

docs/reference/plate166_mean_raw_mfi_df.html

docs/reference/plate166_r_mfi_df.html

docs/reference/pooled_Y_or_N.html

docs/reference/pooled_bleed_date_to_sample_date.html

docs/reference/print_bad_animal_ids.html

docs/reference/print_bad_sample_dates.html

docs/reference/r_mfi_df.html

docs/reference/readRunPropertiesFile.html

docs/reference/read_sample_file.html

docs/reference/remove_bad_animal_ids.html

docs/reference/remove_bn_and_dash_R.html

docs/reference/remove_pdl_report_headers.html

docs/reference/replace_bad_csv_files.html

docs/reference/report_missing_samples.html

docs/reference/report_unexpected_samples.html

docs/reference/save_excel_sheet.html

docs/reference/setMaxSeverity.html

docs/reference/sort_occurances.html

docs/reference/spf_odbcConnect.html

docs/reference/strip_column_labels.html

docs/reference/subtract_background.html

docs/reference/test_for_bleed_date.html

docs/reference/test_for_cage.html

docs/reference/test_for_snprc_id.html

docs/reference/test_for_yes_no.html

docs/reference/triggerError.html

docs/reference/triggerWarning.html

inst/_pkgdown.yml

inst/extdata/format_test.R installation.Rmd

installation.html

man/add_id_date_repeated.Rd man/add_sqlmed_codes.Rd man/apply_divisor.Rd man/blank_fill_ids.Rd man/combine_lines.Rd man/create_luminex_screen_results_tbl.Rd man/create_pdl_results_tbl.Rd man/create_spf_samples_tbl.Rd man/divisors_match.Rd man/fix_pdl_csv_columns.Rd man/fmt_luminex_results.Rd man/getRunPropertyValue.Rd man/getTransformedOutputFile.Rd man/get_Machine_info.Rd man/get_agents_and_antigen_pairs.Rd man/get_all_combined.Rd man/get_all_df.Rd man/get_all_files.Rd man/get_all_regions.Rd man/get_all_summary_df.Rd man/get_antigen_pairs.Rd man/get_assay_pairs.Rd man/get_bad_date_ids_and_id_ids.Rd man/get_bead_df.Rd man/get_bead_headers.Rd man/get_col_boundaries.Rd man/get_col_names.Rd man/get_combined.Rd man/get_date_from_sample.Rd man/get_divisor_mismatch.Rd man/get_divisors.Rd man/get_empty_pdl_df.Rd man/get_excel_divisors.Rd man/get_file_ids.Rd man/get_followup.Rd man/get_followup_pool_samples.Rd man/get_id_date_repeated.Rd man/get_id_from_sample.Rd man/get_low_positive_controls.Rd man/get_luminex_species.Rd man/get_mean_raw_mfi.Rd man/get_mean_raw_mfi_from_lxd.Rd man/get_mean_raw_mfi_from_xlsx.Rd man/get_melted_bead_2_wide.Rd man/get_most_recent_file.Rd man/get_most_recent_files.Rd man/get_one_record_df.Rd man/get_pdl_csv_data.Rd man/get_pdl_meta_data_from_content.Rd man/get_pdl_nonnegative_reports.Rd man/get_pdl_report_date.Rd man/get_pdl_report_file_name.Rd man/get_pdl_reports.Rd man/get_pdl_results.Rd man/get_pdl_results_test_comment.Rd man/get_plateID.Rd man/get_pooled_sample_df.Rd man/get_positive_antigens.Rd man/get_possible_ids_dates.Rd man/get_raw_mfi.Rd man/get_raw_mfi_df.Rd man/get_raw_mfi_tables.Rd man/get_region_df.Rd man/get_repeated_from_sample.Rd man/get_report_date_from_filename.Rd man/get_result_tables.Rd man/get_sample_df.Rd man/get_sample_type_trans.Rd man/get_session_date_tm.Rd man/get_setup_name.Rd man/get_snprc_id.Rd man/get_start_end_dates.Rd man/get_still_pos.Rd man/get_summary_df.Rd man/get_test_antigens.Rd man/get_usable_files.Rd man/get_version.Rd man/get_wide_df.Rd man/get_workset_desc.Rd man/get_yyyymmdd_from_possible_dates.Rd man/handleErrorsAndWarnings.Rd man/insert_combined_assay_results.Rd man/insert_missing_lines.Rd man/insert_pdl_results.Rd man/insert_spf_samples.Rd man/is_column_labels.Rd man/luminex_agent_to_sqlmed_test_id.Rd man/luminex_agent_to_sqlmed_test_name.Rd man/luminex_to_sqlmed_procedure_id.Rd man/luminex_to_sqlmed_procedure_name.Rd man/make_excel_wkbk.Rd man/mdy_to_yyyymmdd.Rd man/merge_pooled_and_pdl.Rd man/na_to_char.Rd man/pdl_assay_to_sqlmed_procedure_id.Rd man/pdl_assay_to_sqlmed_procedure_name.Rd man/pdl_assay_to_sqlmed_test_id.Rd man/pdl_assay_to_sqlmed_test_name.Rd man/pdl_report_to_df.Rd man/pdl_reports_to_df.Rd man/plate165_dfs.Rd man/plate165_mean_raw_mfi_df.Rd man/plate166_combined_df.Rd man/plate166_dfs.Rd man/plate166_mean_raw_mfi_df.Rd man/plate166_r_mfi_df.Rd man/pooled_Y_or_N.Rd man/pooled_bleed_date_to_sample_date.Rd man/print_bad_animal_ids.Rd man/print_bad_sample_dates.Rd man/readRunPropertiesFile.Rd man/read_sample_file.Rd man/remove_bad_animal_ids.Rd man/remove_bn_and_dash_R.Rd man/remove_pdl_report_headers.Rd man/replace_bad_csv_files.Rd man/report_missing_samples.Rd man/report_unexpected_samples.Rd man/save_excel_sheet.Rd man/setMaxSeverity.Rd man/sort_occurances.Rd man/spf_odbcConnect.Rd man/strip_column_labels.Rd man/subtract_background.Rd man/test_for_bleed_date.Rd man/test_for_cage.Rd man/test_for_snprc_id.Rd man/test_for_yes_no.Rd man/triggerError.Rd man/triggerWarning.Rd

snprcspf.Rproj

tests/testthat.R

tests/testthat/.MySCMServerInfo

tests/testthat/mylinters.R tests/testthat/test_date_conversion.R tests/testthat/test_fmt_luminex_results.R tests/testthat/test_getTransformedOutputFile.R tests/testthat/test_get_antigen_pairs.R tests/testthat/test_get_id_from_sample.R tests/testthat/test_get_report_date_from_filename.R tests/testthat/test_low_positive_detection.R tests/testthat/test_pdl_test_to_sqlmed_test.R tests/testthat/test_possible_dates_to_yyyymmdd.R tests/testthat/test_remove_bn_and_dash_R.R tests/testthat/test_runproperties.R tests/testthat/test_with_lintr.R

rmsharp/snprcspf documentation built on June 15, 2020, 11:21 a.m.