Man pages for PublicHealthEngland/hcaidcs
R functions for the mandatory surveillance of bacteraemia and C. difficile infection
| aec_age_sex_plot | Plot rates by age and sex structure, faceted by financial... |
| aec_age_trend_pc | Graph trend in percentage of cases by age group |
| aec_age_trend_rate | Graph trend in rate of cases by age and sex |
| aec_age_trend_rate_bar | aec_age_trend_rate |
| aec_age_trend_rate_pc_change | aec_age_trend_rate_pc_change |
| aec_create_folder_structure | Set up empty folders for Annual publication |
| aec_ec_source_plot | Plot the most likely primary focus for E. coli bacteraemia by... |
| aec_inpatient | Determine whether record is from an acute trust inpatient for... |
| aec_subregion_plot | Plot rates by NHS subregion |
| aec_tto_plot | AEC time to onset plot |
| age_sex_pyramid | Age sex pyramid |
| age_trends_data | Trends in age of patients with *C. difficile* infection |
| ann_tab_ccg_names | Format CCG names for printing in the annual tables. |
| ann_tab_long | Create long annual tables from line listing data |
| ann_tab_onset_annual | ann_tab_onset_annual |
| ann_tab_onset_qtrly | ann_tab_onset_qtrly |
| ann_tab_pir_org_type | Format pir org type for annual tables |
| apportion | Apportion CDI and MSSA records |
| apportion_phc_date | Apportion cases on basis of prior healthcare interactions by... |
| apportion_prior_healthcare | Apportion CDI cases on basis of prior healthcare interactions |
| area_team_names | Format CCG and NHS area team names into print format. |
| assignment_algorithm | Replicate the PIR assignment algorithm |
| assignment_data | Data for testing assignement algorithm |
| assignment_data2 | Data for testing assignement algorithm |
| at_sp_df | NHS Area Team geographies for England |
| bed_days_fq | Calculates inpatient bed-days from Actue Trust KH03 returns |
| bed_days_fy | Calculates inpatient bed-days from Actue Trust KH03 returns |
| cal_q_long | Format date into calendar year quarter. |
| cdi_prior_hc_data | Data for testing prior healthcare exposure monthly table |
| change | Gives the absolute value of the per cent or total change... |
| cmonth_to_fmonth | cmonth_to_fmonth |
| cmonth_to_string | cmonth_to_string |
| cyear_to_cq | Cyear to long calendar quarter |
| cyear_to_fyear | Convert calendar year to financial year |
| date_end_period | Get the string of the first date in a period |
| date_start_period | Get the string of the first date in a period |
| date_to_cmonth | date_to_cmonth |
| date_to_fmonth | date_to_fmonth |
| date_to_fq | date_to_fq |
| date_to_fyear | date_to_fyear |
| days_in_cy | Get the number of days in a calendar year |
| days_in_fmonth | Calculates number of days in a financial month. |
| days_in_fq | Get the number of days in the quarter of a financial year |
| days_in_fy | Get the number of days in a financial year |
| dcs_popn_boilerplate | Create population boilerplate columns for DCS denominator... |
| dcs_speciality_grouping | Group specialties from the HCAI DCS |
| detach_hcaidcs | Convenience function to detach hcaidcs package |
| factor_apportion_both | factor_apportion_both |
| factor_apportioned | factor_apportioned |
| factor_prior_hc | factor_prior_hc |
| first_wednesday | First Wednesday |
| fmonth_to_string | fmonth_to_string |
| fq5 | Convert a date to five-character financial quarter |
| fq_long | Format date into long quarter. |
| fq_short | Format date into short text financial quarter. |
| fq_short_to_date | fq_short_to_date |
| fq_to_cq | Convert financial year quarters to calendar year quarters |
| fq_to_fyear | Convert financial quarter to six-character financial year |
| fyear_to_cyear | Convert financial year to calendar year |
| fyear_to_fq | Fyear to long financial quarter |
| fy_long | Format date into long text financial year. |
| fy_long_short | Format fy_long into short financial year. |
| fyq_to_fq | Fyear-quarter to long financial quarter |
| fy_short | Format date into short text financial year. |
| fy_six | Create six character financial year from date |
| fy_six_to_long | Format date into long text financial year. |
| graph_age_groups | graph_age_groups |
| graph_species_names | Italicise species names for graphing Producing mixed italics... |
| group_source_bacteraemia | group_source_bacteraemia |
| group_tto_bacteraemia | Provides grouped time to onset for bacteraemia cases |
| group_tto_cdi | Provides grouped time to onset for bacteraemia cases |
| independent_sector_denominator | Inpatient modified bed-days from Independent Sector Providers |
| inpatient | inpatient |
| is_sch | Identifies specialist commissioning hubs |
| is_third_party | Check whether assignment is third party |
| kh03_boilerplate | Adds KH03 boilerplate text columns to a data frame in... |
| kh03_year | Convert KH03-formatted dates to Mandatory data-formatted... |
| klebsiella_sp_group | Create group for Klebsiella species |
| line_listing | Data simulating output from the HCAI DCS line listing report |
| mandatory_age | Calculate patient age in manner that conforms to mandatory... |
| mandatory_age_group | Create age group from age |
| mandatory_age_group_bacteraemia | mandatory_age_group_bacteraemia(0) |
| mandatory_age_group_cdi | Mandatory age group for CDI cases Calculates the mandatory... |
| mf_create_text_values | function to create text objects for monthly factsheets |
| mf_fig1_fun | Monthly factsheet figure 1 function |
| mf_lag_trend | lag mf trend data |
| mf_trend_data | Data for monthly factsheet figure 1 function |
| mo_curr_months | Create months for monthly outputs |
| mo_gnabsi_table | Monthly table for Gram-negative blood stream infection data |
| mo_next_pub_date | Returns the next publication date of the monthly outputs. |
| monthly_ccg_data_raw | Data for monthly CCG table for MRSA |
| mo_prior_hc_table | mo_prior_hc_table |
| mo_pub_date | Nicely formats date of publication for monthly data |
| mo_std_table | Monthly CCG table |
| mo_tab_long | mo_tab_long |
| mrsa_source_bacteraemia | Classify the source of bacteramia for MRSA |
| ordered_fin_qtr | Create factor variable from financial quarter |
| ordered_m_y | Add ordered month and calendar year to a data frame |
| patloc_for_pir_assignment | Check whether a patient location is an NHS Trust or not |
| pir_org_type | Create ordered factor variable for PIR organisation type. |
| popn_boilerplate | Adds population boilerplate text columns to a data frame in... |
| provis_orgname | Check whether provisional organisation is Trust or CCG |
| qec_age_table | Create age group table for QEC |
| show_hcaidcs_package_manual | Display manual for this package in browser |
| subregions_sp_df | NHS subregion geographies for England |
| subregion_test_data | subregion_test_data |
| time_period2fyear | Convert time period variable to fyear for merging with KH03... |
| time_to_onset | Calculates time to onset for inpatients |
| update_independent | Update independent sector providers and independent sector... |
| up_or_down | Calculate whether there has been either an increase, decrease... |
