Man pages for PublicHealthEngland/hcaidcs
R functions for the mandatory surveillance of bacteraemia and C. difficile infection

aec_age_sex_plotPlot rates by age and sex structure, faceted by financial...
aec_age_trend_pcGraph trend in percentage of cases by age group
aec_age_trend_rateGraph trend in rate of cases by age and sex
aec_age_trend_rate_baraec_age_trend_rate
aec_age_trend_rate_pc_changeaec_age_trend_rate_pc_change
aec_create_folder_structureSet up empty folders for Annual publication
aec_ec_source_plotPlot the most likely primary focus for E. coli bacteraemia by...
aec_inpatientDetermine whether record is from an acute Trust inpatient for...
aec_subregion_plotPlot rates by NHS subregion
aec_tto_plotAEC time to onset plot
age_trends_dataTrends in age of patients with *C. difficile* infection
ann_tab_ccg_namesFormat CCG names for printing in the annual tables.
ann_tab_onset_annualann_tab_onset_annual
ann_tab_onset_qtrlyann_tab_onset_qtrly
ann_tab_pir_org_typeFormat pir org type for annual tables
ann_tab_pir_quarterlyann_tab_pir_quarterly
apportionApportion CDI and MSSA records
apportion_prior_healthcareApportion CDI cases on basis of prior healthcare interactions
area_team_namesFormat CCG and NHS area team names into print format.
assignment_algorithmReplicate the PIR assignment algorithm
assignment_dataData for testing assignement algorithm
assignment_data2Data for testing assignement algorithm
at_sp_dfNHS Area Team geographies for England
cal_q_longFormat date into calendar year quarter.
cdi_prior_hc_dataData for testing prior healthcare exposure monthly table
changeGives the absolute value of the per cent or total change...
check_date_classCheck that date variables are in required format
cmonth_to_fmonthcmonth_to_fmonth
cmonth_to_stringcmonth_to_string
cyear_to_cqCyear to long calendar quarter
cyear_to_fyearConvert calendar year to financial year
data_compareCompare two data frames to identify cells which are different
date_end_periodGet the string of the first date in a period
date_start_periodGet the string of the first date in a period
date_to_fmonthdate_to_fmonth
date_to_fqdate_to_fq
date_to_fyeardate_to_fyear
days_in_cyGet the number of days in a calendar year
days_in_fmonthCalculates number of days in a financial month.
days_in_fqGet the number of days in the quarter of a financial year
days_in_fyGet the number of days in a financial year
dcs_popn_boilerplateCreate population boilerplate columns for DCS denominator...
detach_hcaidcsConvenience function to detach hcaidcs package
first_wednesdayFirst Wednesday
fmonth_to_stringfmonth_to_string
fq5Convert a date to five-character financial quarter
fq_longFormat date into long quarter.
fq_shortFormat date into short text financial quarter.
fq_short_to_datefq_short_to_date
fq_to_cqConvert financial year quarters to calendar year quarters
fq_to_fyearConvert financial quarter to six-character financial year
fyear_to_cyearConvert financial year to calendar year
fyear_to_fqFyear to long financial quarter
fy_longFormat date into long text financial year.
fy_long_shortFormat fy_long into short financial year.
fyq_to_fqFyear-quarter to long financial quarter
fy_shortFormat date into short text financial year.
fy_sixCreate six character financial year from date
fy_six_to_longFormat date into long text financial year.
group_source_bacteraemiagroup_source_bacteraemia
group_tto_bacteraemiaProvides grouped time to onset for bacteraemia cases
group_tto_cdiProvides grouped time to onset for bacteraemia cases
is_schIdentifies specialist commissioning hubs
is_third_partyCheck whether assignment is third party
kh03_boilerplateAdds KH03 boilerplate text columns to a data frame in...
kh03_yearConvert KH03-formatted dates to Mandatory data-formatted...
klebsiella_sp_groupCreate group for Klebsiella species
mandatory_ageCalculate patient age in manner that conforms to mandatory...
mandatory_age_groupCreate age group from age
mandatory_age_group_bacteraemiamandatory_age_group_bacteraemia(0)
mandatory_age_group_cdiMandatory age group for CDI cases Calculates the mandatory...
mf_fig1_funMonthly factsheet figure 1 function
mf_trend_dataData for monthly factsheet figure 1 function
mo_curr_monthsCreate months for monthly outputs
mo_gnabsi_tableMonthly table for Gram-negative blood stream infection data
mo_next_pub_dateReturns the next publication date of the monthly outputs Used...
monthly_ccg_data_rawData for monthly CCG table for MRSA
mo_prior_hc_tablemo_prior_hc_table
mo_pub_dateNicely formats date of publication for monthly data
mo_std_tableMonthly CCG table
mrsa_source_bacteraemiaClassify the source of bacteramia for MRSA
ordered_fin_qtrCreate factor variable from financial quarter
ordered_m_yAdd ordered month and calendar year to a data frame
patloc_for_pir_assignmentCheck whether a patient location is an NHS Trust or not
pir_org_typeCreate ordered factor variable for PIR organisation type.
popn_boilerplateAdds population boilerplate text columns to a data frame in...
provis_orgnameCheck whether provisional organisation is Trust or CCG
qec_age_tableCreate age group table for QEC
show_hcaidcs_package_manualDisplay manual for this package in browser
subregions_sp_dfNHS subregion geographies for England
time_period2fyearConvert time period variable to fyear for merging with KH03...
time_to_onsetCalculates time to onset for inpatients
update_independentUpdate independent sector providers and independent sector...
up_or_downCalculate whether there has been either an increase, decrease...
PublicHealthEngland/hcaidcs documentation built on July 4, 2018, 12:09 a.m.