Package index • sirfunctions

All functions

add_rolling_years() experimental: Label rolling year periods
check_afp_geographies() experimental: Check whether the AFP geography matches those of the population dataset
check_afp_guid_ctry_data(): Check GUIDs present in the AFP linelist but not in the pop files
check_missing_rows(): Check for rows with NA values
clean_ctry_data(): Cleans and adds additional age and dosage number columns to the AFP linelist
clean_es_data(): Clean environmental surveillance data
clean_iss_data(): Perform common cleaning tasks for ISS/eSURV data
clean_lab_data(): Clean lab data
clear_local_polio_data_cache(): Clear local polio data cache
compress_png(): Compress PNG files using pngquant
create_60_day_export(): Export 60-day follow up table
create_afp_export(): Export the AFP linelist
create_cg_expansion_map(): Create the consequential geography expansion map
create_cg_super_regions(): Create super regions from subsets of consequential geographies
create_emergence_group_gif(): Generate Emergence Group Movement Gifs
create_npafp_export(): Exports NPAFP indicator data summary tables
create_pop_check_export(): Exports file for checking population roll-ups
create_pot_comp_clust_export(): Export potentially compatible and compatible summary table
create_stool_adequacy_export(): Export stool adequacy data
ctry_data_errors(): Check data quality errors from the country data
duplicate_check(): Assess duplicates in the get_all_polio_data() output
edav_io(): Helper function to read and write key data to the EDAV environment
explore_edav() experimental: Interactive loading of EDAV data
export_kpi_table() experimental: Export KPI tables
extract_country_data(): Extract country specific information from raw polio data
f.color.schemes(): Utility function for colors
f.ev.rate.01(): Calculate EV detection rate function
f.expand.bbox(): Expand bounding box
f.metadata.tag(): Function to add metadata tags to figures and tables
f.npafp.rate.01() stable: Calculate non-polio AFP rate
f.plot.looks(): Set plot looks
f.stool.ad.01(): Calculate percent stool adequacy
f.timely.detection.01(): Function to calculate timeliness of detection
fix_ctry_data_missing_guids(): Fix unknown GUIDs in the AFP linelist
flag_cg_positives(): Flag positives data from identified consequential geographies
force_load_polio_data_cache(): Force load data from the local cache
generate_60_day_tab(): 60-day follow up table
generate_60_day_table_data(): Generate summary table for those requiring 60-day follow-up
generate_ad_final_col(): Helper function to add the adequacy.final column
generate_adhoc_map(): Create adhoc maps for emergences
generate_afp_by_month_summary() stable: Generate AFP case count summary
generate_afp_case_map(): AFP case map
generate_afp_ctry_year(): AFP cases by ctry and year
generate_afp_epicurve(): Epicurve of AFP cases by year
generate_afp_prov_year(): AFP cases by province and year
generate_all_prov_desk_review_ppts(): Generate one AFP desk-review PowerPoint per prov
generate_c1_rollup() experimental: Generate C1 rollup for high-priority countries
generate_c1_table() experimental: GPEI Strategy surveillance KPIs
generate_c2_table() experimental: AFP surveillance KPI summary
generate_c3_rollup() experimental: Create a country level rollup of the C3 label
generate_c3_table() experimental: Environmental surveillance KPIs by site
generate_c4_table() experimental: Laboratory surveillance KPIs
generate_case_num_dose_g(): Immunization case status per year
generate_ctry_timeliness_graph(): Timeliness intervals of samples at the country level
generate_dist_pop_map(): Map district U15 populations
generate_dr_ppt(): Generate the desk review slide deck
generate_dr_ppt2(): Generate the desk review slide deck from the figures folder
generate_es_det_map(): ES detection map
generate_es_site_det(): Virus detection in ES sites
generate_es_tab(): ES surveillance sites summary table
generate_es_timely(): ES timeliness scatterplot
generate_inad_tab(): Issues with stool adequacy at the country level
generate_inad_tab_region(): Generate a stool adequacy summary at the regional level
generate_incidence_map(): Generate incidence map timeline
generate_int_data(): Generate a summary table for sample timeliness intervals
generate_iss_barplot(): Visits to health clinics per year
generate_iss_map(): Map of high priority health facilities
generate_kpi_barchart() experimental: Generate KPI indicator bar charts
generate_kpi_ev_map() experimental: EV detection rate map
generate_kpi_evdetect_bar() experimental: Generate KPI EV rate bar chart summary
generate_kpi_map() experimental: Generate KPI maps
generate_kpi_npafp_bar() experimental: Generate KPI NPAFP bar chart summary
generate_kpi_npafp_map() experimental: Generate district level NPAFP maps by region
generate_kpi_stool_map() experimental: Generate district level stool adequacy maps
generate_kpi_stoolad_bar() experimental: Generate KPI Stool adequacy bar chart summary
generate_kpi_tile(): Generate tile plots for indicators
generate_kpi_violin() experimental: Generates KPI violin plot
generate_lab_culture_violin() experimental: Timeliness of lab samples from collection to virus isolation results
generate_lab_itd_violin() experimental: Timeliness of virus isolation to ITD results
generate_lab_itdres_seqres_violin() experimental: Timeliness of final ITD results to sequencing results
generate_lab_seqres_violin() experimental: Timeliness of arrival at sequencing lab to sequencing results
generate_lab_seqship_violin() experimental: Timeliness of shipment to sequencing results
generate_lab_timeliness(): Summary of lab sample timeliness
generate_npafp_maps(): Maps of NPAFP rates by province and year
generate_npafp_maps_dist(): Maps of NPAFP rates by district and year
generate_pop_map(): Country map with province populations
generate_pop_tab(): Summary table of indicators at the province level
generate_pop_tab_ctry(): Country-Level Population Surveillance Table (wide, multi-year)
generate_potentially_compatibles_cluster(): Creating a table of compatible and potentially compatible cases
generate_prov_60_day_table(): PROV 60-day follow-up table
generate_prov_afp_case_map(): PROV-only paralytic polio and compatible-case map
generate_prov_afp_epicurve(): PROV AFP epicurve
generate_prov_desk_review_outputs(): Generate the complete prov AFP review set
generate_prov_desk_review_ppt(): Generate and write one prov AFP desk-review PowerPoint
generate_prov_district_timeliness_panel(): Annual AFP timeliness map panels by district for one prov
generate_prov_es_detection_chart(): ES detection dot chart for one prov
generate_prov_es_location_map(): ES location and detection-rate map for one prov
generate_prov_es_site_table(): ES site details table for one prov
generate_prov_es_timeliness(): ES sample-transport timeliness for one prov
generate_prov_npafp_age_histogram(): Histogram of NPAFP case age in one prov
generate_prov_npafp_detection_delay_graph(): Delayed detection of NPAFP cases in one prov
generate_prov_npafp_immunization_graph(): Immunization status of NPAFP cases in one prov
generate_prov_npafp_map(): PROV-only annualized NPAFP rate map by district
generate_prov_population_roads_map(): PROV DIST under-15 population, roads, and labels map
generate_prov_population_roads_maps(): Generate DIST population and roads maps for multiple prov_names
generate_prov_stool_adequacy_map(): PROV-only stool adequacy map by district
generate_prov_stool_adequacy_table(): PROV stool adequacy issues table
generate_prov_timeliness_graph(): Timeliness intervals of samples at the province level
generate_sg_priority_map() experimental: SG Prioritization Map
generate_stool_ad_maps(): Stool adequacy maps by province
generate_stool_ad_maps_dist(): Maps of stool adequacy by district and year
generate_stool_data(): Generate stool adequacy columns in the AFP dataset
generate_surv_ind_tab(): Surveillance indicator table
generate_surv_reg_tab(): Regional Surveillance Indicators by Year (Multi-country aggregate)
generate_timeliness_maps(): Maps evaluating timeliness of samples against timeliness targets.
generate_timely_det_violin() experimental: Timely detection of AFP/ES samples
generate_timely_ship_violin() experimental: Timely shipment of AFP stool samples
get_all_polio_data(): Retrieve all pre-processed polio data
get_azure_storage_connection(): Validate connection to EDAV
get_cdc_childvaxview_data(): Pull CDC NCIRD childvaxview immunization coverage data
get_constant(): Obtain a constant variable used in sirfunctions
get_ctry_abbrev() experimental: Get country abbreviations
get_diff_cols(): Get the columns where records differ in a group
get_edav_pins_board(): Obtain a pins board from EDAV
get_lab_date_col_missingness(): Get missingness of date variables in the lab dataset
get_lab_locs(): Table of information regarding testing labs in each country
get_ppt_template(): Get path of the PowerPoint template
get_region(): Determines whether lab data is EMRO or AFRO
get_vpd_data() experimental: Get vaccine preventable diseases dataset
get_vpd_missingness() experimental: Get years with missing data based on variable name and VPD
get_vpd_vars(): Obtain available variables for VPD data
init_dr(): Set up the folders and load polio data for the desk review
init_kpi() experimental: Initialize the KPI analysis pipeline
iss_data_errors(): Checks for errors in the ISS data
lab_data_errors(): Generate a log of potential errors in the lab data
list_desk_review_prov(): List available prov_names in country data
load_clean_ctry_sp(): Download country georgraphic data
load_clean_dist_sp(): Download district geographic data
load_clean_prov_sp(): Download province geographic data
load_iss_data(): Read ISS/eSURV data
load_lab_data(): Function to load the raw lab data locally
send_outlook_email(): Send email through Outlook
send_teams_message(): Send a message on Microsoft Teams
set_emergence_colors(): Set the emergence colors
sirfunctions_io() experimental: sirfunctions i/o handler
test_EDAV_connection(): Test network connection to the EDAV
update_city_spatial_data(): Update City Spatial data
update_polio_data() experimental: Update a local dataset with new data
update_road_spatial_data(): Update Roads Spatial data
update_vacc_cov_data(): Extract vaccine coverage information from IHME estimates
upload_to_sharepoint(): Upload file to Sharepoint
write_prov_desk_review_ppt(): Write prov AFP outputs to a PowerPoint