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Copy pathGECKO_original_unedited_factoring_script.r
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GECKO_original_unedited_factoring_script.r
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#Clear existing data and graphics
rm(list=ls())
graphics.off()
#Load Hmisc library
library(Hmisc)
#Read Data
data=read.csv('GECKOTeamRegistratio-SiteSurveyDataNeil_DATA_2024-03-25_1128.csv')
#Setting Labels
label(data$record_id)="Record ID"
label(data$redcap_data_access_group)="Data Access Group"
label(data$hosp_type)=" Hospital type (Please select the option which best describes your hospital.)"
label(data$hosp_fund)=" Hospital funding"
label(data$hosp_bed)=" Total number of inpatient beds (Please include both surgical and non-surgical beds.)"
label(data$hosp_itu_yn)=" Do you have Level 2 (HDU) or Level 3 (ITU) facilities at your hospital?"
label(data$hosp_itu_bed)=" Total number of Level 2 (HDU) or Level 3 (ITU) beds"
label(data$hosp_hpb)=" Do you have a specialised HPB team at your hospital?"
label(data$hosp_hpb_oncall)=" Are there on-call services from the specialised HPB team?"
label(data$hosp_hpb_path)=" Does the specialised HPB team have a dedicated pathway for management of bile duct injury?"
label(data$hosp_hpb_region)=" Are there on-call surgeons specialised in HPB?"
label(data$hosp_mis_yn)=" Do you have access to minimally invasive surgical equipment?"
label(data$hosp_mis_type)=" Type of minimally invasive surgical equipment available"
label(data$hosp_mis_image)=" Do you routinely take intraoperative images at your hospital?"
label(data$service_chole_n)=" What is the approximate total number of cholecystectomies performed each year at your hospital?"
label(data$service_cons_n)=" What is the number of consultant/attending surgeons who perform cholecystectomies each year at your hospital?"
label(data$service_cons_lap_n)=" What is the number of consultant/attending surgeons who perform laparoscopic cholecystectomy at your hospital?"
label(data$service_cons_type)=" Which specialist consultant/attending surgeons perform cholecystectomies at your hospital?"
label(data$service_type)=" What type of services for cholecystectomy services is provided at your hospital?"
label(data$service_eme_n)=" What is the approximate total number of emergency cholecystectomies performed each year at your hospital?"
label(data$service_eme_theatre)=" Do you have dedicated theatres for these emergency services?"
label(data$service_setting)=" Where are cholecystectomies performed at your hospital? "
label(data$service_fu)=" Do you follow-up after cholecystectomy?"
label(data$diag_us_yn)=" Ultrasound"
label(data$diag_ct_yn)=" Computerised Tomography (CT)"
label(data$diag_mrcp_yn)=" Magnetic Resonance Cholangiopancreatography (MRCP)"
label(data$diag_eus_yn)=" Endoscopic Ultrasound (EUS)"
label(data$diag_hida_yn)=" Hepatobiliary Iminodiacetic Acid (HIDA)"
label(data$diag_ostomy_yn)=" Does your hospital have access to cholecystostomy for gallbladder drainage?"
label(data$diag_ostomy_oncall)=" Are there on-call services for cholecystostomy at your hospital?"
label(data$diag_ostomy_region)=" Are there on-call interventional radiologists who perform cholecystostomy available?"
label(data$diag_ercp)=" Is there a dedicated Endoscopic retrograde cholangiopancreatography (ERCP) list at your hospital?"
label(data$diag_ioc)=" Intraoperative Cholangiogram (IOC)"
label(data$diag_lu)=" Laparoscopic Ultrasound"
label(data$diag_icg)=" Incisionless fluorescent cholangiography"
label(data$diag_hist)=" Do you send gallbladders for histological examination after surgery?"
label(data$train_perform)=" Are there trainees in the department who perform gallbladder surgery?"
label(data$train_n)=" How many trainees are there in the department who perform gallbladder surgery?"
label(data$train_grade)=" What are the trainees grades who perform gallbladder surgery in your department?"
label(data$train_sim_yn)=" Are there facilities for simulations training for cholecystectomies?"
label(data$train_sim_type)=" What are the types of simulation training available?"
label(data$tain_chole)=" Are there structured educational programmes or coaching for cholecystectomy training?"
label(data$train_bdi)=" Are there specific structured educational programmes or coaching for bile duct injury training?"
label(data$green_lap)=" Are reusable laparoscopic ports used?"
label(data$green_surginst)=" Are reusable surgical instruments used?"
label(data$green_drape)=" Are reusable drapes used?"
label(data$green_gown)=" Are reusable gowns used?"
label(data$green_scrubcap)=" Are reusable scrub caps used?"
label(data$green_recycle)=" Are single-use instruments recycled?"
label(data$green_recycle_waste)=" Are clean paper and plastic waste recycled?"
label(data$green_ga)=" Is general anaesthesia given through IV rather than anaesthetic gases for environmental reasons?"
label(data$site_survey_complete)="Complete?"
label(data$data_collection_dag)="Data dag:"
label(data$admin_complete)="Complete?"
#Setting Units
#Setting Factors(will create new variable for factors)
data$redcap_data_access_group.factor = 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data$hosp_type.factor = factor(data$hosp_type,levels=c("1","2","3"))
data$hosp_fund.factor = factor(data$hosp_fund,levels=c("1","2","3"))
data$hosp_itu_yn.factor = factor(data$hosp_itu_yn,levels=c("1","0"))
data$hosp_hpb.factor = factor(data$hosp_hpb,levels=c("1","0"))
data$hosp_hpb_oncall.factor = factor(data$hosp_hpb_oncall,levels=c("1","2","3","4"))
data$hosp_hpb_path.factor = factor(data$hosp_hpb_path,levels=c("1","0"))
data$hosp_hpb_region.factor = factor(data$hosp_hpb_region,levels=c("1","2","3","4"))
data$hosp_mis_yn.factor = factor(data$hosp_mis_yn,levels=c("1","0"))
data$hosp_mis_image.factor = factor(data$hosp_mis_image,levels=c("1","2","3","4"))
data$service_eme_theatre.factor = factor(data$service_eme_theatre,levels=c("1","2","3","4","5"))
data$service_fu.factor = factor(data$service_fu,levels=c("1","2","3"))
data$diag_us_yn.factor = factor(data$diag_us_yn,levels=c("1","2","3"))
data$diag_ct_yn.factor = factor(data$diag_ct_yn,levels=c("1","2","3"))
data$diag_mrcp_yn.factor = factor(data$diag_mrcp_yn,levels=c("1","2","3"))
data$diag_eus_yn.factor = factor(data$diag_eus_yn,levels=c("1","2","3"))
data$diag_hida_yn.factor = factor(data$diag_hida_yn,levels=c("1","2","3"))
data$diag_ostomy_yn.factor = factor(data$diag_ostomy_yn,levels=c("1","0"))
data$diag_ostomy_oncall.factor = factor(data$diag_ostomy_oncall,levels=c("1","2","3","4","5"))
data$diag_ostomy_region.factor = factor(data$diag_ostomy_region,levels=c("1","2","3","4"))
data$diag_ercp.factor = factor(data$diag_ercp,levels=c("1","2","3","4","5"))
data$diag_ioc.factor = factor(data$diag_ioc,levels=c("1","2","3","4"))
data$diag_lu.factor = factor(data$diag_lu,levels=c("1","2","3","4"))
data$diag_icg.factor = factor(data$diag_icg,levels=c("1","2","3","4"))
data$diag_hist.factor = factor(data$diag_hist,levels=c("1","2","3","4"))
data$train_perform.factor = factor(data$train_perform,levels=c("1","0"))
data$green_lap.factor = factor(data$green_lap,levels=c("1","2","3","4"))
data$green_surginst.factor = factor(data$green_surginst,levels=c("1","2","3","4"))
data$green_drape.factor = factor(data$green_drape,levels=c("1","2","3","4"))
data$green_gown.factor = factor(data$green_gown,levels=c("1","2","3","4"))
data$green_scrubcap.factor = factor(data$green_scrubcap,levels=c("1","2","3","4"))
data$green_recycle.factor = factor(data$green_recycle,levels=c("1","2","3","4"))
data$green_recycle_waste.factor = factor(data$green_recycle_waste,levels=c("1","0"))
data$green_ga.factor = factor(data$green_ga,levels=c("1","2","3","4"))
data$site_survey_complete.factor = factor(data$site_survey_complete,levels=c("0","1","2"))
data$admin_complete.factor = factor(data$admin_complete,levels=c("0","1","2"))
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levels(data$hosp_type.factor)=c("District (Rural)","District (Non-rural)","Tertiary (teaching or university hospital)")
levels(data$hosp_fund.factor)=c("Public","Private","Mixed")
levels(data$hosp_itu_yn.factor)=c("Yes","No")
levels(data$hosp_hpb.factor)=c("Yes","No")
levels(data$hosp_hpb_oncall.factor)=c("Every day (24 hour)","Every day (daytime 0800 - 1700)","Weekdays only (24 hour)","Weekdays only (daytime 0800 - 1700)")
levels(data$hosp_hpb_path.factor)=c("Yes","No")
levels(data$hosp_hpb_region.factor)=c("Within the same city","In another city but in the same region","In another region","None")
levels(data$hosp_mis_yn.factor)=c("Yes","No")
levels(data$hosp_mis_image.factor)=c("Yes (Photo only)","Yes (Video only)","Yes (Photo and Video)","No")
levels(data$service_eme_theatre.factor)=c("Yes (Everyday)","Yes (Once a week)","Yes (Once every 2 week)","Yes (More than once every 2 weeks)","No")
levels(data$service_fu.factor)=c("Yes (Routinely)","Yes (Selectively)","No")
levels(data$diag_us_yn.factor)=c("Available on-site","Available off-site","Not available")
levels(data$diag_ct_yn.factor)=c("Available on-site","Available off-site","Not available")
levels(data$diag_mrcp_yn.factor)=c("Available on-site","Available off-site","Not available")
levels(data$diag_eus_yn.factor)=c("Available on-site","Available off-site","Not available")
levels(data$diag_hida_yn.factor)=c("Available on-site","Available off-site","Not available")
levels(data$diag_ostomy_yn.factor)=c("Yes","No")
levels(data$diag_ostomy_oncall.factor)=c("Yes (Everyday)","Yes (Once a week)","Yes (Once every 2 week)","Yes (More than once every 2 weeks)","No")
levels(data$diag_ostomy_region.factor)=c("Within the same city","In another city but in the same region","In another region","None")
levels(data$diag_ercp.factor)=c("Yes (Everyday)","Yes (Once a week)","Yes (Once every 2 week)","Yes (More than once every 2 weeks)","No")
levels(data$diag_ioc.factor)=c("Routine use","Selective use with good supply","Selective use with limited supply","Not available")
levels(data$diag_lu.factor)=c("Routine use","Selective use with good supply","Selective use with limited supply","Not available")
levels(data$diag_icg.factor)=c("Routine use","Selective use with good supply","Selective use with limited supply","Not available")
levels(data$diag_hist.factor)=c("Yes (Routinely)","Yes (Selectively)","No (Not sent for histology)","No (No access to histology)")
levels(data$train_perform.factor)=c("Yes","No")
levels(data$green_lap.factor)=c("Yes (Always)","Yes (Sometimes)","No (Not used but available)","No (Not available)")
levels(data$green_surginst.factor)=c("Yes (Always)","Yes (Sometimes)","No (Not used but available)","No (Not available)")
levels(data$green_drape.factor)=c("Yes (Always)","Yes (Sometimes)","No (Not used but available)","No (Not available)")
levels(data$green_gown.factor)=c("Yes (Always)","Yes (Sometimes)","No (Not used but available)","No (Not available)")
levels(data$green_scrubcap.factor)=c("Yes (Always)","Yes (Sometimes)","No (Not used but available)","No (Not available)")
levels(data$green_recycle.factor)=c("Yes (Always)","Yes (Sometimes)","No (Not recycled but recycling service available)","No (No recycling service available)")
levels(data$green_recycle_waste.factor)=c("Yes","No")
levels(data$green_ga.factor)=c("Yes (Always)","Yes (Sometimes)","No (Anaesthetic gases used but IV anaesthesia available)","No (No IV anaesthesia available)")
levels(data$site_survey_complete.factor)=c("Incomplete","Unverified","Complete")
levels(data$admin_complete.factor)=c("Incomplete","Unverified","Complete")