Man pages for n8thangreen/HESmanip
Hospital length of stay data preprocessing and analysis
| adminCens | Administrative censoring |
| AgeCatModify | Age category modification |
| antibioticLookup.dat | Antibiotic look-up table |
| artifCens | Artificial censoring |
| boot.clos | Bootstrap LOS |
| boot.clos.dtable | Bootstrap LOS with data.table |
| byGroupHR | Calculate Cox regression by groups |
| byGroupHR.boxplot | Hazard ratio boxplots |
| byGroupLOS | Length of stay by groups |
| byGroupLOS.boxplot | Boxplot of length of stay by groups |
| capwords | Capitalise words |
| catcodes | Concatenate codes |
| catStays | Concatenate hospital stays |
| charlson | Calculate Charlson comorbidity score |
| clean.data | Clean ICD10 codes |
| clean.ref | Clean reference table codes |
| cLOS | Extension of clos() with medians |
| commonlist | commonlist |
| dat.icu.pneu | Sample ICU pneumonia time to event data from kmi package in... |
| etmFormat | Transform to etm format |
| extractCox | Extract subset of Cox regression statistics. |
| facFlags | Group patients across multiple columns |
| findDuplicates | Find patient record duplicates |
| getGrams | Otain Grams-negative or Gram-positive patient organism status |
| getHES | Read-in HES data |
| getPatientGroupings | Group patients by risk factors |
| getSurvData | Transform to survival data format |
| HCAIsummary | HCAIsummary |
| HESmanip-package | Hospital length of stay data preprocessing and analysis |
| highlevelHCAI | Combined length of stay calculations |
| HRboxplot.batch | Hazard ratio boxplots for all groups as a batch run |
| hr.naive | Time-independent Cox regression |
| hr.tv.causespecific | Time-dependent Cox regression for the cause-specific model |
| hr.tv.subdistribution | Time-dependent Cox regression for the subdistribution model |
| ICDwordmatch | ICD10 word match against patient codes |
| infdata_sample | Exposure/infected sample of patients in linked HES-LabBase2... |
| iqr | Interquartile range |
| listLOS | Length of stay multistate model statistics |
| long2wide | Convert length of stay data from "new" long format to "old"... |
| LOSboot.plot | Length of stay envelope plot |
| LOSboot.plot.wide | Length of stay bootstrap plot with envelope bounds for "old"... |
| LOStable | Hospital length of stay table |
| multistateplots.org | Multistate plots by organism types |
| my.ephi | my.ephi |
| my_recode | Group together codes |
| na.mean | Mean calculation excluding NAs |
| na.median | Median calculation excluding NAs |
| na.sd | standard deviation calculation excluding NAs |
| plot.FollowUpChart | plot.FollowUpChart |
| plot.FollowUpChartBatch | plot.FollowUpChartBatch |
| rmAllButOne | Remove all but one patient record |
| rmDuplicates | Remove duplicate patient records |
| rmOrganism | Remove duplicate entries which only differ by HCAI organism... |
| spellLength | Find actual start and end of a patients in-hospital spell |
| splitByGroup | Split patient record data in subsets which all contain all... |
| splitByOrg | Stratify the patient sample by organism type |
| stratSurvData | Stratify patient survival data |
| subdistn | Fine & Gray subdistribution model time to event times |
| summaryTableAll | summaryTableAll |
| summaryTableGroup | summaryTableGroup |
| summaryTableRF | summaryTableRF |
| survDataByGender | Survival analysis format stratified by gender |
| suscdata_sample | Unexposed/uninfected sample of patients in HES format |
| table2.HR | table2.HR |
| table3.HR | More condensed table format of hazard ratio values for... |
| table.HR | table.HR |
| totaldata_sample | Combined exposed and unexposed sample data |
| trim.boxplot | trim.boxplot |
| trimSurv | trimSurv |
| tvCox | Time-varying regression data representation |
| whichPatientDrug | Match patients against a look-up table of treatments |
| whichPatientDrug.joins | Identify which patients have anti-microbial resistance and... |
