Man pages for TalhoukLab/biostatUtil
Utility Functions Used in Biostatistics Projects
| addTableNumber | Add table number |
| assessSurvTime | Assess survival time |
| barplotSum | Annotated Barplot |
| best_cut | Find the best cutpoint for a covariate |
| binaryCM | Confusion matrix summaries |
| binaryCMAsHTML | Confusion matrix results in HTML |
| biostatUtil | biostatUtil: utility functions for biostatistical projects |
| bootMean | Mean and bootstrap confidence interval |
| boxplotSum | Annotated Boxplot |
| build_cuts | Build cutpoint variables |
| censor_date | Date of censoring |
| chr_to_date | Change character to date |
| cleanDate | Clean dates |
| coxphOut | Nice output from Cox regression object |
| date_compute | Date computations |
| date_extremes | Latest and Earliest Dates |
| design_matrix | Design Matrix with interactions |
| diff_years | Date difference in years |
| doBarplot | Barplot with counts |
| doBoxplotAmongSubtypes | Do a boxplot among subtypes |
| doCohortCharacteristics | Generate cohort characteristics |
| doCoxph | Fit a Cox proportional hazards regression model |
| doHist | Do histogram with median |
| doInteractionCox | Do interaction test with cox model likelihood ratio test only... |
| doJitterplotAmongSubtypes | Do a jitterplot among subtypes |
| doKMPlots | Make Kaplan-Meier plots |
| escapeForGrep | Escape string for regular expression |
| exploreData | Graphical Exploration of a Dataset |
| extract_results | Extract results for executive summary |
| findCutpointByCoxph | Find cutpoint by Cox model statistics |
| formatDate | Format a date. |
| formatNA | Missing Value Formatting |
| freqTable | Generate a Frequency Table |
| geoMean | Geometric mean |
| getFormat | Get date format from character text |
| getPval | Get the p-value |
| gg_diagnostic_prev | Diagnostic Prevalence |
| ggkm | Kaplan-Meier Plots using ggplot |
| g_legend | Generate a legend |
| grhoTests | Summary of Survival Curve differences using G-rho tests |
| histSum | Summary histogram |
| indepTests | Tests for Independence in Contingency Tables |
| indexOf | Find occurences of string within another string |
| isFirstLetterUpperCase | Is the first letter uppercase? |
| kappaBootCI | Bootstrapped confidence interval for kappa statistic. |
| knit_with_date | Knit R markdown report with today's date |
| lifetable | Generate lifetables for multiclass variables |
| logistfPrint | Print summaries from logistf |
| medianCtr | Median center rows |
| ms_condition | Sample count condition for MS analyses |
| ms_plot | Plots for MS analyses |
| ms_process | Process mass spectrometry data |
| ms_summarize | Summarize mass spectrometry data |
| ms_top | Top variables in mass spectrometry analysis |
| multiClassCM | Confusion matrix summaries |
| multiplot | Multiple plots |
| name_cuts | Name cutpoint variables |
| numericToDate | Change numeric to date |
| pairwiseCor | Pairwise Correlations |
| parse_rd | Parse all Rd files in package |
| PCAplot | Plot Principal Components |
| percents | Row and Column Percentages |
| plotKM | Plot Kaplan-Meier curves |
| plotKMDetail | Plot detailed Kaplan-Meier curves |
| plotSchoenfeld | Do Schoenfeld residual plot |
| prettyCoxph | Nicer outputs from coxph model fits |
| pro | Protein file from Mass Spectrometry experiment |
| psm | Peptide-Spectrum Match (PSM) file from Mass Spectrometry... |
| R2_to_D | Convert R2 to D |
| remove_dup | Remove duplicates |
| round_small | Rounding of Small Numbers |
| sample_size_prop | Sample Size for Multiple Proportions in One-Way Design |
| sdFromCI | Standard deviation of log hazard ratio |
| sem | Standard error of the mean |
| simpleCap | Simple capitalization |
| ssize_D | Sample Size Calculation |
| statsWithMissing | Calculates statistics with specifying missing values |
| summaryAsHTML | Summary table in HTML format |
| SummaryStatsBy | Generate summary statistics |
| tableAsHTML | Table as HTML format |
| wrap_ggkm | Wrap list of 'ggkm' plots into a single patchwork |
| Xunivcoxph | Univariate cox proprtional hazards model |
