multisurvival: Multivariable Survival Analysis
In sbalci/jsurvival: Survival Module of ClinicoPath for jamovi

View source: R/multisurvival.h.R

multisurvival

R Documentation

Multivariable Survival Analysis

Description

Function for Multivariable Survival Analysis using Cox-regression.

Usage

multisurvival(
  data,
  elapsedtime,
  tint = FALSE,
  dxdate,
  fudate,
  timetypedata = "ymd",
  timetypeoutput = "months",
  uselandmark = FALSE,
  landmark = 3,
  outcome,
  outcomeLevel,
  dod,
  dooc,
  awd,
  awod,
  analysistype = "overall",
  explanatory,
  contexpl,
  multievent = FALSE,
  hr = FALSE,
  sty = "t1",
  ph_cox = FALSE,
  km = FALSE,
  endplot = 60,
  byplot = 12,
  ci95 = FALSE,
  risktable = FALSE,
  censored = FALSE,
  medianline = "none",
  pplot = TRUE,
  cutp = "12, 36, 60",
  calculateRiskScore = FALSE,
  numRiskGroups = "four",
  plotRiskGroups = FALSE,
  ac = FALSE,
  adjexplanatory,
  ac_method = "average",
  showNomogram = FALSE,
  use_stratify = FALSE,
  stratvar
)

Arguments

`data`	The dataset to be analyzed, provided as a data frame. Must contain the variables specified in the options below.
`elapsedtime`	The numeric variable representing follow-up time until the event or last observation. If `tint` = false, this should be a pre-calculated numeric time variable. If `tint` = true, `dxdate` and `fudate` will be used to calculate this time.
`tint`	If true, survival time will be calculated from `dxdate` and `fudate`. If false, `elapsedtime` should be provided as a pre-calculated numeric variable.
`dxdate`	Date of diagnosis. Required if `tint` = true. Must match the format specified in `timetypedata`.
`fudate`	Follow-up date or date of last observation. Required if `tint` = true. Must match the format specified in `timetypedata`.
`timetypedata`	Specifies the format of the date variables in the input data. This is critical if `tint = true`, as `dxdate` and `fudate` will be parsed according to this format to calculate survival time. For example, if your data files record dates as "YYYY-MM-DD", select `ymd`.
`timetypeoutput`	The units in which survival time is reported in the output. Choose from days, weeks, months, or years.
`uselandmark`	If true, applies a landmark analysis starting at a specified time point.
`landmark`	The time point (in the units defined by `timetypeoutput`) at which to start landmark analyses. Only used if `uselandmark` = true.
`outcome`	The outcome variable. Typically indicates event status (e.g., death, recurrence). For survival analysis, this may be a factor or numeric event indicator.
`outcomeLevel`	The level of `outcome` considered as the event. For example, if `outcome` is a factor, specify which level indicates the event occurrence.
`dod`	The level of `outcome` corresponding to death due to disease, if applicable.
`dooc`	The level of `outcome` corresponding to death due to other causes, if applicable.
`awd`	The level of `outcome` corresponding to alive with disease, if applicable.
`awod`	The level of `outcome` corresponding to alive without disease, if applicable.
`analysistype`	Type of survival analysis: - overall: All-cause survival - cause: Cause-specific survival - compete: Competing risks analysis
`explanatory`	Categorical explanatory (predictor) variables included in the Cox model.
`contexpl`	Continuous explanatory (predictor) variables included in the Cox model.
`multievent`	If true, multiple event levels will be considered for competing risks analysis. Requires specifying `dod`, `dooc`, etc.
`hr`	If true, generates a plot of hazard ratios for each explanatory variable in the Cox model.
`sty`	The style of the hazard ratio (forest) plot. "finalfit" or "survminer forestplot".
`ph_cox`	If true, tests the proportional hazards assumption for the Cox model. Use if you suspect violations of the PH assumption.
`km`	If true, produces a Kaplan-Meier survival plot. Useful for visualization of survival functions without covariate adjustment.
`endplot`	The maximum follow-up time (in units defined by `timetypeoutput`) to display on survival plots.
`byplot`	The interval (in units defined by `timetypeoutput`) at which time points or labels are shown on plots.
`ci95`	If true, displays 95\ estimates on plots.
`risktable`	If true, displays the number of subjects at risk at each time point below the survival plot.
`censored`	If true, marks censored observations (e.g., using tick marks) on the survival plot.
`medianline`	If true, displays a line indicating the median survival time on the survival plot.
`pplot`	If true, displays the p-value from the survival comparison test on the survival plot.
`cutp`	.
`calculateRiskScore`	If true, calculates a risk score from the Cox model coefficients for each individual.
`numRiskGroups`	Select the number of risk groups to create from the risk scores. The data will be divided into equal quantiles based on this selection.
`plotRiskGroups`	If true, stratifies individuals into risk groups based on their calculated risk scores and plots their survival curves.
`ac`	.
`adjexplanatory`	.
`ac_method`	Method for computing adjusted survival curves
`showNomogram`	.
`use_stratify`	If true, uses stratification to handle variables that violate the proportional hazards assumption. Stratification creates separate baseline hazard functions for different groups.
`stratvar`	Variables used for stratification. When proportional hazards are not met, stratification can adjust the model to better fit the data by allowing different baseline hazards.

Value

A results object containing:

`results$todo`					a html
`results$text`					a html
`results$text2`					a html
`results$plot`					an image
`results$plot3`					an image
`results$cox_ph`					a preformatted
`results$plot8`					an image
`results$plotKM`					an image
`results$risk_score_analysis`					a preformatted
`results$risk_score_analysis2`					a html
`results$riskScoreTable`					a table
`results$riskScoreMetrics`					a html
`results$riskGroupPlot`					an image
`results$stratificationExplanation`					a html
`results$calculatedtime`					an output
`results$outcomeredefined`					an output
`results$addRiskScore`					an output
`results$addRiskGroup`					an output
`results$plot_adj`					an image
`results$mydataview_nomogram2`					a preformatted
`results$mydataview_nomogram`					a preformatted
`results$plot_nomogram`					an image
`results$nomogram_display`					a html