run_fcm function

Run Function Cox Models

Fit a functional Cox regression model.

run_fcm(
  mxFDAobject,
  model_name,
  formula,
  event = "event",
  metric = "uni k",
  r = "r",
  value = "fundiff",
  afcm = FALSE,
  smooth = FALSE,
  filter_cols = NULL,
  ...,
  knots = NULL
)

Arguments

• mxFDAobject: Dataframe of spatial summary functions from multiplex imaging data, in long format. Can be estimated using the function extract_summary_functions or provided separately.
• model_name: character string to give the fit model in the functional cox slot
• formula: Formula to be fed to mgcv in the form of survival_time ~ x1 + x2. Does not contain functional predictor. Character valued. Data must contain censoring variable called "event".
• event: character string for the column in Metadata that contains 1/0 for the survival event
• metric: name of calculated spatial metric to use
• r: Character string, the name of the variable that identifies the function domain (usually a radius for spatial summary functions). Default is "r".
• value: Character string, the name of the variable that identifies the spatial summary function values. Default is "fundiff".
• afcm: If TRUE, runs additive functional Cox model. If FALSE, runs linear functional cox model. Defaults to linear functional cox model.
• smooth: Option to smooth data using FPCA. Defaults to FALSE.
• filter_cols: a named vector of factors to filter summary functions to in c(Derived_Column = "Level_to_Filter") format
• ...: Optional other arguments to be passed to fpca.face
• knots: Number of knots for defining spline basis.

Returns

A list which is a linear or additive functional Cox model fit. See mgcv::gam for more details.

Details

Examples

#load ovarian mxFDA object
data('ovarian_FDA')

#run the lfcm model
ovarian_FDA = run_fcm(ovarian_FDA, model_name = "fit_lfcm",
                      formula = survival_time ~ age, event = "event",
                      metric = "uni g", r = "r", value = "fundiff",
                      afcm = FALSE)

Author(s)

Julia Wrobel julia.wrobel@emory.edu

Alex Soupir alex.soupir@moffitt.org