Residual Cancer Burden (RCB) — residualcancerburden • ClinicoPath

Computes the Residual Cancer Burden (RCB) index and class (Symmans et al., 2007) from the standard post-neoadjuvant pathology variables: the two dimensions of the primary tumour bed, overall cancer cellularity, the in-situ fraction, the number of positive lymph nodes, and the diameter of the largest nodal metastasis. The continuous index is classified into RCB-0 (pathologic complete response), RCB-I (minimal), RCB-II (moderate), and RCB-III (extensive) residual disease using the established cut points (1.36 and 3.28). Works on a cohort (one row per patient) or as a single-case calculator, and can optionally relate RCB class to a survival outcome.

Usage

residualcancerburden(
  data,
  inputMode = "data",
  d1 = NULL,
  d2 = NULL,
  cellularity = NULL,
  cis = NULL,
  positiveNodes = NULL,
  metSize = NULL,
  mD1 = 20,
  mD2 = 15,
  mCellularity = 10,
  mCis = 0,
  mNodes = 0,
  mMetSize = 0,
  survivalTime = NULL,
  survivalStatus = NULL,
  eventLevel,
  showDistribution = TRUE,
  showPlot = TRUE,
  survivalLink = FALSE,
  showSummary = FALSE,
  showExplanation = FALSE
)

Arguments

data: The data as a data frame (one row per patient in cohort mode).
inputMode: Compute RCB for every row using data variables, or for a single entered case.
d1: First bidimensional diameter of the primary tumour bed (mm).
d2: Second bidimensional diameter of the primary tumour bed (mm).
cellularity: Overall percentage of the tumour bed area that is carcinoma (0-100).
cis: Percentage of the carcinoma that is in-situ disease (0-100). Defaults to 0.
positiveNodes: Number of regional lymph nodes containing metastatic carcinoma.
metSize: Diameter of the largest nodal metastasis (mm). Defaults to 0.
mD1: Single-case first tumour-bed dimension (mm).
mD2: Single-case second tumour-bed dimension (mm).
mCellularity: Single-case overall cellularity (percent).
mCis: Single-case in-situ fraction (percent).
mNodes: Single-case number of positive nodes.
mMetSize: Single-case largest nodal metastasis (mm).
survivalTime: Follow-up time, to relate RCB class to outcome (cohort mode).
survivalStatus: Event indicator for the survival linkage.
eventLevel: Level of the status variable representing the event.
showDistribution: Tabulate the RCB class distribution across the cohort.
showPlot: Plot the RCB class distribution (cohort) or the case position (single case).
survivalLink: If survival time and status are supplied, show a log-rank test across classes.
showSummary: Plain-language summary of the result.
showExplanation: Explanation of the RCB formula and classes.

Value

A results object containing:

`results$todo`					a html
`results$caseTable`					a table
`results$distributionTable`					a table
`results$survivalTable`					a table
`results$plot`					an image
`results$summary`					a html
`results$explanation`					a html
`results$addIndexToData`					an output
`results$addClassToData`					an output

Tables can be converted to data frames with asDF or as.data.frame. For example:

results$caseTable$asDF

as.data.frame(results$caseTable)

Examples

# \donttest{
residualcancerburden(
    data = mydata,
    d1 = "tumor_dim1", d2 = "tumor_dim2",
    cellularity = "pct_cellularity", cis = "pct_insitu",
    positiveNodes = "n_pos_nodes", metSize = "largest_met_mm")
#> Error in residualcancerburden(data = mydata, d1 = "tumor_dim1", d2 = "tumor_dim2",     cellularity = "pct_cellularity", cis = "pct_insitu", positiveNodes = "n_pos_nodes",     metSize = "largest_met_mm"): argument "eventLevel" is missing, with no default
# }