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Therapy dose-response model

Source: R/dose-response.R
doseResponse.Rd

Fits an outcome (or change from baseline) as a function of a continuous / ordinal therapy dose, with optional confounder adjustment, subject random intercepts and a non-linear dose form. Returns the fitted dose effect, a predicted dose-response curve and the coefficient table.

Usage

doseResponse(
  data,
  outcome,
  dose,
  covariates = NULL,
  subject = NULL,
  baseline = NULL,
  form = c("linear", "log", "spline", "emax"),
  df = 3,
  n_grid = 50
)

Arguments

data

A data.frame with the columns named below.

outcome

Name of the outcome column.

dose

Name of the therapy-dose column (hours / repetitions / sessions).

covariates

Optional character vector of confounder columns to adjust for (added linearly).

subject

Optional subject-id column; when given, a random intercept per subject is fit via fitMixedModel() (needs lme4).

baseline

Optional baseline column; when given it is added as an adjustment covariate (ANCOVA-style change analysis).

form

Dose form: "linear", "log" (needs positive dose), "spline" (natural cubic spline, df terms) or "emax" (E0 + Emax*dose/(ED50+dose), fit by stats::nls(); no subject/covariates).

df

Spline degrees of freedom for form = "spline" (default 3).

n_grid

Number of dose points in the predicted curve (default 50).

Value

A PhysioCore::AnalysisResult of type = "dose_response": estimate is the dose effect (slope, spline coefficients, or E0/Emax/ED50); result holds coefficients, the curve (dose, predicted), the fit and the form.

References

Ruberg SJ (1995) Dose response studies. J Biopharm Stat 5:1-14.

See also

fitMixedModel(), proportionalRecoveryRule()

Examples

set.seed(1)
d <- data.frame(dose = rep(c(0, 5, 10, 20), each = 15))
d$change <- 0.4 * d$dose + rnorm(nrow(d), 0, 2)
dr <- doseResponse(d, outcome = "change", dose = "dose", form = "linear")
PhysioCore::resultValue(dr)$coefficients
#>          term  estimate         se  statistic            p
#> 1 (Intercept) 0.1382792 0.34475004  0.4010999 6.898205e-01
#> 2        dose 0.4087947 0.03009225 13.5847166 1.137395e-19