inst/doc/mult_regimen.R

In DoseFinding: Planning and Analyzing Dose Finding Experiments

## ----settings-knitr, include=FALSE--------------------------------------------
library(ggplot2)
knitr::opts_chunk$set(echo = TRUE, message = FALSE, cache = FALSE,
                      comment = NA,
                      dev = "png", dpi = 150, fig.asp = 0.618, fig.width = 7, out.width = "85%", fig.align = "center")
options(rmarkdown.html_vignette.check_title = FALSE)
theme_set(theme_bw())

## ----data---------------------------------------------------------------------
library(DoseFinding)
library(ggplot2)
## collect estimates and dosage information in one place
example_estimates <- function() {
  ## ANOVA mean estimates and ci bounds extracted from fig. 3 of Bays (2020).
  ## clinicaltrials.gov page already seems to contain values from the dose-response model fit
  mn <- c(-0.55, -1.78, -1.95, -3.29, -4.43, -1.14, -2.74, -4.03, -4.47)
  lb <- c(-1.56, -3.15, -3.36, -4.85, -5.40, -2.49, -4.10, -5.50, -5.50)
  ub <- c( 0.40, -0.30, -0.54, -1.76, -3.48, 0.24, -1.38, -2.65, -3.44)
  se <- (ub - lb)/(2*qnorm(0.975)) # approximate standard error
  return(list(mu_hat = mn,
              daily_dose = c(0, 2.5, 10, 50, 150, 5, 10, 50, 100),
              S_hat = diag(se^2),
              # keep track of which elements correspond to which regimen:
              index = list(placebo = 1, od = 2:5, bid = 6:9)))
}

## restructure estimates for easy plotting with ggplot
tidy_estimates <- function(est) {
  se <- sqrt(diag(est$S_hat))
  tidy <- data.frame(daily_dose = est$daily_dose, mu_hat = est$mu_hat,
                     ub = est$mu_hat + qnorm(0.975) * se, lb = est$mu_hat - qnorm(0.975) * se)
  tidy <- rbind(tidy[1, ], tidy) # duplicate placebo
  tidy$regimen <- c("od", "bid", rep("od", length(est$index$od)), rep("bid", length(est$index$bid)))
  return(tidy)
}

plot_estimates <- function(est) {
  df <- tidy_estimates(est)
  ggplot(df, aes(daily_dose, mu_hat)) + geom_point() +
    geom_errorbar(aes(ymin = lb, ymax = ub)) +
    facet_wrap(vars(regimen), labeller = label_both) +
    xlab("daily dose") + ylab("percent body weight cange") +
    labs(title = "ANOVA estimates with 95% confindence intervals")
}

est <- example_estimates()
plot_estimates(est)

## ----candidate_models---------------------------------------------------------
mods <- list(
  od = Mods(emax = c(5, 50),
            sigEmax = rbind(c(75, 3.5), c(25, 0.7)),
            maxEff = -1,
            doses = est$daily_dose[c(est$index$placebo, est$index$od)]),
  bid = Mods(emax = c(5, 50),
             sigEmax = rbind(c(75, 3.5), c(25, 0.7)),
             maxEff = -1,
             doses=est$daily_dose[c(est$index$placebo, est$index$bid)]))

plotMods(mods$od, superpose = TRUE, xlab = "daily dose")
plotMods(mods$bid, superpose = TRUE, xlab = "daily dose")

## ----contrasts----------------------------------------------------------------
calculate_contrasts <- function(est, mods) {
  S_hat <- est$S_hat
  i <- est$index
  cm_od <- optContr(mods$od, S=S_hat[c(i$placebo, i$od), c(i$placebo, i$od)])$contMat
  cm_bid <- optContr(mods$bid, S=S_hat[c(i$placebo, i$bid), c(i$placebo, i$bid)])$contMat
  colnames(cm_od) <- paste0("od_", colnames(cm_od))
  rownames(cm_od)[-1] <- paste0("od_", rownames(cm_od)[-1])
  colnames(cm_bid) <- paste0("bid_", colnames(cm_bid))
  rownames(cm_bid)[-1] <- paste0("bid_", rownames(cm_bid)[-1])
  # now build a block matrix (contrasts in columns) like this:
  # [ row of placebo coefficients od   | row of placebo coefficients bid   ]
  # [----------------------------------+-----------------------------------]
  # [ remaining doses' coefficents od  | fill with all zeros               ]
  # [----------------------------------+-----------------------------------]
  # [ fill with all zeros              | remaining doses' coefficients bid ]
  cm_full <- rbind(
    "0"=c(cm_od[1,],                                cm_bid[1,]                              ),
    cbind(cm_od[-1,],                               matrix(0, nrow(cm_od) - 1, ncol(cm_bid))),
    cbind(matrix(0, nrow(cm_bid) - 1, ncol(cm_od)), cm_bid[-1, ]                            ))
  return(cm_full)
}

cont_mat <- calculate_contrasts(est, mods)
print(round(cont_mat, 2))

## ----test---------------------------------------------------------------------
mct_test <- function(cont_mat, est) {
  cont_cov <- t(cont_mat) %*% est$S_hat %*% cont_mat
  t_stat <- drop(est$mu_hat %*% cont_mat) / sqrt(diag(cont_cov))
  # FIXME: calling non-exported function
  p <- MCTpval(contMat = cont_mat, corMat = cov2cor(cont_cov),
               df=Inf, tStat=t_stat, alternative = "one.sided")
  ord <- rev(order(t_stat))
  return(data.frame(tStat = t_stat[ord], pVals = p[ord]))
}
mct_test(cont_mat, est)

## ----estimation_1-------------------------------------------------------------
## calculate response under `model` for od/bid with common e0, but separate remaining parameters
## arguments:
## - model: as a string like "emax",
## - i_par: list of vectors named "placebo", "od", "bid", used for indexing `par`
## - par: numeric, model parameter structured as c(e0, pars_od, pars_bid)
## returns: response at placebo, dose_od, dose_bid (in this order)
eval_model_shared_e0 <- function(model, dose_od, dose_bid, par, i_par) {
  resp_placebo <- par[1] # e0
  resp_od <- do.call(model, append(list(dose_od, par[1]), as.list(par[i_par$od])))
  resp_bid <- do.call(model, append(list(dose_bid, par[1]), as.list(par[i_par$bid])))
  resp <- c(resp_placebo, resp_od, resp_bid)
  return(resp)
}

## ----estimation_2-------------------------------------------------------------
## find sensible starting values for `fit_model_shared_e0` by fitting separate models,
## index:  list of vectors named "placebo", "od", "bid", used for indexing `dose`
## bounds: passed through to `fitMod`
calc_start_values <- function(model, full_mu, full_S, dose, index, bounds) {
  separate_coefs <- sapply(c("od", "bid"), function(regimen) {
    inds <- c(index$placebo, index[[regimen]])
    coef(fitMod(dose[inds], full_mu[inds], S = full_S[inds, inds],
                type = "general",  model = model, bnds = bounds))[-1] # drop e0 estimate
  })
  ## remove names to prevent error in do.call() in eval_model_shared_e0;
  ## od, bid coefs are in 1st / second column
  start <- c(full_mu[1], as.numeric(separate_coefs), use.names=FALSE)
  return(start)
}

## fits 'model' to mu_hat with GLS (using S_hat_inv as weight matrix), using a common e0 for od and bid regimens.
## i_reg:  list of vectors named "placebo", "od", "bid", used for indexing `dose`
## i_par: passed through to `eval_model_shared_e0`
## dose: numeric with doses for placebo, od, bid
## lower, upper, start: control parameters fro `nlminb`
fit_model_shared_e0 <- function(model, dose, mu_hat, S_hat_inv, lower, upper, start, i_reg, i_par) {
  opt_fun <- function(par) { # make use of lexical scope
    resp <- eval_model_shared_e0(model, dose[i_reg$od], dose[i_reg$bid], par, i_par)
    delta <- resp - mu_hat
    return(drop(t(delta) %*% S_hat_inv %*% delta))
  }
  fit <- nlminb(start, opt_fun, lower = lower, upper = upper)
  return(fit)
}

## ----estimation_3-------------------------------------------------------------
## predict population response in each regimen for dose_seq_*
## note: both dose_seq_* vectors should contain a 0 if response at placebo is of interest
one_bootstrap_sample <- function(est, dose_seq_od, dose_seq_bid) {
  mu_new <- drop(mvtnorm::rmvnorm(1, est$mu_hat, est$S_hat))
  mod_info <- list(list(name = "emax", bounds = rbind(c(0.15, 225)),
                        i_par = list(od = 2:3, bid = 4:5), n_par_gaic = 5),
                   list(name = "sigEmax", bounds = rbind(c(0.15, 225), c(0.5, 5)),
                        i_par = list(od = 2:4, bid = 5:7), n_par_gaic = 7))
  fit <- lapply(mod_info, function(m) {
    start <- calc_start_values(m$name, mu_new, est$S_hat, est$daily_dose, est$index, m$bounds)
    low <- c(-Inf, -Inf, m$bounds[,1]) # no bounds on e0, eMax
    up <- c(Inf, Inf, m$bounds[,2])
    fit_model_shared_e0(m$name, est$daily_dose, mu_new, solve(est$S_hat), lower = low,  upper = up,
                        start = start, i_reg = est$index, i_par = m$i_par)
  })
  ## calculate gAICs
  gaics <- sapply(fit, `[[`, "objective") + 2 * sapply(mod_info, `[[`, "n_par_gaic")
  sel <- which.min(gaics)
  mod <- mod_info[[sel]]
  ## drop the placebo element
  pred <- eval_model_shared_e0(mod$name, dose_seq_od, dose_seq_bid, fit[[sel]]$par, mod$i_par)[-1]
  return(pred)
}

summarize_bootstrap_samples <- function(samples, probs = c(0.025, 0.25, 0.75, 0.975)) {
  stopifnot(length(probs) == 4)
  med <- apply(samples, 1, median)
  quants <- apply(samples, 1, quantile, probs = probs)
  bs_df <- as.data.frame(cbind(med, t(quants)))
  names(bs_df) <- c("median", "low_out", "low_in", "high_in", "high_out")
  return(bs_df)
}

dose_seq_od <- seq(0, 150, length.out = 21) # do include placebo!
dose_seq_bid <- seq(0, 100, length.out = 21)
set.seed(1, kind = "Mersenne-Twister", sample.kind = "Rejection", normal.kind = "Inversion")
reps <- replicate(1000, one_bootstrap_sample(est, dose_seq_od, dose_seq_bid))
bs_sum <- summarize_bootstrap_samples(reps)
bs_sum$daily_dose <- c(dose_seq_od, dose_seq_bid)
bs_sum$regimen <- c(rep("od", length(dose_seq_od)), rep("bid", length(dose_seq_bid)))

ggplot(bs_sum) + geom_ribbon(aes(daily_dose, ymin=low_out, ymax=high_out), alpha = 0.2) +
  geom_ribbon(aes(daily_dose, ymin=low_in, ymax=high_in), alpha = 0.2) +
  geom_line(aes(daily_dose, median)) +
  geom_point(aes(daily_dose, mu_hat), tidy_estimates(est)) +
  facet_wrap(vars(regimen), labeller = label_both) +
  labs(title = "Bootstrap estimates for population response",
       subtitle = "Least squares estimates plus 50% and 95% confidence bands") +
  xlab("daily dose") + ylab("percent body weigh change") +
  coord_cartesian(ylim = c(-6, 0))