R/getStdErrClp.R

In TIMP: Fitting Separable Nonlinear Models in Spectroscopy and Microscopy

"getStdErrClp" <- function(group, multimodel, thetalist,
                           clpindepX, rlist, rawtheta) {
  QR.temp <- rlist$QR
  m <- multimodel@modellist
  dset <- group[[1]][2]
  clpind <- group[[1]][1]
  cp <- multimodel@fit@resultlist[[dset]]@cp[[clpind]]
  sigma_2 <- multimodel@fit@nlsres$sumonls$sigma^2
  if (is(multimodel@fit@nlsres$onls, "timp.nls")) {
    R <- multimodel@fit@nlsres$onls$m$Rmat()
    R_inv <- chol2inv(R)
  } else {
    R <- multimodel@fit@nlsres$onls$hessian
    R_inv <- solve(R)
  }
  R_X <- qr.R(QR.temp)
  R_X_inv <- backsolve(R_X, diag(ncol(R_X)))
  X_pseudo <- tcrossprod(R_X_inv, qr.Q(QR.temp))
  numenv <- new.env()
  assign("model", m[[dset]], envir = numenv)
  assign("group", group, envir = numenv)
  assign("rawtheta", rawtheta, envir = numenv)
  assign("multimodel", multimodel, envir = numenv)
  assign("thetalist", thetalist, envir = numenv)
  assign("clpindepX", clpindepX, envir = numenv)
  assign("finished", FALSE, envir = numenv)
  assign("returnX", TRUE, envir = numenv)
  if (m[[dset]]@clpdep) {
    s_e <- body(selectMethod("residPart", m[[dset]]@mod_type)@.Data)
  } else {
    s_e <- body(selectMethod("residPart", m[[dset]]@mod_type)@.Data)
  }
  X_gradient <- attr(numericDeriv(
    expr = s_e, rho = numenv,
    theta = c("rawtheta")
  ), "gradient")
  dim(X_gradient) <- c(dim(QR.temp$qr), length(rawtheta))
  G <- matrix(nrow = length(cp), ncol = length(rawtheta))
  for (i in 1:length(rawtheta)) {
    G[, i] <- X_pseudo %*% (as.matrix(X_gradient[, , i]) %*% cp)
  }
  G_R_inv <- G %*% R_inv
  ## if A R = G, R^T A^T = G^T
  ## G R_inv R_inv^T G^T
  ## A A^T
  A_T <- solve(t(R), t(G))
  Bloc1 <- tcrossprod(X_pseudo, X_pseudo)
  std_err_clp <- sqrt(sigma_2 * diag(Bloc1 + crossprod(A_T, A_T)))
  for (i in 1:length(group)) {
    multimodel@fit@resultlist[[group[[i]][2]]]@std_err_clp[[group[[i]][1]]] <- std_err_clp
  }
  multimodel
}