From 7a1d3d031aa23fce723ac4f4c8e4bb5d64959447 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 4 Apr 2019 15:42:23 +0200
Subject: Direct error model fitting works

- No IRLS required
- Removed optimization algorithms other than Port
- Removed the dependency on FME
- Fitting the error model 'obs' is much faster for the FOCUS_2006_D
  dataset and the FOMC_SFO model (1 second versus 3.4 seconds)
- Vignettes build slower. Compiled models needs 3 minutes instead of 1.5
- For other vignettes, the trend is less clear. Some fits are faster,
  even for error_model = "const". FOCUS_Z is faster (34.9 s versus
  44.1 s)
- Standard errors and confidence intervals are slightly smaller
- Removed code for plotting during the fit, as I hardly ever used it
- Merged the two cost functions (using transformed and untransformed
  parameters) into one log-likelihood function
---
 R/mkinfit.R | 499 ++++++++++++++++--------------------------------------------
 1 file changed, 133 insertions(+), 366 deletions(-)

(limited to 'R/mkinfit.R')

diff --git a/R/mkinfit.R b/R/mkinfit.R
index 4ac54ce2..796b25c7 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -30,19 +30,12 @@ mkinfit <- function(mkinmod, observed,
   solution_type = c("auto", "analytical", "eigen", "deSolve"),
   method.ode = "lsoda",
   use_compiled = "auto",
-  method.modFit = c("Port", "Marq", "SANN", "Nelder-Mead", "BFGS", "CG", "L-BFGS-B"),
-  maxit.modFit = "auto",
-  control.modFit = list(),
+  control = list(eval.max = 300, iter.max = 200),
   transform_rates = TRUE,
   transform_fractions = TRUE,
   plot = FALSE, quiet = FALSE,
-  err = NULL,
-  weight = c("none", "manual", "std", "mean", "tc"),
-  tc = c(sigma_low = 0.5, rsd_high = 0.07),
-  scaleVar = FALSE,
   atol = 1e-8, rtol = 1e-10, n.outtimes = 100,
-  reweight.method = NULL,
-  reweight.tol = 1e-8, reweight.max.iter = 10,
+  error_model = c("const", "obs", "tc", "obs_tc"),
   trace_parms = FALSE,
   ...)
 {
@@ -61,19 +54,6 @@ mkinfit <- function(mkinmod, observed,
     }
   }
 
-  # Check optimisation method and set maximum number of iterations if specified
-  method.modFit = match.arg(method.modFit)
-  if (maxit.modFit != "auto") {
-    if (method.modFit == "Marq") control.modFit$maxiter = maxit.modFit
-    if (method.modFit == "Port") {
-      control.modFit$iter.max = maxit.modFit
-      control.modFit$eval.max = maxit.modFit
-    }
-    if (method.modFit %in% c("SANN", "Nelder-Mead", "BFGS", "CG", "L-BFGS-B")) {
-        control.modFit$maxit = maxit.modFit
-    }
-  }
-
   # Get the names of the state variables in the model
   mod_vars <- names(mkinmod$diffs)
 
@@ -96,6 +76,9 @@ mkinfit <- function(mkinmod, observed,
     observed$time <- observed$time - t_of_max
   }
 
+  # Number observations used for fitting
+  n_observed <- nrow(observed)
+
   # Define starting values for parameters where not specified by the user
   if (parms.ini[[1]] == "auto") parms.ini = vector()
 
@@ -254,32 +237,42 @@ mkinfit <- function(mkinmod, observed,
     }
   }
 
+  # Get the error model and specify starting values as well as fixed components
+  err_mod <- match.arg(error_model)
+  if (err_mod == "const") {
+    errparms = c(sigma = 1)
+  }
+  if (err_mod == "obs") {
+    errparms <- rep(1, length(obs_vars))
+    names(errparms) = paste0("sigma_", obs_vars)
+  }
+  if (err_mod == "tc") {
+    errparms <- c(sigma_low = 0.5, rsd_high = 0.07)
+  }
+  if (err_mod == "obs_tc") {
+    errparms <- rep(1, length(obs_vars))
+    names(errparms) = paste0("sigma_", obs_vars)
+    errparms <- c(errparms, a = 0.1)
+  }
+
   # Define outtimes for model solution.
   # Include time points at which observed data are available
   outtimes = sort(unique(c(observed$time, seq(min(observed$time),
                                               max(observed$time),
                                               length.out = n.outtimes))))
 
-  weight.ini <- weight <- match.arg(weight)
-  if (weight.ini == "tc") {
-     observed$err = sigma_twocomp(observed$value, tc["sigma_low"], tc["rsd_high"])
-     err <- "err"
-  } else {
-    if (!is.null(err)) weight.ini = "manual"
-  }
-
-  cost.old <- 1e100 # The first model cost should be smaller than this value
   calls <- 0 # Counter for number of model solutions
   out_predicted <- NA
 
-  # Define the model cost function for optimisation, including (back)transformations
-  cost <- function(P)
+  # Define log-likelihood function for optimisation, including (back)transformations
+  nlogLik <- function(P, trans = TRUE)
   {
     assign("calls", calls+1, inherits=TRUE) # Increase the model solution counter
 
     # Trace parameter values if requested
     if(trace_parms) cat(P, "\n")
 
+    # Initial states for t0
     if(length(state.ini.optim) > 0) {
       odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed)
       names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
@@ -288,13 +281,18 @@ mkinfit <- function(mkinmod, observed,
       names(odeini) <- state.ini.fixed.boxnames
     }
 
-    odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], transparms.fixed)
+    odeparms.optim <- P[(length(state.ini.optim) + 1):(length(P) - length(errparms))]
 
-    parms <- backtransform_odeparms(odeparms, mkinmod,
-                                    transform_rates = transform_rates,
-                                    transform_fractions = transform_fractions)
+    if (trans == TRUE) {
+      odeparms <- c(odeparms.optim, transparms.fixed)
+      parms <- backtransform_odeparms(odeparms, mkinmod,
+                                      transform_rates = transform_rates,
+                                      transform_fractions = transform_fractions)
+    } else {
+      parms <- c(odeparms.optim, parms.fixed)
+    }
 
-    # Solve the system with current transformed parameter values
+    # Solve the system with current parameter values
     out <- mkinpredict(mkinmod, parms,
                        odeini, outtimes,
                        solution_type = solution_type,
@@ -302,82 +300,55 @@ mkinfit <- function(mkinmod, observed,
                        method.ode = method.ode,
                        atol = atol, rtol = rtol, ...)
 
-    assign("out_predicted", out, inherits=TRUE)
-
-    mC <- modCost(out, observed, y = "value",
-      err = err, weight = weight, scaleVar = scaleVar)
-
-    # Report and/or plot if the model is improved
-    if (mC$model < cost.old) {
-      if(!quiet) cat("Model cost at call ", calls, ": ", mC$model, "\n")
-
-      # Plot the data and current model output if requested
-      if(plot) {
-        outtimes_plot = seq(min(observed$time), max(observed$time), length.out=100)
-
-        out_plot <- mkinpredict(mkinmod, parms,
-                                odeini, outtimes_plot,
-                                solution_type = solution_type,
-                                use_compiled = use_compiled,
-                                method.ode = method.ode,
-                                atol = atol, rtol = rtol, ...)
-
-        plot(0, type="n",
-          xlim = range(observed$time), ylim = c(0, max(observed$value, na.rm=TRUE)),
-          xlab = "Time", ylab = "Observed")
-        col_obs <- pch_obs <- 1:length(obs_vars)
-        lty_obs <- rep(1, length(obs_vars))
-        names(col_obs) <- names(pch_obs) <- names(lty_obs) <- obs_vars
-        for (obs_var in obs_vars) {
-          points(subset(observed, name == obs_var, c(time, value)),
-                 pch = pch_obs[obs_var], col = col_obs[obs_var])
-        }
-        matlines(out_plot$time, out_plot[-1], col = col_obs, lty = lty_obs)
-        legend("topright", inset=c(0.05, 0.05), legend=obs_vars,
-          col=col_obs, pch=pch_obs, lty=1:length(pch_obs))
-      }
+    out_long <- mkin_wide_to_long(out, time = "time")
 
-      assign("cost.old", mC$model, inherits=TRUE)
-    }
-    return(mC)
-  }
+    assign("out_predicted", out_long, inherits=TRUE)
 
-  # Define the model cost function for the t-test, without parameter transformation
-  cost_notrans <- function(P)
-  {
-    if(length(state.ini.optim) > 0) {
-      odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed)
-      names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
-    } else {
-      odeini <- state.ini.fixed
-      names(odeini) <- state.ini.fixed.boxnames
+    if (err_mod == "const") {
+      observed$std <- P["sigma"]
+    }
+    if (err_mod == "obs") {
+      std_names <- paste0("sigma_", observed$name)
+      observed$std <- P[std_names]
+    }
+    if (err_mod == "tc") {
+      tmp <- merge(observed, out_long, by = c("time", "name"))
+      tmp$name <- ordered(tmp$name, levels = obs_vars)
+      tmp <- tmp[order(tmp$name, tmp$time), ]
+      observed$std <- sqrt(P["sigma_low"]^2 + tmp$value.y^2 * P["rsd_high"]^2)
+    }
+    if (err_mod == "obs_tc") {
+      tmp <- merge(observed, out_long, by = c("time", "name"))
+      tmp$name <- ordered(tmp$name, levels = obs_vars)
+      tmp <- tmp[order(tmp$name, tmp$time), ]
+      std_names <- paste0("sigma_", observed$name)
+      observed$std <- sqrt(P[std_names] * (1 + P["a"] * tmp$value.y^2))
     }
 
-    odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], parms.fixed)
-
-    # Solve the system with current parameter values
-    out <- mkinpredict(mkinmod, odeparms,
-                       odeini, outtimes,
-                       solution_type = solution_type,
-                       use_compiled = use_compiled,
-                       method.ode = method.ode,
-                       atol = atol, rtol = rtol, ...)
-
-    mC <- modCost(out, observed, y = "value",
-      err = err, weight = weight, scaleVar = scaleVar)
+    data_log_lik <- merge(observed[c("name", "time", "value", "std")], out_long,
+                         by = c("name", "time"))
 
-    return(mC)
+    nlogLik <- - with(data_log_lik,
+      sum(dnorm(x = value.x, mean = value.y, sd = std, log = TRUE)))
+    return(nlogLik)
   }
 
+  n_optim <- length(c(state.ini.optim, transparms.optim, errparms))
+  names_optim <- c(names(state.ini.optim),
+                   names(transparms.optim),
+                   names(errparms))
+
   # Define lower and upper bounds other than -Inf and Inf for parameters
-  # for which no internal transformation is requested in the call to mkinfit.
-  lower <- rep(-Inf, length(c(state.ini.optim, transparms.optim)))
-  upper <- rep(Inf, length(c(state.ini.optim, transparms.optim)))
-  names(lower) <- names(upper) <- c(names(state.ini.optim), names(transparms.optim))
+  # for which no internal transformation is requested in the call to mkinfit
+  # and for error model parameters
+  lower <- rep(-Inf, n_optim)
+  upper <- rep(Inf, n_optim)
+  names(lower) <- names(upper) <- names_optim
 
   # IORE exponentes are not transformed, but need a lower bound of zero
   index_N <- grep("^N", names(lower))
   lower[index_N] <- 0
+
   if (!transform_rates) {
     index_k <- grep("^k_", names(lower))
     lower[index_k] <- 0
@@ -396,151 +367,44 @@ mkinfit <- function(mkinmod, observed,
     upper[other_fraction_parms] <- 1
   }
 
+  if (err_mod == "const") {
+    lower["sigma"] <- 0
+  }
+  if (err_mod == "obs") {
+    index_sigma <- grep("^sigma_", names(lower))
+    lower[index_sigma] <- 0
+  }
+  if (err_mod == "tc") {
+    lower["sigma_low"] <- 0
+    lower["rsd_high"] <- 0
+  }
+  if (err_mod == "obs_tc") {
+    index_sigma <- grep("^sigma_", names(lower))
+    lower[index_sigma] <- 0
+    lower["a"] <- 0
+  }
+
   # Show parameter names if tracing is requested
-  if(trace_parms) cat(names(c(state.ini.optim, transparms.optim)), "\n")
+  if(trace_parms) cat(names_optim, "\n")
 
   # Do the fit and take the time
   fit_time <- system.time({
-    fit <- modFit(cost, c(state.ini.optim, transparms.optim),
-                  method = method.modFit, control = control.modFit,
-                  lower = lower, upper = upper, ...)
-
-    # Reiterate the fit until convergence of the variance components (IRLS)
-    # if requested by the user
-
-    if (!is.null(reweight.method)) {
-      if (! reweight.method %in% c("obs", "tc")) stop("Only reweighting methods 'obs' and 'tc' are implemented")
-
-      if (reweight.method  == "obs") {
-        tc_fit <- NA
-        if(!quiet) {
-          cat("IRLS based on variance estimates for each observed variable\n")
-          cat("Initial variance estimates are:\n")
-          print(signif(fit$var_ms_unweighted, 8))
-        }
-      }
-      if (reweight.method  == "tc") {
-        tc_fit <- .fit_error_model_mad_obs(cost(fit$par)$residuals, tc, 0)
-
-        if (is.character(tc_fit)) {
-          if (!quiet) {
-            cat(tc_fit, ".\n", "No reweighting will be performed.")
-          }
-          tc_fitted <- c(sigma_low = NA, rsd_high = NA)
-        } else {
-          tc_fitted <- coef(tc_fit)
-          if(!quiet) {
-            cat("IRLS based on variance estimates according to the two component error model\n")
-            cat("Initial variance components are:\n")
-            print(signif(tc_fitted))
-          }
-        }
-      }
-      reweight.diff = 1
-      n.iter <- 0
-      if (!is.null(err)) observed$err.ini <- observed[[err]]
-      err = "err.irls"
-
-      while (reweight.diff > reweight.tol &
-             n.iter < reweight.max.iter &
-             !is.character(tc_fit)) {
-        n.iter <- n.iter + 1
-        # Store squared residual predictors used for weighting in sr_old and define new weights
-        if (reweight.method == "obs") {
-          sr_old <- fit$var_ms_unweighted
-          observed[err] <- sqrt(fit$var_ms_unweighted[as.character(observed$name)])
-        }
-        if (reweight.method == "tc") {
-          sr_old <- tc_fitted
-
-          tmp_predicted <- mkin_wide_to_long(out_predicted, time = "time")
-          tmp_data <- suppressMessages(join(observed, tmp_predicted, by = c("time", "name")))
-
-          #observed[err] <- predict(tc_fit, newdata = data.frame(mod = tmp_data[[4]]))
-          observed[err] <- predict(tc_fit, newdata = data.frame(obs = observed$value))
-
-        }
-        fit <- modFit(cost, fit$par, method = method.modFit,
-                      control = control.modFit, lower = lower, upper = upper, ...)
+    fit <- nlminb(c(state.ini.optim, transparms.optim, errparms),
+                  nlogLik, control = control,
+                  lower = lower, upper = upper, ...)})
 
-        if (reweight.method == "obs") {
-          sr_new <- fit$var_ms_unweighted
-        }
-        if (reweight.method == "tc") {
-          tc_fit <- .fit_error_model_mad_obs(cost(fit$par)$residuals, tc_fitted, n.iter)
-
-          if (is.character(tc_fit)) {
-            if (!quiet) {
-              cat(tc_fit, ".\n")
-            }
-            break
-          } else {
-            tc_fitted <- coef(tc_fit)
-            sr_new <- tc_fitted
-          }
-        }
-
-        reweight.diff = sum((sr_new - sr_old)^2)
-        if (!quiet) {
-          cat("Iteration", n.iter, "yields variance estimates:\n")
-          print(signif(sr_new, 8))
-          cat("Sum of squared differences to last variance (component) estimates:",
-              signif(reweight.diff, 2), "\n")
-        }
-      }
-    }
-  })
-
-  # Check for convergence
-  if (method.modFit == "Marq") {
-    if (!fit$info %in% c(1, 2, 3)) {
-      fit$warning = paste0("Optimisation by method ", method.modFit,
-                           " did not converge.\n",
-                           "The message returned by nls.lm is:\n",
-                                    fit$message)
-      warning(fit$warning)
-    }
-    else {
-      if(!quiet) cat("Optimisation by method", method.modFit, "successfully terminated.\n")
-    }
-  }
-  if (method.modFit == "Port") {
-    if (fit$convergence != 0) {
-      fit$warning = paste0("Optimisation by method ", method.modFit,
-                           " did not converge:\n",
-                           if(is.character(fit$counts)) fit$counts # FME bug
-                           else fit$message)
-      warning(fit$warning)
-    } else {
-      if(!quiet) cat("Optimisation by method", method.modFit, "successfully terminated.\n")
-    }
-  }
-  if (method.modFit %in% c("SANN", "Nelder-Mead", "BFGS", "CG", "L-BFGS-B")) {
-    if (fit$convergence != 0) {
-      fit$warning = paste0("Optimisation by method ", method.modFit,
-                           " did not converge.\n",
-                           "Convergence code returned by optim() is", fit$convergence)
-      warning(fit$warning)
-    } else {
-      if(!quiet) cat("Optimisation by method", method.modFit, "successfully terminated.\n")
-    }
-  }
-
-  # Return number of iterations for SANN method and alert user to check if
-  # the approximation to the optimum is sufficient
-  if (method.modFit == "SANN") {
-    fit$iter = maxit.modFit
-    fit$warning <- paste0("Termination of the SANN algorithm does not imply convergence.\n",
-      "Make sure the approximation of the optimum is adequate.")
+  if (fit$convergence != 0) {
+    fit$warning = paste0("Optimisation did not converge:\n", fit$message)
     warning(fit$warning)
+  } else {
+    if(!quiet) cat("Optimisation successfully terminated.\n")
   }
 
   # We need to return some more data for summary and plotting
   fit$solution_type <- solution_type
   fit$transform_rates <- transform_rates
   fit$transform_fractions <- transform_fractions
-  fit$method.modFit <- method.modFit
-  fit$maxit.modFit <- maxit.modFit
+  fit$control <- control
   fit$calls <- calls
   fit$time <- fit_time
 
@@ -550,40 +414,30 @@ mkinfit <- function(mkinmod, observed,
   # We need data and predictions for summary and plotting
   fit$observed <- observed
   fit$obs_vars <- obs_vars
-  fit$predicted <- mkin_wide_to_long(out_predicted, time = "time")
+  fit$predicted <- out_predicted
 
   # Backtransform parameters
   bparms.optim = backtransform_odeparms(fit$par, fit$mkinmod,
-                                        transform_rates = transform_rates,
-                                        transform_fractions = transform_fractions)
+    transform_rates = transform_rates,
+    transform_fractions = transform_fractions)
   bparms.fixed = c(state.ini.fixed, parms.fixed)
   bparms.all = c(bparms.optim, parms.fixed)
 
-  # Attach the cost functions to the fit for post-hoc parameter uncertainty analysis
-  fit$cost <- cost
-  fit$cost_notrans <- cost_notrans
-
-  # Estimate the Hessian for the model cost without parameter transformations
-  # to make it possible to obtain the usual t-test
-  # Code ported from FME::modFit
-  Jac_notrans <- try(gradient(function(p, ...) cost_notrans(p)$residuals$res,
-                              bparms.optim, centered = TRUE), silent = TRUE)
-  if (inherits(Jac_notrans, "try-error")) {
-    warning("Calculation of the Jacobian failed for the cost function of the untransformed model.\n",
-            "No t-test results will be available")
-    fit$hessian_notrans <- NA
-  } else {
-    fit$hessian_notrans <- 2 * t(Jac_notrans) %*% Jac_notrans
-  }
+  # Attach the negative log-likelihood function for post-hoc parameter uncertainty analysis
+  fit$nlogLik <- nlogLik
+
+  fit$hessian <- hessian(nlogLik, fit$par)
+  fit$hessian_notrans <- hessian(nlogLik, c(bparms.optim, fit$par[names(errparms)]), trans = FALSE)
 
   # Collect initial parameter values in three dataframes
   fit$start <- data.frame(value = c(state.ini.optim,
-                                    parms.optim))
+                                    parms.optim, errparms))
   fit$start$type = c(rep("state", length(state.ini.optim)),
-                     rep("deparm", length(parms.optim)))
+                     rep("deparm", length(parms.optim)),
+                     rep("error", length(errparms)))
 
   fit$start_transformed = data.frame(
-      value = c(state.ini.optim, transparms.optim),
+      value = c(state.ini.optim, transparms.optim, errparms),
       lower = lower,
       upper = upper)
 
@@ -596,28 +450,16 @@ mkinfit <- function(mkinmod, observed,
   data$name <- ordered(data$name, levels = obs_vars)
   data <- data[order(data$name, data$time), ]
 
-  # Add a column named "value" holding the observed values for the case
-  # that this column was selected for manual weighting, so it can be
-  # shown in the summary as "err"
-  data$value <- data$value.x
-
   fit$data <- data.frame(time = data$time,
                          variable = data$name,
                          observed = data$value.x,
                          predicted = data$value.y)
 
   fit$data$residual <- fit$data$observed - fit$data$predicted
-  if (!is.null(data$err.ini)) fit$data$err.ini <- data$err.ini
-  if (!is.null(err)) fit$data[["err"]] <- data[[err]]
 
   fit$atol <- atol
   fit$rtol <- rtol
-  fit$weight.ini <- weight.ini
-  fit$tc.ini <- tc
-  fit$reweight.method <- reweight.method
-  fit$reweight.tol <- reweight.tol
-  fit$reweight.max.iter <- reweight.max.iter
-  if (exists("tc_fitted")) fit$tc_fitted <- tc_fitted
+  fit$err_mod <- err_mod
 
   # Return different sets of backtransformed parameters for summary and plotting
   fit$bparms.optim <- bparms.optim
@@ -629,6 +471,9 @@ mkinfit <- function(mkinmod, observed,
                         state.ini.fixed)
   names(fit$bparms.state) <- gsub("_0$", "", names(fit$bparms.state))
 
+  fit$errparms.optim <- fit$par[names(errparms)]
+  fit$df.residual <- n_observed - n_optim
+
   fit$date <- date()
   fit$version <- as.character(utils::packageVersion("mkin"))
   fit$Rversion <- paste(R.version$major, R.version$minor, sep=".")
@@ -641,39 +486,41 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, alpha = 0.05,
   param  <- object$par
   pnames <- names(param)
   bpnames <- names(object$bparms.optim)
+  epnames <- names(object$errparms.optim)
   p      <- length(param)
   mod_vars <- names(object$mkinmod$diffs)
-  covar  <- try(solve(0.5*object$hessian), silent = TRUE)   # unscaled covariance
-  covar_notrans  <- try(solve(0.5*object$hessian_notrans), silent = TRUE)   # unscaled covariance
-  rdf    <- object$df.residual
-  resvar <- object$ssr / rdf
+  covar  <- try(solve(object$hessian), silent = TRUE)
+  covar_notrans  <- try(solve(object$hessian_notrans), silent = TRUE)
+  rdf <- object$df.residual
+
   if (!is.numeric(covar) | is.na(covar[1])) {
     covar <- NULL
     se <- lci <- uci <- rep(NA, p)
   } else {
     rownames(covar) <- colnames(covar) <- pnames
-    se     <- sqrt(diag(covar) * resvar)
+    se     <- sqrt(diag(covar))
     lci    <- param + qt(alpha/2, rdf) * se
     uci    <- param + qt(1-alpha/2, rdf) * se
   }
-
+  
+  beparms.optim <- c(object$bparms.optim, object$par[epnames])
   if (!is.numeric(covar_notrans) | is.na(covar_notrans[1])) {
     covar_notrans <- NULL
     se_notrans <- tval <- pval <- rep(NA, p)
   } else {
-    rownames(covar_notrans) <- colnames(covar_notrans) <- bpnames
-    se_notrans     <- sqrt(diag(covar_notrans) * resvar)
-    tval   <- object$bparms.optim/se_notrans
-    pval   <- pt(abs(tval), rdf, lower.tail = FALSE)
+    rownames(covar_notrans) <- colnames(covar_notrans) <- c(bpnames, epnames)
+    se_notrans <- sqrt(diag(covar_notrans))
+    tval  <- beparms.optim / se_notrans
+    pval  <- pt(abs(tval), rdf, lower.tail = FALSE)
   }
 
   names(se) <- pnames
-  modVariance <- object$ssr / length(object$residuals)
 
   param <- cbind(param, se, lci, uci)
   dimnames(param) <- list(pnames, c("Estimate", "Std. Error", "Lower", "Upper"))
 
-  bparam <- cbind(Estimate = object$bparms.optim, se_notrans, "t value" = tval, "Pr(>t)" = pval, Lower = NA, Upper = NA)
+  bparam <- cbind(Estimate = beparms.optim, se_notrans,
+                  "t value" = tval, "Pr(>t)" = pval, Lower = NA, Upper = NA)
 
   # Transform boundaries of CI for one parameter at a time,
   # with the exception of sets of formation fractions (single fractions are OK).
@@ -699,6 +546,7 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, alpha = 0.05,
       bparam[names(bpu), "Upper"] <- bpu
     }
   }
+  bparam[epnames, c("Lower", "Upper")] <- param[epnames, c("Lower", "Upper")]
 
   ans <- list(
     version = as.character(utils::packageVersion("mkin")),
@@ -706,26 +554,14 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, alpha = 0.05,
     date.fit = object$date,
     date.summary = date(),
     solution_type = object$solution_type,
-    method.modFit = object$method.modFit,
     warning = object$warning,
     use_of_ff = object$mkinmod$use_of_ff,
-    weight.ini = object$weight.ini,
-    reweight.method = object$reweight.method,
-    tc.ini = object$tc.ini,
-    var_ms_unweighted = object$var_ms_unweighted,
-    tc_fitted = object$tc_fitted,
-    residuals = object$residuals,
-    residualVariance = resvar,
-    sigma = sqrt(resvar),
-    modVariance = modVariance,
     df = c(p, rdf),
     cov.unscaled = covar,
-    cov.scaled = covar * resvar,
-    info = object$info,
+    #cov.scaled = covar * resvar,
     niter = object$iterations,
     calls = object$calls,
     time = object$time,
-    stopmess = message,
     par = param,
     bpar = bparam)
 
@@ -789,24 +625,8 @@ print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), .
   cat("\nFitted with method", x$method.modFit,
       "using", x$calls, "model solutions performed in", x$time[["elapsed"]],  "s\n")
 
-  cat("\nWeighting:", x$weight.ini)
-  if (x$weight.ini == "tc")  {
-    cat(" with variance components\n")
-    print(x$tc.ini)
-  } else {
-    cat ("\n")
-  }
-  if(!is.null(x$reweight.method)) {
-    cat("\nIterative reweighting with method", x$reweight.method, "\n")
-    if (x$reweight.method == "obs") {
-      cat("Final mean squared residuals of observed variables:\n")
-      print(x$var_ms_unweighted)
-    }
-    if (x$reweight.method == "tc") {
-      cat("Final components of fitted standard deviation:\n")
-      print(x$tc_fitted)
-    }
-  }
+  cat("\nError model:\n")
+  print(x$err_mod)
 
   cat("\nStarting values for parameters to be optimised:\n")
   print(x$start)
@@ -830,9 +650,6 @@ print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), .
     }
   }
 
-  cat("\nResidual standard error:",
-      format(signif(x$sigma, digits)), "on", rdf, "degrees of freedom\n")
-
   cat("\nBacktransformed parameters:\n")
   cat("Confidence intervals for internally transformed parameters are asymmetric.\n")
   if ((x$version) < "0.9-36") {
@@ -874,54 +691,4 @@ print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), .
 
   invisible(x)
 }
-
-# Fit the median absolute deviation against the observed values,
-# using the current error model for weighting
-.fit_error_model_mad_obs <- function(tmp_res, tc, iteration) {
-  mad_agg <- aggregate(tmp_res$res.unweighted,
-                       by = list(name = tmp_res$name, time = tmp_res$x),
-                       FUN = function(x) mad(x, center = 0))
-  names(mad_agg) <- c("name", "time", "mad")
-  error_data <- suppressMessages(
-    join(data.frame(name = tmp_res$name,
-                    time = tmp_res$x,
-                    obs = tmp_res$obs),
-         mad_agg))
-  error_data_complete <- na.omit(error_data)
-
-  tc_fit <- tryCatch(
-    nls(mad ~ sigma_twocomp(obs, sigma_low, rsd_high),
-      start = list(sigma_low = tc["sigma_low"], rsd_high = tc["rsd_high"]),
-      weights = 1/sigma_twocomp(error_data_complete$obs,
-                                tc["sigma_low"],
-                                tc["rsd_high"])^2,
-      data = error_data_complete,
-      lower = 0,
-      algorithm = "port"),
-    error = function(e) paste("Fitting the error model failed in iteration", iteration))
-  return(tc_fit)
-}
-# Alternative way to fit the error model, fitting to modelled instead of
-# observed values
-# .fit_error_model_mad_mod <- function(tmp_res, tc) {
-#   mad_agg <- aggregate(tmp_res$res.unweighted,
-#                        by = list(name = tmp_res$name, time = tmp_res$x),
-#                        FUN = function(x) mad(x, center = 0))
-#   names(mad_agg) <- c("name", "time", "mad")
-#   mod_agg <- aggregate(tmp_res$mod,
-#                        by = list(name = tmp_res$name, time = tmp_res$x),
-#                        FUN = mean)
-#   names(mod_agg) <- c("name", "time", "mod")
-#   mod_mad <- merge(mod_agg, mad_agg)
-# 
-#   tc_fit <- tryCatch(
-#     nls(mad ~ sigma_twocomp(mod, sigma_low, rsd_high),
-#       start = list(sigma_low = tc["sigma_low"], rsd_high = tc["rsd_high"]),
-#       data = mod_mad,
-#       weights = 1/mod_mad$mad,
-#       lower = 0,
-#       algorithm = "port"),
-#     error = "Fitting the error model failed in iteration")
-#   return(tc_fit)
-# }
 # vim: set ts=2 sw=2 expandtab:
-- 
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