From 06327bc9d4269e2c8652c9af8cb038fe097729f3 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 27 Feb 2019 13:21:38 +0100
Subject: Comment out unused code

---
 R/mkinfit.R | 42 +++++++++++++++++++++---------------------
 R/mkinmod.R | 12 ++++++------
 2 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/R/mkinfit.R b/R/mkinfit.R
index b5020418..4ac54ce2 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -903,25 +903,25 @@ print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), .
 }
 # 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$mad,
-      lower = 0,
-      algorithm = "port"),
-    error = "Fitting the error model failed in iteration")
-  return(tc_fit)
-}
+# .fit_error_model_mad_mod <- function(tmp_res, tc) {
+#   mad_agg <- aggregate(tmp_res$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:
diff --git a/R/mkinmod.R b/R/mkinmod.R
index 2805ef54..26148f18 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -164,12 +164,12 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb
         # The problems were: Calculation of dissipation times did not work in this case
         # and the coefficient matrix is not generated correctly by the code present
         # in this file in this case
-        f_free_bound <- paste("f", varname, "free", "bound", sep = "_")
-        k_bound_free <- paste("k", varname, "bound", "free", sep = "_")
-        parms <- c(parms, f_free_bound, k_bound_free)
-        reversible_binding_term_1 <- paste("+", k_bound_free, "*", box_2)
-        reversible_binding_term_2 <- paste("+", f_free_bound, "*", k_compound, "*", box_1, "-",
-          k_bound_free, "*", box_2)
+        #f_free_bound <- paste("f", varname, "free", "bound", sep = "_")
+        #k_bound_free <- paste("k", varname, "bound", "free", sep = "_")
+        #parms <- c(parms, f_free_bound, k_bound_free)
+        #reversible_binding_term_1 <- paste("+", k_bound_free, "*", box_2)
+        #reversible_binding_term_2 <- paste("+", f_free_bound, "*", k_compound, "*", box_1, "-",
+        #  k_bound_free, "*", box_2)
       }
       diffs[[box_1]] <- paste(diffs[[box_1]], reversible_binding_term_1)
       diffs[[box_2]] <- paste(diffs[[box_2]], reversible_binding_term_2)
-- 
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