From fc692554ecdaff66548cc3e6d666e44b7aaaa9af Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Tue, 3 Jan 2023 17:52:39 +0100
Subject: Neutral names for code chunks in the template

---
 .../templates/hierarchical_kinetics/skeleton/skeleton.Rmd        | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

(limited to 'inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd')

diff --git a/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd
index e26213f5..38a6bd20 100644
--- a/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd
@@ -186,8 +186,7 @@ parms(parent_best_pH_2, ci = TRUE) |> kable(digits = 3)
 As an example of a pathway fit, a model with SFORB for the parent compound and
 parallel formation of two metabolites is set up.
 
-
-```{r m_sforb_sfo2}
+```{r path-1-degmod}
 if (!dir.exists("dlls")) dir.create("dlls")
 
 m_sforb_sfo2 = mkinmod(
@@ -203,7 +202,7 @@ m_sforb_sfo2 = mkinmod(
 Separate evaluations of all datasets are performed with constant variance
 and using two-component error.
 
-```{r path-sep, dependson = c("m_sforb_all", "ds")}
+```{r path-1-sep, dependson = c("path-1-degmod", "ds")}
 sforb_sep_const <- mmkin(list(sforb_path = m_sforb_sfo2), ds,
   cluster = cl, quiet = TRUE)
 sforb_sep_tc <- update(sforb_sep_const, error_model = "tc")
@@ -211,7 +210,7 @@ sforb_sep_tc <- update(sforb_sep_const, error_model = "tc")
 
 The separate fits with constant variance are plotted.
 
-```{r dependson = "path-sep", fig.height = 9}
+```{r dependson = "path-1-sep", fig.height = 9}
 plot(mixed(sforb_sep_const))
 ```
 
@@ -219,7 +218,7 @@ The two corresponding hierarchical fits, with the random effects for the parent
 degradation parameters excluded as discussed above, and including the covariate
 model that was identified for the parent degradation, are attempted below.
 
-```{r path-1, dependson = "path-sep"}
+```{r path-1, dependson = "path-1-sep"}
 path_1 <- mhmkin(list(sforb_sep_const, sforb_sep_tc),
   no_random_effect = c("lambda_free_0", "log_k_lambda_free_bound"),
   covariates = covariates, covariate_models = list(log_k_lambda_bound_free ~ pH),
-- 
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