use expressly revision tag for links

1 files changed, 12 insertions, 12 deletions

diff --git a/loael.Rmd b/loael.Rmd
index 3179530..08087eb 100644
--- a/loael.Rmd
+++ b/loael.Rmd
@@ -137,9 +137,9 @@ of `r length(m$SMILES)` LOAEL values for `r length(unique(m$SMILES))` unique
 chemical structures.
 The Nestlé database can be obtained from the following GitHub links:
 
-  - original data: [https://github.com/opentox/loael-paper/tree/master/data/LOAEL_mg_corrected_smiles_mmol.csv](https://github.com/opentox/loael-paper/tree/master/data/LOAEL_mg_corrected_smiles_mmol.csv)
-  - unique smiles: [https://github.com/opentox/loael-paper/tree/master/data/mazzatorta.csv](https://github.com/opentox/loael-paper/tree/master/data/mazzatorta.csv)
-  - -log10 transfomed LOAEL: [https://github.com/opentox/loael-paper/tree/master/data/mazzatorta_log10.csv](https://github.com/opentox/loael-paper/tree/master/data/mazzatorta_log10.csv).
+  - original data: [https://github.com/opentox/loael-paper/blob/revision/data/LOAEL_mg_corrected_smiles_mmol.csv](https://github.com/opentox/loael-paper/blob/revision/data/LOAEL_mg_corrected_smiles_mmol.csv)
+  - unique smiles: [https://github.com/opentox/loael-paper/blob/revision/data/mazzatorta.csv](https://github.com/opentox/loael-paper/blob/revision/data/mazzatorta.csv)
+  - -log10 transfomed LOAEL: [https://github.com/opentox/loael-paper/blob/revision/data/mazzatorta_log10.csv](https://github.com/opentox/loael-paper/blob/revision/data/mazzatorta_log10.csv).
 
 ### Swiss Food Safety and Veterinary Office (FSVO) database
 
@@ -152,9 +152,9 @@ described elsewhere [@Zarn2011, @Zarn2013]. The
 FSVO-database consists of `r length(s$SMILES)` rat LOAEL values for `r length(unique(s$SMILES))` unique chemical
 structures. It can be obtained from the following GitHub links:
 
-  - original data: [https://github.com/opentox/loael-paper/tree/master/data/NOAEL-LOAEL_SMILES_rat_chron.csv](https://github.com/opentox/loael-paper/tree/master/data/NOAEL-LOAEL_SMILES_rat_chron.csv)
-  - unique smiles and mmol/kg_bw/day units: [https://github.com/opentox/loael-paper/tree/master/data/swiss.csv](https://github.com/opentox/loael-paper/tree/master/data/swiss.csv)
-  - -log10 transfomed LOAEL: [https://github.com/opentox/loael-paper/tree/master/data/swiss_log10.csv](https://github.com/opentox/loael-paper/tree/master/data/swiss_log10.csv)
+  - original data: [https://github.com/opentox/loael-paper/blob/revision/data/NOAEL-LOAEL_SMILES_rat_chron.csv](https://github.com/opentox/loael-paper/blob/revision/data/NOAEL-LOAEL_SMILES_rat_chron.csv)
+  - unique smiles and mmol/kg_bw/day units: [https://github.com/opentox/loael-paper/blob/revision/data/swiss.csv](https://github.com/opentox/loael-paper/blob/revision/data/swiss.csv)
+  - -log10 transfomed LOAEL: [https://github.com/opentox/loael-paper/blob/revision/data/swiss_log10.csv](https://github.com/opentox/loael-paper/blob/revision/data/swiss_log10.csv)
 
 
 ### Preprocessing
@@ -175,7 +175,7 @@ significant digits. For prediction, validation and visualisation purposes
 Two derived datasets were obtained from the original databases:
 
 The [*test*
-dataset](https://github.com/opentox/loael-paper/tree/master/data/test_log10.csv)
+dataset](https://github.com/opentox/loael-paper/blob/revision/data/test_log10.csv)
 contains data from compounds that occur in both databases. LOAEL values equal
 at five significant digits were considered as duplicates originating from the
 same study/publication and only one instance was kept in the test dataset. The
@@ -186,7 +186,7 @@ unique chemical structures and was used for
 - comparing model predictions with experimental variability.
 
 The [*training*
-dataset](https://github.com/opentox/loael-paper/tree/master/data/training_log10.csv)
+dataset](https://github.com/opentox/loael-paper/blob/revision/data/training_log10.csv)
 is the union of the Nestlé and the FSVO databases and it was used to build
 predictive models. LOAEL duplicates were removed using the same criteria as for
 the test dataset.  The training dataset has `r length(c$SMILES)` LOAEL values
@@ -218,7 +218,7 @@ modelling. Algorithms used within this study are described in the following sect
 
 ### Neighbor identification
 
-Similarity calculations are based on [MolPrint2D fingerprints](https://github.com/opentox/lazar/blob/loael-paper/lib/compound.rb#L38-L42)
+Similarity calculations are based on [MolPrint2D fingerprints](https://github.com/opentox/lazar/blob/loael-paper.revision/lib/compound.rb#L38-L42)
 [@doi:10.1021/ci034207y] from the OpenBabel chemoinformatics library
 [@OBoyle2011].
 
@@ -258,7 +258,7 @@ closely related neighbors, we follow a tiered approach:
 - Similarity thresholds of 0.5 and 0.2 are the default values chosen by the software developers and remained unchanged during the course of these experiments.
 
 Compounds with the same structure as the query structure are automatically
-[eliminated from neighbors](https://github.com/opentox/lazar/blob/loael-paper/lib/model.rb#L231-L236)
+[eliminated from neighbors](https://github.com/opentox/lazar/blob/loael-paper.revision/lib/model.rb#L231-L236)
 to obtain unbiased predictions in the presence of
 duplicates.
 
@@ -316,7 +316,7 @@ validation errors. As we have only a single test set no model or parameter
 optimisations were performed in order to avoid overfitting a single dataset.
 
 Results from 3 repeated [10-fold
-crossvalidations](https://github.com/opentox/lazar/blob/loael-paper.revision/lib/crossvalidation.rb#L95-L113)
+crossvalidations](https://github.com/opentox/lazar/blob/loael-paper.revision/lib/crossvalidation.rb#L85-L93)
 with independent training/test set splits are provided as additional
 information to the test set results.
 
@@ -363,7 +363,7 @@ frequency of functional groups from the OpenBabel FP4 fingerprint. [@fig:fg]
 shows the frequency of functional groups in both databases. `r length(fg$V1)`
 functional groups with a frequency > 25 are depicted, the complete table for
 all functional groups can be found in the supplemental
-material at [GitHub](https://github.com/opentox/loael-paper/tree/master/data/functional-groups.csv).
+material at [GitHub](https://github.com/opentox/loael-paper/blob/revision/data/functional-groups.csv).
  
 ![Frequency of functional groups.](figures/functional-groups.pdf){#fig:fg}