diff --git a/NAMESPACE b/NAMESPACE
index cc6984a0..3c3fd87c 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.1.1): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 S3method(candidate_for_synth,study_meta)
 S3method(flags,match_names)
diff --git a/man/get_study.Rd b/man/get_study.Rd
index 5e9938e9..8d625a20 100644
--- a/man/get_study.Rd
+++ b/man/get_study.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/studies.R
 \name{get_study}
 \alias{get_study}
diff --git a/man/get_study_meta.Rd b/man/get_study_meta.Rd
index 84e8f09b..debb7c62 100644
--- a/man/get_study_meta.Rd
+++ b/man/get_study_meta.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/studies-methods.R, R/studies.R
 \name{get_tree_ids}
 \alias{candidate_for_synth}
diff --git a/man/get_study_subtree.Rd b/man/get_study_subtree.Rd
index 04ba9327..45573d70 100644
--- a/man/get_study_subtree.Rd
+++ b/man/get_study_subtree.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/studies.R
 \name{get_study_subtree}
 \alias{get_study_subtree}
@@ -12,7 +12,7 @@ get_study_subtree(study_id, tree_id, subtree_id, object_format = c("phylo"),
 
 \item{tree_id}{the tree identifier (character)}
 
-\item{subtree_id,}{either a node id that specifies a subtree or
+\item{subtree_id, }{either a node id that specifies a subtree or
 \dQuote{ingroup} which returns the ingroup for this subtree.}
 
 \item{object_format}{the class of the object returned by the
diff --git a/man/get_study_tree.Rd b/man/get_study_tree.Rd
index 2ecfde0f..8c3dcd57 100644
--- a/man/get_study_tree.Rd
+++ b/man/get_study_tree.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/studies.R
 \name{get_study_tree}
 \alias{get_study_tree}
diff --git a/man/gol_about.Rd b/man/gol_about.Rd
index 08cb6418..14ad194c 100644
--- a/man/gol_about.Rd
+++ b/man/gol_about.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/gol.R
 \name{gol_about}
 \alias{gol_about}
@@ -44,7 +44,7 @@ Returns summary information about the entire graph
     trees used to build it.
 }
 \examples{
-\dontrun{
+  \dontrun{
     res <- gol_about()
   }
 }
diff --git a/man/gol_node_info.Rd b/man/gol_node_info.Rd
index ccd1da75..19719e43 100644
--- a/man/gol_node_info.Rd
+++ b/man/gol_node_info.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/gol.R
 \name{gol_node_info}
 \alias{gol_node_info}
@@ -69,7 +69,7 @@ the node from the synthetic tree. Optional; default = FALSE.}
 
     }
 
-	\item {tax_source} {String. Source taxonomy IDs (if it is a
+\item {tax_source} {String. Source taxonomy IDs (if it is a
     named node), e.g. "ncbi:9242,gbif:5289,irmng:104628".}
 
    \item {synth_sources} {A list of supporting synthesis source
diff --git a/man/list_trees.Rd b/man/list_trees.Rd
index aa0de2b9..822264e9 100644
--- a/man/list_trees.Rd
+++ b/man/list_trees.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/studies-methods.R
 \name{list_trees}
 \alias{list_trees}
diff --git a/man/match_names-methods.Rd b/man/match_names-methods.Rd
index 0f78bad5..d4d73342 100644
--- a/man/match_names-methods.Rd
+++ b/man/match_names-methods.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/match_names.R
 \name{ott_id.match_names}
 \alias{flags}
diff --git a/man/match_names.Rd b/man/match_names.Rd
index 14634a7d..500fdb08 100644
--- a/man/match_names.Rd
+++ b/man/match_names.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/match_names.R
 \name{inspect.match_names}
 \alias{inspect}
@@ -63,7 +63,7 @@ To update one of the name, you also need to provide the row number
 in which the name to be replaced appear or its ott id.
 }
 \examples{
-\dontrun{
+  \dontrun{
    matched_names <- tnrs_match_names(c("holothuria", "diadema", "boletus"))
    inspect(matched_names, taxon_name="diadema")
    new_matched_names <- update(matched_names, taxon_name="diadema",
diff --git a/man/rotl.Rd b/man/rotl.Rd
index 57bfcc48..c4f8f9ee 100644
--- a/man/rotl.Rd
+++ b/man/rotl.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/rotl-package.R
 \docType{package}
 \name{rotl}
diff --git a/man/strip_ott_ids.Rd b/man/strip_ott_ids.Rd
index edf98256..ae297f63 100644
--- a/man/strip_ott_ids.Rd
+++ b/man/strip_ott_ids.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/tol.R
 \name{strip_ott_ids}
 \alias{strip_ott_ids}
@@ -7,7 +7,7 @@
 strip_ott_ids(tip_labels)
 }
 \arguments{
-\item{tip_labels}{a character vector containing tip labels (most likely
+\item{tip_labels}{a character vector containing tip labels (most likely 
 the \code{tip.label} element from a tree returned by
 \code{\link{tol_induced_subtree}}}
 }
diff --git a/man/studies_find_studies.Rd b/man/studies_find_studies.Rd
index bc9cac8b..e6e8be98 100644
--- a/man/studies_find_studies.Rd
+++ b/man/studies_find_studies.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/studies.R
 \name{studies_find_studies}
 \alias{studies_find_studies}
diff --git a/man/studies_find_trees.Rd b/man/studies_find_trees.Rd
index aacbdc73..8de6e591 100644
--- a/man/studies_find_trees.Rd
+++ b/man/studies_find_trees.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/studies.R
 \name{studies_find_trees}
 \alias{studies_find_trees}
diff --git a/man/study_list.Rd b/man/study_list.Rd
index 3d2d4a7d..92269892 100644
--- a/man/study_list.Rd
+++ b/man/study_list.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/tol.R
 \name{study_list}
 \alias{study_list}
diff --git a/man/synonyms.match_names.Rd b/man/synonyms.match_names.Rd
index be055f2d..5aa77766 100644
--- a/man/synonyms.match_names.Rd
+++ b/man/synonyms.match_names.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/match_names.R
 \name{synonyms.match_names}
 \alias{synonyms.match_names}
diff --git a/man/taxonomy-methods.Rd b/man/taxonomy-methods.Rd
index a9859040..297dbdcc 100644
--- a/man/taxonomy-methods.Rd
+++ b/man/taxonomy-methods.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/taxonomy.R
 \name{tax_rank}
 \alias{ott_id}
diff --git a/man/taxonomy_about.Rd b/man/taxonomy_about.Rd
index 12d447bd..1d970b8c 100644
--- a/man/taxonomy_about.Rd
+++ b/man/taxonomy_about.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/taxonomy.R
 \name{taxonomy_about}
 \alias{taxonomy_about}
diff --git a/man/taxonomy_lica.Rd b/man/taxonomy_lica.Rd
index 2530a99a..6687df32 100644
--- a/man/taxonomy_lica.Rd
+++ b/man/taxonomy_lica.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/taxonomy.R
 \name{taxonomy_lica}
 \alias{ott_id.taxon_lica}
diff --git a/man/taxonomy_subtree.Rd b/man/taxonomy_subtree.Rd
index 1227d905..32aa3197 100644
--- a/man/taxonomy_subtree.Rd
+++ b/man/taxonomy_subtree.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/taxonomy.R
 \name{taxonomy_subtree}
 \alias{taxonomy_subtree}
diff --git a/man/taxonomy_taxon.Rd b/man/taxonomy_taxon.Rd
index 91fa0460..85600d29 100644
--- a/man/taxonomy_taxon.Rd
+++ b/man/taxonomy_taxon.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/taxonomy.R
 \name{taxonomy_taxon}
 \alias{ott_taxon_name.taxon_info}
diff --git a/man/tnrs_contexts.Rd b/man/tnrs_contexts.Rd
index 6638cb1d..5fa0eefc 100644
--- a/man/tnrs_contexts.Rd
+++ b/man/tnrs_contexts.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/tnrs.R
 \name{tnrs_contexts}
 \alias{tnrs_contexts}
diff --git a/man/tnrs_infer_context.Rd b/man/tnrs_infer_context.Rd
index d3de002f..43d79642 100644
--- a/man/tnrs_infer_context.Rd
+++ b/man/tnrs_infer_context.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/tnrs.R
 \name{tnrs_infer_context}
 \alias{tnrs_infer_context}
diff --git a/man/tnrs_match_names.Rd b/man/tnrs_match_names.Rd
index a695eed9..7286ab94 100644
--- a/man/tnrs_match_names.Rd
+++ b/man/tnrs_match_names.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/tnrs.R
 \name{tnrs_match_names}
 \alias{tnrs_match_names}
diff --git a/man/tol_about.Rd b/man/tol_about.Rd
index 9465dd5d..9691ef78 100644
--- a/man/tol_about.Rd
+++ b/man/tol_about.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/tol.R
 \name{tol_about}
 \alias{tol_about}
@@ -8,10 +8,10 @@ tol_about(study_list = FALSE, ...)
 }
 \arguments{
 \item{study_list}{Whether to return the list of source
-    studies. (Logical, default = FALSE).}
+studies. (Logical, default = FALSE).}
 
 \item{...}{additional arguments to customize the API call (see
-    \code{\link{rotl}} for more information).}
+\code{\link{rotl}} for more information).}
 }
 \value{
 An invisible list of synthetic tree summary statistics:
diff --git a/man/tol_induced_subtree.Rd b/man/tol_induced_subtree.Rd
index cc85fb1b..f91e2892 100644
--- a/man/tol_induced_subtree.Rd
+++ b/man/tol_induced_subtree.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/tol.R
 \name{tol_induced_subtree}
 \alias{tol_induced_subtree}
@@ -33,7 +33,7 @@ synthetic tree. This tree is equivalent to the minimal subtree
 induced on the draft tree by the set of identified nodes. Ott ids
 that do not correspond to any nodes found in the graph, or which
 are in the graph but are absent from the synthetic tree (e.g. groups
-included in the Open Tree Taxonomy but found to be paraphyletic in
+included in the Open Tree Taxonomy but found to be paraphyletic in 
 in studies contributing to the synthetic tree) , will be
 identified in the output (but obvisouly will be absent from the
 resulting induced tree). Branch lengths in the result may be
diff --git a/man/tol_mrca.Rd b/man/tol_mrca.Rd
index 0c064923..2bced8c1 100644
--- a/man/tol_mrca.Rd
+++ b/man/tol_mrca.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/tol.R
 \name{tol_mrca}
 \alias{tol_mrca}
diff --git a/man/tol_subtree.Rd b/man/tol_subtree.Rd
index 64351632..e682e94e 100644
--- a/man/tol_subtree.Rd
+++ b/man/tol_subtree.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/tol.R
 \name{tol_subtree}
 \alias{tol_subtree}
@@ -38,7 +38,7 @@ Return a complete subtree of the draft tree descended
     an error will be returned.
 }
 \examples{
-\dontrun{
+   \dontrun{
       res <- tol_subtree(ott_id=81461)
     }
 }