diff --git a/DESCRIPTION b/DESCRIPTION
index 132921c..0dc38a9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -10,7 +10,8 @@ Description: A PEP, or Portable Encapsulated Project, is a dataset that
     subscribes to the PEP structure for organizing metadata. It is written using
     a simple YAML + CSV format, it is your one-stop solution to metadata 
     management across data analysis environments. This package reads this 
-    standardized project configuration structure into R.
+    standardized project configuration structure into R. 
+    Described in Sheffield et al. (2021) <doi:10.1093/gigascience/giab077>.
 Imports:
     yaml,
     stringr,
diff --git a/man/Project.Rd b/man/Project.Rd
index 238f0d0..cd10f9f 100644
--- a/man/Project.Rd
+++ b/man/Project.Rd
@@ -22,6 +22,9 @@ to index the sample table}
 \item{subSampleTableIndex}{a string indicating the sample attribute that is used
 to index the sample table}
 }
+\value{
+an object of \code{"\linkS4class{Project}"}
+}
 \description{
 This is a helper that creates the project with empty samples and config slots
 }
diff --git a/man/activateAmendments.Rd b/man/activateAmendments.Rd
index ca7579f..8625478 100644
--- a/man/activateAmendments.Rd
+++ b/man/activateAmendments.Rd
@@ -14,6 +14,9 @@ activateAmendments(.Object, amendments)
 
 \item{amendments}{character with the amendment name}
 }
+\value{
+an object of class \code{"\linkS4class{Project}"} with activated amendments
+}
 \description{
 This method switches between the amendments
 within the \code{"\linkS4class{Project}"} object
diff --git a/man/dot-printNestedList.Rd b/man/dot-printNestedList.Rd
index 5cbcfb7..e563709 100644
--- a/man/dot-printNestedList.Rd
+++ b/man/dot-printNestedList.Rd
@@ -11,6 +11,9 @@
 
 \item{level}{the indentation level}
 }
+\value{
+No return value, called for side effects
+}
 \description{
 Prints a nested list in a way that looks nice
 }
diff --git a/man/dot-strformat.Rd b/man/dot-strformat.Rd
index c83e762..4281e8c 100644
--- a/man/dot-strformat.Rd
+++ b/man/dot-strformat.Rd
@@ -13,6 +13,9 @@
 
 \item{parent}{a directory that will be used to make the path absolute}
 }
+\value{
+Formatted string
+}
 \description{
 Given a string with environment variables (encoded like \code{${VAR}} or \code{$VAR}), and
 other variables (encoded like \code{{VAR}}) this function will substitute
diff --git a/man/fetchSamples.Rd b/man/fetchSamples.Rd
index e62319d..15088af 100644
--- a/man/fetchSamples.Rd
+++ b/man/fetchSamples.Rd
@@ -15,6 +15,9 @@ fetchSamples(samples, attr = NULL, func = NULL, action = "include")
 
 \item{action}{a string (either \code{include} or \code{exclude}) that specifies whether the function should select the row or exclude it.}
 }
+\value{
+an object of \code{\link[data.table]{data.table-class}} class filtered according to specified requirements
+}
 \description{
 This funciton collects the samples from a \code{\link[data.table]{data.table-class}} object that
 fulfill the requirements of an attribute \code{attr} specified with