From 150b52dccee40c5c7cc82806b6ef6ae3411c4857 Mon Sep 17 00:00:00 2001 From: nsheff Date: Tue, 21 Nov 2023 07:54:43 -0500 Subject: [PATCH] add citation as requested by cran, redoc --- DESCRIPTION | 3 ++- man/Project.Rd | 3 +++ man/activateAmendments.Rd | 3 +++ man/dot-printNestedList.Rd | 3 +++ man/dot-strformat.Rd | 3 +++ man/fetchSamples.Rd | 3 +++ 6 files changed, 17 insertions(+), 1 deletion(-) 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) . 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