Minor updates to documentation

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MGnifyR
 Type: Package
-Version: 0.99.24
+Version: 0.99.25
 Authors@R:
     c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
              email = "[email protected]",

R/MgnifyClient.R

@@ -39,9 +39,9 @@
 #'
 #' @param ... optional arguments:
 #' \itemize{
-#'   \item{url}{ A single character value specifying an url address of the
-#'   the database.
-#'   (By default: \code{url = "https://www.ebi.ac.uk/metagenomics/api/v1"})}
+#'   \item \strong{url} A single character value specifying an url address of
+#'   the database. (By default:
+#'   \code{url = "https://www.ebi.ac.uk/metagenomics/api/v1"})
 #' }
 #'
 #' @return A MgnifyClient object.
@@ -51,7 +51,7 @@
 #'     useCache = TRUE, cacheDir = "/scratch/MGnify_cache_location"
 #'     )
 #'
-#' \donttest{
+#' \dontrun{
 #' # Use username and password to get access to non-public data
 #' my_client <- MgnifyClient(
 #'     username = "Webin-1122334", password = "SecretPassword",

R/doQuery.R

@@ -91,7 +91,7 @@
 #'     mg, "studies", biome_name="Agricultural wastewater"
 #'     )
 #'
-#' \donttest{
+#' \dontrun{
 #' # Get all samples from a particular study
 #' samps <- doQuery(mg, "samples", accession="MGYS00004521")
 #'

R/getFile.R

@@ -54,7 +54,7 @@
 #' supplied_filename <- getFile(
 #'     mg, url_list[[1]], file="SSU_file.fasta.gz")
 #'
-#' \donttest{
+#' \dontrun{
 #' # Example 2:
 #' # Just use local caching
 #' cached_filename <- getFile(mg, url_list[[2]])

R/getResult.R

@@ -31,29 +31,30 @@
 #'
 #' @param ... optional arguments:
 #' \itemize{
-#'   \item{taxa.su}{ A single character value specifying which taxa subunit
-#'   results should be selected? Currently, taxonomy assignments in the
+#'   
+#'   \item \strong{taxa.su} A single character value specifying which taxa
+#'   subunit results should be selected? Currently, taxonomy assignments in the
 #'   MGnify pipelines rely on rRNA matches to existing databases
 #'   (GreenGenes and SILVA), with later pipelines checking both the SSU and
 #'   LSU portions of the rRNA sequence. \code{taxa.su} allows then selection
 #'   of either the Small subunit (SSU) or Large subunit results
 #'   in the final \code{TreeSummarizedExperiment} object. Older pipeline
 #'   versions do not report results for both subunits, and thus for some
-#'   accessions this value will have no effect.}
+#'   accessions this value will have no effect.
 #'
-#'   \item{get.tree}{ A single boolean value specifying whether to include
-#'   available phylogenetic trees in the \code{TreeSummarizedExperiment}
-#'   object. (By default: \code{get.tree = TRUE})}
+#'   \item \strong{get.tree} A single boolean value specifying whether to
+#'   include available phylogenetic trees in the \code{TreeSummarizedExperiment}
+#'   object. (By default: \code{get.tree = TRUE})
 #'
-#'   \item{as.df}{ A single boolean value enabled when \code{output = "list"}.
-#'   The argument specifies whether return functional data as a named list
-#'   (one entry per element in the output list) of data.frames,
-#'   with each data.frame containing results for all requested accessions.
-#'   If \code{FALSE}, The function returns a list of lists, each element
-#'   consisting of results for a single accession.
-#'   (By default: \code{as.df = TRUE})}
+#'   \item \strong{as.df} A single boolean value enabled when
+#'   \code{output = "list"}. The argument specifies whether return functional
+#'   data as a named list (one entry per element in the output list) of
+#'   data.frames, with each data.frame containing results for all requested
+#'   accessions. If \code{FALSE}, The function returns a list of lists, each
+#'   element consisting of results for a single accession. (By default:
+#'   \code{as.df = TRUE})
 #'
-#'   \item{bulk.dl}{ A single boolean value specifying should
+#'   \item \strong{bulk.dl} A single boolean value specifying should
 #'   MGnifyR attempt to speed things up by downloading
 #'   relevant studies TSV results and only extracting the required columns,
 #'   rather than using the JSONAPI interface. When getting results where
@@ -63,7 +64,7 @@
 #'   expected accession names. This will hopefully be fixed in the future,
 #'   but for now \code{bulk.dl} defaults to TRUE. When it does work, it can
 #'   be orders of magnitude more efficient.
-#'   (By default: \code{buld_dl = TRUE})}
+#'   (By default: \code{buld_dl = TRUE})
 #'
 #' }
 #'
@@ -90,7 +91,7 @@
 #' accession_list <- c("MGYA00377505")
 #' tse <- getResult(mg, accession_list, get.func=FALSE, get.taxa=TRUE)
 #'
-#' \donttest{
+#' \dontrun{
 #' # Get functional data along with OTU tables as MAE
 #' mae <- getResult(mg, accession_list, get.func=TRUE, get.taxa=TRUE)
 #'

R/searchAnalysis.R

@@ -24,7 +24,7 @@
 #' # Retrieve analysis ids from study MGYS00005058
 #' result <- searchAnalysis(mg, "studies", c("MGYS00005058"))
 #'
-#' \donttest{
+#' \dontrun{
 #' # Retrieve all analysis ids from samples
 #' result <- searchAnalysis(
 #'     mg, "samples", c("SRS4392730", "SRS4392743"))

vignettes/MGnifyR.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "MGnifyR: interface to MGnify database"
+title: "MGnifyR"
 date: "`r Sys.Date()`"
 package: MGnifyR
 output:
@@ -10,7 +10,7 @@ output:
         toc_depth: 2
         number_sections: true
 vignette: >
-    %\VignetteIndexEntry{mia}
+    %\VignetteIndexEntry{MGnifyR}
     %\VignetteEngine{knitr::rmarkdown}
     %\VignetteEncoding{UTF-8}
 bibliography: references.bib

vignettes/MGnifyR_long.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "MGnifyR: interface to MGnify database"
+title: "MGnifyR, extended vignette"
 date: "`r Sys.Date()`"
 package: MGnifyR
 output:
@@ -10,7 +10,7 @@ output:
         toc_depth: 2
         number_sections: true
 vignette: >
-    %\VignetteIndexEntry{mia}
+    %\VignetteIndexEntry{MGnifyR, extended vignette}
     %\VignetteEngine{knitr::rmarkdown}
     %\VignetteEncoding{UTF-8}
 bibliography: references.bib