diff --git a/.Rbuildignore b/.Rbuildignore index 91114bf..33cc41e 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,2 +1,5 @@ ^.*\.Rproj$ ^\.Rproj\.user$ +^_pkgdown\.yml$ +^docs$ +^pkgdown$ diff --git a/.gitignore b/.gitignore index 543d1f3..5c9f4a1 100644 --- a/.gitignore +++ b/.gitignore @@ -48,3 +48,4 @@ po/*~ # RStudio Connect folder rsconnect/ +docs diff --git a/R/HoloFoodR.R b/R/HoloFoodR.R index 70e5340..c1f5ac3 100644 --- a/R/HoloFoodR.R +++ b/R/HoloFoodR.R @@ -8,7 +8,7 @@ #' details on the JSONAPI implementation. #' #' @name HoloFoodR-package -#' @docType _PACKAGE +#' @docType package #' @seealso #' \link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment} #' \link[MultiAssayExperiment:MultiAssayExperiment-class]{MultiAssaySummarizedExperiment} diff --git a/R/doQuery.R b/R/doQuery.R index 7aa2147..c1f012d 100644 --- a/R/doQuery.R +++ b/R/doQuery.R @@ -19,26 +19,26 @@ #' #' @param ... optional arguments: #' \itemize{ -#' -#' \item{\code{max.hits}: }{\code{NULL} or \code{integer scalar} specifying the +#' +#' \item \code{max.hits}: \code{NULL} or \code{integer scalar} specifying the #' maximum number of results to fetch. When NULL, all results are fetched. -#' (Default: \code{NULL})} -#' -#' \item{\code{spread.sample.types}: }{\code{Logical scalar} specifying whether +#' (Default: \code{NULL}) +#' +#' \item \code{spread.sample.types}: \code{Logical scalar} specifying whether #' to create spread sample types column of animals data. In animals data, #' sample types column might have multiple values that might be hard to #' explore. This argument specifies whether to create presence/absence table -#' from sample types. (Default: \code{TRUE})} -#' -#' \item{\code{use.cache}: }{\code{Logical scalar} specifying whether to -#' use.cache (Default: \code{FALSE})} -#' -#' \item{\code{cache.dir}: }{\code{Character scalar} specifying cache directory. -#' (Default: \code{tempdir()})} -#' -#' \item{\code{clear.cache}: }{\code{Logical scalar} specifying whether to -#' use.cache (Default: \code{FALSE})} -#' +#' from sample types. (Default: \code{TRUE}) +#' +#' \item \code{use.cache}: \code{Logical scalar} specifying whether to +#' use.cache (Default: \code{FALSE}) +#' +#' \item \code{cache.dir}: \code{Character scalar} specifying cache directory. +#' (Default: \code{tempdir()}) +#' +#' \item \code{clear.cache}: \code{Logical scalar} specifying whether to +#' use.cache (Default: \code{FALSE}) +#' #' } #' #' @return \code{data.frame} diff --git a/R/getData.R b/R/getData.R index c0f9922..3b46bae 100644 --- a/R/getData.R +++ b/R/getData.R @@ -33,20 +33,20 @@ #' #' @param ... optional arguments: #' \itemize{ -#' -#' \item{\code{max.hits}: }{\code{NULL} or \code{integer scalar} specifying the +#' +#' \item \code{max.hits}: \code{NULL} or \code{integer scalar} specifying the #' maximum number of results to fetch. When NULL, all results are fetched. -#' (Default: \code{NULL})} -#' -#' \item{\code{use.cache}: }{\code{Logical scalar} specifying whether to -#' use.cache (Default: \code{FALSE})} -#' -#' \item{\code{cache.dir}: }{\code{Character scalar} specifying cache directory. -#' (Default: \code{tempdir()})} -#' -#' \item{\code{clear.cache}: }{\code{Logical scalar} specifying whether to -#' use.cache (Default: \code{FALSE})} -#' +#' (Default: \code{NULL}) +#' +#' \item \code{use.cache}: \code{Logical scalar} specifying whether to +#' use.cache (Default: \code{FALSE}) +#' +#' \item \code{cache.dir}: \code{Character scalar} specifying cache directory. +#' (Default: \code{tempdir()}) +#' +#' \item \code{clear.cache}: \code{Logical scalar} specifying whether to +#' use.cache (Default: \code{FALSE}) +#' #' } #' #' @return \code{list} or \code{data.frame} diff --git a/R/getResult.R b/R/getResult.R index 17ca45b..1a41646 100644 --- a/R/getResult.R +++ b/R/getResult.R @@ -21,16 +21,16 @@ #' #' @param ... optional arguments: #' \itemize{ -#' -#' \item{\code{use.cache}: }{\code{Logical scalar} specifying whether to -#' use.cache (Default: \code{FALSE})} -#' -#' \item{\code{cache.dir}: }{\code{Character scalar} specifying cache directory. -#' (Default: \code{tempdir()})} -#' -#' \item{\code{clear.cache}: }{\code{Logical scalar} specifying whether to -#' use.cache (Default: \code{FALSE})} -#' +#' +#' \item \code{use.cache}: \code{Logical scalar} specifying whether to +#' use.cache (Default: \code{FALSE}) +#' +#' \item \code{cache.dir}: \code{Character scalar} specifying cache directory. +#' (Default: \code{tempdir()}) +#' +#' \item \code{clear.cache}: \code{Logical scalar} specifying whether to +#' use.cache (Default: \code{FALSE}) +#' #' } #' #' @return \code{MultiAssayExperiment} diff --git a/_pkgdown.yml b/_pkgdown.yml new file mode 100644 index 0000000..d71acfb --- /dev/null +++ b/_pkgdown.yml @@ -0,0 +1,4 @@ +url: ~ +template: + bootstrap: 5 + diff --git a/man/HoloFoodR-package.Rd b/man/HoloFoodR-package.Rd index 9080212..9a6fb9e 100644 --- a/man/HoloFoodR-package.Rd +++ b/man/HoloFoodR-package.Rd @@ -1,7 +1,8 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/HoloFoodR.R -\docType{_PACKAGE} +\docType{package} \name{HoloFoodR-package} +\alias{HoloFoodR} \alias{HoloFoodR-package} \title{\code{HoloFoodR} package} \description{ @@ -16,3 +17,12 @@ details on the JSONAPI implementation. \link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment} \link[MultiAssayExperiment:MultiAssayExperiment-class]{MultiAssaySummarizedExperiment} } +\author{ +\strong{Maintainer}: Tuomas Borman \email{tuomas.v.borman@utu.fi} (\href{https://orcid.org/0000-0002-8563-8884}{ORCID}) + +Authors: +\itemize{ + \item Leo Lahti \email{leo.lahti@iki.fi} (\href{https://orcid.org/0000-0001-5537-637X}{ORCID}) +} + +} diff --git a/man/doQuery.Rd b/man/doQuery.Rd index e288972..a0ec9e1 100644 --- a/man/doQuery.Rd +++ b/man/doQuery.Rd @@ -19,25 +19,25 @@ are separated to multiple columns. (Default: \code{TRUE})} \item{...}{optional arguments: \itemize{ - \item{\code{max.hits}: }{\code{NULL} or \code{integer scalar} specifying the + \item \code{max.hits}: \code{NULL} or \code{integer scalar} specifying the maximum number of results to fetch. When NULL, all results are fetched. - (Default: \code{NULL})} - - \item{\code{spread.sample.types}: }{\code{Logical scalar} specifying whether + (Default: \code{NULL}) + + \item \code{spread.sample.types}: \code{Logical scalar} specifying whether to create spread sample types column of animals data. In animals data, sample types column might have multiple values that might be hard to explore. This argument specifies whether to create presence/absence table - from sample types. (Default: \code{TRUE})} - - \item{\code{use.cache}: }{\code{Logical scalar} specifying whether to - use.cache (Default: \code{FALSE})} - - \item{\code{cache.dir}: }{\code{Character scalar} specifying cache directory. - (Default: \code{tempdir()})} - - \item{\code{clear.cache}: }{\code{Logical scalar} specifying whether to - use.cache (Default: \code{FALSE})} - + from sample types. (Default: \code{TRUE}) + + \item \code{use.cache}: \code{Logical scalar} specifying whether to + use.cache (Default: \code{FALSE}) + + \item \code{cache.dir}: \code{Character scalar} specifying cache directory. + (Default: \code{tempdir()}) + + \item \code{clear.cache}: \code{Logical scalar} specifying whether to + use.cache (Default: \code{FALSE}) + }} } \value{ diff --git a/man/getData.Rd b/man/getData.Rd index 9d46323..aaa481b 100644 --- a/man/getData.Rd +++ b/man/getData.Rd @@ -35,19 +35,19 @@ are separated to multiple columns. (Default: \code{FALSE})} \item{...}{optional arguments: \itemize{ - \item{\code{max.hits}: }{\code{NULL} or \code{integer scalar} specifying the + \item \code{max.hits}: \code{NULL} or \code{integer scalar} specifying the maximum number of results to fetch. When NULL, all results are fetched. - (Default: \code{NULL})} - - \item{\code{use.cache}: }{\code{Logical scalar} specifying whether to - use.cache (Default: \code{FALSE})} - - \item{\code{cache.dir}: }{\code{Character scalar} specifying cache directory. - (Default: \code{tempdir()})} - - \item{\code{clear.cache}: }{\code{Logical scalar} specifying whether to - use.cache (Default: \code{FALSE})} - + (Default: \code{NULL}) + + \item \code{use.cache}: \code{Logical scalar} specifying whether to + use.cache (Default: \code{FALSE}) + + \item \code{cache.dir}: \code{Character scalar} specifying cache directory. + (Default: \code{tempdir()}) + + \item \code{clear.cache}: \code{Logical scalar} specifying whether to + use.cache (Default: \code{FALSE}) + }} } \value{ diff --git a/man/getResult.Rd b/man/getResult.Rd index eb0d7f9..925d3c0 100644 --- a/man/getResult.Rd +++ b/man/getResult.Rd @@ -12,16 +12,16 @@ accession IDs of type samples.} \item{...}{optional arguments: \itemize{ - - \item{\code{use.cache}: }{\code{Logical scalar} specifying whether to - use.cache (Default: \code{FALSE})} - - \item{\code{cache.dir}: }{\code{Character scalar} specifying cache directory. - (Default: \code{tempdir()})} - - \item{\code{clear.cache}: }{\code{Logical scalar} specifying whether to - use.cache (Default: \code{FALSE})} - + + \item \code{use.cache}: \code{Logical scalar} specifying whether to + use.cache (Default: \code{FALSE}) + + \item \code{cache.dir}: \code{Character scalar} specifying cache directory. + (Default: \code{tempdir()}) + + \item \code{clear.cache}: \code{Logical scalar} specifying whether to + use.cache (Default: \code{FALSE}) + }} } \value{