Merge pull request #77 from willpearse/master

docs changes

R/ft_get_si.R

@@ -11,12 +11,17 @@
 #' @param si number of the supplement to be downloaded (1, 2, 3, etc.),
 #' or (for ESA and Science journals) the name of the supplment (e.g.,
 #' "S1_data.csv"). Can be a \code{character} or \code{numeric}.
-#' @param from Publisher of article (\code{character}). Optional,
-#' except for ESA journals (see \code{doi}), but supplying it will
-#' speed up downloads. Must be one of: auto (i.e., auto-detect
-#' journal; default), plos, wiley, science, proceedings, figshare,
-#' esa_data_archives, esa_archives. Only use this argument if \code{x}
-#' isn't a vector of DOI(s).
+#' @param from Publisher of article (\code{character}). The default
+#' (\code{auto}) uses crossref (\code{\link[rcrossref]{cr_works}}) to
+#' detect the journal's publisher. Specifying the journal can somewhat
+#' speed up your download, or be used to force a download from EPMC
+#' (see details). You *must* specify if downloading from an ESA
+#' journal (\code{esa_data_archives}, \code{esa_archives}). You can
+#' only use this argument if \code{x} is a vector of DOI(s). Must be
+#' one of: \code{auto} (i.e., auto-detect journal; default),
+#' \code{plos}, \code{wiley}, \code{science}, \code{proceedings},
+#' \code{figshare}, \code{esa_data_archives}, \code{esa_archives},
+#' \code{biorxiv}, or \code{epmc}.
 #' @param save.name a name for the file to download
 #' (\code{character}). If \code{NULL} (default) this will be a
 #' combination of the DOI and SI number
@@ -108,7 +113,7 @@ ft_get_si.character <- function(x, si, from=c("auto","plos","wiley","science","p
 #' @rdname ft_get_si
 ft_get_si.ft_data <- function(x, si, from=NA, save.name=NA, dir=NA, cache=TRUE, vol=NA, issue=NA, list=FALSE, timeout=10){
     if(!is.na(from))
-        warning("Ignoring 'from' argument")
+        stop("Cannot use 'from' argument with 'ft_data' input")
     from <- names(x)
     x <- unlist(sapply(x, function(x) x$dois))
     from <- .fix.param(x, from, "from")
@@ -118,7 +123,7 @@ ft_get_si.ft_data <- function(x, si, from=NA, save.name=NA, dir=NA, cache=TRUE,
 #' @rdname ft_get_si
 ft_get_si.ft <- function(x, si, from=NA, save.name=NA, dir=NA, cache=TRUE, vol=NA, issue=NA, list=FALSE, timeout=10){
     if(!is.na(from))
-        warning("Ignoring 'from' argument")
+        stop("Cannot use 'from' argument with 'ft' input")
     x <- unlist(sapply(x, function(x) x$data$id))
     from <- names(x)
     return(setNames(unlist(mapply(ft_get_si.character, x=x,si=si,from=from,save.name=save.name,dir=dir,cache=cache,vol=vol,issue=issue,list=list,timeout=timeout)),x))

man/ft_get_si.Rd

@@ -33,12 +33,17 @@ use the ESA-specific article code (e.g., E092-201).}
 or (for ESA and Science journals) the name of the supplment (e.g.,
 "S1_data.csv"). Can be a \code{character} or \code{numeric}.}
 
-\item{from}{Publisher of article (\code{character}). Optional,
-except for ESA journals (see \code{doi}), but supplying it will
-speed up downloads. Must be one of: auto (i.e., auto-detect
-journal; default), plos, wiley, science, proceedings, figshare,
-esa_data_archives, esa_archives. Only use this argument if \code{x}
-isn't a vector of DOI(s).}
+\item{from}{Publisher of article (\code{character}). The default
+(\code{auto}) uses crossref (\code{\link[rcrossref]{cr_works}}) to
+detect the journal's publisher. Specifying the journal can somewhat
+speed up your download, or be used to force a download from EPMC
+(see details). You *must* specify if downloading from an ESA
+journal (\code{esa_data_archives}, \code{esa_archives}). You can
+only use this argument if \code{x} is a vector of DOI(s). Must be
+one of: \code{auto} (i.e., auto-detect journal; default),
+\code{plos}, \code{wiley}, \code{science}, \code{proceedings},
+\code{figshare}, \code{esa_data_archives}, \code{esa_archives},
+\code{biorxiv}, or \code{epmc}.}
 
 \item{save.name}{a name for the file to download
 (\code{character}). If \code{NULL} (default) this will be a