udpated vignette and readme, fixes

.Rbuildignore

@@ -7,10 +7,6 @@ man-roxygen
 CONTRIBUTING.md
 README.html
 Makefile
-inst/vign/
-vignettes/rbhl_vignette.md
-vignettes/margins.sty
-vignettes/cache/
 ^appveyor\.yml$
 README.Rmd
 NEWS.md

DESCRIPTION

@@ -16,11 +16,12 @@ LazyData: true
 VignetteBuilder: knitr
 Imports:
     httr (>= 1.1.0),
-    XML,
-    jsonlite (>= 0.9.19),
-    plyr,
-    tibble
+    xml2 (>= 1.0.0),
+    jsonlite (>= 1.1),
+    plyr (>= 1.8.4),
+    tibble (>= 1.2)
 Suggests:
+    roxygen2 (>= 5.0.1),
     testthat,
     knitr,
     covr

NAMESPACE

@@ -39,14 +39,11 @@ export(bhl_partsearch)
 export(bhl_subjectsearch)
 export(bhl_titlesearchsimple)
 export(getpages)
-importFrom(XML,xmlParse)
-importFrom(XML,xmlSize)
-importFrom(XML,xmlValue)
-importFrom(XML,xpathApply)
-importFrom(XML,xpathSApply)
 importFrom(httr,GET)
 importFrom(httr,content)
 importFrom(httr,stop_for_status)
 importFrom(jsonlite,fromJSON)
-importFrom(plyr,ldply)
 importFrom(plyr,rbind.fill)
+importFrom(xml2,read_xml)
+importFrom(xml2,xml_find_all)
+importFrom(xml2,xml_text)

R/bhl_getsubjecttitles.R

@@ -9,9 +9,8 @@
 #' bhl_getsubjecttitles('diptera', 'json')
 #' }
 
-bhl_getsubjecttitles <- function(subject = NULL, as = "table", key = NULL, ...)
-{
-  args <- bhlc(list(op = "GetSubjectTitles", apikey = check_key(key), format = as_f(as),
-                       subject = subject))
+bhl_getsubjecttitles <- function(subject = NULL, as = "table", key = NULL, ...) {
+  args <- bhlc(list(op = "GetSubjectTitles", apikey = check_key(key),
+                    format = as_f(as), subject = subject))
   bhl_GET(as, args, ...)
 }

R/bhl_gettitleitems.R

@@ -9,8 +9,8 @@
 #' bhl_gettitleitems(1726, as='list')
 #' }
 
-bhl_gettitleitems <- function(titleid, as = "table", key = NULL, ...)
-{
-  args <- bhlc(list(op = "GetTitleItems", apikey = check_key(key), format = as_f(as), titleid=titleid))
+bhl_gettitleitems <- function(titleid, as = "table", key = NULL, ...) {
+  args <- bhlc(list(op = "GetTitleItems", apikey = check_key(key),
+                    format = as_f(as), titleid = titleid))
   bhl_GET(as, args, ...)
 }

R/getpages.R

@@ -2,18 +2,19 @@
 #'
 #' @export
 #' @param itemid the item id (character). Required
-#' @param key Your BHL API key, either enter, or loads from your \code{.Renviron} as \code{BHL_KEY}
-#' or from \code{.Rprofile} as \code{bhl_key}.
+#' @param key Your BHL API key, either enter, or loads from your
+#' \code{.Renviron} as \code{BHL_KEY} or from \code{.Rprofile} as
+#' \code{bhl_key}
 #' @param ... Curl options passed on to \code{\link[httr]{GET}}
 #' @examples \dontrun{
-#' books <- bhl_booksearch(title='Selborne', lname='White', volume=2, edition='new', year=1825,
-#'    collectionid=4, language='eng')
-#' getpages(itemid=16800)
+#' books <- bhl_booksearch(title='Selborne', lname='White', volume=2,
+#'   edition='new', year=1825, collectionid=4, language='eng')
+#' getpages(itemid = 16800)
 #' }
 
 getpages <- function(itemid, key = NULL, ...){
   res <- bhl_getitempages(itemid, ...)
-  out <- lapply(res$data$PageID, function(x){
+  out <- lapply(res$PageID, function(x){
     tmp <- bhl_getpageocrtext(page = x)
     if (grepl("OCR text unavailable for this page", tmp))
       NULL

R/rbhl-package.R

@@ -3,14 +3,14 @@
 #' You need an API key to use the Biodiversity Heritage Library API. Get your
 #' BHL API key at \url{http://www.biodiversitylibrary.org/getapikey.aspx}.
 #' Put your API key in your .Rprofile file using e.g.,
-#' `options(BioHerLibKey = "YOURBHLAPIKEY")`, and the functions within this package
-#' will be able to use your API key without you having to enter it every time
-#' you run a search.
+#' `options(BioHerLibKey = "YOURBHLAPIKEY")`, and the functions within
+#' this package will be able to use your API key without you having to enter
+#' it every time you run a search.
 #'
 #' @importFrom httr GET content stop_for_status
 #' @importFrom jsonlite fromJSON
-#' @importFrom plyr ldply rbind.fill
-#' @importFrom XML xmlSize xpathSApply xpathApply xmlParse xmlValue
+#' @importFrom plyr rbind.fill
+#' @importFrom xml2 xml_find_all read_xml xml_text
 #' @name rbhl-package
 #' @aliases rbhl
 #' @docType package
@@ -20,6 +20,7 @@
 NULL
 
 #' Data.frame of all the BHL API methods from the BHL website.
+#'
 #' @name rbhlmethods
 #' @docType data
 #' @keywords datasets

R/zzz.R

@@ -1,25 +1,3 @@
-query2message <- function(url, x) {
-  mylist <- list()
-  for (i in 1:length(x)) {
-    mylist[i] <- paste(names(x[i]), '=', x[i][[1]], sep = '')
-  }
-  paste('API call:\n', paste(url, "?", paste(mylist, collapse = "&"), sep = ''))
-}
-
-return_results <- function(x, y, z) {
-  if (y == 'raw') {
-    return( x )
-  } else if (y == 'list') {
-    return( jsonlite::fromJSON(I(x)) )
-  } else {
-    if (z == "json") {
-      return(jsonlite::fromJSON(I(x)))
-    } else {
-      return(XML::xmlTreeParse(I(x)))
-    }
-  }
-}
-
 check_key <- function(x) {
   tmp <- if (is.null(x)) Sys.getenv("BHL_KEY", "") else x
   if (tmp == "") getOption("bhl_key", stop("need an API key for BHL")) else tmp
@@ -29,7 +7,7 @@ bhl_GET <- function(as, args, ...){
   out <- GET(bhl_url(), query = args, ...)
   stop_for_status(out)
   res <- switch(as,
-         xml = xmlSize(xpathSApply(xmlParse(content_utf8(out)), "//Result")[[1]]),
+         xml = length(xml_children(xml_find_all(read_xml(content_utf8(out)), "//Result"))),
          json = length(jsonlite::fromJSON(content_utf8(out))$Result),
          list = length(jsonlite::fromJSON(content_utf8(out))$Result),
          table = length(jsonlite::fromJSON(content_utf8(out))$Result))
@@ -52,7 +30,6 @@ todf <- function(x){
     } else {
       do.call(rbind.fill, lapply(bhlc(temp), data.frame))
     }
-    #structure(list(data = tmp), class = "bhldf")
     tibble::as_data_frame(tmp)
   }
 }

README.md

@@ -53,12 +53,17 @@ The default is usually `table`:
 
 ```r
 bhl_authorsearch(name='dimmock')
-#> <bhl data> [2, 12]
-#>   CreatorID             Name Role Numeration Unit Title Location
-#> 1      1970 Dimmock, George,   NA                               
-#> 2      8126 Dimmock, George,   NA                               
-#> Variables not shown: FullerForm (chr), Relationship (lgl), TitleOfWork
-#>      (lgl), Dates (chr), CreatorUrl (chr)
+#> # A tibble: 6 × 12
+#>   CreatorID                    Name  Role Numeration  Unit Title Location
+#> *     <int>                   <chr> <lgl>      <chr> <chr> <chr>    <chr>
+#> 1    189035 Dimmock, Anna Katherina    NA                                
+#> 2     59023              Dimmock, G    NA                                
+#> 3    189042           Dimmock, Geo     NA                                
+#> 4    189021         Dimmock, George    NA                                
+#> 5      1970        Dimmock, George,    NA                                
+#> 6      8126        Dimmock, George,    NA                                
+#> # ... with 5 more variables: FullerForm <chr>, Relationship <lgl>,
+#> #   TitleOfWork <lgl>, Dates <chr>, CreatorUrl <chr>
 ```
 
 list output
@@ -67,10 +72,10 @@ list output
 ```r
 bhl_authorsearch(name='dimmock', as='list')$Result[[1]]
 #> $CreatorID
-#> [1] 1970
+#> [1] 189035
 #> 
 #> $Name
-#> [1] "Dimmock, George,"
+#> [1] "Dimmock, Anna Katherina"
 #> 
 #> $Role
 #> NULL
@@ -97,26 +102,26 @@ bhl_authorsearch(name='dimmock', as='list')$Result[[1]]
 #> NULL
 #> 
 #> $Dates
-#> [1] "1852-"
+#> [1] ""
 #> 
 #> $CreatorUrl
-#> [1] "http://www.biodiversitylibrary.org/creator/1970"
+#> [1] "http://www.biodiversitylibrary.org/creator/189035"
 ```
 
 XML output
 
 
 ```r
 bhl_authorsearch(name='dimmock', as='xml')
-#> [1] "<?xml version=\"1.0\" encoding=\"utf-8\"?><Response xmlns:xsd=\"http://www.w3.org/2001/XMLSchema\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"><Status>ok</Status><Result><Creator><CreatorID>1970</CreatorID><Name>Dimmock, George,</Name><Numeration /><Unit /><Title /><Location /><FullerForm /><Dates>1852-</Dates><CreatorUrl>http://www.biodiversitylibrary.org/creator/1970</CreatorUrl></Creator><Creator><CreatorID>8126</CreatorID><Name>Dimmock, George,</Name><Numeration /><Unit /><Title /><Location /><FullerForm /><Dates>1852-1930</Dates><CreatorUrl>http://www.biodiversitylibrary.org/creator/8126</CreatorUrl></Creator></Result></Response>"
+#> [1] "<?xml version=\"1.0\" encoding=\"utf-8\"?><Response xmlns:xsd=\"http://www.w3.org/2001/XMLSchema\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"><Status>ok</Status><Result><Creator><CreatorID>189035</CreatorID><Name>Dimmock, Anna Katherina</Name><Numeration /><Unit /><Title /><Location /><FullerForm /><Dates /><CreatorUrl>http://www.biodiversitylibrary.org/creator/189035</CreatorUrl></Creator><Creator><CreatorID>59023</CreatorID><Name>Dimmock, G</Name><Numeration /><Unit /><Title /><Location /><FullerForm /><Dates /><CreatorUrl>http://www.biodiversitylibrary.org/creator/59023</CreatorUrl></Creator><Creator><CreatorID>189042</CreatorID><Name>Dimmock, Geo </Name><Numeration /><Unit /><Title /><Location /><FullerForm /><Dates /><CreatorUrl>http://www.biodiversitylibrary.org/creator/189042</CreatorUrl></Creator><Creator><CreatorID>189021</CreatorID><Name>Dimmock, George</Name><Numeration /><Unit /><Title /><Location /><FullerForm /><Dates /><CreatorUrl>http://www.biodiversitylibrary.org/creator/189021</CreatorUrl></Creator><Creator><CreatorID>1970</CreatorID><Name>Dimmock, George,</Name><Numeration /><Unit /><Title /><Location /><FullerForm /><Dates>1852-</Dates><CreatorUrl>http://www.biodiversitylibrary.org/creator/1970</CreatorUrl></Creator><Creator><CreatorID>8126</CreatorID><Name>Dimmock, George,</Name><Numeration /><Unit /><Title /><Location /><FullerForm /><Dates>1852-1930</Dates><CreatorUrl>http://www.biodiversitylibrary.org/creator/8126</CreatorUrl></Creator></Result></Response>"
 ```
 
 JSON output
 
 
 ```r
 bhl_authorsearch(name='dimmock', as='json')
-#> [1] "{\"Status\":\"ok\",\"ErrorMessage\":null,\"Result\":[{\"CreatorID\":1970,\"Name\":\"Dimmock, George,\",\"Role\":null,\"Numeration\":\"\",\"Unit\":\"\",\"Title\":\"\",\"Location\":\"\",\"FullerForm\":\"\",\"Relationship\":null,\"TitleOfWork\":null,\"Dates\":\"1852-\",\"CreatorUrl\":\"http://www.biodiversitylibrary.org/creator/1970\"},{\"CreatorID\":8126,\"Name\":\"Dimmock, George,\",\"Role\":null,\"Numeration\":\"\",\"Unit\":\"\",\"Title\":\"\",\"Location\":\"\",\"FullerForm\":\"\",\"Relationship\":null,\"TitleOfWork\":null,\"Dates\":\"1852-1930\",\"CreatorUrl\":\"http://www.biodiversitylibrary.org/creator/8126\"}]}"
+#> [1] "{\"Status\":\"ok\",\"ErrorMessage\":null,\"Result\":[{\"CreatorID\":189035,\"Name\":\"Dimmock, Anna Katherina\",\"Role\":null,\"Numeration\":\"\",\"Unit\":\"\",\"Title\":\"\",\"Location\":\"\",\"FullerForm\":\"\",\"Relationship\":null,\"TitleOfWork\":null,\"Dates\":\"\",\"CreatorUrl\":\"http://www.biodiversitylibrary.org/creator/189035\"},{\"CreatorID\":59023,\"Name\":\"Dimmock, G\",\"Role\":null,\"Numeration\":\"\",\"Unit\":\"\",\"Title\":\"\",\"Location\":\"\",\"FullerForm\":\"\",\"Relationship\":null,\"TitleOfWork\":null,\"Dates\":\"\",\"CreatorUrl\":\"http://www.biodiversitylibrary.org/creator/59023\"},{\"CreatorID\":189042,\"Name\":\"Dimmock, Geo \",\"Role\":null,\"Numeration\":\"\",\"Unit\":\"\",\"Title\":\"\",\"Location\":\"\",\"FullerForm\":\"\",\"Relationship\":null,\"TitleOfWork\":null,\"Dates\":\"\",\"CreatorUrl\":\"http://www.biodiversitylibrary.org/creator/189042\"},{\"CreatorID\":189021,\"Name\":\"Dimmock, George\",\"Role\":null,\"Numeration\":\"\",\"Unit\":\"\",\"Title\":\"\",\"Location\":\"\",\"FullerForm\":\"\",\"Relationship\":null,\"TitleOfWork\":null,\"Dates\":\"\",\"CreatorUrl\":\"http://www.biodiversitylibrary.org/creator/189021\"},{\"CreatorID\":1970,\"Name\":\"Dimmock, George,\",\"Role\":null,\"Numeration\":\"\",\"Unit\":\"\",\"Title\":\"\",\"Location\":\"\",\"FullerForm\":\"\",\"Relationship\":null,\"TitleOfWork\":null,\"Dates\":\"1852-\",\"CreatorUrl\":\"http://www.biodiversitylibrary.org/creator/1970\"},{\"CreatorID\":8126,\"Name\":\"Dimmock, George,\",\"Role\":null,\"Numeration\":\"\",\"Unit\":\"\",\"Title\":\"\",\"Location\":\"\",\"FullerForm\":\"\",\"Relationship\":null,\"TitleOfWork\":null,\"Dates\":\"1852-1930\",\"CreatorUrl\":\"http://www.biodiversitylibrary.org/creator/8126\"}]}"
 ```
 
 ## Get title metadata
@@ -146,9 +151,18 @@ bhl_gettitlemetadata(titleid = 1726, items = TRUE, as="list")$Result$Items
 #> [[1]]$Year
 #> NULL
 #> 
+#> [[1]]$CopySpecificInformation
+#> NULL
+#> 
 #> [[1]]$Contributor
 #> [1] "MBLWHOI Library"
 #> 
+#> [[1]]$RightsHolder
+#> NULL
+#> 
+#> [[1]]$ScanningInstitution
+#> NULL
+#> 
 #> [[1]]$Sponsor
 #> [1] "MBLWHOI Library"
 #> 
@@ -197,24 +211,26 @@ bhl_gettitlemetadata(titleid = 1726, items = TRUE, as="list")$Result$Items
 
 ```r
 bhl_booksearch(title='Selborne', lname='White', volume=2, edition='new', year=1825, collectionid=4, language='eng')
-#> <bhl data> [1, 22]
+#> # A tibble: 1 × 22
 #>   TitleID BibliographicLevel
+#> *   <int>              <chr>
 #> 1   32868                   
-#> Variables not shown: FullTitle (chr), ShortTitle (lgl), SortTitle (lgl),
-#>      PartNumber (chr), PartName (chr), CallNumber (lgl), Edition (chr),
-#>      PublisherPlace (chr), PublisherName (chr), PublicationDate (chr),
-#>      PublicationFrequency (lgl), Doi (lgl), TitleUrl (chr), Authors
-#>      (list), Subjects (lgl), Identifiers (lgl), Collections (lgl),
-#>      Variants (lgl), Items (list), Notes (lgl)
+#> # ... with 20 more variables: FullTitle <chr>, ShortTitle <lgl>,
+#> #   SortTitle <lgl>, PartNumber <chr>, PartName <chr>, CallNumber <lgl>,
+#> #   Edition <chr>, PublisherPlace <chr>, PublisherName <chr>,
+#> #   PublicationDate <chr>, PublicationFrequency <lgl>, Doi <lgl>,
+#> #   TitleUrl <chr>, Authors <list>, Subjects <lgl>, Identifiers <lgl>,
+#> #   Collections <lgl>, Variants <lgl>, Items <list>, Notes <lgl>
 ```
 
 ## Search titles
 
 
 ```r
 bhl_titlesearchsimple('husbandry')
-#> <bhl data> [151, 22]
+#> # A tibble: 153 × 22
 #>    TitleID BibliographicLevel
+#> *    <int>              <chr>
 #> 1    25997     Monograph/Item
 #> 2    44403     Monograph/Item
 #> 3    27062     Monograph/Item
@@ -225,33 +241,34 @@ bhl_titlesearchsimple('husbandry')
 #> 8    58205     Monograph/Item
 #> 9    51946     Monograph/Item
 #> 10   55665     Monograph/Item
-#> ..     ...                ...
-#> Variables not shown: FullTitle (chr), ShortTitle (chr), SortTitle (chr),
-#>      PartNumber (chr), PartName (chr), CallNumber (lgl), Edition (chr),
-#>      PublisherPlace (chr), PublisherName (chr), PublicationDate (chr),
-#>      PublicationFrequency (chr), Doi (lgl), TitleUrl (lgl), Authors (lgl),
-#>      Subjects (lgl), Identifiers (lgl), Collections (lgl), Variants (lgl),
-#>      Items (lgl), Notes (lgl)
+#> # ... with 143 more rows, and 20 more variables: FullTitle <chr>,
+#> #   ShortTitle <chr>, SortTitle <chr>, PartNumber <chr>, PartName <chr>,
+#> #   CallNumber <lgl>, Edition <chr>, PublisherPlace <chr>,
+#> #   PublisherName <chr>, PublicationDate <chr>,
+#> #   PublicationFrequency <chr>, Doi <lgl>, TitleUrl <lgl>, Authors <lgl>,
+#> #   Subjects <lgl>, Identifiers <lgl>, Collections <lgl>, Variants <lgl>,
+#> #   Items <lgl>, Notes <lgl>
 ```
 
 ## Get languages
 
 
 ```r
 bhl_getlanguages()
-#> <bhl data> [68, 2]
-#>    LanguageCode   LanguageName
-#> 1           AFR      Afrikaans
-#> 2           ARA         Arabic
-#> 3           ARC        Aramaic
-#> 4           BUL      Bulgarian
-#> 5           BUR        Burmese
-#> 6           CAR          Carib
-#> 7           CAT        Catalan
-#> 8           CEL Celtic (Other)
-#> 9           CHI        Chinese
-#> 10          HRV       Croatian
-#> ..          ...            ...
+#> # A tibble: 69 × 2
+#>    LanguageCode         LanguageName
+#> *         <chr>                <chr>
+#> 1           AFR            Afrikaans
+#> 2           ARA               Arabic
+#> 3           ARC              Aramaic
+#> 4           MAP Austronesian (Other)
+#> 5           BUL            Bulgarian
+#> 6           BUR              Burmese
+#> 7           CAR                Carib
+#> 8           CAT              Catalan
+#> 9           CEL       Celtic (Other)
+#> 10          CHI              Chinese
+#> # ... with 59 more rows
 ```
 
 ## Meta

inst/vign/rbhl_vignette.Rmd

@@ -34,13 +34,13 @@ knitr::opts_chunk$set(
   comment = "#>", 
   warning = FALSE, 
   message = FALSE,
-  cache = TRUE
+  cache = FALSE
 )
 
 ```
 
 rbhl Introduction
-======
+=================
 
 `rbhl` is an R interface to the Biodiversity Heritage Library.