Merge pull request #314 from stitam/newrelease

ropensci · Feb 7, 2021 · ee2d0d8 · ee2d0d8
2 parents 9e1694b + ffd65b2
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diff --git a/R/alanwood.R b/R/alanwood.R
@@ -18,7 +18,7 @@
 #' @references Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller,
 #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical
 #' Information from the Web. Journal of Statistical Software, 93(13).
-#' <doi:10.18637/jss.v093.i13>.
+#' \doi{10.18637/jss.v093.i13}.
 #' @export
 #' @examples
 #' \dontrun{

diff --git a/R/chebi.R b/R/chebi.R
@@ -52,7 +52,7 @@
 #' @references Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller,
 #'   Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical
 #'   Information from the Web. Journal of Statistical Software, 93(13).
-#'   <doi:10.18637/jss.v093.i13>.
+#'   \doi{10.18637/jss.v093.i13}.
 #' @export
 #' @examples
 #' \donttest{
@@ -225,7 +225,7 @@ get_chebiid <- function(query,
 #' @references Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller,
 #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical
 #' Information from the Web. Journal of Statistical Software, 93(13).
-#' <doi:10.18637/jss.v093.i13>.
+#' \doi{10.18637/jss.v093.i13}.
 #' @export
 #' @examples
 #' \donttest{

diff --git a/R/chemspider.R b/R/chemspider.R
@@ -164,7 +164,7 @@ cs_control <- function(datasources = vector(),
 #' @references Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller,
 #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical
 #' Information from the Web. Journal of Statistical Software, 93(13).
-#' <doi:10.18637/jss.v093.i13>.
+#' \doi{10.18637/jss.v093.i13}.
 #'
 #' @export
 #' @examples
@@ -336,7 +336,7 @@ get_csid <- function(query,
 #' @references Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller,
 #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical
 #' Information from the Web. Journal of Statistical Software, 93(13).
-#' <doi:10.18637/jss.v093.i13>.
+#' \doi{10.18637/jss.v093.i13}.
 #' @export
 #' @examples
 #' \dontrun{

diff --git a/R/etox.R b/R/etox.R
@@ -25,7 +25,7 @@
 #' @references Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller,
 #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical
 #' Information from the Web. Journal of Statistical Software, 93(13).
-#' <doi:10.18637/jss.v093.i13>.
+#' \doi{10.18637/jss.v093.i13}.
 #' @export
 #' @examples
 #' \dontrun{
@@ -153,7 +153,7 @@ get_etoxid <- function(query,
 #' @references Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller,
 #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical
 #' Information from the Web. Journal of Statistical Software, 93(13).
-#' <doi:10.18637/jss.v093.i13>.
+#' \doi{10.18637/jss.v093.i13}.
 #' @export
 #' @examples
 #' \dontrun{
@@ -278,7 +278,7 @@ etox_basic <- function(id, verbose = TRUE) {
 #' @references Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller,
 #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical
 #' Information from the Web. Journal of Statistical Software, 93(13).
-#' <doi:10.18637/jss.v093.i13>.
+#' \doi{10.18637/jss.v093.i13}.
 #' @export
 #' @examples
 #' \dontrun{

diff --git a/R/extractors.R b/R/extractors.R
@@ -7,7 +7,7 @@
 #' @references Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller,
 #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical
 #' Information from the Web. Journal of Statistical Software, 93(13).
-#' <doi:10.18637/jss.v093.i13>.
+#' \doi{10.18637/jss.v093.i13}.
 #' @export
 cas <- function(x, ...){
   UseMethod("cas")

diff --git a/R/nist.R b/R/nist.R
@@ -309,7 +309,7 @@ tidy_ritable <- function(ri_xml) {
 #'   "Retention Indices" in NIST Chemistry WebBook, NIST Standard Reference
 #'   Database Number 69, Eds. P.J. Linstrom and W.G. Mallard,
 #'   National Institute of Standards and Technology, Gaithersburg MD, 20899,
-#'   \url{https://doi.org/10.18434/T4D303}.
+#'   \doi{10.18434/T4D303}.
 #'
 #' @export
 #' @note Copyright for NIST Standard Reference Data is governed by the Standard

diff --git a/R/opsin.R b/R/opsin.R
@@ -15,7 +15,7 @@
 #'
 #' @references Lowe, D. M., Corbett, P. T., Murray-Rust, P., & Glen, R. C. (2011).
 #' Chemical Name to Structure: OPSIN, an Open Source Solution. Journal of Chemical Information and Modeling,
-#' 51(3), 739–753. \url{https://doi.org/10.1021/ci100384d}
+#' 51(3), 739–753. \doi{10.1021/ci100384d}
 #' @examples
 #' \donttest{
 #' opsin_query('Cyclopropane')

diff --git a/R/pan.R b/R/pan.R
@@ -1,6 +1,6 @@
 #' Query the PAN Pesticide database
 #'
-#' Retrieve information from the PAN database (\url{http://www.pesticideinfo.org/}).
+#' Retrieve information from the PAN database (\url{https://www.pesticideinfo.org/}).
 #' This function is currently broken.
 #' @import xml2
 #' @importFrom utils adist
@@ -13,7 +13,7 @@
 #' @param verbose logical; should a verbose output be printed on the console?
 #' @param ... currently not used.
 #' @return a named list of 73 entries,
-#'   see \url{http://www.pesticideinfo.org/Docs/ref_overview.html} for more information.
+#'   see \url{https://www.pesticideinfo.org/about/overview.html} for more information.
 #'   If \code{match="best"} an additional entry \code{match_score} with the normalized
 #'   Levenshtein distance (0 = perfect match, 1 = worst match).
 #'
@@ -84,7 +84,7 @@ pan_query <- function(query, from = c("name", "cas"),
       if (verbose) webchem_message("na")
       return(NA)
     }
-    baseurl <- 'http://www.pesticideinfo.org/List_Chemicals.jsp?'
+    baseurl <- 'https://www.pesticideinfo.org/List_Chemicals.jsp?'
     baseq <- paste0('ChooseSearchType=Begin&ResultCnt=50&dCAS_No=y&dEPA_PCCode=y&',
                     'dDPR_Chem_Code=y&dUseList=y&dClassList=y&dMol_weight=y&',
                     'dEPA_Reg=y&dCA_Reg=y&dPIC=y&dPOP=y&dWHOObsolete=y&dEPA_HAP=y&',
@@ -141,7 +141,7 @@ pan_query <- function(query, from = c("name", "cas"),
       # return also source url
       # xmlview::xml_view(nd, add_filter = TRUE)
       source_url <- xml_attr(xml_find_all(nd, ".//a[contains(., 'Details')]"), 'href')
-      out[['source_url']] <- paste0('http://www.pesticideinfo.org/', source_url)
+      out[['source_url']] <- paste0('https://www.pesticideinfo.org/', source_url)
 
       ind <-
         matcher(

diff --git a/R/pubchem.R b/R/pubchem.R
@@ -64,7 +64,7 @@
 #' @references Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller,
 #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical
 #' Information from the Web. Journal of Statistical Software, 93(13).
-#' <doi:10.18637/jss.v093.i13>.
+#' \doi{10.18637/jss.v093.i13}.
 #' @note Please respect the Terms and Conditions of the National Library of
 #' Medicine, \url{https://www.nlm.nih.gov/databases/download.html} the data
 #' usage policies of National Center for Biotechnology Information,
@@ -296,7 +296,7 @@ get_cid <-
 #' @references Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller,
 #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical
 #' Information from the Web. Journal of Statistical Software, 93(13).
-#' <doi:10.18637/jss.v093.i13>.
+#' \doi{10.18637/jss.v093.i13}.
 #' @note Please respect the Terms and Conditions of the National Library of
 #' Medicine, \url{https://www.nlm.nih.gov/databases/download.html} the data
 #' usage policies of National Center for Biotechnology Information,
@@ -541,7 +541,7 @@ pc_synonyms <- function(query,
 #' \url{https://pubchem.ncbi.nlm.nih.gov/sources/}.
 #' @references Kim, S., Thiessen, P.A., Cheng, T. et al. PUG-View: programmatic
 #' access to chemical annotations integrated in PubChem. J Cheminform 11, 56
-#' (2019). https://doi.org/10.1186/s13321-019-0375-2.
+#' (2019). \doi{10.1186/s13321-019-0375-2}.
 #' @seealso \code{\link{get_cid}}, \code{\link{pc_prop}}
 #' @examples
 #' # might fail if API is not available
@@ -592,7 +592,7 @@ pc_sect <- function(id,
 #' \url{https://pubchem.ncbi.nlm.nih.gov/classification/#hid=72}.
 #' @references Kim, S., Thiessen, P.A., Cheng, T. et al. PUG-View: programmatic
 #' access to chemical annotations integrated in PubChem. J Cheminform 11, 56
-#' (2019). https://doi.org/10.1186/s13321-019-0375-2.
+#' (2019). \doi{10.1186/s13321-019-0375-2}.
 #' @examples
 #' # might fail if API is not available
 #' \donttest{
@@ -671,7 +671,7 @@ pc_page <- function(id,
 #' be found at \url{https://pubchem.ncbi.nlm.nih.gov/classification/#hid=72}.
 #' @references Kim, S., Thiessen, P.A., Cheng, T. et al. PUG-View: programmatic
 #' access to chemical annotations integrated in PubChem. J Cheminform 11, 56
-#' (2019). https://doi.org/10.1186/s13321-019-0375-2.
+#' (2019). \doi{10.1186/s13321-019-0375-2}.
 #' @examples
 #' # might fail if API is not available
 #' \donttest{

diff --git a/R/utils.R b/R/utils.R
@@ -21,7 +21,7 @@
 #' @references Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller,
 #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical
 #' Information from the Web. Journal of Statistical Software, 93(13).
-#' <doi:10.18637/jss.v093.i13>.
+#' \doi{10.18637/jss.v093.i13}.
 #' @export
 #' @examples
 #' is.inchikey('BQJCRHHNABKAKU-KBQPJGBKSA-N')
@@ -190,7 +190,7 @@ is.inchikey_format = function(x, verbose = TRUE) {
 #' @references Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller,
 #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical
 #' Information from the Web. Journal of Statistical Software, 93(13).
-#' <doi:10.18637/jss.v093.i13>.
+#' \doi{10.18637/jss.v093.i13}.
 #'
 #' @export
 #' @examples
@@ -336,7 +336,7 @@ extr_num <- function(x) {
 #' @references Grabner, M., Varmuza, K., & Dehmer, M. (2012). RMol:
 #' a toolset for transforming SD/Molfile structure information into R objects.
 #' Source Code for Biology and Medicine, 7, 12.
-#' \url{https://doi.org/10.1186/1751-0473-7-12}
+#' \doi{10.1186/1751-0473-7-12}
 #' @export
 
 parse_mol <- function(string) {

diff --git a/R/wikidata.R b/R/wikidata.R
@@ -135,7 +135,7 @@ get_wdid <-
 #' @seealso \code{\link{get_wdid}}
 #'
 #' @references Willighagen, E., 2015. Getting CAS registry numbers out of WikiData. The Winnower.
-#' \url{http://dx.doi.org/10.15200/winn.142867.72538}
+#' \doi{10.15200/winn.142867.72538}
 #'
 #' Mitraka, Elvira, Andra Waagmeester, Sebastian Burgstaller-Muehlbacher, et al. 2015
 #' Wikidata: A Platform for Data Integration and Dissemination for the Life Sciences and beyond. bioRxiv: 031971.

diff --git a/man/aw_query.Rd b/man/aw_query.Rd
diff --git a/man/chebi_comp_entity.Rd b/man/chebi_comp_entity.Rd
diff --git a/man/cs_convert.Rd b/man/cs_convert.Rd
diff --git a/man/etox_basic.Rd b/man/etox_basic.Rd
diff --git a/man/etox_targets.Rd b/man/etox_targets.Rd
diff --git a/man/extractors.Rd b/man/extractors.Rd
diff --git a/man/get_chebiid.Rd b/man/get_chebiid.Rd
diff --git a/man/get_cid.Rd b/man/get_cid.Rd
diff --git a/man/get_csid.Rd b/man/get_csid.Rd
diff --git a/man/get_etoxid.Rd b/man/get_etoxid.Rd
diff --git a/man/is.cas.Rd b/man/is.cas.Rd
diff --git a/man/is.inchikey.Rd b/man/is.inchikey.Rd
diff --git a/man/nist_ri.Rd b/man/nist_ri.Rd
diff --git a/man/opsin_query.Rd b/man/opsin_query.Rd
diff --git a/man/pan_query.Rd b/man/pan_query.Rd
diff --git a/man/parse_mol.Rd b/man/parse_mol.Rd
diff --git a/man/pc_prop.Rd b/man/pc_prop.Rd
diff --git a/man/pc_sect.Rd b/man/pc_sect.Rd
diff --git a/man/wd_ident.Rd b/man/wd_ident.Rd