Merge pull request #298 from stitam/new_release

Final edits before v1.1
ropensci · Oct 1, 2020 · 6433e7e · 6433e7e
2 parents a931d81 + 62c70cb
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -25,3 +25,4 @@ README_cache
 ^\.github$
 
 codemeta.json
+^codemeta\.json$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -7,8 +7,8 @@ Description: Chemical information from around the web. This package interacts
     Flavornet, NIST Chemistry WebBook, OPSIN, PAN Pesticide Database, PubChem,
     SRS, Wikidata.
 Type: Package
-Version: 1.0.0.9001
-Date: 2020-05-27
+Version: 1.1.0
+Date: 2020-10-01
 License: MIT + file LICENSE
 URL: https://docs.ropensci.org/webchem, https://github.com/ropensci/webchem
 BugReports: https://github.com/ropensci/webchem/issues

diff --git a/NEWS.md b/NEWS.md
diff --git a/R/alanwood.R b/R/alanwood.R
@@ -20,7 +20,6 @@
 #' 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>.
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
 #' @export
 #' @examples
 #' \dontrun{
@@ -176,7 +175,6 @@ aw_query <- function(query, from = c("name", "cas"), verbose = TRUE,
 #' @param force_build logical; force building a new index?
 #' @return a data.frame
 #' @seealso \code{\link{aw_query}}, \code{\link{tempdir}}
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
 #' @source \url{http://www.alanwood.net/pesticides}
 #' @noRd
 build_aw_idx <- function(verbose = TRUE, force_build = FALSE) {

diff --git a/R/chebi.R b/R/chebi.R
@@ -55,7 +55,6 @@
 #'   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>.
-#' @author Andreas Scharmüller, \email{andschar@@protonmail.com}
 #' @export
 #' @examples
 #' \donttest{
@@ -230,7 +229,6 @@ get_chebiid <- function(query,
 #' 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>.
-#' @author Andreas Scharmüller, \email{andschar@@protonmail.com}
 #' @export
 #' @examples
 #' \donttest{
@@ -356,7 +354,6 @@ chebi_comp_entity <- function(chebiid,
 #' @param x list; a list to bind into a data.frame
 #' @return a data.frame
 #' @seealso \code{\link{chebi_comp_entity}}
-#' @author Andreas Scharmüller, \email{andschar@@protonmail.com}
 #' @noRd
 #'
 l2df <- function(x) {
@@ -375,7 +372,6 @@ l2df <- function(x) {
 #' https://stackoverflow.com/questions/17308551/do-callrbind-list-for-uneven-number-of-column
 #' @param x list; a list to bind into a data.frame
 #' @seealso \code{\link{l2df}}
-#' @author Andreas Scharmüller, \email{andschar@@protonmail.com}
 #' @noRd
 #'
 rbind_named_fill <- function(x) {

diff --git a/R/chemspider.R b/R/chemspider.R
@@ -44,7 +44,6 @@ cs_check_key <- function() {
 #' for an API key. Please respect the Terms & Conditions. The Terms & Conditions
 #' can be found at \url{https://developer.rsc.org/terms}.
 #' @references \url{https://developer.rsc.org/compounds-v1/apis}
-#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com}
 #' @export
 #' @examples
 #' \dontrun{
@@ -101,7 +100,6 @@ cs_datasources <- function(apikey = NULL) {
 #' The controls that are available for a given function are indicated within the
 #' documentation of the function.
 #' @references \url{https://developer.rsc.org/compounds-v1/apis}
-#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com}
 #' @seealso \code{\link{get_csid}}
 #' @export
 #' @examples
@@ -161,8 +159,6 @@ cs_control <- function(datasources = vector(),
 #' 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>.
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
-#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com}
 #' @importFrom httr POST add_headers http_status
 #' @importFrom jsonlite toJSON
 #' @importFrom tibble enframe
@@ -243,7 +239,6 @@ get_csid <- function(query,
 #' for an API key.
 #' Please respect the Terms & conditions \url{https://developer.rsc.org/terms}.
 #' @references \url{https://developer.rsc.org/compounds-v1/apis}
-#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com}
 #' @noRd
 cs_query_csid <- function(postres, headers) {
   query_id <- jsonlite::fromJSON(rawToChar(postres$content))$queryId
@@ -315,7 +310,6 @@ cs_query_csid <- function(postres, headers) {
 #' for an API key. Please respect the Terms & conditions
 #' \url{https://developer.rsc.org/terms}.
 #' @references https://developer.rsc.org/compounds-v1/apis
-#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com}
 #' @note This is a low level function and is not exported.
 #' @examples
 #' \dontrun{
@@ -364,7 +358,6 @@ cs_name_csid <- function(name, apikey = NULL, control = cs_control()) {
 #' for an API key. Please respect the Terms & conditions
 #' \url{https://developer.rsc.org/terms}.
 #' @references \url{https://developer.rsc.org/compounds-v1/apis}
-#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com}
 #' @note This is a low level function and is not exported.
 #' @examples
 #' \dontrun{
@@ -409,7 +402,6 @@ cs_formula_csid <- function(formula, apikey = NULL, control = cs_control()) {
 #' for an API key. Please respect the Terms & conditions
 #' \url{https://developer.rsc.org/terms}.
 #' @references \url{https://developer.rsc.org/compounds-v1/apis}
-#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com}
 #' @note This is a low level function and is not exported.
 #' @examples
 #' \dontrun{
@@ -451,7 +443,6 @@ cs_smiles_csid <- function(smiles, apikey = NULL) {
 #' for an API key. Please respect the Terms & conditions
 #' \url{https://developer.rsc.org/terms}.
 #' @references \url{https://developer.rsc.org/compounds-v1/apis}
-#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com}
 #' @note This is a low level function and is not exported.
 #' @examples
 #' \dontrun{
@@ -495,7 +486,6 @@ cs_inchi_csid <- function(inchi, apikey = NULL) {
 #' for an API key. Please respect the Terms & conditions
 #' \url{https://developer.rsc.org/terms}.
 #' @references \url{https://developer.rsc.org/compounds-v1/apis}
-#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com}
 #' @note This is a low level function and is not exported.
 #' @examples
 #' \dontrun{
@@ -550,7 +540,6 @@ cs_inchikey_csid <- function(inchikey, apikey = NULL) {
 #' for an API key. Please respect the Terms & Conditions. The Terms & Conditions
 #' can be found at \url{https://developer.rsc.org/terms}.
 #' @references \url{https://developer.rsc.org/compounds-v1/apis}
-#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com}
 #' @seealso This is a low level function and is not exported. See
 #' \code{\link{cs_convert}} for the top level function.
 #' @seealso \code{\link{parse_mol}}
@@ -618,8 +607,6 @@ cs_convert_multiple <- function(input, from, to, apikey = NULL) {
 #' 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>.
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
-#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com}
 #' @export
 #' @examples
 #' \dontrun{
@@ -710,7 +697,6 @@ cs_convert <- function(query, from, to, apikey = NULL) {
 #' for an API key. Please respect the Terms & Conditions. The Terms & Conditions
 #' can be found at \url{https://developer.rsc.org/terms}.
 #' @references \url{https://developer.rsc.org/compounds-v1/apis}
-#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com}
 #' @export
 #' @examples
 #' \dontrun{
@@ -772,7 +758,6 @@ cs_compinfo <- function(csid, fields, apikey = NULL) {
 #' for a security token.
 #' Please respect the Terms & conditions
 #' \url{https://www.rsc.org/help-legal/legal/terms-conditions/}.
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
 #' @seealso \code{\link{get_csid}} to retrieve ChemSpider IDs,
 #' \code{\link{cs_compinfo}} for extended compound information.
 #' @note use \code{\link{cs_compinfo}} to retrieve standard inchikey.
@@ -850,7 +835,6 @@ use 'cs_commpinfo()' instead.")
 #' for an API key. Please respect the Terms & Conditions. The Terms & Conditions
 #' can be found at \url{https://developer.rsc.org/terms}.
 #' @references \url{https://developer.rsc.org/compounds-v1/apis}
-#' @author Tamas Stirling, \email{stirling.tamas@@gmail.com}
 #' @seealso \code{\link{get_csid}}, \code{\link{cs_check_key}}
 #' @importFrom httr GET add_headers message_for_status content
 #' @importFrom jsonlite fromJSON

diff --git a/R/cir.R b/R/cir.R
@@ -96,7 +96,6 @@
 #' \url{http://cactus.nci.nih.gov/blog/?p=1386}, \cr
 #' \url{http://cactus.nci.nih.gov/blog/?p=1456}, \cr
 #'
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
 #'
 #' @examples
 #' \donttest{
@@ -234,7 +233,6 @@ cir_query <- function(identifier, representation = "smiles",
 #' \url{http://cactus.nci.nih.gov/blog/?p=1386}, \cr
 #' \url{http://cactus.nci.nih.gov/blog/?p=1456}, \cr
 #'
-#' @author Andreas Scharmueller, \email{andschar@@protonmail.com}
 #'
 #' @examples
 #' \donttest{

diff --git a/R/cts.R b/R/cts.R
@@ -10,7 +10,6 @@
 #' @param inchikey deprecated
 #' @return a list of lists (for each supplied inchikey):
 #' a list of 7. inchikey, inchicode, molweight, exactmass, formula, synonyms and externalIds
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
 #'
 #' @references Wohlgemuth, G., P. K. Haldiya, E. Willighagen, T. Kind, and O. Fiehn 2010The Chemical Translation Service
 #' -- a Web-Based Tool to Improve Standardization of Metabolomic Reports. Bioinformatics 26(20): 2647–2648.
@@ -97,7 +96,6 @@ cts_compinfo <- function(query, from = "inchikey", verbose = TRUE, inchikey){
 #' @param verbose logical; should a verbose output be printed on the console?
 #' @param ... currently not used.
 #' @return a list of character vectors or if \code{choices} is used, then a single named vector.
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
 #' @details See also \url{http://cts.fiehnlab.ucdavis.edu/}
 #' for possible values of from and to.
 #'
@@ -205,7 +203,6 @@ cts_convert <- function(query,
 #' @import jsonlite
 #' @param verbose logical; should a verbose output be printed on the console?
 #' @return a character vector.
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
 #' @details See also \url{http://cts.fiehnlab.ucdavis.edu/services}
 #'
 #' @seealso \code{\link{cts_convert}}
@@ -242,7 +239,6 @@ cts_from <- function(verbose = TRUE){
 #' @import jsonlite
 #' @param verbose logical; should a verbose output be printed on the console?
 #' @return a character vector.
-#' @author Eduard Szoecs, \email{eduardszoecs@@gmail.com}
 #' @details See also \url{http://cts.fiehnlab.ucdavis.edu/services}
 #'
 #' @seealso \code{\link{cts_convert}}

diff --git a/R/etox.R b/R/etox.R
@@ -27,9 +27,6 @@
 #' 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>.
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
-#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com}
-#' @author Andreas Scharmüller, \email{andschar@@protonmail.com}
 #' @export
 #' @examples
 #' \dontrun{
@@ -159,7 +156,6 @@ get_etoxid <- function(query,
 #' 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>.
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
 #' @export
 #' @examples
 #' \dontrun{
@@ -286,7 +282,6 @@ etox_basic <- function(id, verbose = TRUE) {
 #' 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>.
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
 #' @export
 #' @examples
 #' \dontrun{
@@ -386,7 +381,6 @@ etox_targets <- function(id, verbose = TRUE) {
 #' @seealso \code{\link{get_etoxid}} to retrieve ETOX IDs, \code{\link{etox_basic}} for basic information,
 #' \code{\link{etox_targets}} for quality targets and \code{\link{etox_tests}} for test results
 #'
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
 #' @export
 #' @examples
 #' \dontrun{

diff --git a/R/flavornet.R b/R/flavornet.R
@@ -1,7 +1,7 @@
 #' Retrieve flavor percepts from www.flavornet.org
 #'
 #' Retreive flavor percepts from \url{http://www.flavornet.org}.  Flavornet is a database of 738 compounds with odors
-#' perceptible to humans detected using gas chromatography ofactometry (GCO).
+#' perceptible to humans detected using gas chromatography olfactometry (GCO).
 #'
 #' @import xml2
 #' @importFrom stats rgamma
@@ -13,7 +13,6 @@
 #'
 #' @return A named character vector containing flavor percepts or NA's in the case of CAS numbers that are not found
 #'
-#' @author Eric Scott, \email{eric.scott@@tufts.edu}
 #'
 #' @examples
 #' \dontrun{

diff --git a/R/pan.R b/R/pan.R
@@ -49,7 +49,6 @@
 #' Fresh Water Guidelines (ug/L); Salt Water Guidelines (ug/L);
 #' Irrigation Water Guidelines (ug/L); Livestock Water Guidelines (ug/L);
 #' Chemical Name; matching synonym; source URL
-#' @author Eduard Szoecs, \email{eduardszoecs@@gmail.com}
 #' @export
 #' @examples
 #' \dontrun{

diff --git a/R/pubchem.R b/R/pubchem.R
@@ -72,8 +72,6 @@
 #' \url{https://pubchemdocs.ncbi.nlm.nih.gov/programmatic-access}, and the data
 #' usage policies of the indicidual data sources
 #' \url{https://pubchem.ncbi.nlm.nih.gov/sources/}.
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
-#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com}
 #' @import httr
 #' @importFrom purrr map map2
 #' @importFrom jsonlite fromJSON
@@ -283,7 +281,6 @@ get_cid <-
 #' @param ... currently not used.
 #'
 #' @return a data.frame
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
 #' @seealso \code{\link{get_cid}}, \code{\link{pc_sect}}
 #' @references Wang, Y., J. Xiao, T. O. Suzek, et al. 2009 PubChem: A Public
 #' Information System for
@@ -442,7 +439,6 @@ pc_prop <- function(cid, properties = NULL, verbose = TRUE, ...) {
 #' \url{https://pubchemdocs.ncbi.nlm.nih.gov/programmatic-access}, and the data
 #' usage policies of the indicidual data sources
 #' \url{https://pubchem.ncbi.nlm.nih.gov/sources/}.
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
 #' @export
 #' @examples
 #' \donttest{
@@ -547,7 +543,6 @@ pc_synonyms <- function(query,
 #' @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.
-#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com}
 #' @seealso \code{\link{get_cid}}, \code{\link{pc_prop}}
 #' @examples
 #' # might fail if API is not available
@@ -600,7 +595,6 @@ pc_sect <- function(id,
 #' @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.
-#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com}
 #' @examples
 #' # might fail if API is not available
 #' \donttest{
@@ -680,7 +674,6 @@ pc_page <- function(id,
 #' @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.
-#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com}
 #' @examples
 #' # might fail if API is not available
 #' \donttest{

diff --git a/R/srs.R b/R/srs.R
@@ -13,7 +13,6 @@
 #'  categoryClass, kingdomCode, iupacName, pubChemId, molecularWeight,
 #'  molecularFormula, inchiNotation, smilesNotation, classifications,
 #'  characteristics, synonyms, casNumbers, taxonomicSerialNumbers, relationships
-#'@author Gordon Getzinger, \email{gjg3@@duke.edu}
 #'@export
 #'
 #' @examples

diff --git a/R/utils.R b/R/utils.R
@@ -22,7 +22,6 @@
 #' 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>.
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
 #' @export
 #' @examples
 #' is.inchikey('BQJCRHHNABKAKU-KBQPJGBKSA-N')
@@ -53,7 +52,6 @@ is.inchikey = function(x, type = c('format', 'chemspider'), verbose = TRUE) {
 #' @return a logical
 #'
 #' @seealso \code{\link{is.inchikey}} for a pure-R implementation.
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
 #' @export
 #' @examples
 #' \donttest{
@@ -118,7 +116,6 @@ is.inchikey_cs <- function(x, verbose = TRUE){
 #' @return a logical
 #'
 #' @seealso \code{\link{is.inchikey}} for a pure-R implementation.
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
 #' @export
 #' @examples
 #' \donttest{
@@ -194,7 +191,6 @@ is.inchikey_format = function(x, verbose = TRUE) {
 #' 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>.
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
 #'
 #' @export
 #' @examples
@@ -275,8 +271,6 @@ is.cas <-  function(x, verbose = TRUE) {
 #'
 #' @note This function can handle only one SMILES string.
 #'
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
-#'
 #' @references Egon Willighagen (2015). How to test SMILES strings in
 #' Supplementary Information.
 #' \url{https://chem-bla-ics.blogspot.nl/2015/10/how-to-test-smiles-strings-in.html}
@@ -339,7 +333,6 @@ extr_num <- function(x) {
 #' 1 = first atom, 2 = second atom, t = bond type, s = stereo type, x = not
 #' used, r = bond typology, c = reacting center status.
 #'
-#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com}
 #' @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.
@@ -383,7 +376,6 @@ parse_mol <- function(string) {
 #' @return character vector of valid CAS numbers
 #' @seealso \code{\link{is.cas}}
 #' @export
-#' @author Eric Scott, \email{scottericr@@gmail.com}
 #' @examples
 #' x = c(58082, 123456, "hexenol")
 #' as.cas(x)