documentation fixes

Author: fmichonneau

DESCRIPTION

@@ -1,4 +1,3 @@
-Roxygen: list(wrap = FALSE)
 Package: rncl
 Title: An Interface to the Nexus Class Library
 Version: 0.8.4
@@ -30,4 +29,5 @@ License: BSD_2_clause + file LICENSE
 URL: https://github.com/fmichonneau/rncl
 BugReports: https://github.com/fmichonneau/rncl/issues
 LazyData: true
-RoxygenNote: 6.0.1
+RoxygenNote: 7.0.2.9000
+Encoding: UTF-8

R/RcppExports.R

@@ -1,6 +1,10 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
+RNCL <- function(params, paramsVecR) {
+    .Call('_rncl_RNCL', PACKAGE = 'rncl', params, paramsVecR)
+}
+
 n_singletons <- function(ances) {
     .Call('_rncl_n_singletons', PACKAGE = 'rncl', ances)
 }
@@ -9,7 +13,3 @@ collapse_single_cpp <- function(ances, desc, elen, nnode, show_progress) {
     .Call('_rncl_collapse_single_cpp', PACKAGE = 'rncl', ances, desc, elen, nnode, show_progress)
 }
 
-RNCL <- function(params, paramsVecR) {
-    .Call('_rncl_RNCL', PACKAGE = 'rncl', params, paramsVecR)
-}
-

R/rncl.R

@@ -32,7 +32,7 @@
 ##' @references Maddison DR, Swofford DL, Maddison WP (1997).
 ##'     "NEXUS: An extensible file format for systematic information".
 ##'     Systematic Biology 46(4) : 590-621.
-##'     doi:\href{http://dx.doi.org/10.1093/sysbio/46.4.590}{10.1093/sysbio/46.4.590}
+##'     doi:\href{https://doi.org/10.1093/sysbio/46.4.590}{10.1093/sysbio/46.4.590}
 ##'
 ##' Lewis, P. O. 2003. NCL: a C++ class library for interpreting data
 ##' files in NEXUS format. Bioinformatics 19 (17) : 2330-2331.

man/read_nexus_phylo.Rd

@@ -5,6 +5,18 @@
 
 using namespace Rcpp;
 
+// RNCL
+Rcpp::List RNCL(SEXP params, SEXP paramsVecR);
+RcppExport SEXP _rncl_RNCL(SEXP paramsSEXP, SEXP paramsVecRSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< SEXP >::type params(paramsSEXP);
+    Rcpp::traits::input_parameter< SEXP >::type paramsVecR(paramsVecRSEXP);
+    rcpp_result_gen = Rcpp::wrap(RNCL(params, paramsVecR));
+    return rcpp_result_gen;
+END_RCPP
+}
 // n_singletons
 int n_singletons(Rcpp::IntegerVector ances);
 RcppExport SEXP _rncl_n_singletons(SEXP ancesSEXP) {
@@ -31,15 +43,3 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
-// RNCL
-Rcpp::List RNCL(SEXP params, SEXP paramsVecR);
-RcppExport SEXP _rncl_RNCL(SEXP paramsSEXP, SEXP paramsVecRSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< SEXP >::type params(paramsSEXP);
-    Rcpp::traits::input_parameter< SEXP >::type paramsVecR(paramsVecRSEXP);
-    rcpp_result_gen = Rcpp::wrap(RNCL(params, paramsVecR));
-    return rcpp_result_gen;
-END_RCPP
-}