Doc updates, bump version to 1.5

.Rbuildignore

@@ -3,4 +3,5 @@
 ^LICENSE\.md$
 ^.gitignore$
 ^img/*$
-^readme.md$
+^readme.md$
+^.github

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rpeaks
 Type: Package
 Title: Fast detection of R peaks in ecg data
-Version: 1.4
+Version: 1.5
 Date: 2020-04-29
 Author: Erik-Jan van Kesteren
 Maintainer: Erik-Jan van Kesteren <e.vankesteren1@uu.nl>
@@ -13,4 +13,6 @@ Imports:
     Rcpp,
     signal
 LinkingTo: Rcpp, RcppArmadillo
-RoxygenNote: 7.1.0
+Encoding: UTF-8
+RoxygenNote: 7.3.0
+Roxygen: list(markdown = TRUE)

R/pantompkins.R

@@ -26,6 +26,15 @@ NULL
 #' @references Pan, J., & Tompkins, W. J. (1985). A real-time QRS detection 
 #' algorithm. IEEE transactions on biomedical engineering, (3), 230-236.
 #' 
+#' @examples
+#' ecg_url <- "https://physionet.org/files/ecgiddb/1.0.0/Person_01/rec_2.dat?download"
+#' ecg_dat <- readBin(ecg_url, integer(), 500*30)
+#' ecg_sec <- (0:(length(ecg_dat) - 1)) / 500 # rel. time in seconds
+#' r_peaks <- rpeaks_pan_tompkins(ecg = ecg_dat, sample_rate = 500)
+#' plot(x = ecg_sec, y = ecg_dat, type = "l", xlab = "time (seconds)", ylab = "ecg")
+#' abline(v = r_peaks, col = "blue", lty = 3)
+#' 
+#' 
 #' @export
 rpeaks_pan_tompkins <- function(ecg, sample_rate, integration_window = 0.15,
                                 refractory = 0.2, band_low = 5, 

readme.md

@@ -2,12 +2,33 @@
   <img src="./img/logo.png" width="200px"></img>
 </p>
 
+[![R-CMD-check](https://github.com/vankesteren/rpeaks/actions/workflows/rcmdcheck.yml/badge.svg)](https://github.com/vankesteren/rpeaks/actions/workflows/rcmdcheck.yml)
+
 Fast implementation of Pan & Tompkins (1985). It is programmed relatively efficiently, using `Rcpp` and `RcppArmadillo` to process long ecg data much faster than alternatives. Default processing parameters are taken directly from the original paper.
 
 This package gratefully borrows parts of the processing code from `rsleep::detect_rpeaks()`.
 
 _NB: use at your own risk. This method has not been officially validated!_
 
+## Installation
+
+Install `rpeaks` from `r-universe` like so:
+```r
+install.packages("rpeaks", repos = c('https://vankesteren.r-universe.dev', 'https://cloud.r-project.org'))
+```
+
+## Usage
+
+```r
+library(rpeaks)
+ecg_url <- "https://physionet.org/files/ecgiddb/1.0.0/Person_01/rec_2.dat?download"
+ecg_dat <- readBin(ecg_url, integer(), 500*30)
+ecg_sec <- (0:(length(ecg_dat) - 1)) / 500 # rel. time in seconds
+r_peaks <- rpeaks_pan_tompkins(ecg = ecg_dat, sample_rate = 500)
+plot(x = ecg_sec, y = ecg_dat, type = "l")
+abline(v = r_peaks, col = "blue", lty = 3)
+```
+
 ## Speed comparison
 <p align="center">
   <img src="./img/speedcomparison.png" width="700px"></img>

src/RcppExports.cpp

@@ -6,6 +6,11 @@
 
 using namespace Rcpp;
 
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
 // fast_conv
 arma::vec fast_conv(const arma::vec& x, const arma::vec& y);
 RcppExport SEXP _rpeaks_fast_conv(SEXP xSEXP, SEXP ySEXP) {