Rough draft

Former-commit-id: 3b8b997db2f0ae536a7b0ed5a850970cc33275bd

Author: Max Czapanskiy

.Rbuildignore

@@ -7,3 +7,4 @@
 ^CONTRIBUTING\.md$
 analysis
 ^data-raw$
+^runtime\.txt$

.gitignore

@@ -3,3 +3,4 @@
 .Rdata
 .httr-oauth
 .DS_Store
+analysis/paper/paper_cache/*

DESCRIPTION

@@ -7,15 +7,13 @@ Authors@R:
            role = c("aut", "cre"),
            email = "[email protected]",
            comment = c("ORCID-ID" = "0000-0002-6302-905X"))
-Description: Code and data for [Authors] [Title] [Journal] [doi]
+Description: Code and data for Czapanskiy et al. "Accelerometer-derived
+    ballistocardiogram confirms blue whale (*Balaenoptera musculus*) heart
+    rate during diving bradycardia".
 License: MIT + file LICENSE
-ByteCompile: true
-Encoding: UTF-8
-LazyData: true
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+Depends: 
+    R (>= 2.10)
 Imports: 
-    akima,
     bookdown,
     cowplot,
     dplyr,
@@ -32,12 +30,20 @@ Imports:
     RcppRoll,
     readxl,
     RobustLinearReg,
-    scales,
     signal
 Suggests: 
-    tidyverse,
+    bib2df,
+    crul,
     devtools,
     git2r,
-    shiny
-Depends: 
-    R (>= 2.10)
+    rcrossref,
+    shiny,
+    stringr,
+    tidyverse
+Remotes: 
+    FlukeAndFeather/crul
+ByteCompile: true
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.1

NAMESPACE

@@ -12,5 +12,4 @@ export(s2n)
 export(shannon_entropy)
 export(split_dives)
 export(tma)
-import(tidyverse)
 importFrom(magrittr,"%>%")

R/bib.R

@@ -0,0 +1,44 @@
+#' Create crossref.bib
+#'
+#' Uses package rcrossref to look up DOIs in dois.txt and create crossref.bib.
+write_crossref <- function() {
+  for (pkg in c("rcrossref", "bib2df")) {
+    if (!requireNamespace(pkg, quietly = TRUE)) {
+      stop(sprintf("write_crossref() requires package '%s'", pkg))
+    }
+  }
+  # Fetch from crossref
+  dois <- readLines("analysis/paper/dois.txt")
+  refs <- rcrossref::cr_cn(dois = dois, format = "bibtex")
+  bib_path <- "analysis/paper/crossref.bib"
+  if (file.exists(bib_path)) {
+    message("Overwriting crossref.bib")
+    file.remove(bib_path)
+  }
+  file.create(bib_path)
+  for (ref in refs) {
+    write(paste0(ref, "\n"), file = bib_path, append = TRUE)
+  }
+
+  # Fix entry names
+  get_first_author <- function(author_list) {
+    author_list[1] %>% stringr::str_match(".* ([^ ]+)$") %>% `[`(1, 2)
+  }
+  append_suffix <- function(keys) {
+    if (length(keys) > 1) {
+      paste0(keys, letters[seq(length(keys))])
+    } else {
+      keys
+    }
+  }
+  bibdf <- bib2df::bib2df(bib_path) %>%
+    dplyr::mutate(BIBTEXKEY = paste(purrr::map_chr(AUTHOR, get_first_author),
+                                    YEAR,
+                                    sep = "-")) %>%
+    dplyr::group_by(BIBTEXKEY) %>%
+    dplyr::mutate(BIBTEXKEY = append_suffix(BIBTEXKEY)) %>%
+    dplyr::ungroup()
+  bib2df::df2bib(bibdf, bib_path)
+}
+
+

R/dives.R

@@ -10,7 +10,7 @@
 #'   to individual dives. Inter-dive periods marked as NA.
 #' @export
 split_dives <- function(dt, depth, surface = 0, min_depth = 0, min_dur = 0) {
-  dive_start <- depth >= surface & lag(depth) < surface
+  dive_start <- depth >= surface & dplyr::lag(depth) < surface
   dive_start[1] <- FALSE
   dive_id <- cumsum(dive_start)
   dive_id[depth < surface | dive_id == 0] <- NA
@@ -28,7 +28,7 @@ split_dives <- function(dt, depth, surface = 0, min_depth = 0, min_dur = 0) {
 
 #' Normalize dive time
 #'
-#' Normalize the time in each dive to [0, 1] where 0 is start of dive and 1 is
+#' Normalize the time in each dive to `[0, 1]` where 0 is start of dive and 1 is
 #' the end.
 #'
 #' @param dive_id A factor of dive id's, as from \code{split_dives()}.

R/find_beats.R

@@ -14,7 +14,7 @@ find_beats <- function(cue, fs_hz, minperiod) {
   # Skip if less than 50 peaks
   if (nrow(peaks) >= 50) {
     dist_max <- sqrt((max(peaks[, 1]) - peaks[, 1])^2 + (max(proms) - proms)^2)
-    dist_dens <- density(dist_max)
+    dist_dens <- stats::density(dist_max)
     dist_thr <- dist_dens$x[pracma::findpeaks(-dist_dens$y)[, 2]]
     is_beat <- peaks[, 2][dist_max <= dist_thr]
   } else {
@@ -57,7 +57,7 @@ filter_acc <- function(acc, fs, upper) {
 choose_peaks <- function(x) {
   x_sorted <- sort(x)
   steps <- diff(x_sorted)
-  thr <- if (max(steps) > mean(steps) + 2 * sd(steps)) {
+  thr <- if (max(steps) > mean(steps) + 2 * stats::sd(steps)) {
     x_sorted[which.max(steps)]
   } else {
     x_sorted[1]

R/psd.R

@@ -6,19 +6,19 @@
 #' @return `[spec]` see `psd::pspectrum`
 #' @export
 pspectrum <- function(x, fs_hz) {
-  suppressMessages(psd::pspectrum(ts(x, frequency = fs_hz)))
+  suppressMessages(psd::pspectrum(stats::ts(x, frequency = fs_hz)))
 }
 
 #' Calculate signal-to-noise ratio from power spectral density
 #'
 #' @param psd `[spec]` power spectral density
 #' @param signal_bpm `[numeric(2)]` signal band (bpm)
 #'
-#' @return
+#' @return `[numeric(1)]`
 #' @export
 s2n <- function(psd, signal_bpm) {
   signal_hz <- signal_bpm / 60
-  is_signal <- between(psd$freq, signal_hz[1], signal_hz[2])
+  is_signal <- dplyr::between(psd$freq, signal_hz[1], signal_hz[2])
   is_noise <- !is_signal
 
   psignal <- pracma::trapz(psd$freq[is_signal], psd$spec[is_signal])