Dev1.2.2.9000

.Rbuildignore

@@ -1,6 +1,7 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^README\.Rmd$
+^README\.html$
 ^README_sync\.Rmd$
 ^_pkgdown\.yml$
 ^docs$
@@ -11,3 +12,6 @@
 ^LICENSE\.md$
 ^LICENSE$
 ^\.github$
+^codecov\.yml$
+^\.travis\.yml$
+^cran-comments\.md$

.github/workflows/check-standard.yaml

@@ -14,8 +14,10 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: windows-latest, r: '3.6'}
           - {os: windows-latest, r: 'release'}
           - {os: windows-latest, r: 'devel'}
+          - {os: macOS-latest, r: '3.6'}
           - {os: macOS-latest, r: 'release'}
           - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
@@ -24,6 +26,8 @@ jobs:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      # don't treat missing suggested packages as error
+      _R_CHECK_FORCE_SUGGESTS_: false
 
     steps:
       - uses: actions/checkout@v2
@@ -54,11 +58,6 @@ jobs:
         # env:
           # RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
         run: |
-          # # # # custom hack to ensure correct version of Matrix for TMB
-          # sudo apt-get install -y --allow-downgrades r-cran-matrix=1.2-18-1focal0
-          # R -e "install.packages('TMB', type = 'source')"
-          # # # # custom hack end
-
           while read -r cmd
           do
             eval sudo $cmd
@@ -76,6 +75,16 @@ jobs:
         run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
+      - name: Run codecov
+        if: runner.os == 'Linux'
+        run: |
+          covr::codecov()
+        shell: Rscript {0}
+
+      - name: Upload coverage to Codecov
+        if: runner.os == 'Linux'
+        uses: codecov/codecov-action@v1
+
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@main

.gitignore

@@ -31,13 +31,15 @@ vignettes/*.pdf
 # Temporary files created by R markdown
 *.utf8.md
 *.knit.md
-man/figures/
-/man/figures/
-man/figures/*.png
-/man/figures/*.png
+# man/figures/
+# /man/figures/
+# man/figures/*.png
+# /man/figures/*.png
 
 # Shiny token, see https://shiny.rstudio.com/articles/shinyapps.html
 rsconnect/
 .Rproj.user
 inst/doc
 debug.log
+
+README.html

.travis.yml

@@ -0,0 +1,9 @@
+# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
+
+language: R
+cache: packages
+addons:
+  apt:
+    packages:
+      - libgit2-dev
+

DESCRIPTION

@@ -1,12 +1,12 @@
 Package: yaps
 Title: Track Estimation using YAPS (Yet Another Positioning Solver)
-Version: 1.2.2
-Authors@R: c(	person("Henrik", "Baktoft", email = "[email protected]", role = c("cre", "aut")),
+Version: 1.2.3
+Authors@R: c(	person("Henrik", "Baktoft", email = "[email protected]", role = c("cre", "aut"), comment=c(ORCID = "0000-0002-3644-4960")),
 				person("Karl", "Gjelland", role=c("aut")),
 				person("Uffe H.", "Thygesen", role=c("aut")),
 				person("Finn", "Økland", role=c("aut"))
 			)
-Description: Estimate track from acoustic data using YAPS.
+Description: Estimate tracks of animals tagged with acoustic transmitters. 'yaps' was introduced in 2017 as a transparent open-source tool to estimate positions of fish (and other aquatic animals) tagged with acoustic transmitters. Based on registrations of acoustic transmitters on hydrophones positioned in a fixed array, 'yaps' enables users to synchronize the collected data (i.e. correcting for drift in the internal clocks of the hydrophones/receivers) and subsequently to estimate tracks of the tagged animals. The paper introducing 'yaps' is available in open access at Baktoft, Gjelland, Økland & Thygesen (2017) <doi:10.1038/s41598-017-14278-z>. Also check out our cookbook with a completely worked through example at Baktoft, Gjelland, Økland, Rehage, Rodemann, Corujo, Viadero & Thygesen (2019) <DOI:10.1101/2019.12.16.877688>. Additional tutorials will eventually make their way onto the project website at <https://baktoft.github.io/yaps/>.
 Depends: R (>= 3.5.0)
 License: GPL-3
 Encoding: UTF-8
@@ -15,8 +15,10 @@ RoxygenNote: 7.1.1
 LinkingTo: Rcpp, TMB, RcppEigen
 Imports: circular, cowplot, data.table, ggplot2, ggrepel, nloptr, plyr, Rcpp, reshape2, splusTimeSeries, stats, tictoc, TMB, viridis, zoo
 Suggests: 
-    testthat (>= 2.1.0),
+    covr,
     knitr,
-    rmarkdown
-URL: https://github.com/baktoft/yaps
+    rmarkdown,
+    testthat (>= 2.1.0),
+    vdiffr
+URL: https://github.com/baktoft/yaps, https://baktoft.github.io/yaps/
 BugReports: https://github.com/baktoft/yaps/issues

NAMESPACE

@@ -2,14 +2,12 @@
 
 export(alignBurstSeq)
 export(applySync)
+export(checkInp)
 export(checkInpSync)
 export(fineTuneSyncModel)
 export(getBbox)
-export(getDatTmb)
-export(getInits)
 export(getInp)
 export(getInpSync)
-export(getParams)
 export(getSyncCoverage)
 export(getSyncModel)
 export(getToaYaps)
@@ -35,6 +33,7 @@ importFrom(data.table,.I)
 importFrom(data.table,.N)
 importFrom(data.table,.SD)
 importFrom(ggplot2,aes)
+importFrom(ggplot2,coord_fixed)
 importFrom(ggplot2,facet_grid)
 importFrom(ggplot2,facet_wrap)
 importFrom(ggplot2,geom_bar)

NEWS.md

@@ -1,3 +1,10 @@
+# yaps v1.2.3
+
+## New stuff
+* Moved example data `hald` to an external package with yaps example data `yapsdata`. Available from github using devtools::install_github('baktoft/yapsdata')
+* Lots of examples and tests added
+
+
 # yaps v1.2.2
 
 ## New stuff
@@ -31,7 +38,7 @@
 * Add option to use alternative optimization function (EXPERIMENTAL). Try nloptr() instead of default nlminb(), if you have issues with e.g. false convergence.
 * Add option to use linear correction information when running the sync model (EXPERIMENTAL).
 * Add option to specify all three ping types in testYaps(). PingType can be 'sbi' (default), 'rbi' or 'pbi'
-* Not related to package development, but check out [yaps-live](https://baktoft.shinyapps.io/yapslive/) to see `yaps` in action.
+* Not related to package development, but check out yaps-live https://baktoft.shinyapps.io/yapslive/ to see `yaps` in action.
 
 
 ## Minor new stuff

R/alignBurstSeq.R

@@ -10,6 +10,7 @@
 #' @param plot_diag Logical indicating if visual diagnosis plots should be created.
 #' return data.table like input, but with extra columns seq_ping_idx and seq_epo
 #' @export
+#' @example man/examples/example-alignBurstSeq.R
 alignBurstSeq <- function(synced_dat, burst_seq, seq_lng_min=10, rbi_min, rbi_max, plot_diag=TRUE){
 	burst_seq_dt <- data.table::data.table(bi=burst_seq)
 	burst_seq_dt[, seq_ping_idx := 1:.N]
@@ -55,7 +56,7 @@ alignBurstSeq <- function(synced_dat, burst_seq, seq_lng_min=10, rbi_min, rbi_ma
 		plot(log(seq_diffs))
 		points(log(seq_diffs[seq_fix_idx]) ~ seq_fix_idx, col="red", pch=20, cex=2)
 
-		plot(synced_dat[, eposync - seq_epo] ~ synced_dat$ts, pch=".", main="NOTE: If the line suddenly shifts, \n tag time drift is too large!")
+		plot(synced_dat[, eposync - seq_epo] ~ synced_dat$ts, pch=".")
 		par(mfrow=c(1,1))
 	}
 

R/applySync.R

@@ -2,6 +2,8 @@
 #' @param toa Object containing data to be synchronized. Typically a `data.table` as e.g. `ssu1$detections`, but can also be a matrix dim=(n_ping, n_hydo).
 #' @param hydros data.table formatted as `ssu1$hydros`
 #' @param sync_model Synchronization model obtained using `getSyncModel()`
+#' @example man/examples/example-yaps_ssu1.R
+
 #' @export
 applySync <- function(toa, hydros="", sync_model){
 	if(is.matrix(toa)) {type <- "toa_matrix"

R/checkInp.R

@@ -1,6 +1,8 @@
 #' Check consistency of `inp` object obtained from `getInp()`
 #' 
 #' @param inp Object obtained using `getInp()`
+#' @export
+#' @example man/examples/example-yaps_ssu1.R
 checkInp <- function(inp){
 
 	stopifnot(ncol(inp$datTmb$toa) == inp$datTmb$np)
@@ -11,5 +13,7 @@ checkInp <- function(inp){
 		stopifnot(dim(inp$datTmb$H)[2] == 3)
 		stopifnot(length(inp$datTmb$z_vec) == inp$datTmb$np)
 	}
+
+	print("checkInp passed!")
 
 }

R/checkInpSync.R

@@ -3,6 +3,7 @@
 #' @inheritParams getInpSync
 #' @param inp_sync Object obtained using `getInpSync()`
 #' @export
+#' @example man/examples/example-yaps_ssu1.R
 checkInpSync <- function(inp_sync, silent_check){
 	# speed of sound stuff
 	if(!silent_check & inp_sync$dat_tmb_sync$ss_data_what != "data"){cat("WARNING: getSyncModel() will estimate speed of sound. It is strongly advised to use data instead!\n")}

R/data.R

@@ -32,34 +32,20 @@
 #' }
 "ssu1"
 
-#' Test data from Lake Hald, Denmark
-#'
-#' 
+
+#' Example data for showcasing yaps function alignBurstSeq()
 #' 
-#' @format A list containing 3 data.tables:
+#' Function alignBurstSeq() is used to align synced detection data with a sequence of known random burst intervals (BI). \cr
+#' This step is needed to take advantage of the extra information available when working with random BI data with a known sequence. \cr
+#' This small sample is obtained from the accompanying data package `yapsdata`.
+#'
+#' @format A list containing 2 items:
 #' \describe{
-#'   \item{hydros}{
-#'     \itemize{
-#'        \item serial Hydrophone serial number.
-#'        \item x,y,z Position of hydrophones in UTM.
-#'        \item sync_tag ID of co-located sync tag. Must be identical to entries in data.table detections$tag.
-#'        \item idx Unique values from 1:nrow(hydros).
-#'      }
-#'   }
-#'   \item{detections}{
-#'     \itemize{
-#'        \item ts Timestamp of detection in POSIXct().
-#'        \item tag ID of detected tag.
-#'        \item epo Timestamp as number of seconds since Unix epoch. Can be obtained using as.numeric(ts).
-#'        \item frac Sub-second part of detection timestamp in fractions of second [0-1].
-#'        \item serial Serial number of detecting hydrophone. Must match entry in data.table hydros.
-#'      }
+#'   \item{synced_dat_1315}{
+#'      data.table containing synced detections of tag 1315.
 #'   }
-#'   \item{gps}{
-#'     \itemize{
-#'        \item ts Timestamp of gps position in POSIXct().
-#'        \item utm_x, utm_y Coordinates of position. Same projection and coordinate system as used in hydros.
-#'      }
+#'   \item{synced_dat_1315}{
+#'      vector of small part of the complete sequence of known random BIs.
 #'   }
 #' }
-"hald"
+"dat_align"

R/fineTuneSyncModel.R

@@ -3,7 +3,9 @@
 #' @param sync_model sync_model obtained using getSyncModel()
 #' @param eps_threshold Maximum value of residual measured in meter assuming speed of sound = 1450 m/s
 #' @param silent logical whether to make getSyncModel() silent
+#' @example man/examples/example-yaps_ssu1.R
 #' @export
+#' @example man/examples/example-yaps_ssu1.R
 fineTuneSyncModel <- function(sync_model, eps_threshold, silent=TRUE){
 	# original inp_sync
 	inp_sync <- sync_model$inp_synced
@@ -42,11 +44,11 @@ fineTuneSyncModel <- function(sync_model, eps_threshold, silent=TRUE){
 	# inp_sync$params_tmb_sync$SLOPE2 				<- sync_model$pl$SLOPE2
 	# inp_sync$params_tmb_sync$SS 					<- sync_model$pl$SS  # Disabled because option to use ss_data is implemented...
 	# inp_sync$params_tmb_sync$LOG_SIGMA_HYDROS_XY	<- sync_model$pl$LOG_SIGMA_HYDROS_XY
-	inp_sync$params_tmb_sync$TRUE_H					<- sync_model$pl$TRUE_H 
-	inp_sync$params_tmb_sync$LOG_SIGMA_TOA			<- sync_model$pl$LOG_SIGMA_TOA
+	# inp_sync$params_tmb_sync$TRUE_H					<- sync_model$pl$TRUE_H 
+	# inp_sync$params_tmb_sync$LOG_SIGMA_TOA			<- sync_model$pl$LOG_SIGMA_TOA
 
 	# run getSyncModel() using the tuned inp_sync
-	sync_model_tuned <- getSyncModel(inp_sync, silent=silent)
+	sync_model_tuned <- getSyncModel(inp_sync, silent=silent, tmb_smartsearch=inp_sync$inp_params$tmb_smartsearch, max_iter=inp_sync$inp_params$max_iter)
 
 	return(sync_model_tuned)
 }

R/getBbox.R

@@ -7,6 +7,7 @@
 #' @param pen Specifies the penalty multiplier.
 #' @inheritParams getInp
 #' @export
+#' @example man/examples/example-bbox.R
 getBbox <- function(hydros, buffer=5, eps=1E-3, pen=1){
 	x_min <- hydros[which.min(hydros$hx), hx] - buffer
 	x_max <- hydros[which.max(hydros$hx), hx] + buffer

R/getToaYaps.R

@@ -3,6 +3,7 @@
 #' @param synced_dat `data.table` containing synchronized data formatted as output from/or obtained using `applySync()`
 #' @inheritParams getInp
 #' @export
+#' @example man/examples/example-yaps_ssu1.R
 getToaYaps <- function(synced_dat, hydros, rbi_min, rbi_max){
 
 	# remove NAs in eposync

R/plotBbox.R

@@ -1,6 +1,7 @@
 #' Graphical representation of spatial constraints
 #' @inheritParams getInp
 #' @export
+#' @example man/examples/example-bbox.R
 plotBbox <- function(hydros, bbox){
 	Var1 <- Var2 <- NULL
 	softplus <- function(x, eps){return (0.5*(x+sqrt(x*x+eps*eps)))	}

R/plotYaps.R

@@ -1,12 +1,14 @@
 #' Basic plots of yaps output
 #' 
-#' @param inp Input object obtained using \code{getInp()}
 #' @param yaps_out Output from succesful run of \code{runYaps()}
 #' @param type Plot type. \code{type="map"} prodces a basic map of estimated track and hydrophones; \code{type="coord_X"}, \code{type="coord_Y"} produces plots of X and Y coordinated including +- 1 standard error.
 #' @param xlim,ylim Optional vectors of length 2 to set xlim and/or ylim. 
 #' @param main Title of plot - optional.
 #' @export
-plotYaps <- function(inp, yaps_out, type="map", xlim=NULL, ylim=NULL, main=NULL){
+#' @example man/examples/example-plotYaps.R
+plotYaps <- function(yaps_out, type="map", xlim=NULL, ylim=NULL, main=NULL){
+	inp <- yaps_out$inp
+
 	pl <- yaps_out$pl
 	plsd <- yaps_out$plsd
 

R/prepFiles.R

@@ -1,7 +1,10 @@
-#' Prepare detections data.table from raw data - csv-files exported from vendor software
+#' Experimental! Prepare detections data.table from raw data - csv-files exported from vendor software
 #' @param raw_dat Data file from vendor supplied software
 #' @param type Type of the vendor file. Currently only 'vemco_vue' is supported.
 #' @export
+#' @examples \dontrun{
+#' prepped_detections <- prepDetection("path-to-raw-data-file", type="vemco_vue")
+#' }
 prepDetections <- function(raw_dat, type){
 	detections <- data.table::data.table()
 	if (type == "vemco_vue"){