version 0.0.1

DESCRIPTION

@@ -0,0 +1,30 @@
+Package: mort
+Title: Identifying Potential Mortalities and Expelled Tags in Aquatic
+        Acoustic Telemetry Arrays
+Version: 0.0.1
+Authors@R: c(
+    person("Rosie", "Smith", , "rosieluain@gmail.com", role = c("aut", "cre", "cph"),
+           comment = c(ORCID = "0000-0003-2675-4452")),
+    person("Heidi", "Swanson", role = "fnd")
+  )
+Description: A toolkit for identifying potential mortalities and expelled tags in aquatic acoustic telemetry arrays. 
+    Designed for arrays with non-overlapping receivers. 
+License: GPL (>= 3)
+Encoding: UTF-8
+URL: https://github.com/rosieluain/mort,
+        https://rosieluain.github.io/mort/
+BugReports: https://github.com/rosieluain/mort/issues
+RoxygenNote: 7.2.3
+LazyData: true
+Imports: lubridate, methods, rlang
+Suggests: ggplot2, knitr, plotly, rmarkdown, testthat (>= 3.0.0)
+VignetteBuilder: knitr
+Depends: R (>= 3.5.0)
+Config/testthat/edition: 3
+NeedsCompilation: no
+Packaged: 2023-09-02 17:53:51 UTC; rosie
+Author: Rosie Smith [aut, cre, cph] (<https://orcid.org/0000-0003-2675-4452>),
+  Heidi Swanson [fnd]
+Maintainer: Rosie Smith <rosieluain@gmail.com>
+Repository: CRAN
+Date/Publication: 2023-09-04 09:00:02 UTC

MD5

@@ -0,0 +1,85 @@
+029f94b0ae61ff6245090ff24d6273ee *DESCRIPTION
+d828fc95e1ca9cebdc78dc81d440f554 *NAMESPACE
+1ceaa516aabe7961b7cf0b1f945243f8 *NEWS.md
+b494f2731d8431c7adf234e4b62cb285 *R/data.R
+cdb756bbd86d89e289891f5a1acbec53 *R/helper.R
+edff660648ccb7da73f7044492283ffc *R/mort.R
+685ddac1dc4711a88fbd5f2b1090f853 *R/options.R
+0ade5db5d30ea7e2d4305a943999f48c *R/plot.R
+22181625a1b0bc0d7ae26d3589db0b4c *R/residences.R
+0b7e8fb12645394a97981bcef2d2bcde *R/review.R
+551f305e720430e85139c2afd0a5a4ee *R/stationchange.R
+488965bcd80ef54b79589b6924eab750 *README.md
+f955bb4f6520270611cf13cea280cbe1 *build/vignette.rds
+6ff1355f479f60c629ca9f9004f3c9df *data/ddd.rda
+6ffeb1d8e114f1134282f80fd4fd8096 *data/detections.rda
+3f13e2b93534f2b413d49983c5f5e886 *data/events.rda
+1f96ced813fcb1574140b2044efd9860 *data/new.data.rda
+f7bb40b1fac19b4967572f0a5cdc2150 *data/seasons.rda
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+1a5a2d49e769f6b04bf71f7b2e20d991 *inst/doc/a3_drift.R
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+a87b01ccbfd4494d4422fe206461cdd2 *inst/doc/a4_season.html
+9fe6d07576603ba5bcec5706fb6fc1ca *inst/doc/a5_plots.R
+07b5683f0b0b22e3bbcafef20b1beb0d *inst/doc/a5_plots.Rmd
+d53998594c7c736963f3592336c4b00e *inst/doc/a5_plots.html
+b1b8a5008610c6f7d30ec6b477923843 *inst/doc/a6_digging.R
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+7b59224fc8a31a341a77219867d41ab2 *inst/doc/a6_digging.html
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+bf6abae5eb102db1be3b39b0a17d7ec3 *man/backwards.Rd
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+22585b1aa4853afb16b01a0642afe170 *man/detections.Rd
+186caeb1fcce856bcfedacddfe1f071c *man/drift.Rd
+2a4e34dd8732f5321a99571ff6ebaf22 *man/events.Rd
+9f37b603f442d7f3cee6d07bc590fd35 *man/figures/hex-mort.png
+ad17d261ae700596a4b7a0d5a080e8ea *man/figures/interactive_plot_ex.png
+3ff2c6c71b0aa769792d2189a0df5dc9 *man/figures/logo.png
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+a335c01b3e4315b2b798091460adeb34 *tests/testthat.R
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+74cc3a31d9e25ea8b6e2cbb4dbb87930 *tests/testthat/fixtures/ssn_Ymd.rds
+4c194e558e404aa1de22b5f671103be3 *tests/testthat/fixtures/ssn_ddmm.rds
+05e02376d64e3b64f71075c357c3db2f *tests/testthat/fixtures/stnchange.rds
+e5fce82f41987b9fee6797cdc6a07b4e *tests/testthat/test-helper.R
+f22c76100432b54a23f81daaf3075aaf *tests/testthat/test-mort.R
+fb3ed3ead42647c293e972f24c4d4644 *tests/testthat/test-options.R
+d7e886f9944f18f3e24cc54e78255cbf *tests/testthat/test-residences.R
+7bd04be4df4a86c9e00398a5abf29627 *tests/testthat/test-review.R
+cc12796c48c30be8ab4bf1ba562d07c3 *tests/testthat/test-stationchange.R
+e86f4abd7210037e31b57b6b0a02bdd0 *vignettes/a1_data-prep.Rmd
+0ae5b89d349711829c4ac9dc07ae8f6d *vignettes/a2_morts.Rmd
+2373cd5b563634987464d2348f55dddf *vignettes/a3_drift.Rmd
+795a9c48ddb36fbc26c9cc442be7c363 *vignettes/a4_season.Rmd
+07b5683f0b0b22e3bbcafef20b1beb0d *vignettes/a5_plots.Rmd
+8265ec9d2e67a7c95efb591e6b5b2e94 *vignettes/a6_digging.Rmd
+87b4b6213e8cc4d22e71fd194be637b9 *vignettes/a7_review.Rmd

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(backwards)
+export(drift)
+export(infrequent)
+export(morts)
+export(mortsplot)
+export(residences)
+export(resmax)
+export(resmaxcml)
+export(review)
+export(season)
+export(stationchange)
+import(lubridate)
+import(methods)
+importFrom(lubridate,hms)
+importFrom(lubridate,period_to_seconds)
+importFrom(methods,is)
+importFrom(rlang,.data)
+importFrom(stats,na.omit)
+importFrom(utils,setTxtProgressBar)
+importFrom(utils,txtProgressBar)

NEWS.md

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+# mort 0.0.1
+
+* Added a `NEWS.md` file to track changes to the package.

R/data.R

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+#'Sample acoustic telemetry detection data
+#'
+#'These detection data were subset from a real acoustic telemetry dataset of Arctic
+#'Char near Kugluktuk, Nunavut. The data were from a project that was a
+#'collaboration between the Kugluktuk Hunters and Trappers Organization, the
+#'University of Waterloo, and Fisheries and Oceans Canada. The data are valuable
+#'to the community of Kugluktuk, and are also sensitive due to their pertinence
+#'to the local fishery for Arctic Char. For this reason, the detections have been
+#'given generic station names and fish IDs so locations and sample information
+#'is anonymous. The year has also been changed, but otherwise, the detections are
+#'real, and therefore have all the challenges and intricacies of biological
+#'data.
+#'
+#'The variables are as follows:
+#'
+#'\itemize{
+#'\item DateTimeUTC. The date and time of each detection, in POSIXct format. The
+#'data are in UTC, as downloaded from the receivers.
+#'\item Station.Name Name of the receiver location.
+#'\item ID Unique ID of the fish.
+#'}
+#'
+#'@docType data
+#'@keywords datasets
+#'@name detections
+#'@usage data(detections)
+#'@format A data frame with 447 627 rows (observations) and 3 variables.
+NULL
+
+#'Sample residence events
+#'
+#'Events generated from the sample detection file provided. Events were generated
+#'using the residences() function in mort.
+#'
+#'The detection data were subset from a real acoustic telemetry dataset of Arctic
+#'Char near Kugluktuk, Nunavut. The data were from a project that was a
+#'collaboration between the Kugluktuk Hunters and Trappers Organization, the
+#'University of Waterloo, and Fisheries and Oceans Canada. The data are valuable
+#'to the community of Kugluktuk, and are also sensitive due to their pertinence
+#'to the local fishery for Arctic Char. For this reason, the detections have been
+#'given generic station names and fish IDs so locations and sample information
+#'is anonymous. The year has also been changed, but otherwise, the detections are
+#'real, and therefore have all the challenges and intricacies of biological
+#'data.
+#'
+#'The variables are as follows:
+#'
+#'\itemize{
+#'\item ResidenceStart. The start time of the residence events, in POSIXct.
+#'\item Station.Name. Name of the receiver location.
+#'\item ID. Unique ID of the fish.
+#'\item ResidenceEnd. The end time of the residence events, in POSIXct.
+#'\item ResidenceLength.days. The duration of the residence events. The units are
+#'days, as indicated by the variable name (which is automatically generated
+#'by mort::residences())
+#'}
+#'
+#'@docType data
+#'@keywords datasets
+#'@name events
+#'@usage data(events)
+#'@format A data frame with 11 487 rows (events) and 5 variables.
+NULL
+
+#'Sample dead drift direction dataframe
+#'
+#'The locations have been given generic station names, due to the sensitive nature
+#'of the dataset. The connections between stations (i.e., which stations are
+#'connected by drift and in which direction) are real.
+#'
+#'The variables are as follows:
+#'
+#'\itemize{
+#'\item From. The station where a tag may drift from.
+#'\item To. The station where a tag may drift to, from the station in From.
+#'}
+#'
+#'@docType data
+#'@keywords datasets
+#'@name ddd
+#'@usage data(ddd)
+#'@format A data frame with 18 rows and 2 variables.
+NULL
+
+#'Ice-free seasons
+#'
+#'The year has been changed, due to the sensitive nature of the dataset. The
+#'years have been changed in the same manner as the detection dates, so
+#'the ice-free dates correspond to the dataset in the same way as the original
+#'dataset.
+#'
+#'The variables are as follows:
+#'
+#'\itemize{
+#'\item Start. The date of ice break-up (the start of the period of interest).
+#'\item End. The date of ice freeze-up (the end of the period of interest).
+#'}
+#'
+#'@docType data
+#'@keywords datasets
+#'@name seasons
+#'@usage data(seasons)
+#'@format A data frame with 5 rows (years) and 2 variables.
+NULL
+
+#'Example of new acoustic telemetry detection data
+#'
+#'These are fabricated detection data to demonstrate the use of the review
+#'function.
+#'
+#'The variables are as follows:
+#'
+#'\itemize{
+#'\item ResidenceStart. The start time of the residence events, in POSIXct.
+#'\item Station.Name. Name of the receiver location.
+#'\item ID. Unique ID of the fish.
+#'\item ResidenceEnd. The end time of the residence events, in POSIXct.
+#'\item ResidenceLength.days. The duration of the residence events. The units are
+#'days, as indicated by the variable name (which is automatically generated
+#'by mort::residences())
+#'}
+#'
+#'@docType data
+#'@keywords datasets
+#'@name new.data
+#'@usage data(new.data)
+#'@format A data frame with 35 rows (observations) and 3 variables.
+NULL