From 6525afd732af525de909f5a69350d3efad735bbf Mon Sep 17 00:00:00 2001 From: chrisholbrook Date: Thu, 19 Sep 2024 23:00:10 -0400 Subject: [PATCH] sneak detection_range_model into 0.8.0 --- DESCRIPTION | 4 +++- NEWS.md | 8 ++++++-- ReadMe.md | 6 ++++++ inst/supplemental_docs/render_supplemental_docs.R | 5 ++++- man/glatos.Rd | 4 ++++ 5 files changed, 23 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 98fc98c3..1ee034e1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Type: Package Title: A package for the Great Lakes Acoustic Telemetry Observation System Description: Functions useful to members of the Great Lakes Acoustic Telemetry Observation System https://glatos.glos.us; many more broadly relevant to simulating, processing, analysing, and visualizing acoustic telemetry data. Version: 0.8.0 -Date: 2024-09-18 +Date: 2024-09-19 Depends: R (>= 3.6.0) Imports: av, @@ -24,6 +24,7 @@ Suggests: ggplot2, gifski, knitr, + mapview, methods, png, purrr, @@ -41,6 +42,7 @@ Authors@R: c( person("Jon", "Pye", role = "aut"), person("Mike", "O'Brien", role = "ctb"), person("Alex", "Nunes", role = "ctb"), + person("Benjamin", "Hlina", role = "ctb"), person("Angela", "Dini", role = "ctb"), person("Ryan", "Gosse", role = "ctb")) License: GPL-2 diff --git a/NEWS.md b/NEWS.md index 547aae6e..2909c85b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,6 @@ ---- -# glatos 0.8.9011 (2024-09-18) +# glatos 0.8.0 (2024-09-19) ## Breaking changes @@ -81,7 +81,7 @@ from earlier versions. - fixes [issue #126](https://github.com/ocean-tracking-network/glatos/issues/126) - fixes [issue #78](https://github.com/ocean-tracking-network/glatos/issues/78) -- New function `jarasterize()` to allow rasterization +- Add new function `jarasterize()` to allow rasterization (esp. with `all_touched = TRUE`) using only `sf` and `raster`. Used by `make_transition()`. @@ -91,6 +91,10 @@ from earlier versions. - In `make_frames()`, allow `terra::SpatVector` input for background map (`bg_map` arg). - add test for `terra::SpatVector` input + +- Add new function `detection_range_model()` for estimating detection range at + which a certain detection efficiency is expected, using output from + Innovasea's range testing software. ### Bug fixes and minor changes diff --git a/ReadMe.md b/ReadMe.md index 53aa575e..9212da72 100644 --- a/ReadMe.md +++ b/ReadMe.md @@ -74,6 +74,11 @@ exported from Innovasea's VUE software. 6. [`REI`](https://github.com/ocean-tracking-network/glatos/blob/main/R/REI.r) calculates the relative activity at each receiver based on number of unique species and individual animals. +7. `detection_range_model` for estimating detection range at which a certain +detection efficiency is expected, using output from Innovasea's range testing +software. + + #### Simulation functions for system design and evaluation 1. [`calc_collision_prob`](https://github.com/ocean-tracking-network/glatos/blob/main/R/sim-calc_collision_prob.r) estimates the probability of collisions for pulse-position-modulation type co-located telemetry transmitters. This is useful for determining the number of fish to release or tag specifications (e.g., delay). @@ -82,6 +87,7 @@ species and individual animals. 3. [`crw_in_polygon`](https://github.com/ocean-tracking-network/glatos/blob/main/R/simutil-crw_in_polygon.r), [`transmit_along_path`](https://github.com/ocean-tracking-network/glatos/blob/main/R/sim-transmit_along_path.r), and [`detect_transmissions`](https://github.com/ocean-tracking-network/glatos/blob/main/R/sim-detect_transmissions.r) individually simulate random fish movement paths within a water body (*crw_in_polygon*: a random walk in a polygon), tag signal transmissions along those paths (*transmit_along_path*: time series and locations of transmissions based on tag specs), and detection of those transmittions by receivers in a user-defined receiver network (*detect_transmissions*: time series and locations of detections based on detection range curve). Collectively, these functions can be used to explore, compare, and contrast theoretical performance of a wide range of transmitter and receiver network designs. + #### Visualization and data exploration 1. [`abacus_plot`](https://github.com/ocean-tracking-network/glatos/blob/main/R/vis-abacus_plot.r) is useful for exploring movement patterns of individual tagged animals through time. diff --git a/inst/supplemental_docs/render_supplemental_docs.R b/inst/supplemental_docs/render_supplemental_docs.R index 7ed05607..0d7fd64b 100644 --- a/inst/supplemental_docs/render_supplemental_docs.R +++ b/inst/supplemental_docs/render_supplemental_docs.R @@ -25,4 +25,7 @@ render(input = "vignettes/data_requirements_vignette.Rmd", output_format = "all") #output format -> make sure html_document is first in Rmd - +render(input = "vignettes/detection_efficiency_vignette.Rmd", + output_dir = "vignettes", + output_format = "all") +#output format -> make sure html_document is first in Rmd diff --git a/man/glatos.Rd b/man/glatos.Rd index 4b6aa0a0..bd389c98 100644 --- a/man/glatos.Rd +++ b/man/glatos.Rd @@ -64,6 +64,9 @@ exported from Innovasea's VUE software. \item \href{https://github.com/ocean-tracking-network/glatos/blob/main/R/summ-residence_index.r}{\code{residence_index}} calculates the relative proportion of time spent at each location. \item \href{https://github.com/ocean-tracking-network/glatos/blob/main/R/REI.r}{\code{REI}} calculates the relative activity at each receiver based on number of unique species and individual animals. +\item \code{detection_range_model} for estimating detection range at which a certain +detection efficiency is expected, using output from Innovasea's range testing +software. } } @@ -122,6 +125,7 @@ Other contributors: \itemize{ \item Mike O'Brien [contributor] \item Alex Nunes [contributor] + \item Benjamin Hlina [contributor] \item Angela Dini [contributor] \item Ryan Gosse [contributor] }