diff --git a/DESCRIPTION b/DESCRIPTION index c503026c..0abaacd5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -7,7 +7,8 @@ Date: 2024-01-04 Depends: R (>= 3.5.0) Imports: av, - data.table, + data.table, + dplyr, fasterize, fasttime, gdalUtilities, @@ -20,7 +21,6 @@ Imports: magrittr, methods, plotrix, - plyr, purrr, raster, readxl, @@ -52,4 +52,4 @@ RoxygenNote: 7.2.3 VignetteBuilder: knitr Encoding: UTF-8 Roxygen: list(markdown = TRUE) -Config/testthat/edition: 3 \ No newline at end of file +Config/testthat/edition: 3 diff --git a/man/REI.Rd b/man/REI.Rd index 16f31a17..77c5bd22 100644 --- a/man/REI.Rd +++ b/man/REI.Rd @@ -42,16 +42,17 @@ REI = (Tr/Ta) x (Sr/Sa) x (DDr/DDa) x (Da/Dr) } \examples{ det_file <- system.file("extdata", "hfx_detections.csv", -package = "glatos") + package = "glatos" +) dep_file <- system.file("extdata", "hfx_deployments.csv", - package = "glatos") + package = "glatos" +) hfx_deployments <- glatos::read_otn_deployments(dep_file) dets <- glatos::read_otn_detections(det_file) -hfx_receiver_efficiency_index <- glatos::REI(dets,hfx_deployments) - +hfx_receiver_efficiency_index <- glatos::REI(dets, hfx_deployments) } \author{ diff --git a/man/abacus_plot.Rd b/man/abacus_plot.Rd index cfb38e6d..2f362898 100644 --- a/man/abacus_plot.Rd +++ b/man/abacus_plot.Rd @@ -117,63 +117,77 @@ optional graphical parameters to "points" (see ?points). } \examples{ -#get path to example detection file +# get path to example detection file det_file <- system.file("extdata", "walleye_detections.csv", - package = "glatos") + package = "glatos" +) det <- read_glatos_detections(det_file) -#subset one transmitter +# subset one transmitter det2 <- det[det$animal_id == 153, ] -#plot without control table and main tile and change color to red -abacus_plot(det2, locations=NULL, - main = "TagID: 32054", col = "red") +# plot without control table and main tile and change color to red +abacus_plot(det2, + locations = NULL, + main = "TagID: 32054", col = "red" +) -#example with locations specified -abacus_plot(det2, locations=c("DRF", "DRL", "FMP", "MAU", "PRS", "RAR", - "DRM", "FDT"), main = "TagID: 32054", col = "red") +# example with locations specified +abacus_plot(det2, locations = c( + "DRF", "DRL", "FMP", "MAU", "PRS", "RAR", + "DRM", "FDT" +), main = "TagID: 32054", col = "red") -#plot with custom y-axis label and lines connecting symbols -abacus_plot(det2, main = "TagID: 32054", type = "o", pch = 20, col = "red") +# plot with custom y-axis label and lines connecting symbols +abacus_plot(det2, main = "TagID: 32054", type = "o", pch = 20, col = "red") -#plot with custom x-axis resolution - 10 bins +# plot with custom x-axis resolution - 10 bins abacus_plot(det2, main = "TagID: 32054", x_res = 10) -#plot with custom x-axis resolution - monthly bins +# plot with custom x-axis resolution - monthly bins abacus_plot(det2, main = "TagID: 32054", x_res = "month") -#plot with custom x-axis resolution - 8-week bins +# plot with custom x-axis resolution - 8-week bins abacus_plot(det2, main = "TagID: 32054", x_res = "8 weeks") -#plot with custom x-axis format +# plot with custom x-axis format abacus_plot(det2, main = "TagID: 32054", x_res = "months", x_format = "\%b-\%y") -#plot with custom x axis limits +# plot with custom x axis limits xLim <- as.POSIXct(c("2012-01-01", "2014-01-01"), tz = "UTC") abacus_plot(det2, main = "TagID: 32054", xlim = xLim) -#example with receiver locations +# example with receiver locations # get example receiver location data rec_file <- system.file("extdata", "sample_receivers2.csv", - package = "glatos") + package = "glatos" +) rec <- read_glatos_receivers(rec_file) -abacus_plot(det2, locations=c("DRF", "DRL", "FMP", "MAU", "PRS", "RAR", - "DRM", "FDT"), receiver_history = rec, - main = "TagID: 32054", col = "red") - -#example with grey box plotted in background (using panel.first) +abacus_plot(det2, + locations = c( + "DRF", "DRL", "FMP", "MAU", "PRS", "RAR", + "DRM", "FDT" + ), receiver_history = rec, + main = "TagID: 32054", col = "red" +) + +# example with grey box plotted in background (using panel.first) -#set time range covered by rectangle +# set time range covered by rectangle rect_x_rng <- as.POSIXct(c("2012-07-31", "2013-04-15"), tz = "UTC") -#get number of unique locations (y-axis) +# get number of unique locations (y-axis) n_locs <- length(unique(det2$glatos_array)) -#plot as grey box in background -abacus_plot(det2, locations=NULL, - main = "TagID: 32054", col = "red", - panel.first = rect(rect_x_rng[1], 1, rect_x_rng[2], n_locs, col = "grey", - border = NA)) +# plot as grey box in background +abacus_plot(det2, + locations = NULL, + main = "TagID: 32054", col = "red", + panel.first = rect(rect_x_rng[1], 1, rect_x_rng[2], n_locs, + col = "grey", + border = NA + ) +) } \author{ diff --git a/man/adjust_playback_time.Rd b/man/adjust_playback_time.Rd index 476048bf..50fddd73 100644 --- a/man/adjust_playback_time.Rd +++ b/man/adjust_playback_time.Rd @@ -50,7 +50,6 @@ specifying a different file extension in \code{output}. Input argument 'ffmpeg' was removed in glatos version 0.7.0. } \examples{ - \dontrun{ # load example frames @@ -58,34 +57,42 @@ frames <- system.file("extdata", "frames", package = "glatos") # make video animation out_file <- file.path(tempdir(), "animation_av.mp4") -make_video(input_dir = frames, - input_ext = ".png", - output = out_file) +make_video( + input_dir = frames, + input_ext = ".png", + output = out_file +) # slow video down by a factor of 10 path <- file.path(tempdir(), "animation_av.mp4") -adjust_playback_time(scale_factor = 10, - input = path, - output_dir = tempdir(), - output = "animation_av_slow.mp4", - diagnostic_mode = FALSE, - overwrite = TRUE) +adjust_playback_time( + scale_factor = 10, + input = path, + output_dir = tempdir(), + output = "animation_av_slow.mp4", + diagnostic_mode = FALSE, + overwrite = TRUE +) # slow video down by a factor of 10 and change format of output video -adjust_playback_time(scale_factor = 10, - input = path, - output_dir = tempdir(), - output = "animation_av_slow.wmv", - diagnostic_mode = FALSE, - overwrite = TRUE) +adjust_playback_time( + scale_factor = 10, + input = path, + output_dir = tempdir(), + output = "animation_av_slow.wmv", + diagnostic_mode = FALSE, + overwrite = TRUE +) # speed up video -adjust_playback_time(scale_factor = 0.5, - input = path, - output_dir = tempdir(), - output = "animation_av_fast.mp4", - diagnostic_mode = FALSE, - overwrite = TRUE) +adjust_playback_time( + scale_factor = 0.5, + input = path, + output_dir = tempdir(), + output = "animation_av_fast.mp4", + diagnostic_mode = FALSE, + overwrite = TRUE +) } } diff --git a/man/check_vdat.Rd b/man/check_vdat.Rd index 48e07607..3f7c6a4c 100644 --- a/man/check_vdat.Rd +++ b/man/check_vdat.Rd @@ -19,21 +19,18 @@ Character string with command for calling VDAT.exe via Check path to Innovasea program VDAT.exe } \examples{ - \dontrun{ -#use Windows system PATH variable +# use Windows system PATH variable check_vdat() -#use path to directory containing VDAT.exe +# use path to directory containing VDAT.exe check_vdat(vdat_exe_path = "C:/Program Files/Innovasea/Fathom") -#use full path to VDAT.exe +# use full path to VDAT.exe check_vdat(vdat_exe_path = "C:/Program Files/Innovasea/Fathom/VDAT.exe") - - } } diff --git a/man/check_vue.Rd b/man/check_vue.Rd index 2c9ee41b..dc254ceb 100644 --- a/man/check_vue.Rd +++ b/man/check_vue.Rd @@ -19,20 +19,18 @@ Character string with command for calling VUE.exe via Check path to Innovasea program VUE.exe } \examples{ - \dontrun{ -#use Windows system PATH variable +# use Windows system PATH variable check_vue() -#use path to directory containing VUE.exe +# use path to directory containing VUE.exe check_vue(vue_exe_path = "C:/Program Files (x86)/VEMCO/VUE") -#use full path to VUE.exe +# use full path to VUE.exe check_vue(vue_exe_path = "C:/Program Files (x86)/VEMCO/VUE/VUE.exe") - } } diff --git a/man/convert_glatos_to_att.Rd b/man/convert_glatos_to_att.Rd index 27d91834..b745720b 100644 --- a/man/convert_glatos_to_att.Rd +++ b/man/convert_glatos_to_att.Rd @@ -40,11 +40,13 @@ in a comment by Ryan Gosse. library(glatos) wal_det_file <- system.file("extdata", "walleye_detections.csv", - package = "glatos") + package = "glatos" +) walleye_detections <- read_glatos_detections(wal_det_file) # load walleye data rec_file <- system.file("extdata", "sample_receivers.csv", - package = "glatos") + package = "glatos" +) rcv <- read_glatos_receivers(rec_file) # load receiver data ATTdata <- convert_glatos_to_att(walleye_detections, rcv) diff --git a/man/convert_otn_erddap_to_att.Rd b/man/convert_otn_erddap_to_att.Rd index 48158ed9..ba0d3b46 100644 --- a/man/convert_otn_erddap_to_att.Rd +++ b/man/convert_otn_erddap_to_att.Rd @@ -54,31 +54,37 @@ that this only contains public data. library(glatos) -#get path to example files from OTN ERDDAP +# get path to example files from OTN ERDDAP ani_erd_file <- system.file("extdata", "otn_aat_animals.csv", - package = "glatos") + package = "glatos" +) animals <- read.csv(ani_erd_file) # load the CSVs from ERDDAP tags_erd_file <- system.file("extdata", "otn_aat_tag_releases.csv", - package = "glatos") + package = "glatos" +) tags <- read.csv(tags_erd_file) rcv_erd_file <- system.file("extdata", "otn_aat_receivers.csv", - package = "glatos") + package = "glatos" +) stations <- read.csv(rcv_erd_file) -#Remove first row; (blank or metadata about the column) -animals <- animals[-1,] -tags <- tags[-1,] -stations <- stations[-1,] +# Remove first row; (blank or metadata about the column) +animals <- animals[-1, ] +tags <- tags[-1, ] +stations <- stations[-1, ] -#get blue shark example data +# get blue shark example data shrk_det_file <- system.file("extdata", "blue_shark_detections.csv", - package = "glatos") + package = "glatos" +) blue_shark_detections <- read_otn_detections(shrk_det_file) # load shark data -ATTdata <- convert_otn_erddap_to_att(blue_shark_detections, - tags, stations, animals) +ATTdata <- convert_otn_erddap_to_att( + blue_shark_detections, + tags, stations, animals +) } \author{ Ryan Gosse diff --git a/man/convert_otn_to_att.Rd b/man/convert_otn_to_att.Rd index c3360aa8..0d3a0bf8 100644 --- a/man/convert_otn_to_att.Rd +++ b/man/convert_otn_to_att.Rd @@ -59,11 +59,14 @@ in a comment by Ryan Gosse. library(glatos) dets_path <- system.file("extdata", "blue_shark_detections.csv", - package = "glatos") + package = "glatos" +) deploy_path <- system.file("extdata", "hfx_deployments.csv", - package = "glatos") + package = "glatos" +) tag_path <- system.file("extdata", "otn_nsbs_tag_metadata.xls", - package = "glatos") + package = "glatos" +) dets <- read_otn_detections(dets_path) tags <- prepare_tag_sheet(tag_path, 5, 2) @@ -77,11 +80,14 @@ ATTdata <- convert_otn_to_att(dets, tags, deploymentObj = deploy) library(glatos) dets_path <- system.file("extdata", "blue_shark_detections.csv", - package = "glatos") + package = "glatos" +) deploy_path <- system.file("extdata", "hfx_deploy_simplified.xlsx", - package = "glatos") + package = "glatos" +) tag_path <- system.file("extdata", "otn_nsbs_tag_metadata.xls", - package = "glatos") + package = "glatos" +) dets <- read_otn_detections(dets_path) tags <- prepare_tag_sheet(tag_path, 5, 2) diff --git a/man/crw.Rd b/man/crw.Rd index 04f6836c..c5c822a2 100644 --- a/man/crw.Rd +++ b/man/crw.Rd @@ -44,9 +44,11 @@ to obtain the simualted path. Adapted from code provided by Tom Binder. } \examples{ -foo <- crw(theta=c(0,5), stepLen=10, initPos=c(0,0), initHeading=0, - nsteps=10) -plot(foo,type="o",pch=20,asp=c(1,1)) +foo <- crw( + theta = c(0, 5), stepLen = 10, initPos = c(0, 0), initHeading = 0, + nsteps = 10 +) +plot(foo, type = "o", pch = 20, asp = c(1, 1)) } \author{ diff --git a/man/crw_in_polygon.Rd b/man/crw_in_polygon.Rd index 77bd4c5b..fca0b6ec 100644 --- a/man/crw_in_polygon.Rd +++ b/man/crw_in_polygon.Rd @@ -93,84 +93,104 @@ River system. \examples{ # Example 1 - data.frame input -mypolygon <- data.frame(x = c(-50,-50, 50, 50), y = c(-50,50,50,-50)) +mypolygon <- data.frame(x = c(-50, -50, 50, 50), y = c(-50, 50, 50, -50)) -path_df <- crw_in_polygon(mypolygon, theta = c(0, 20), stepLen = 10, - initPos=c(0,0), initHeading=0, nsteps=50, sp_out = FALSE) +path_df <- crw_in_polygon(mypolygon, + theta = c(0, 20), stepLen = 10, + initPos = c(0, 0), initHeading = 0, nsteps = 50, sp_out = FALSE +) -class(path_df) #note object is data.frame +class(path_df) # note object is data.frame -plot(path_df, type = "o", pch = 20, asp = c(1,1), - xlim = range(mypolygon$x), ylim = range(mypolygon$y)) +plot(path_df, + type = "o", pch = 20, asp = c(1, 1), + xlim = range(mypolygon$x), ylim = range(mypolygon$y) +) polygon(mypolygon, border = "red") # Example 2 - data.frame input; input CRS specified -mypolygon <- data.frame(x = c(-84,-85, -85, -84), - y = c(45, 44, 45, 45)) -path_df <- crw_in_polygon(mypolygon, - theta = c(0, 20), - stepLen = 1000, - initPos = c(-84.75, 44.75), - initHeading = 0, - nsteps = 50, - inputCRS = 4326, - cartesianCRS = 3175, - sp_out = FALSE) -plot(path_df, type = "o", pch = 20, asp = c(1,1), - xlim = range(mypolygon$x), ylim = range(mypolygon$y)) -class(path_df) #note object is data.frame +mypolygon <- data.frame( + x = c(-84, -85, -85, -84), + y = c(45, 44, 45, 45) +) +path_df <- crw_in_polygon(mypolygon, + theta = c(0, 20), + stepLen = 1000, + initPos = c(-84.75, 44.75), + initHeading = 0, + nsteps = 50, + inputCRS = 4326, + cartesianCRS = 3175, + sp_out = FALSE +) +plot(path_df, + type = "o", pch = 20, asp = c(1, 1), + xlim = range(mypolygon$x), ylim = range(mypolygon$y) +) +class(path_df) # note object is data.frame polygon(mypolygon, border = "red") # Example 3 - sf POLYGON input data(great_lakes_polygon) -#simulate in great lakes polygon +# simulate in great lakes polygon path_sf <- crw_in_polygon(great_lakes_polygon, - theta = c(0, 25), - stepLen = 10000, - initHeading = 0, - nsteps = 100, - cartesianCRS = 3175) + theta = c(0, 25), + stepLen = 10000, + initHeading = 0, + nsteps = 100, + cartesianCRS = 3175 +) -#plot +# plot plot(sf::st_geometry(great_lakes_polygon), - col = "lightgrey", - border = "grey") + col = "lightgrey", + border = "grey" +) points(sf::st_coordinates(path_sf), type = "o", pch = 20, col = "red") -#zoom in -plot(sf::st_geometry(great_lakes_polygon), col = "lightgrey", - xlim = sf::st_bbox(path_sf)[c("xmin", "xmax")], - ylim = sf::st_bbox(path_sf)[c("ymin", "ymax")]) -points(sf::st_coordinates(path_sf),type="o", pch = 20, col = "red") +# zoom in +plot(sf::st_geometry(great_lakes_polygon), + col = "lightgrey", + xlim = sf::st_bbox(path_sf)[c("xmin", "xmax")], + ylim = sf::st_bbox(path_sf)[c("ymin", "ymax")] +) +points(sf::st_coordinates(path_sf), type = "o", pch = 20, col = "red") # Example 4 - SpatialPolygonsDataFrame input data(greatLakesPoly) -#simulate in great lakes polygon -path_sp <- crw_in_polygon(greatLakesPoly, - theta = c(0, 25), - stepLen = 10000, - initHeading = 0, - nsteps = 100, - cartesianCRS = 3175, - sp_out = TRUE) +# simulate in great lakes polygon +path_sp <- crw_in_polygon(greatLakesPoly, + theta = c(0, 25), + stepLen = 10000, + initHeading = 0, + nsteps = 100, + cartesianCRS = 3175, + sp_out = TRUE +) -#plot +# plot plot(sf::st_as_sfc(greatLakesPoly), col = "lightgrey", border = "grey") -points(sf::st_coordinates(sf::st_as_sf(path_sp)), type = "o", pch = 20, - col = "red") - -#zoom in -plot(sf::st_as_sfc(greatLakesPoly), col = "lightgrey", border = "grey", - xlim = sf::st_bbox(path_sp)[c("xmin", "xmax")], - ylim = sf::st_bbox(path_sp)[c("ymin", "ymax")]) -points(sf::st_coordinates(sf::st_as_sf(path_sp)), type = "o", pch = 20, - col = "red") +points(sf::st_coordinates(sf::st_as_sf(path_sp)), + type = "o", pch = 20, + col = "red" +) + +# zoom in +plot(sf::st_as_sfc(greatLakesPoly), + col = "lightgrey", border = "grey", + xlim = sf::st_bbox(path_sp)[c("xmin", "xmax")], + ylim = sf::st_bbox(path_sp)[c("ymin", "ymax")] +) +points(sf::st_coordinates(sf::st_as_sf(path_sp)), + type = "o", pch = 20, + col = "red" +) } \seealso{ diff --git a/man/detect_transmissions.Rd b/man/detect_transmissions.Rd index e67be6e4..015ea514 100644 --- a/man/detect_transmissions.Rd +++ b/man/detect_transmissions.Rd @@ -98,105 +98,123 @@ This function was written to be used along with } \examples{ -#Example 1 - data.frame input (make a simple path in polygon) +# Example 1 - data.frame input (make a simple path in polygon) -mypoly <- data.frame(x = c(0, 0, 1000, 1000), - y = c(0, 1000, 1000, 0)) +mypoly <- data.frame( + x = c(0, 0, 1000, 1000), + y = c(0, 1000, 1000, 0) +) + +mypath <- crw_in_polygon(mypoly, + stepLen = 100, + nsteps = 50, + sp_out = FALSE +) -mypath <- crw_in_polygon(mypoly, - stepLen = 100, - nsteps = 50, - sp_out = FALSE) - plot(mypath, type = "l", xlim = c(0, 1000), ylim = c(0, 1000)) -#add receivers +# add receivers recs <- expand.grid(x = c(250, 750), y = c(250, 750)) points(recs, pch = 15, col = "blue") -#simulate tag transmissions -mytrns <- transmit_along_path(mypath, vel = 2.0, delayRng = c(60, 180), - burstDur = 5.0, sp_out = FALSE) -points(mytrns, pch = 21) #add to plot +# simulate tag transmissions +mytrns <- transmit_along_path(mypath, + vel = 2.0, delayRng = c(60, 180), + burstDur = 5.0, sp_out = FALSE +) +points(mytrns, pch = 21) # add to plot -#Define detection range function (to pass as detRngFun) +# Define detection range function (to pass as detRngFun) # that returns detection probability for given distance # assume logistic form of detection range curve where # dm = distance in meters # b = intercept and slope -pdrf <- function(dm, b=c(0.5, -1/120)){ - p <- 1/(1+exp(-(b[1]+b[2]*dm))) +pdrf <- function(dm, b = c(0.5, -1 / 120)) { + p <- 1 / (1 + exp(-(b[1] + b[2] * dm))) return(p) } -pdrf(c(100,200,300,400,500)) #view detection probs. at some distances - -#simulate detection -mydtc <- detect_transmissions(trnsLoc = mytrns, - recLoc = recs, - detRngFun = pdrf, - sp_out = FALSE) - +pdrf(c(100, 200, 300, 400, 500)) # view detection probs. at some distances + +# simulate detection +mydtc <- detect_transmissions( + trnsLoc = mytrns, + recLoc = recs, + detRngFun = pdrf, + sp_out = FALSE +) + points(mydtc[, c("trns_x", "trns_y")], pch = 21, bg = "red") -#link transmitter and receiver locations for each detection\ -with(mydtc, segments(x0 = trns_x, - y0 = trns_y, - x1 = rec_x, - y1 = rec_y, - col = "red")) - - -#Example 2 - spatial (sf) input +# link transmitter and receiver locations for each detection\ +with(mydtc, segments( + x0 = trns_x, + y0 = trns_y, + x1 = rec_x, + y1 = rec_y, + col = "red" +)) + + +# Example 2 - spatial (sf) input data(great_lakes_polygon) set.seed(610) -mypath <- crw_in_polygon(great_lakes_polygon, - stepLen = 100, - initPos = c(-83.7, 43.8), - initHeading = 0, - nsteps = 50, - cartesianCRS = 3175) - +mypath <- crw_in_polygon(great_lakes_polygon, + stepLen = 100, + initPos = c(-83.7, 43.8), + initHeading = 0, + nsteps = 50, + cartesianCRS = 3175 +) + plot(sf::st_geometry(mypath), type = "l") -#add receivers -recs <- expand.grid(x = c(-83.705, -83.70), - y = c(43.810, 43.815)) +# add receivers +recs <- expand.grid( + x = c(-83.705, -83.70), + y = c(43.810, 43.815) +) points(recs, pch = 15, col = "blue") -#simulate tag transmissions -mytrns <- transmit_along_path(mypath, vel = 2.0, delayRng = c(60, 180), - burstDur = 5.0) -points(sf::st_coordinates(mytrns), pch = 21) #add to plot +# simulate tag transmissions +mytrns <- transmit_along_path(mypath, + vel = 2.0, delayRng = c(60, 180), + burstDur = 5.0 +) +points(sf::st_coordinates(mytrns), pch = 21) # add to plot -#Define detection range function (to pass as detRngFun) +# Define detection range function (to pass as detRngFun) # that returns detection probability for given distance # assume logistic form of detection range curve where # dm = distance in meters # b = intercept and slope -pdrf <- function(dm, b=c(2, -1/120)){ - p <- 1/(1+exp(-(b[1]+b[2]*dm))) +pdrf <- function(dm, b = c(2, -1 / 120)) { + p <- 1 / (1 + exp(-(b[1] + b[2] * dm))) return(p) } -pdrf(c(100,200,300,400,500)) #view detection probs. at some distances - -#simulate detection -mydtc <- detect_transmissions(trnsLoc = mytrns, - recLoc = recs, - detRngFun = pdrf) - -#view transmissions that were detected +pdrf(c(100, 200, 300, 400, 500)) # view detection probs. at some distances + +# simulate detection +mydtc <- detect_transmissions( + trnsLoc = mytrns, + recLoc = recs, + detRngFun = pdrf +) + +# view transmissions that were detected sf::st_geometry(mydtc) <- "trns_geometry" points(sf::st_coordinates(mydtc$trns_geometry), pch = 21, bg = "red") -#link transmitter and receiver locations for each detection -segments(x0 = sf::st_coordinates(mydtc$trns_geometry)[,"X"], - y0 = sf::st_coordinates(mydtc$trns_geometry)[,"Y"], - x1 = sf::st_coordinates(mydtc$rec_geometry)[,"X"], - y1 = sf::st_coordinates(mydtc$rec_geometry)[,"Y"], - col = "red") +# link transmitter and receiver locations for each detection +segments( + x0 = sf::st_coordinates(mydtc$trns_geometry)[, "X"], + y0 = sf::st_coordinates(mydtc$trns_geometry)[, "Y"], + x1 = sf::st_coordinates(mydtc$rec_geometry)[, "X"], + y1 = sf::st_coordinates(mydtc$rec_geometry)[, "Y"], + col = "red" +) } \seealso{ diff --git a/man/detection_bubble_plot.Rd b/man/detection_bubble_plot.Rd index b859e3c5..4716f7bd 100644 --- a/man/detection_bubble_plot.Rd +++ b/man/detection_bubble_plot.Rd @@ -91,7 +91,7 @@ and upper right coordinates of the rectangle of colors } \value{ A data frame produced by -\code{glatos::summarize_detections(det, location_col = location_col, receiver_locs = receiver_locs, summ_type = "location")} +\code{glatos::summarize_detections(det, location_col = location_col, receiver_locs = receiver_locs, summ_type = "location")} If not out_file is specified, then an image is printed to the default plot device. If out_file is specified, then an image of @@ -120,22 +120,24 @@ which will accept a vector containing any two colors return by } \examples{ -#get path to example detection file +# get path to example detection file det_file <- system.file("extdata", "walleye_detections.csv", - package = "glatos") + package = "glatos" +) det <- read_glatos_detections(det_file) -#call with defaults +# call with defaults detection_bubble_plot(det, map = great_lakes_polygon) -#change symbol size and color +# change symbol size and color detection_bubble_plot(det, symbol_radius = 2, col_grad = c("grey90", "grey10")) -#Add all receivers +# Add all receivers # get path to example receiver file rec_file <- system.file("extdata", "sample_receivers.csv", - package = "glatos") + package = "glatos" +) rec <- read_glatos_receivers(rec_file) detection_bubble_plot(det, receiver_locs = rec) @@ -146,7 +148,8 @@ detection_bubble_plot(det, receiver_locs = rec) # get path to example receiver file rec_file <- system.file("extdata", "sample_receivers.csv", - package = "glatos") + package = "glatos" +) rec <- read_glatos_receivers(rec_file) first <- min(det$detection_timestamp_utc) # time of first detection @@ -155,9 +158,9 @@ last <- max(det$detection_timestamp_utc) # time of last detection # Subset receiver deployments oustide the detection period. # !is.na(rec$recover_date_time) eliminates receivers that have been # deployed but not yet recovered. -plot_rec <- rec[rec$deploy_date_time < last & - rec$recover_date_time > first & - !is.na(rec$recover_date_time),] +plot_rec <- rec[rec$deploy_date_time < last & + rec$recover_date_time > first & + !is.na(rec$recover_date_time), ] detection_bubble_plot(det, receiver_locs = plot_rec) diff --git a/man/detection_events.Rd b/man/detection_events.Rd index b70209a8..a687b63d 100644 --- a/man/detection_events.Rd +++ b/man/detection_events.Rd @@ -66,8 +66,10 @@ detection event.} \item{res_time_sec}{The elapsed time in seconds between the first and last detection in a given event.} -If \code{condense = FALSE}, a data.frame, data.table, or tibble matching the -input data frame \code{det} with the following columns added: +\if{html}{\out{
}}\preformatted{If `condense = FALSE`, a data.frame, data.table, or tibble matching the +input data frame `det` with the following columns added: +}\if{html}{\out{
}} + \item{time_diff}{Lagged time difference in seconds between successive detections of each animal_id.} \item{arrive}{Flag (0 or 1) representing the first detection in each @@ -93,18 +95,19 @@ detections that occurred on each station). } \examples{ -#get path to example detection file +# get path to example detection file det_file <- system.file("extdata", "walleye_detections.csv", - package = "glatos") + package = "glatos" +) det <- read_glatos_detections(det_file) -filt0 <- detection_events(det) #no time filter +filt0 <- detection_events(det) # no time filter -#7-day filter -filt_7d <- detection_events(det , time_sep = 604800) +# 7-day filter +filt_7d <- detection_events(det, time_sep = 604800) -#7-day filter but return do not condense result -filt_7d <- detection_events(det , time_sep = 604800, condense = FALSE) +# 7-day filter but return do not condense result +filt_7d <- detection_events(det, time_sep = 604800, condense = FALSE) } \author{ diff --git a/man/false_detections.Rd b/man/false_detections.Rd index 2b91317b..9b5ba8a5 100644 --- a/man/false_detections.Rd +++ b/man/false_detections.Rd @@ -72,15 +72,16 @@ sensitivity of the proportion of detections removed to the choice of \code{tf}. } \examples{ -#get path to example detection file +# get path to example detection file det_file <- system.file("extdata", "walleye_detections.csv", - package = "glatos") + package = "glatos" +) det <- read_glatos_detections(det_file) det <- false_detections(det, 3600) head(det) -#plot sensitivity to tf +# plot sensitivity to tf det <- false_detections(det, 3600, show_plot = TRUE) } diff --git a/man/format_POSIXt.Rd b/man/format_POSIXt.Rd index e26ea2f6..f2e60711 100644 --- a/man/format_POSIXt.Rd +++ b/man/format_POSIXt.Rd @@ -43,10 +43,14 @@ format(t2, digits = 6) t3 <- format_POSIXt(t1, digits = 5) format(t3, digits = 6) -#Example 2 -t1 <- as.POSIXct(c("2011-03-08 23:59:58", - "2011-03-08 23:59:58.828867"), - tz = "UTC") +# Example 2 +t1 <- as.POSIXct( + c( + "2011-03-08 23:59:58", + "2011-03-08 23:59:58.828867" + ), + tz = "UTC" +) format_POSIXt(t1, digits = 5, drop0trailing = FALSE) format_POSIXt(t1, digits = 5, drop0trailing = TRUE) diff --git a/man/get_local_vdat_schema.Rd b/man/get_local_vdat_schema.Rd index fa9535aa..d4cef8aa 100644 --- a/man/get_local_vdat_schema.Rd +++ b/man/get_local_vdat_schema.Rd @@ -20,13 +20,14 @@ Get schema from local installation of Innovsea program VDAT.exe \examples{ \dontrun{ -#use if VDAT.exe in Windows system PATH variable +# use if VDAT.exe in Windows system PATH variable get_local_vdat_schema() -#or specify path to VDAT.exe -get_local_vdat_schema(vdat_exe_path = - "C:/Program Files/Innovasea/Fathom/VDAT.exe") - +# or specify path to VDAT.exe +get_local_vdat_schema( + vdat_exe_path = + "C:/Program Files/Innovasea/Fathom/VDAT.exe" +) } } diff --git a/man/get_local_vdat_version.Rd b/man/get_local_vdat_version.Rd index ca55a01f..82aa832d 100644 --- a/man/get_local_vdat_version.Rd +++ b/man/get_local_vdat_version.Rd @@ -19,15 +19,16 @@ string returned by VDAT.exe). Get version of local installation of Innovasea program VDAT.exe } \examples{ - \dontrun{ -#use if VDAT.exe in Windows system PATH variable +# use if VDAT.exe in Windows system PATH variable get_local_vdat_version() -#or specify path to VDAT.exe -get_local_vdat_version(vdat_exe_path = - "C:/Program Files/Innovasea/Fathom/VDAT.exe") +# or specify path to VDAT.exe +get_local_vdat_version( + vdat_exe_path = + "C:/Program Files/Innovasea/Fathom/VDAT.exe" +) } } diff --git a/man/get_local_vue_version.Rd b/man/get_local_vue_version.Rd index 3372165c..15321894 100644 --- a/man/get_local_vue_version.Rd +++ b/man/get_local_vue_version.Rd @@ -19,16 +19,16 @@ string returned by VUE.exe). Get version of local installation of Innovasea program VUE.exe } \examples{ - \dontrun{ -#use if VUE.exe in Windows system PATH variable +# use if VUE.exe in Windows system PATH variable get_local_vue_version() -#or specify path to VUE.exe -get_local_vue_version(vue_exe_path = - "C:/Program Files (x86)/Vemco/VUE") - +# or specify path to VUE.exe +get_local_vue_version( + vue_exe_path = + "C:/Program Files (x86)/Vemco/VUE" +) } } diff --git a/man/glatos_animals.Rd b/man/glatos_animals.Rd index fbde1400..207f92eb 100644 --- a/man/glatos_animals.Rd +++ b/man/glatos_animals.Rd @@ -61,20 +61,28 @@ required column names and classes using \code{validate_glatos_animals()}. \examples{ # glatos_animals -x = data.frame(animal_id = c("120", "107", "109"), - tag_id_code = c("32024", "32012", "32014"), - tag_code_space = c("A69-9001", "A69-9001", "A69-9001"), - utc_release_date_time = as.POSIXct(c("2011-03-28 00:00:00", - "2011-03-28 00:01:00", - "2011-03-28 00:05:00"), - tz = "UTC"), - release_latitude = c(41.56093, 41.56093, 41.56093), - release_longitude = c(-83.645, -83.645, -83.645)) - -ga_df1 <- glatos_animals(animal_id = x$animal_id, - tag_id_code = x$tag_id_code, - tag_code_space = x$tag_code_space, - utc_release_date_time = x$utc_release_date_time) +x <- data.frame( + animal_id = c("120", "107", "109"), + tag_id_code = c("32024", "32012", "32014"), + tag_code_space = c("A69-9001", "A69-9001", "A69-9001"), + utc_release_date_time = as.POSIXct( + c( + "2011-03-28 00:00:00", + "2011-03-28 00:01:00", + "2011-03-28 00:05:00" + ), + tz = "UTC" + ), + release_latitude = c(41.56093, 41.56093, 41.56093), + release_longitude = c(-83.645, -83.645, -83.645) +) + +ga_df1 <- glatos_animals( + animal_id = x$animal_id, + tag_id_code = x$tag_id_code, + tag_code_space = x$tag_code_space, + utc_release_date_time = x$utc_release_date_time +) # as_glatos_animals @@ -86,7 +94,8 @@ ga_df2 <- as_glatos_animals(x) library(sf) x_sf <- sf::st_as_sf(x, - coords = c("release_longitude", "release_latitude")) + coords = c("release_longitude", "release_latitude") +) ga_sf <- as_glatos_animals(x_sf) @@ -100,17 +109,20 @@ ga_tbl <- as_glatos_animals(x_tbl) # data.frame input; missing column name -library(dplyr) #for rename +library(dplyr) # for rename x2 <- rename(x, - fish_name = animal_id, - release_timestamp = utc_release_date_time) + fish_name = animal_id, + release_timestamp = utc_release_date_time +) ga2 <- as_glatos_animals(x2) # data.grame input; wrong column class -x3 <- mutate(x, animal_id = as.integer(animal_id), - utc_release_date_time = as.character(utc_release_date_time)) +x3 <- mutate(x, + animal_id = as.integer(animal_id), + utc_release_date_time = as.character(utc_release_date_time) +) ga3 <- as_glatos_animals(x3) @@ -119,7 +131,7 @@ ga3 <- as_glatos_animals(x3) validate_glatos_animals(x) -is_glatos_animals(x) #FALSE +is_glatos_animals(x) # FALSE -is_glatos_animals(ga_df1) #TRUE +is_glatos_animals(ga_df1) # TRUE } diff --git a/man/glatos_detections.Rd b/man/glatos_detections.Rd index 3360047a..edbf8d43 100644 --- a/man/glatos_detections.Rd +++ b/man/glatos_detections.Rd @@ -61,20 +61,28 @@ required column names and classes using \code{validate_glatos_detections()}. \examples{ # glatos_detections -x = data.frame(animal_id = c("153", "153", "153", "153"), - detection_timestamp_utc = as.POSIXct(c("2012-04-29 01:48:37", - "2012-04-29 01:52:55", - "2012-04-29 01:55:12", - "2012-04-29 01:56:42"), - tz = "UTC"), - deploy_lat =c(43.39165, 43.39165, 43.39165, 43.39165), - deploy_long = c(-83.99264, -83.99264, -83.99264, -83.99264)) - -gd_df1 <- glatos_detections(animal_id = x$animal_id, - detection_timestamp_utc = - x$detection_timestamp_utc, - deploy_lat = x$deploy_lat, - deploy_long = x$deploy_long) +x <- data.frame( + animal_id = c("153", "153", "153", "153"), + detection_timestamp_utc = as.POSIXct( + c( + "2012-04-29 01:48:37", + "2012-04-29 01:52:55", + "2012-04-29 01:55:12", + "2012-04-29 01:56:42" + ), + tz = "UTC" + ), + deploy_lat = c(43.39165, 43.39165, 43.39165, 43.39165), + deploy_long = c(-83.99264, -83.99264, -83.99264, -83.99264) +) + +gd_df1 <- glatos_detections( + animal_id = x$animal_id, + detection_timestamp_utc = + x$detection_timestamp_utc, + deploy_lat = x$deploy_lat, + deploy_long = x$deploy_long +) # as_glatos_detections @@ -87,8 +95,9 @@ library(sf) # use remove = FALSE to keep required columns x_sf <- sf::st_as_sf(x, - coords = c("deploy_long", "deploy_lat"), - remove = FALSE) + coords = c("deploy_long", "deploy_lat"), + remove = FALSE +) gd_sf <- as_glatos_detections(x_sf) @@ -102,18 +111,20 @@ gd_tbl <- as_glatos_detections(x_tbl) # data.frame input; missing column name -library(dplyr) #for rename +library(dplyr) # for rename x2 <- rename(x, - fish_id = animal_id, - det_date_time = detection_timestamp_utc) + fish_id = animal_id, + det_date_time = detection_timestamp_utc +) gd2 <- as_glatos_detections(x2) # data.frame input; wrong column class -x3 <- mutate(x, - animal_id = as.integer(animal_id), - detection_timestamp_utc = as.character(detection_timestamp_utc)) +x3 <- mutate(x, + animal_id = as.integer(animal_id), + detection_timestamp_utc = as.character(detection_timestamp_utc) +) gr3 <- as_glatos_detections(x3) @@ -122,7 +133,7 @@ gr3 <- as_glatos_detections(x3) validate_glatos_detections(x) -is_glatos_detections(x) #FALSE +is_glatos_detections(x) # FALSE -is_glatos_detections(gd_df1) #TRUE +is_glatos_detections(gd_df1) # TRUE } diff --git a/man/glatos_receivers.Rd b/man/glatos_receivers.Rd index 854c890c..70cbe91e 100644 --- a/man/glatos_receivers.Rd +++ b/man/glatos_receivers.Rd @@ -64,27 +64,39 @@ required column names and classes using \code{validate_glatos_receivers()}. \examples{ # glatos_receivers -x = data.frame(station = c("WHT-009", "FDT-001", "FDT-004", "FDT-003"), - deploy_lat = c(43.7, 45.9, 45.9, 45.9), - deploy_long = c(-82.5, -83.5, -83.5, -83.5), - deploy_date_time = as.POSIXct(c("2010-09-22 18:05:00", - "2010-11-12 15:07:00", - "2010-11-12 15:36:00", - "2010-11-12 15:56:00"), - tz = "UTC"), - recover_date_time = as.POSIXct(c("2012-08-15 16:52:00", - "2012-05-15 13:25:00", - "2012-05-15 14:15:00", - "2012-05-15 14:40:00"), - tz = "UTC"), - ins_serial_no = c("109450", "442", "441", "444")) - -gr_df1 <- glatos_receivers(station = x$station, - deploy_lat = x$deploy_lat, - deploy_long = x$deploy_long, - deploy_date_time = x$deploy_date_time, - recover_date_time = x$recover_date_time, - ins_serial_no = x$ins_serial_no) +x <- data.frame( + station = c("WHT-009", "FDT-001", "FDT-004", "FDT-003"), + deploy_lat = c(43.7, 45.9, 45.9, 45.9), + deploy_long = c(-82.5, -83.5, -83.5, -83.5), + deploy_date_time = as.POSIXct( + c( + "2010-09-22 18:05:00", + "2010-11-12 15:07:00", + "2010-11-12 15:36:00", + "2010-11-12 15:56:00" + ), + tz = "UTC" + ), + recover_date_time = as.POSIXct( + c( + "2012-08-15 16:52:00", + "2012-05-15 13:25:00", + "2012-05-15 14:15:00", + "2012-05-15 14:40:00" + ), + tz = "UTC" + ), + ins_serial_no = c("109450", "442", "441", "444") +) + +gr_df1 <- glatos_receivers( + station = x$station, + deploy_lat = x$deploy_lat, + deploy_long = x$deploy_long, + deploy_date_time = x$deploy_date_time, + recover_date_time = x$recover_date_time, + ins_serial_no = x$ins_serial_no +) # as_glatos_receivers @@ -97,8 +109,9 @@ library(sf) # use remove = FALSE to keep required columns x_sf <- sf::st_as_sf(x, - coords = c("deploy_long", "deploy_lat"), - remove = FALSE) + coords = c("deploy_long", "deploy_lat"), + remove = FALSE +) gr_sf <- as_glatos_receivers(x_sf) @@ -112,17 +125,20 @@ gr_tbl <- as_glatos_receivers(x_tbl) # data.frame input; missing column name -library(dplyr) #for rename +library(dplyr) # for rename x2 <- rename(x, - receiver_loc = station, - deploy_timestamp = deploy_date_time) + receiver_loc = station, + deploy_timestamp = deploy_date_time +) gr2 <- as_glatos_receivers(x2) # data.frame input; wrong column class -x3 <- mutate(x, ins_serial_no = as.integer(ins_serial_no), - deploy_date_time = as.character(deploy_date_time)) +x3 <- mutate(x, + ins_serial_no = as.integer(ins_serial_no), + deploy_date_time = as.character(deploy_date_time) +) gr3 <- as_glatos_receivers(x3) @@ -131,7 +147,7 @@ gr3 <- as_glatos_receivers(x3) validate_glatos_receivers(x) -is_glatos_receivers(x) #FALSE +is_glatos_receivers(x) # FALSE -is_glatos_receivers(gr_df1) #TRUE +is_glatos_receivers(gr_df1) # TRUE } diff --git a/man/kml_to_csv.Rd b/man/kml_to_csv.Rd index f8d4eae8..b2f470aa 100644 --- a/man/kml_to_csv.Rd +++ b/man/kml_to_csv.Rd @@ -34,10 +34,11 @@ saved as kml. Or extract (unzip) kml from kmz. } \examples{ -#Get example kml with two polygons +# Get example kml with two polygons kml_file <- system.file("inst/extdata", "example_polygons.kml", - package = "glatos") - + package = "glatos" +) + kml_to_csv(kml_file) } diff --git a/man/kml_workbook.Rd b/man/kml_workbook.Rd index 4bd97b0a..90bfab84 100644 --- a/man/kml_workbook.Rd +++ b/man/kml_workbook.Rd @@ -74,23 +74,26 @@ timestamps at each location. Release locations will be displayed when the display window includes the date of release. } \examples{ - \dontrun{ -#get path to example GLATOS Data Workbook -wb_file <- system.file("extdata", -"walleye_workbook.xlsm", package = "glatos") +# get path to example GLATOS Data Workbook +wb_file <- system.file("extdata", + "walleye_workbook.xlsm", + package = "glatos" +) -#read workbook directly +# read workbook directly kml_workbook(wb_file = wb_file) -#now with bigger label and point and out_file -kml_workbook(wb_file = wb_file, labelSize = 20, iconSize = 1, - out_file = "bigger.kml") +# now with bigger label and point and out_file +kml_workbook( + wb_file = wb_file, labelSize = 20, iconSize = 1, + out_file = "bigger.kml" +) -#read workbook directly; output kmz +# read workbook directly; output kmz kml_workbook(wb_file = wb_file, kmz = TRUE) -#get path to example GLATOS Data Workbook +# get path to example GLATOS Data Workbook wb <- read_glatos_workbook(wb_file) kml_workbook(wb = wb, kmz = TRUE, out_file = "bigger.kmz") } diff --git a/man/make_frames.Rd b/man/make_frames.Rd index 196d4bb8..5414ab52 100644 --- a/man/make_frames.Rd +++ b/man/make_frames.Rd @@ -170,12 +170,12 @@ input argument \code{preview = TRUE} will be useful while exploring optional plo arguments. } \examples{ - \dontrun{ # load detection data det_file <- system.file("extdata", "walleye_detections.csv", - package = "glatos") + package = "glatos" +) dtc <- read_glatos_detections(det_file) # take a look @@ -183,37 +183,44 @@ head(dtc) # load receiver location data rec_file <- system.file("extdata", - "sample_receivers.csv", package = "glatos") + "sample_receivers.csv", + package = "glatos" +) recs <- read_glatos_receivers(rec_file) # call with defaults; linear interpolation pos1 <- interpolate_path(dtc) # make frames, preview the first frame -myDir <- paste0(getwd(),"/frames1") -make_frames(pos1, recs=recs, out_dir=myDir, preview = TRUE) +myDir <- paste0(getwd(), "/frames1") +make_frames(pos1, recs = recs, out_dir = myDir, preview = TRUE) # make frames but not animation -myDir <- paste0(getwd(),"/frames2") -make_frames(pos1, recs=recs, out_dir=myDir, animate = FALSE) +myDir <- paste0(getwd(), "/frames2") +make_frames(pos1, recs = recs, out_dir = myDir, animate = FALSE) # make sequential frames, and animate. Make animation and frames. -#change default color of fish markers to red and change marker and size. +# change default color of fish markers to red and change marker and size. myDir <- paste0(getwd(), "/frames3") -make_frames(pos1, recs=recs, out_dir=myDir, animate = TRUE, - ani_name = "animation3.mp4", col="red", pch = 16, cex = 3) +make_frames(pos1, + recs = recs, out_dir = myDir, animate = TRUE, + ani_name = "animation3.mp4", col = "red", pch = 16, cex = 3 +) # make sequential frames, animate, add 5-day tail myDir <- paste0(getwd(), "/frames4") -make_frames(pos1, recs=recs, out_dir=myDir, animate = TRUE, - ani_name = "animation4.mp4", tail_dur=5) +make_frames(pos1, + recs = recs, out_dir = myDir, animate = TRUE, + ani_name = "animation4.mp4", tail_dur = 5 +) # make animation, remove frames. myDir <- paste0(getwd(), "/frames5") -make_frames(pos1, recs=recs, out_dir=myDir, animate = TRUE, - ani_name = "animation5.mp4", frame_delete = TRUE) - +make_frames(pos1, + recs = recs, out_dir = myDir, animate = TRUE, + ani_name = "animation5.mp4", frame_delete = TRUE +) } } diff --git a/man/make_transition.Rd b/man/make_transition.Rd index 074321cb..c366dffc 100644 --- a/man/make_transition.Rd +++ b/man/make_transition.Rd @@ -81,14 +81,14 @@ next version of \code{glatos}. Use \code{\link{make_transition3}} instead. \examples{ \dontrun{ -#Example 1 - read from sf polygon +# Example 1 - read from sf polygon # use example polygon for Great lakes -library(sf) #for loading great_lakes_polygon +library(sf) # for loading great_lakes_polygon library(raster) # for plotting rasters # Get polygon of the Great Lakes -data(great_lakes_polygon) #glatos example data; an sf polygons object +data(great_lakes_polygon) # glatos example data; an sf polygons object # Make transition layer tst <- make_transition(great_lakes_polygon, res = c(0.1, 0.1)) @@ -97,17 +97,17 @@ tst <- make_transition(great_lakes_polygon, res = c(0.1, 0.1)) # notice land = 1, water = 0 plot(tst$rast) -#compare to polygon +# compare to polygon plot(sf::st_geometry(great_lakes_polygon), add = TRUE) -#Example 2 - read from SpatialPolygonsDataFrame +# Example 2 - read from SpatialPolygonsDataFrame # use example polygon for Great lakes library(raster) # for plotting rasters -#get polygon of the Great Lakes -data(greatLakesPoly) #glatos example data; a SpatialPolygonsDataFrame +# get polygon of the Great Lakes +data(greatLakesPoly) # glatos example data; a SpatialPolygonsDataFrame # make_transition layer tst <- make_transition(greatLakesPoly, res = c(0.1, 0.1)) @@ -116,13 +116,13 @@ tst <- make_transition(greatLakesPoly, res = c(0.1, 0.1)) # notice land = 1, water = 0 plot(tst$rast) -#compare to polygon +# compare to polygon plot(greatLakesPoly, add = TRUE) # increase resolution and repeat if needed #------------------------------------------ -#Example 3 - read from ESRI Shapefile +# Example 3 - read from ESRI Shapefile # path to polygon shapefile poly <- system.file("extdata", "shoreline.zip", package = "glatos") poly <- unzip(poly, exdir = tempdir()) diff --git a/man/make_transition2.Rd b/man/make_transition2.Rd index 3abfe548..f4f46416 100644 --- a/man/make_transition2.Rd +++ b/man/make_transition2.Rd @@ -63,7 +63,7 @@ next version of \code{glatos}. Use \code{\link{make_transition3}} instead. library(raster) # for plotting rasters # get polygon of the Great Lakes -data(greatLakesPoly) #glatos example data; a SpatialPolygonsDataFrame +data(greatLakesPoly) # glatos example data; a SpatialPolygonsDataFrame # make_transition layer tst <- make_transition2(greatLakesPoly, res = c(0.1, 0.1)) @@ -86,7 +86,6 @@ plot(tst1$rast) plot(raster(tst1$transition)) } - } \seealso{ \link{make_transition} diff --git a/man/make_video.Rd b/man/make_video.Rd index 4e6a1aed..40b5f1b3 100644 --- a/man/make_video.Rd +++ b/man/make_video.Rd @@ -97,69 +97,85 @@ duration may also be controlled by setting the \code{framerate} argument of \link[=encoding]{av::av_encode_video}. See \code{...} above. } \examples{ - \dontrun{ # load frames frames <- system.file("extdata", "frames", package = "glatos") # make .mp4 video -make_video(input_dir = frames, - input_ext = ".png", - output = file.path(tempdir(), "animation1.mp4")) +make_video( + input_dir = frames, + input_ext = ".png", + output = file.path(tempdir(), "animation1.mp4") +) # set duration to 10 seconds -make_video(input_dir = frames, - input_ext = ".png", - output = file.path(tempdir(), "animation2.mp4"), - duration = 10) +make_video( + input_dir = frames, + input_ext = ".png", + output = file.path(tempdir(), "animation2.mp4"), + duration = 10 +) # set size of ouput video -make_video(input_dir = frames, - input_ext = ".png", - output = file.path(tempdir(), "animation3.mp4"), - size = c(320, 240)) +make_video( + input_dir = frames, + input_ext = ".png", + output = file.path(tempdir(), "animation3.mp4"), + size = c(320, 240) +) # start animation on frame 10, end on frame 20 -make_video(input_dir = frames, - input_ext = ".png", - output = file.path(tempdir(), "animation_4.mp4"), - start_frame = 10, - end_frame = 20) +make_video( + input_dir = frames, + input_ext = ".png", + output = file.path(tempdir(), "animation_4.mp4"), + start_frame = 10, + end_frame = 20 +) # make move backwards- start animation of frame 20 and end on frame 10 -make_video(input_dir = frames, - input_ext = ".png", - output = file.path(tempdir(), "animation_5.mp4"), - start_frame = 20, - end_frame = 10) +make_video( + input_dir = frames, + input_ext = ".png", + output = file.path(tempdir(), "animation_5.mp4"), + start_frame = 20, + end_frame = 10 +) # make .wmv video -make_video(input_dir = frames, - input_ext = ".png", - output = file.path(tempdir(), "animation1.wmv")) +make_video( + input_dir = frames, + input_ext = ".png", + output = file.path(tempdir(), "animation1.wmv") +) #--- Examples using more advanced features of av_encode_video # resize output video by specifying a scale filter -make_video(input_dir = frames, - input_ext = ".png", - output = file.path(tempdir(), "animation_6.mp4"), - vfilter = "scale=320:240") +make_video( + input_dir = frames, + input_ext = ".png", + output = file.path(tempdir(), "animation_6.mp4"), + vfilter = "scale=320:240" +) # slow the video by 10 times -make_video(input_dir = frames, - input_ext = ".png", - output = file.path(tempdir(), "animation_7.mp4"), - vfilter = "setpts=10*PTS") +make_video( + input_dir = frames, + input_ext = ".png", + output = file.path(tempdir(), "animation_7.mp4"), + vfilter = "setpts=10*PTS" +) # slow video by 10 times and scale to 320x240 resolution -make_video(input_dir = frames, - input_ext = ".png", - output = file.path(tempdir(), "animation_8.mp4"), - vfilter = "scale=320:240, setpts=10*PTS") - +make_video( + input_dir = frames, + input_ext = ".png", + output = file.path(tempdir(), "animation_8.mp4"), + vfilter = "scale=320:240, setpts=10*PTS" +) } } diff --git a/man/min_lag.Rd b/man/min_lag.Rd index 4ec6b73c..b81ecde9 100644 --- a/man/min_lag.Rd +++ b/man/min_lag.Rd @@ -49,7 +49,8 @@ standard glatos export. # load example detection file det_file <- system.file("extdata", "walleye_detections.csv", - package = "glatos") + package = "glatos" +) det <- read_glatos_detections(det_file) # rename existing min_lag column diff --git a/man/point_offset.Rd b/man/point_offset.Rd index 3ae0ae24..de2ce249 100644 --- a/man/point_offset.Rd +++ b/man/point_offset.Rd @@ -36,11 +36,13 @@ great circle distances. lat <- rep(44.0, 17) lon <- rep(-83.0, 17) -offsetDir <- c(NA,"N", "NNE", "NE", "ENE", "E", "ESE", "SE", "SSE", "S", -"SSW", "SW", "WSW", "W", "WNW", "NW", "NNW") +offsetDir <- c( + NA, "N", "NNE", "NE", "ENE", "E", "ESE", "SE", "SSE", "S", + "SSW", "SW", "WSW", "W", "WNW", "NW", "NNW" +) -offsetDist <- seq(100, 1700, by = 100) -distUnit <- 'm' +offsetDist <- seq(100, 1700, by = 100) +distUnit <- "m" point_offset(lon, lat, offsetDist, offsetDir, distUnit) diff --git a/man/prepare_deploy_sheet.Rd b/man/prepare_deploy_sheet.Rd index d1fa1f75..c3c1c160 100644 --- a/man/prepare_deploy_sheet.Rd +++ b/man/prepare_deploy_sheet.Rd @@ -40,11 +40,13 @@ to be used by \code{convert_otn_to_att}. library(glatos) deploy_path <- system.file("extdata", "hfx_deploy_simplified.xlsx", - package = "glatos") + package = "glatos" +) -deploy <- prepare_deploy_sheet(deploy_path, - header_line = 1, - sheet_name = 1) +deploy <- prepare_deploy_sheet(deploy_path, + header_line = 1, + sheet_name = 1 +) } \author{ diff --git a/man/prepare_tag_sheet.Rd b/man/prepare_tag_sheet.Rd index b6ee55fa..9fc4e378 100644 --- a/man/prepare_tag_sheet.Rd +++ b/man/prepare_tag_sheet.Rd @@ -33,7 +33,8 @@ to be used by \code{convert_otn_to_att}. library(glatos) tag_path <- system.file("extdata", "otn_nsbs_tag_metadata.xls", - package = "glatos") + package = "glatos" +) tags <- prepare_tag_sheet(tag_path, 5, 2) diff --git a/man/read_glatos_detections.Rd b/man/read_glatos_detections.Rd index 7acff2d5..3dd8270b 100644 --- a/man/read_glatos_detections.Rd +++ b/man/read_glatos_detections.Rd @@ -37,13 +37,14 @@ When created, it will be constructed from \code{transmitter_codespace} and \code{transmitter_id}, separated by '-'. } \examples{ -#get path to example detection file +# get path to example detection file det_file <- system.file("extdata", "walleye_detections.csv", - package = "glatos") + package = "glatos" +) -#note that code above is needed to find the example file -#for real glatos data, use something like below -#det_file <- "c:/path_to_file/HECWL_detectionsWithLocs_20150321_132242.csv" +# note that code above is needed to find the example file +# for real glatos data, use something like below +# det_file <- "c:/path_to_file/HECWL_detectionsWithLocs_20150321_132242.csv" det <- read_glatos_detections(det_file) diff --git a/man/read_glatos_receivers.Rd b/man/read_glatos_receivers.Rd index 89102e5d..7a442ddc 100644 --- a/man/read_glatos_receivers.Rd +++ b/man/read_glatos_receivers.Rd @@ -32,13 +32,15 @@ timestamps must be 'YYYY-MM-DD HH:MM' format and in UTC timezone per GLATOS standard. } \examples{ -#get path to example receiver_locations file +# get path to example receiver_locations file rec_file <- system.file("extdata", - "sample_receivers.csv", package = "glatos") + "sample_receivers.csv", + package = "glatos" +) -#note that code above is needed to find the example file -#for real glatos data, use something like below -#rec_file <- "c:/path_to_file/GLATOS_receiverLocations_20150321_132242.csv" +# note that code above is needed to find the example file +# for real glatos data, use something like below +# rec_file <- "c:/path_to_file/GLATOS_receiverLocations_20150321_132242.csv" rcv <- read_glatos_receivers(rec_file) diff --git a/man/read_glatos_workbook.Rd b/man/read_glatos_workbook.Rd index ca387a7c..654a709b 100644 --- a/man/read_glatos_workbook.Rd +++ b/man/read_glatos_workbook.Rd @@ -85,13 +85,15 @@ that need reformatting, (2) select 'Text-to-columns' in the 'Data' menu, (5) choose 'Date: YMD' in the 'Column data format' box, and (6) 'Finish'. } \examples{ -#get path to example GLATOS Data Workbook +# get path to example GLATOS Data Workbook wb_file <- system.file("extdata", - "walleye_workbook.xlsm", package = "glatos") + "walleye_workbook.xlsm", + package = "glatos" +) -#note that code above is needed to find the example file -#for real glatos data, use something like below -#wb_file <- "c:/path_to_file/HECWL_GLATOS_20150321.csv" +# note that code above is needed to find the example file +# for real glatos data, use something like below +# wb_file <- "c:/path_to_file/HECWL_GLATOS_20150321.csv" wb <- read_glatos_workbook(wb_file) diff --git a/man/read_otn_deployments.Rd b/man/read_otn_deployments.Rd index d9cf36c8..aa9c88b6 100644 --- a/man/read_otn_deployments.Rd +++ b/man/read_otn_deployments.Rd @@ -42,9 +42,10 @@ Column names are changed to match GLATOS standard columns when possible. Otherwise, OTN columns and column names are retained. } \examples{ -#get path to example deployments file +# get path to example deployments file deployment_file <- system.file("extdata", "hfx_deployments.csv", - package = "glatos") + package = "glatos" +) dep <- read_otn_deployments(deployment_file) } diff --git a/man/read_otn_detections.Rd b/man/read_otn_detections.Rd index b976d327..85325692 100644 --- a/man/read_otn_detections.Rd +++ b/man/read_otn_detections.Rd @@ -28,9 +28,10 @@ Column names are changed to match GLATOS standard columns when possible. Otherwise, OTN columns and column names are retained. } \examples{ -#get path to example detection file +# get path to example detection file det_file <- system.file("extdata", "blue_shark_detections.csv", - package = "glatos") + package = "glatos" +) det <- read_otn_detections(det_file) } diff --git a/man/read_vemco_tag_specs.Rd b/man/read_vemco_tag_specs.Rd index 50bd5914..a92b9080 100644 --- a/man/read_vemco_tag_specs.Rd +++ b/man/read_vemco_tag_specs.Rd @@ -72,9 +72,11 @@ purchasers by Vemco. This function is not endorsed or supported by any transmitter manufacturer. } \examples{ -#get path to example Vemco tag spec file -spec_file <- system.file("extdata", - "lamprey_tag_specs.xls", package = "glatos") +# get path to example Vemco tag spec file +spec_file <- system.file("extdata", + "lamprey_tag_specs.xls", + package = "glatos" +) my_tags <- read_vemco_tag_specs(spec_file, file_format = "vemco_xls") } diff --git a/man/read_vue_detection_csv.Rd b/man/read_vue_detection_csv.Rd index 2f9a7de7..676e172b 100644 --- a/man/read_vue_detection_csv.Rd +++ b/man/read_vue_detection_csv.Rd @@ -27,7 +27,9 @@ All timestamp columns are assumed to be in UTC. } \examples{ csv_file <- system.file("extdata", - "VR2W_109924_20110718_1.csv", package="glatos") + "VR2W_109924_20110718_1.csv", + package = "glatos" +) vue_det <- read_vue_detection_csv(csv_file) diff --git a/man/read_vue_event_csv.Rd b/man/read_vue_event_csv.Rd index 57aa5575..3891df1d 100644 --- a/man/read_vue_event_csv.Rd +++ b/man/read_vue_event_csv.Rd @@ -28,7 +28,9 @@ All timestamp columns are assumed to be in UTC. } \examples{ csv_file <- system.file("extdata", - "VR2W_receiverEvents_109924_20110718_1.csv", package="glatosDS") + "VR2W_receiverEvents_109924_20110718_1.csv", + package = "glatosDS" +) vue_evn <- read_vue_event_csv(csv_file) diff --git a/man/real_sensor_values.Rd b/man/real_sensor_values.Rd index b0f0b2ba..3590272e 100644 --- a/man/real_sensor_values.Rd +++ b/man/real_sensor_values.Rd @@ -93,23 +93,27 @@ ensure that the each combination of those columns occurs only once in } \examples{ -#get path to example detection file -det_file <- system.file("extdata", - "lamprey_detections.csv", package="glatos") - +# get path to example detection file +det_file <- system.file("extdata", + "lamprey_detections.csv", + package = "glatos" +) + lamprey_detections <- read_glatos_detections(det_file) -#get path to example Vemco tag spec file -spec_file <- system.file("extdata", - "lamprey_tag_specs.xls", package="glatos") - +# get path to example Vemco tag spec file +spec_file <- system.file("extdata", + "lamprey_tag_specs.xls", + package = "glatos" +) + lamprey_tags <- read_vemco_tag_specs(spec_file, file_format = "vemco_xls") -#note use of '$specs' in tag_specs argument +# note use of '$specs' in tag_specs argument dtc <- real_sensor_values(lamprey_detections, lamprey_tags$specs) -#now view records with sensor measurements -dtc[!is.na(dtc$sensor_value_real),] +# now view records with sensor measurements +dtc[!is.na(dtc$sensor_value_real), ] } \author{ diff --git a/man/receiver_line_det_sim.Rd b/man/receiver_line_det_sim.Rd index a6c9a07a..70a4811c 100644 --- a/man/receiver_line_det_sim.Rd +++ b/man/receiver_line_det_sim.Rd @@ -77,98 +77,111 @@ Detection or non-detection on each receiver is determined by a draw from a Bernoulli distribution with probability p. } \examples{ -#EXAMPLE 1 - simulate detection on line of ten receivers - - #Define detection range function (to pass as rngFun) - # that returns detection probability for given distance - # assume logistic form of detection range curve where - # dm = distance in meters - # b = intercept and slope - pdrf <- function(dm, b=c(5.5, -1/120)){ - p <- 1/(1+exp(-(b[1]+b[2]*dm))) - return(p) - } - - #preview detection range curve - plot(pdrf(0:2000),type="l",ylab="Probability of detecting each coded burst", -xlab="Distance between receiver and transmitter") - - #Simulate detection using pdrf; default values otherwise - dp <- receiver_line_det_sim(rngFun=pdrf) - dp - - #Again with only 10 virtual fish and optional plot to see simulated data - dp <- receiver_line_det_sim(rngFun=pdrf, nsim=10, showPlot=T) #w/ optional plot - dp - - #Again but six receivers and allow fish to pass to left and right of line - dp <- receiver_line_det_sim(rngFun=pdrf, recSpc=rep(1000,5), - outerLim=c(1000, 1000), nsim=10, showPlot=T) - dp - - #Again but four receivers with irregular spacing - dp <- receiver_line_det_sim(rngFun=pdrf, recSpc=c(2000,4000,2000), - outerLim=c(1000, 1000), nsim=10, showPlot=T) - dp - - -#EXAMPLE 2 - summarize detection probability vs. receiver spacing - - #two receivers only, spaced 'spc' m apart - #define scenarios where two receiver are spaced - spc <- seq(100,5000, 100) #two receivers spaced 100, 200, ... 5000 m - #loop through scenarios, estimate detection probability for each - for(i in 1:length(spc)){ - if(i==1) dp <- numeric(length(spc)) #pre-allocate - dp[i] <- receiver_line_det_sim(recSpc=spc[i], rngFun=pdrf) - } - cbind(spc,dp) #view results - #plot results - plot(spc, dp, type="o",ylim=c(0,1), - xlab="distance between receivers in meters", - ylab="proportion of virtual fish detected") - # e.g., >95\% virtual fish detected up to 1400 m spacing in this example - - -#EXAMPLE 3 - summarize detection probability vs. fish swim speed - - #define scenarios of fish movement rate - swim <- seq(0.1, 5.0, 0.1) #constant velocity - for(i in 1:length(swim)){ - if(i==1) dp <- numeric(length(swim)) #pre-allocate - dp[i] <- receiver_line_det_sim(vel=swim[i], rngFun=pdrf) - } - cbind(swim,dp) #view results - #plot results - plot(swim, dp, type="o", ylim=c(0,1), xlab="fish movement rate, m/s", - ylab="proportion of virtual fish detected") - # e.g., >95\% virtual fish detected up to 1.7 m/s rate in this example - # e.g., declines linearly above 1.7 m/s - - -#EXAMPLE 4 - empirical detection range curve instead of logistic - - #create data frame with observed det. efficiency (p) at each distance (x) - edr <- data.frame( - x=c(0,363,444,530,636,714,794,889,920), #tag-receiver distance - p=c(1,1,0.96,0.71,0.67,0.75,0.88,0.21,0)) # detection prob - - #now create a function to return the detection probability - # based on distance and linear interpolation within edr - # i.e., estimate p at given x by "connecting the dots" - edrf <- function(dm, my.edr=edr) { - p <- approx(x=my.edr$x,y=my.edr$p,xout=dm, rule=2)$y - return(p) - } - - #preview empirical detection range curve - plot(edrf(0:2000),type="l", - ylab="probability of detecting each coded burst", - xlab="distance between receiver and transmitter, meters") - - #use empirical curve (edrf) in simulation - dp <- receiver_line_det_sim(rngFun=edrf, nsim=10, showPlot=T) #w/ optional plot - dp +# EXAMPLE 1 - simulate detection on line of ten receivers + +# Define detection range function (to pass as rngFun) +# that returns detection probability for given distance +# assume logistic form of detection range curve where +# dm = distance in meters +# b = intercept and slope +pdrf <- function(dm, b = c(5.5, -1 / 120)) { + p <- 1 / (1 + exp(-(b[1] + b[2] * dm))) + return(p) +} + +# preview detection range curve +plot(pdrf(0:2000), + type = "l", ylab = "Probability of detecting each coded burst", + xlab = "Distance between receiver and transmitter" +) + +# Simulate detection using pdrf; default values otherwise +dp <- receiver_line_det_sim(rngFun = pdrf) +dp + +# Again with only 10 virtual fish and optional plot to see simulated data +dp <- receiver_line_det_sim(rngFun = pdrf, nsim = 10, showPlot = T) # w/ optional plot +dp + +# Again but six receivers and allow fish to pass to left and right of line +dp <- receiver_line_det_sim( + rngFun = pdrf, recSpc = rep(1000, 5), + outerLim = c(1000, 1000), nsim = 10, showPlot = T +) +dp + +# Again but four receivers with irregular spacing +dp <- receiver_line_det_sim( + rngFun = pdrf, recSpc = c(2000, 4000, 2000), + outerLim = c(1000, 1000), nsim = 10, showPlot = T +) +dp + + +# EXAMPLE 2 - summarize detection probability vs. receiver spacing + +# two receivers only, spaced 'spc' m apart +# define scenarios where two receiver are spaced +spc <- seq(100, 5000, 100) # two receivers spaced 100, 200, ... 5000 m +# loop through scenarios, estimate detection probability for each +for (i in 1:length(spc)) { + if (i == 1) dp <- numeric(length(spc)) # pre-allocate + dp[i] <- receiver_line_det_sim(recSpc = spc[i], rngFun = pdrf) +} +cbind(spc, dp) # view results +# plot results +plot(spc, dp, + type = "o", ylim = c(0, 1), + xlab = "distance between receivers in meters", + ylab = "proportion of virtual fish detected" +) +# e.g., >95\% virtual fish detected up to 1400 m spacing in this example + + +# EXAMPLE 3 - summarize detection probability vs. fish swim speed + +# define scenarios of fish movement rate +swim <- seq(0.1, 5.0, 0.1) # constant velocity +for (i in 1:length(swim)) { + if (i == 1) dp <- numeric(length(swim)) # pre-allocate + dp[i] <- receiver_line_det_sim(vel = swim[i], rngFun = pdrf) +} +cbind(swim, dp) # view results +# plot results +plot(swim, dp, + type = "o", ylim = c(0, 1), xlab = "fish movement rate, m/s", + ylab = "proportion of virtual fish detected" +) +# e.g., >95\% virtual fish detected up to 1.7 m/s rate in this example +# e.g., declines linearly above 1.7 m/s + + +# EXAMPLE 4 - empirical detection range curve instead of logistic + +# create data frame with observed det. efficiency (p) at each distance (x) +edr <- data.frame( + x = c(0, 363, 444, 530, 636, 714, 794, 889, 920), # tag-receiver distance + p = c(1, 1, 0.96, 0.71, 0.67, 0.75, 0.88, 0.21, 0) +) # detection prob + +# now create a function to return the detection probability +# based on distance and linear interpolation within edr +# i.e., estimate p at given x by "connecting the dots" +edrf <- function(dm, my.edr = edr) { + p <- approx(x = my.edr$x, y = my.edr$p, xout = dm, rule = 2)$y + return(p) +} + +# preview empirical detection range curve +plot(edrf(0:2000), + type = "l", + ylab = "probability of detecting each coded burst", + xlab = "distance between receiver and transmitter, meters" +) + +# use empirical curve (edrf) in simulation +dp <- receiver_line_det_sim(rngFun = edrf, nsim = 10, showPlot = T) # w/ optional plot +dp } \references{ diff --git a/man/residence_index.Rd b/man/residence_index.Rd index d2ce5fee..b052f2a7 100644 --- a/man/residence_index.Rd +++ b/man/residence_index.Rd @@ -90,9 +90,9 @@ among all sites. For each location, residency index (RI) is calculated: \deqn{ RI = L/T} \deqn{ RI = Residence Index} -\deqn{L = Distinct number of time intervals in which detection observed at +\deqn{L = Distinct number of time intervals in which detection observed at this location} -\deqn{T = Distinct number of time intervals in which detection observed at +\deqn{T = Distinct number of time intervals in which detection observed at any location} For consistency with other \code{calculation_method}s, @@ -146,21 +146,27 @@ RI = AnOS/AnOT} \deqn{AnOT = Sum of length of time of each detection among all locations, excluding any overlap} } \examples{ -#get path to example detection file +# get path to example detection file det_file <- system.file("extdata", "walleye_detections.csv", - package = "glatos") + package = "glatos" +) det <- read_glatos_detections(det_file) detection_events <- glatos::detection_events(det) -rik_data <- glatos::residence_index(detection_events, - calculation_method = 'kessel') -rit_data <- glatos::residence_index(detection_events, - calculation_method = 'time_interval') -rit_data <- glatos::residence_index(detection_events, - calculation_method = 'timedelta') -riawo_data <- glatos::residence_index(detection_events, - calculation_method = 'aggregate_with_overlap') -riano_data <- glatos::residence_index(detection_events, - calculation_method = 'aggregate_no_overlap') +rik_data <- glatos::residence_index(detection_events, + calculation_method = "kessel" +) +rit_data <- glatos::residence_index(detection_events, + calculation_method = "time_interval" +) +rit_data <- glatos::residence_index(detection_events, + calculation_method = "timedelta" +) +riawo_data <- glatos::residence_index(detection_events, + calculation_method = "aggregate_with_overlap" +) +riano_data <- glatos::residence_index(detection_events, + calculation_method = "aggregate_no_overlap" +) } \references{ diff --git a/man/rotate_points.Rd b/man/rotate_points.Rd index a33a448d..868a606a 100644 --- a/man/rotate_points.Rd +++ b/man/rotate_points.Rd @@ -33,11 +33,11 @@ rotation matrix, then shifted back to original focus. This function is called from \code{\link[=crw_in_polygon]{crw_in_polygon()}} } \examples{ -x <- runif(10,0,10) -y <- runif(10,0,10) -plot(x,y,type="b",pch=20) +x <- runif(10, 0, 10) +y <- runif(10, 0, 10) +plot(x, y, type = "b", pch = 20) foo <- rotate_points(x, y, 20, c(5, 5)) -points(foo$x,foo$y,type="b",pch=20,col="red") +points(foo$x, foo$y, type = "b", pch = 20, col = "red") } \author{ diff --git a/man/summarize_detections.Rd b/man/summarize_detections.Rd index e0cbde40..76bf76ea 100644 --- a/man/summarize_detections.Rd +++ b/man/summarize_detections.Rd @@ -137,60 +137,69 @@ the output summary. } \examples{ -#get path to example detection file - det_file <- system.file("extdata", "walleye_detections.csv", - package = "glatos") - det <- read_glatos_detections(det_file) - - #Basic summaries - - # by animal - ds <- summarize_detections(det) - - # by location - ds <- summarize_detections(det, summ_type = "location") - - # by animal and location - ds <- summarize_detections(det, summ_type = "both") - - - #Include user-defined location_col - - # by animal - det$some_place <- ifelse(grepl("^S", det$glatos_array), "s", "not_s") - - ds <- summarize_detections(det, location_col = "some_place") - - # by location - ds <- summarize_detections(det, location_col = "some_place", - summ_type = "location") - - # by animal and location - ds <- summarize_detections(det, location_col = "some_place", - summ_type = "both") - - - #Include locations where no animals detected - - #get example receiver data - rec_file <- system.file("extdata", "sample_receivers.csv", - package = "glatos") - rec <- read_glatos_receivers(rec_file) - - ds <- summarize_detections(det, receiver_locs = rec, summ_type = "location") - - - #Include animals that were not detected - #get example animal data from walleye workbook - wb_file <- system.file("extdata", "walleye_workbook.xlsm", - package = "glatos") - wb <- read_glatos_workbook(wb_file) - - ds <- summarize_detections(det, animals = wb$animals, summ_type = "animal") - - #Include by animals and locations that were not detected - ds <- summarize_detections(det, receiver_locs = rec, animals = wb$animals, - summ_type = "both") +# get path to example detection file +det_file <- system.file("extdata", "walleye_detections.csv", + package = "glatos" +) +det <- read_glatos_detections(det_file) + +# Basic summaries + +# by animal +ds <- summarize_detections(det) + +# by location +ds <- summarize_detections(det, summ_type = "location") + +# by animal and location +ds <- summarize_detections(det, summ_type = "both") + + +# Include user-defined location_col + +# by animal +det$some_place <- ifelse(grepl("^S", det$glatos_array), "s", "not_s") + +ds <- summarize_detections(det, location_col = "some_place") + +# by location +ds <- summarize_detections(det, + location_col = "some_place", + summ_type = "location" +) + +# by animal and location +ds <- summarize_detections(det, + location_col = "some_place", + summ_type = "both" +) + + +# Include locations where no animals detected + +# get example receiver data +rec_file <- system.file("extdata", "sample_receivers.csv", + package = "glatos" +) +rec <- read_glatos_receivers(rec_file) + +ds <- summarize_detections(det, receiver_locs = rec, summ_type = "location") + + +# Include animals that were not detected +# get example animal data from walleye workbook +wb_file <- system.file("extdata", "walleye_workbook.xlsm", + package = "glatos" +) +wb <- read_glatos_workbook(wb_file) + +ds <- summarize_detections(det, animals = wb$animals, summ_type = "animal") + +# Include by animals and locations that were not detected +ds <- summarize_detections(det, + receiver_locs = rec, animals = wb$animals, + summ_type = "both" +) } \author{ diff --git a/man/transmit_along_path.Rd b/man/transmit_along_path.Rd index dc43202b..cbc23e43 100644 --- a/man/transmit_along_path.Rd +++ b/man/transmit_along_path.Rd @@ -82,89 +82,108 @@ which was designed to accept the result as input (\code{trnsLoc}). } \examples{ -#Example 1 - data.frame input (default column names) - -mypath <- data.frame(x = seq(0, 1000, 100), - y = seq(0, 1000, 100)) - -mytrns <- transmit_along_path(mypath, vel = 0.5, - delayRng = c(60, 180), - burstDur = 5.0, - sp_out = FALSE) +# Example 1 - data.frame input (default column names) + +mypath <- data.frame( + x = seq(0, 1000, 100), + y = seq(0, 1000, 100) +) + +mytrns <- transmit_along_path(mypath, + vel = 0.5, + delayRng = c(60, 180), + burstDur = 5.0, + sp_out = FALSE +) plot(mypath, type = "o") points(mytrns, pch = 20, col = "red") -#Example 2 - data.frame input (non-default column names) +# Example 2 - data.frame input (non-default column names) -mypath <- data.frame(Easting = seq(0, 1000, 100), - Northing = seq(0, 1000, 100)) - -mytrns <- transmit_along_path(mypath, vel = 0.5, delayRng = c(60, 180), - burstDur = 5.0, - colNames = list(x = "Easting", - y = "Northing"), - sp_out = FALSE) +mypath <- data.frame( + Easting = seq(0, 1000, 100), + Northing = seq(0, 1000, 100) +) + +mytrns <- transmit_along_path(mypath, + vel = 0.5, delayRng = c(60, 180), + burstDur = 5.0, + colNames = list( + x = "Easting", + y = "Northing" + ), + sp_out = FALSE +) plot(mypath, type = "o") points(mytrns, pch = 20, col = "red") -#Example 3 - data.frame input using pathCRS arg +# Example 3 - data.frame input using pathCRS arg -mypath <- data.frame(deploy_long = c(-87, -87.1, -87), - deploy_lat = c(44, 44.1, 44.2)) +mypath <- data.frame( + deploy_long = c(-87, -87.1, -87), + deploy_lat = c(44, 44.1, 44.2) +) -mytrns <- transmit_along_path(mypath, vel = 0.5, delayRng = c(600, 1800), - burstDur = 5.0, - colNames = list(x = "deploy_long", - y = "deploy_lat"), - pathCRS = 4326, - sp_out = FALSE) +mytrns <- transmit_along_path(mypath, + vel = 0.5, delayRng = c(600, 1800), + burstDur = 5.0, + colNames = list( + x = "deploy_long", + y = "deploy_lat" + ), + pathCRS = 4326, + sp_out = FALSE +) plot(mypath, type = "o") points(mytrns, pch = 20, col = "red") -#Example 4 - sf POINT input +# Example 4 - sf POINT input -#simulate in great lakes polygon +# simulate in great lakes polygon data(great_lakes_polygon) mypath_sf <- crw_in_polygon(great_lakes_polygon, - theta = c(0, 25), - stepLen = 100, - initHeading = 0, - nsteps = 10, - cartesianCRS = 3175) - -mytrns_sf <- transmit_along_path(mypath_sf, - vel = 0.5, - delayRng = c(60, 180), - burstDur = 5.0) + theta = c(0, 25), + stepLen = 100, + initHeading = 0, + nsteps = 10, + cartesianCRS = 3175 +) + +mytrns_sf <- transmit_along_path(mypath_sf, + vel = 0.5, + delayRng = c(60, 180), + burstDur = 5.0 +) plot(mypath_sf, type = "o") points(sf::st_coordinates(mytrns_sf), pch = 20, col = "red") -#Example 5 - SpatialPointsDataFrame input +# Example 5 - SpatialPointsDataFrame input -#simulate in great lakes polygon +# simulate in great lakes polygon data(greatLakesPoly) mypath_sp <- crw_in_polygon(greatLakesPoly, - theta = c(0, 25), - stepLen = 100, - initHeading = 0, - nsteps = 10, - cartesianCRS = 3175) + theta = c(0, 25), + stepLen = 100, + initHeading = 0, + nsteps = 10, + cartesianCRS = 3175 +) -mytrns_sp <- transmit_along_path(mypath_sp, - vel = 0.5, - delayRng = c(60, 180), - burstDur = 5.0) +mytrns_sp <- transmit_along_path(mypath_sp, + vel = 0.5, + delayRng = c(60, 180), + burstDur = 5.0 +) plot(sf::st_coordinates(sf::st_as_sf(mypath_sp)), type = "o") points(sf::st_coordinates(mytrns_sp), pch = 20, col = "red") - } \author{ C. Holbrook \email{cholbrook@usgs.gov} diff --git a/man/vdat_convert.Rd b/man/vdat_convert.Rd index e713817f..da385a92 100644 --- a/man/vdat_convert.Rd +++ b/man/vdat_convert.Rd @@ -104,86 +104,91 @@ extension) as the source file (e.g., } \examples{ - \dontrun{ # Check vdat.exe check_vdat() -#all examples below assume path to VDAT.exe is in system PATH environment +# all examples below assume path to VDAT.exe is in system PATH environment # variable. If not (you get an error), add input argument 'vdat_exe_path' # with path directory with VDAT.exe. # e.g., -#vdat_convert(vrl_files, +# vdat_convert(vrl_files, # vdat_exe_path = "C:/Program Files/Innovasea/Fathom") -#get path to example VRL files in glatos +# get path to example VRL files in glatos vrl_files <- system.file("extdata", "detection_files_raw", - c("VR2W_109924_20110718_1.vrl", - "VR2W180_302187_20180629_1.vrl", - "VR2AR_546310_20190613_1.vrl", - "VR2Tx_480022_20190613_1.vrl"), - package = "glatos") + c( + "VR2W_109924_20110718_1.vrl", + "VR2W180_302187_20180629_1.vrl", + "VR2AR_546310_20190613_1.vrl", + "VR2Tx_480022_20190613_1.vrl" + ), + package = "glatos" +) -#copy to temp_dir +# copy to temp_dir temp_dir <- tempdir() vrl_files2 <- file.path(temp_dir, basename(vrl_files)) file.copy(vrl_files, vrl_files2) -#uncomment to open in file browser -#utils::browseURL(temp_dir) +# uncomment to open in file browser +# utils::browseURL(temp_dir) -#call VDAT.exe; default args +# call VDAT.exe; default args vdat_convert(vrl_files2) -#run again and overwrite +# run again and overwrite vdat_convert(vrl_files2, overwrite = TRUE) -#run again without progress bars +# run again without progress bars vdat_convert(vrl_files2, overwrite = TRUE, show_progress = FALSE) -#use split output format +# use split output format vdat_convert(vrl_files2, output_format = "csv.fathom.split") -#change output directory +# change output directory new_dir <- file.path(temp_dir, "testdir") -if(!dir.exists(new_dir)) dir.create(new_dir) +if (!dir.exists(new_dir)) dir.create(new_dir) -#write to new directory +# write to new directory vdat_convert(vrl_files2, out_dir = new_dir) -#multiple source folders -#make new folder for each vrl file inside temp directory -new_dir2 <- file.path(temp_dir, - "testdir2", - seq_along(vrl_files2)) -for(i in 1:length(new_dir2)){ - if(!dir.exists(new_dir2[i])) dir.create(new_dir2[i], recursive = TRUE) +# multiple source folders +# make new folder for each vrl file inside temp directory +new_dir2 <- file.path( + temp_dir, + "testdir2", + seq_along(vrl_files2) +) +for (i in 1:length(new_dir2)) { + if (!dir.exists(new_dir2[i])) dir.create(new_dir2[i], recursive = TRUE) } -#redistribute files +# redistribute files vrl_files3 <- file.path(new_dir2, basename(vrl_files2)) file.copy(vrl_files2, vrl_files3) -#write each CSV file to same location as corresponding VRL (full path input) +# write each CSV file to same location as corresponding VRL (full path input) vdat_convert(vrl_files3) -#same but use input dir only and overwrite = TRUE +# same but use input dir only and overwrite = TRUE vdat_convert(dirname(vrl_files3), overwrite = TRUE) -#same but write all CSV files to new location +# same but write all CSV files to new location new_dir3 <- file.path(temp_dir, "testdir3") -if(!dir.exists(new_dir3)) dir.create(new_dir3) +if (!dir.exists(new_dir3)) dir.create(new_dir3) vdat_convert(vrl_files3, out_dir = new_dir3) -#same but use input dir only and recursive = TRUE -vdat_convert(src = file.path(temp_dir, "testdir2"), - out_dir = new_dir3, - overwrite = TRUE, - recursive = TRUE) - +# same but use input dir only and recursive = TRUE +vdat_convert( + src = file.path(temp_dir, "testdir2"), + out_dir = new_dir3, + overwrite = TRUE, + recursive = TRUE +) } } diff --git a/man/vector_heading.Rd b/man/vector_heading.Rd index f21ed3a5..b5fea265 100644 --- a/man/vector_heading.Rd +++ b/man/vector_heading.Rd @@ -38,31 +38,37 @@ This function is called from within \code{\link[=crw_in_polygon]{crw_in_polygon( } \examples{ -#example using generic cartesian (regular grid) coordinates -x=c(2,4) -y=c(2,4) +# example using generic cartesian (regular grid) coordinates +x <- c(2, 4) +y <- c(2, 4) vector_heading(x, y) -x2=c(2,4,2) -y2=c(2,4,2) +x2 <- c(2, 4, 2) +y2 <- c(2, 4, 2) vector_heading(x2, y2) -#example using WGS84 lat-lon -#e.g., from Duluth to Toronto to Detroit +# example using WGS84 lat-lon +# e.g., from Duluth to Toronto to Detroit -path1 <- data.frame(city = c("Duluth", "Toronoto", "Detroit"), - longitude = c(-92.1005, -79.3832, -83.0458), - latitude = c(46.7867, 43.6532, 42.3314)) +path1 <- data.frame( + city = c("Duluth", "Toronoto", "Detroit"), + longitude = c(-92.1005, -79.3832, -83.0458), + latitude = c(46.7867, 43.6532, 42.3314) +) -#example using the x, y input method way -vector_heading(x = c(-92.1005, -79.3832, -83.0458), - y = c(46.7867, 43.6532, 42.3314), - coord_sys = "longlat") - -#example using the x-only input method -vector_heading(x = path1[ , c("longitude", "latitude")], - coord_sys = "longlat") +# example using the x, y input method way +vector_heading( + x = c(-92.1005, -79.3832, -83.0458), + y = c(46.7867, 43.6532, 42.3314), + coord_sys = "longlat" +) + +# example using the x-only input method +vector_heading( + x = path1[, c("longitude", "latitude")], + coord_sys = "longlat" +) } \author{ diff --git a/man/vrl2csv-deprecated.Rd b/man/vrl2csv-deprecated.Rd index dc39e091..28f5e77a 100644 --- a/man/vrl2csv-deprecated.Rd +++ b/man/vrl2csv-deprecated.Rd @@ -54,18 +54,18 @@ warning message even if conversion was successful. \examples{ \dontrun{ -#get path to example VRL in this package -myVRL <- system.file("extdata", "detection_files_raw", - "VR2W_109924_20110718_1.vrl", - package = "glatos") - -vrl2csv(dirname(myVRL)) #directory input -vrl2csv(myVRL) #file name input +# get path to example VRL in this package +myVRL <- system.file("extdata", "detection_files_raw", + "VR2W_109924_20110718_1.vrl", + package = "glatos" +) -#setting 'overwrite=FALSE' will make new file with '_n'added to name -vrl2csv(myVRL, overwrite=F) -} +vrl2csv(dirname(myVRL)) # directory input +vrl2csv(myVRL) # file name input +# setting 'overwrite=FALSE' will make new file with '_n'added to name +vrl2csv(myVRL, overwrite = F) +} } \seealso{ diff --git a/man/vue_convert.Rd b/man/vue_convert.Rd index 0b9fa2b1..347e1d7a 100644 --- a/man/vue_convert.Rd +++ b/man/vue_convert.Rd @@ -93,87 +93,91 @@ same (except for extension) as the source file (e.g., } \examples{ - \dontrun{ # Check vue.exe check_vue() -#all examples below assume path to VUE.exe is in system PATH environment +# all examples below assume path to VUE.exe is in system PATH environment # variable. If not (you get an error), add input argument 'vue_exe_path' # with path directory with VUE.exe. # e.g., -#vue_convert(vrl_files, +# vue_convert(vrl_files, # vue_exe_path = "C:/Program Files (x86)/Vemco/VUE") -#get path to example VRL files in glatos +# get path to example VRL files in glatos vrl_files <- system.file("extdata", "detection_files_raw", - c("VR2W_109924_20110718_1.vrl", - "VR2W180_302187_20180629_1.vrl", - "VR2AR_546310_20190613_1.vrl", - "VR2Tx_480022_20190613_1.vrl"), - package = "glatos") + c( + "VR2W_109924_20110718_1.vrl", + "VR2W180_302187_20180629_1.vrl", + "VR2AR_546310_20190613_1.vrl", + "VR2Tx_480022_20190613_1.vrl" + ), + package = "glatos" +) -#copy to temp_dir +# copy to temp_dir temp_dir <- tempdir() vrl_files2 <- file.path(temp_dir, basename(vrl_files)) file.copy(vrl_files, vrl_files2) -#uncomment to open in file browser -#utils::browseURL(temp_dir) +# uncomment to open in file browser +# utils::browseURL(temp_dir) -#call VUE.exe; default args +# call VUE.exe; default args vue_convert(vrl_files2) -#run again and overwrite +# run again and overwrite vue_convert(vrl_files2, overwrite = TRUE) -#run again without progress bars +# run again without progress bars vue_convert(vrl_files2, overwrite = TRUE, show_progress = FALSE) -#change output directory +# change output directory new_dir <- file.path(temp_dir, "testdir") -if(!dir.exists(new_dir)) dir.create(new_dir) +if (!dir.exists(new_dir)) dir.create(new_dir) -#write to new directory +# write to new directory vue_convert(vrl_files2, out_dir = new_dir) -#multiple source folders -#make new folder for each vrl file inside temp directory -new_dir2 <- file.path(temp_dir, - "testdir2", - seq_along(vrl_files2)) -for(i in 1:length(new_dir2)){ - if(!dir.exists(new_dir2[i])) dir.create(new_dir2[i], recursive = TRUE) +# multiple source folders +# make new folder for each vrl file inside temp directory +new_dir2 <- file.path( + temp_dir, + "testdir2", + seq_along(vrl_files2) +) +for (i in 1:length(new_dir2)) { + if (!dir.exists(new_dir2[i])) dir.create(new_dir2[i], recursive = TRUE) } -#redistribute files +# redistribute files vrl_files3 <- file.path(new_dir2, basename(vrl_files2)) file.copy(vrl_files2, vrl_files3) -#write each CSV file to same location as corresponding VRL (full path input) +# write each CSV file to same location as corresponding VRL (full path input) vue_convert(vrl_files3) -#same but use input dir only and overwrite = TRUE +# same but use input dir only and overwrite = TRUE vue_convert(dirname(vrl_files3), overwrite = TRUE) -#same but write all CSV files to new location +# same but write all CSV files to new location new_dir3 <- file.path(temp_dir, "testdir3") -if(!dir.exists(new_dir3)) dir.create(new_dir3) +if (!dir.exists(new_dir3)) dir.create(new_dir3) vue_convert(vrl_files3, out_dir = new_dir3) -#same but use input dir only and recursive = TRUE -vue_convert(src = file.path(temp_dir, "testdir2"), - out_dir = new_dir3, - overwrite = TRUE, - recursive = TRUE) - +# same but use input dir only and recursive = TRUE +vue_convert( + src = file.path(temp_dir, "testdir2"), + out_dir = new_dir3, + overwrite = TRUE, + recursive = TRUE +) } - } \author{ C. Holbrook (cholbrook@usgs.gov) diff --git a/man/write_vdat_csv.Rd b/man/write_vdat_csv.Rd index 16c77846..fdf19361 100644 --- a/man/write_vdat_csv.Rd +++ b/man/write_vdat_csv.Rd @@ -62,24 +62,25 @@ Writing is done via \code{\link[data.table]{fwrite}}. # Example 1. Read and write a single file vrl_file <- system.file("extdata", "detection_files_raw", - "VR2W_109924_20110718_1.vrl", package="glatos") + "VR2W_109924_20110718_1.vrl", + package = "glatos" +) temp_dir <- tempdir() csv_file <- vdat_convert(vrl_file, out_dir = temp_dir) -#utils::browseURL(temp_dir) +# utils::browseURL(temp_dir) -#read all record types +# read all record types vdat <- read_vdat_csv(csv_file) -#write to single file (output_format = "csv.fathom") +# write to single file (output_format = "csv.fathom") write_vdat_csv(vdat) -#write to multiple files +# write to multiple files write_vdat_csv(vdat, output_format = "csv.fathom.split") - } \author{ C. Holbrook (cholbrook@usgs.gov)