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Remove geosphere dependency #236

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merged 10 commits into from
Aug 16, 2024
Merged

Remove geosphere dependency #236

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980a458
rm geosphere
mhpob May 23, 2024
28550d6
drop geosphere in favor of hard-coded haversine
mhpob May 24, 2024
dec4ece
rm geosphere
mhpob May 24, 2024
f88fcb4
rm geosphere. closes #235
mhpob May 24, 2024
9016179
Merge branch 'dev-rm-geosphere' of https://github.com/mhpob/glatos in…
mhpob May 24, 2024
64237d6
Add initial tests for point_offset
mhpob May 24, 2024
0750b57
Add initial interpolate_path tests
mhpob May 24, 2024
c64e8c9
Style code (GHA)
mhpob May 24, 2024
222cd6c
Merge branch 'dev' into dev-rm-geosphere
chrisholbrook Aug 16, 2024
d4ca28b
Style code (GHA)
chrisholbrook Aug 16, 2024
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1 change: 0 additions & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,6 @@ Imports:
gdalUtilities,
geodist,
gdistance,
geosphere,
jsonlite,
lubridate,
plotrix,
Expand Down
33 changes: 27 additions & 6 deletions R/util-point_offset.r
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Original file line number Diff line number Diff line change
@@ -1,8 +1,7 @@
#' @title Identify new location based on distance and bearing from another
#'
#' @description Calculates latitude and longitude for new point that is x meters
#' away at bearing y from a geographic location (Longitude, Latitude). uses
#' "destPoint" function from "geosphere" package and calculations are based on
#' away at bearing y from a geographic location (Longitude, Latitude) using
#' great circle distances.
#'
#' @param lon vector of longitudes (dd) to calculate offset points
Expand Down Expand Up @@ -32,9 +31,7 @@

point_offset <- function(lon = NA, lat = NA, offsetDist = NA, offsetDir = NA,
distUnit = "m") {
# require(geosphere) #for spatialPoints

if (distUnit == "ft") offsetDist <- 0.3048 * offsetDist # conver to m if needed
if (distUnit == "ft") offsetDist <- 0.3048 * offsetDist # convert to m if needed
if (!(distUnit) %in% c("ft", "m")) {
stop("Input attribute 'dirUnit' must be 'm' (meters) or 'ft' (feet).")
}
Expand All @@ -53,6 +50,30 @@ point_offset <- function(lon = NA, lat = NA, offsetDist = NA, offsetDir = NA,

bearing <- dirKey$deg[match(offsetDir, dirKey$txt)]

pos <- geosphere::destPoint(cbind(lon, lat), bearing, offsetDist)
haversine <- function(lon, lat, bearing, offsetDist) {
lat <- lat * pi / 180
lon <- lon * pi / 180
R <- 6378137
bearing <- bearing * pi / 180
lat2 <- asin(sin(lat) * cos(offsetDist / R) + cos(lat) * sin(offsetDist / R) * cos(bearing))
lon2 <- 180 / pi * (
lon + atan2(
sin(bearing) * sin(offsetDist / R) * cos(lat),
cos(offsetDist / R) - sin(lat) * sin(lat2)
)
)

lat2 <- 180 / pi * lat2

coords <- matrix(
c(lon2, lat2),
ncol = 2,
dimnames = list(NULL, c("lon", "lat"))
)

return(coords)
}

pos <- haversine(lon, lat, bearing, offsetDist)
return(pos)
}
28 changes: 23 additions & 5 deletions R/vis-interpolate_path.r
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Expand Up @@ -380,7 +380,15 @@ interpolate_path <- function(det, trans = NULL, start_time = NULL,
# as.matrix(.SD[.N, c("deploy_long", "deploy_lat")])), by = i.start]

# remove geosphere dependency and use geodist. geosphere relies on sp and raster.
dtc[, gcd := geodist::geodist_vec(x1 = .SD[[1, "deploy_long"]], y1 = .SD[[1, "deploy_lat"]], x2 = .SD[[.N, "deploy_long"]], y2 = .SD[[.N, "deploy_lat"]], measure = "haversine"), by = i.start]
dtc[, gcd := geodist::geodist_vec(
x1 = .SD[[1, "deploy_long"]],
y1 = .SD[[1, "deploy_lat"]],
x2 = .SD[[.N, "deploy_long"]],
y2 = .SD[[.N, "deploy_lat"]],
measure = "haversine"
),
by = i.start
]

# calculate least cost (non-linear) distance between points
message("Calculating least-cost (non-linear) distances... (step 1 of 3)")
Expand Down Expand Up @@ -577,10 +585,20 @@ interpolate_path <- function(det, trans = NULL, start_time = NULL,
nln_small[, latitude_lead := data.table::shift(nln_latitude, type = "lag", fill = NA), by = i.start]
nln_small[, longitude_lead := data.table::shift(nln_longitude, type = "lag", fill = NA), by = i.start]

nln_small[, cumdist := geosphere::distGeo(
.SD[, c("nln_longitude", "nln_latitude")],
.SD[, c("longitude_lead", "latitude_lead")]
), by = i.start]
# Switch from geosphere to geodist
# nln_small[, cumdist := geosphere::distGeo(
# .SD[, c("nln_longitude", "nln_latitude")],
# .SD[,c("longitude_lead", "latitude_lead")]), by = i.start]

nln_small[, cumdist := geodist::geodist_vec(
x1 = .SD[["nln_longitude"]],
y1 = .SD[["nln_latitude"]],
x2 = .SD[["longitude_lead"]],
y2 = .SD[["latitude_lead"]],
measure = "geodesic"
),
by = .I
]

nln_small[is.na(cumdist), cumdist := 0]
nln_small[, cumdist := cumsum(cumdist), by = i.start]
Expand Down
6 changes: 2 additions & 4 deletions inst/supplemental_docs/detection_range_handout.Rmd
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Expand Up @@ -167,7 +167,6 @@ https://github.com/ocean-tracking-network/glatos.
# load libraries
library(glatos)
library(data.table)
library(geosphere)
library(ggplot2)

# load detection data from glatos package
Expand All @@ -188,7 +187,7 @@ of columns.
Many of the columns in the dtc object are not needed for this
analysis. In the next code chunk, we will extract only the necessary
columns from the `dtc` object and calculate the geographic distance
between each receiver using the `geosphere::distm` function. The
between each receiver using the `geodist::geodist_vec` function. The
internal tag on 4 receivers was used in this study so distances among
receivers is the same as distances between each tag and receiver.

Expand All @@ -202,8 +201,7 @@ dtc <- dtc[, c("detection_timestamp_utc", "transmitter_id", "receiver_sn",
rec_dist <- unique(dtc[,c("receiver_sn", "deploy_lat", "deploy_long")])

# calculate distance matrix
dist_matrix <- distm(rec_dist[, c("deploy_long", "deploy_lat")],
rec_dist[, c("deploy_long", "deploy_lat")])
dist_matrix <- geodist::geodist_vec(rec_dist$deploy_long, rec_dist$deploy_lat)

# rename columns and rows of matrix
colnames(dist_matrix) <- rec_dist[,get("receiver_sn")]
Expand Down
3 changes: 1 addition & 2 deletions man/point_offset.Rd
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136 changes: 136 additions & 0 deletions tests/testthat/_snaps/interpolate_path.md
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@@ -0,0 +1,136 @@
# linear interpolation works

Code
linear_interp
Output
animal_id bin_timestamp latitude longitude record_type
1 1 2000-01-01 44.00000 -87.00000 detection
2 1 2000-01-02 44.01613 -86.85484 interpolated
3 1 2000-01-03 44.03226 -86.70968 interpolated
4 1 2000-01-04 44.04839 -86.56452 interpolated
5 1 2000-01-05 44.06452 -86.41935 interpolated
6 1 2000-01-06 44.08065 -86.27419 interpolated
7 1 2000-01-07 44.09677 -86.12903 interpolated
8 1 2000-01-08 44.11290 -85.98387 interpolated
9 1 2000-01-09 44.12903 -85.83871 interpolated
10 1 2000-01-10 44.14516 -85.69355 interpolated
11 1 2000-01-11 44.16129 -85.54839 interpolated
12 1 2000-01-12 44.17742 -85.40323 interpolated
13 1 2000-01-13 44.19355 -85.25806 interpolated
14 1 2000-01-14 44.20968 -85.11290 interpolated
15 1 2000-01-15 44.22581 -84.96774 interpolated
16 1 2000-01-16 44.24194 -84.82258 interpolated
17 1 2000-01-17 44.25806 -84.67742 interpolated
18 1 2000-01-18 44.27419 -84.53226 interpolated
19 1 2000-01-19 44.29032 -84.38710 interpolated
20 1 2000-01-20 44.30645 -84.24194 interpolated
21 1 2000-01-21 44.32258 -84.09677 interpolated
22 1 2000-01-22 44.33871 -83.95161 interpolated
23 1 2000-01-23 44.35484 -83.80645 interpolated
24 1 2000-01-24 44.37097 -83.66129 interpolated
25 1 2000-01-25 44.38710 -83.51613 interpolated
26 1 2000-01-26 44.40323 -83.37097 interpolated
27 1 2000-01-27 44.41935 -83.22581 interpolated
28 1 2000-01-28 44.43548 -83.08065 interpolated
29 1 2000-01-29 44.45161 -82.93548 interpolated
30 1 2000-01-30 44.46774 -82.79032 interpolated
31 1 2000-01-31 44.48387 -82.64516 interpolated
32 1 2000-02-01 44.50000 -82.50000 detection
33 1 2000-02-02 44.46552 -82.34483 interpolated
34 1 2000-02-03 44.43103 -82.18966 interpolated
35 1 2000-02-04 44.39655 -82.03448 interpolated
36 1 2000-02-05 44.36207 -81.87931 interpolated
37 1 2000-02-06 44.32759 -81.72414 interpolated
38 1 2000-02-07 44.29310 -81.56897 interpolated
39 1 2000-02-08 44.25862 -81.41379 interpolated
40 1 2000-02-09 44.22414 -81.25862 interpolated
41 1 2000-02-10 44.18966 -81.10345 interpolated
42 1 2000-02-11 44.15517 -80.94828 interpolated
43 1 2000-02-12 44.12069 -80.79310 interpolated
44 1 2000-02-13 44.08621 -80.63793 interpolated
45 1 2000-02-14 44.05172 -80.48276 interpolated
46 1 2000-02-15 44.01724 -80.32759 interpolated
47 1 2000-02-16 43.98276 -80.17241 interpolated
48 1 2000-02-17 43.94828 -80.01724 interpolated
49 1 2000-02-18 43.91379 -79.86207 interpolated
50 1 2000-02-19 43.87931 -79.70690 interpolated
51 1 2000-02-20 43.84483 -79.55172 interpolated
52 1 2000-02-21 43.81034 -79.39655 interpolated
53 1 2000-02-22 43.77586 -79.24138 interpolated
54 1 2000-02-23 43.74138 -79.08621 interpolated
55 1 2000-02-24 43.70690 -78.93103 interpolated
56 1 2000-02-25 43.67241 -78.77586 interpolated
57 1 2000-02-26 43.63793 -78.62069 interpolated
58 1 2000-02-27 43.60345 -78.46552 interpolated
59 1 2000-02-28 43.56897 -78.31034 interpolated
60 1 2000-02-29 43.53448 -78.15517 interpolated
61 1 2000-03-01 43.50000 -78.00000 detection

# Non-linear interpolation works

Code
nonlinear_interp
Output
animal_id bin_timestamp latitude longitude record_type
1 1 2000-01-01 44.00000 -87.00000 detection
2 1 2000-01-02 44.14456 -87.01280 interpolated
3 1 2000-01-03 44.28736 -86.99353 interpolated
4 1 2000-01-04 44.39165 -86.84604 interpolated
5 1 2000-01-05 44.49603 -86.69840 interpolated
6 1 2000-01-06 44.60050 -86.55064 interpolated
7 1 2000-01-07 44.70507 -86.40275 interpolated
8 1 2000-01-08 44.80973 -86.25472 interpolated
9 1 2000-01-09 44.91448 -86.10656 interpolated
10 1 2000-01-10 45.01933 -85.95826 interpolated
11 1 2000-01-11 45.12427 -85.80983 interpolated
12 1 2000-01-12 45.22932 -85.66127 interpolated
13 1 2000-01-13 45.33445 -85.51257 interpolated
14 1 2000-01-14 45.43968 -85.36373 interpolated
15 1 2000-01-15 45.54501 -85.21476 interpolated
16 1 2000-01-16 45.65044 -85.06565 interpolated
17 1 2000-01-17 45.74961 -84.91262 interpolated
18 1 2000-01-18 45.75648 -84.70329 interpolated
19 1 2000-01-19 45.72012 -84.49758 interpolated
20 1 2000-01-20 45.65750 -84.30603 interpolated
21 1 2000-01-21 45.59065 -84.11694 interpolated
22 1 2000-01-22 45.52387 -83.92803 interpolated
23 1 2000-01-23 45.45715 -83.73930 interpolated
24 1 2000-01-24 45.37617 -83.56547 interpolated
25 1 2000-01-25 45.27099 -83.41672 interpolated
26 1 2000-01-26 45.16591 -83.26810 interpolated
27 1 2000-01-27 45.06093 -83.11961 interpolated
28 1 2000-01-28 44.95605 -82.97127 interpolated
29 1 2000-01-29 44.85125 -82.82305 interpolated
30 1 2000-01-30 44.74656 -82.67497 interpolated
31 1 2000-01-31 44.64195 -82.52702 interpolated
32 1 2000-02-01 44.50000 -82.50000 detection
33 1 2000-02-02 44.27598 -82.41394 interpolated
34 1 2000-02-03 44.02721 -82.41394 interpolated
35 1 2000-02-04 43.77843 -82.41394 interpolated
36 1 2000-02-05 43.52964 -82.41394 interpolated
37 1 2000-02-06 43.28084 -82.41394 interpolated
38 1 2000-02-07 43.03202 -82.41394 interpolated
39 1 2000-02-08 42.80359 -82.47917 interpolated
40 1 2000-02-09 42.60977 -82.59843 interpolated
41 1 2000-02-10 42.43783 -82.84162 interpolated
42 1 2000-02-11 42.27309 -83.09093 interpolated
43 1 2000-02-12 42.03710 -83.06659 interpolated
44 1 2000-02-13 41.99075 -82.75061 interpolated
45 1 2000-02-14 42.02156 -82.42462 interpolated
46 1 2000-02-15 42.12825 -82.12284 interpolated
47 1 2000-02-16 42.23508 -81.82064 interpolated
48 1 2000-02-17 42.34205 -81.51804 interpolated
49 1 2000-02-18 42.43982 -81.21055 interpolated
50 1 2000-02-19 42.49761 -80.88362 interpolated
51 1 2000-02-20 42.55545 -80.55641 interpolated
52 1 2000-02-21 42.64289 -80.24305 interpolated
53 1 2000-02-22 42.71383 -79.92129 interpolated
54 1 2000-02-23 42.77186 -79.59301 interpolated
55 1 2000-02-24 42.82994 -79.26443 interpolated
56 1 2000-02-25 42.88807 -78.93556 interpolated
57 1 2000-02-26 43.07781 -79.02641 interpolated
58 1 2000-02-27 43.28679 -78.97607 interpolated
59 1 2000-02-28 43.38565 -78.66456 interpolated
60 1 2000-02-29 43.44428 -78.33286 interpolated
61 1 2000-03-01 43.50000 -78.00000 detection

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