Skip to content

Commit

Permalink
Add initial interpolate_path tests
Browse files Browse the repository at this point in the history
  • Loading branch information
@mhpob
mhpob committed May 24, 2024
1 parent 64237d6 commit 0750b57
Show file tree
Hide file tree
Showing 3 changed files with 367 additions and 1 deletion.
5 changes: 4 additions & 1 deletion R/vis-interpolate_path.r
View file
Original file line number Diff line number Diff line change
Expand Up @@ -199,7 +199,10 @@ interpolate_path <- function(det, trans = NULL, start_time = NULL,

# stop if out_class is not NULL, data.table, or tibble
if(!is.null(out_class)){
if( !(out_class %in% c("data.table", "tibble"))) {stop('out_class is not a "data.table" or "tibble"')}}
if( !(out_class %in% c("data.table", "tibble"))) {
stop('out_class is not a "data.table" or "tibble"')
}
}

# check to see that trans is a transition layer or transition stack
if(!is.null(trans) &
Expand Down
136 changes: 136 additions & 0 deletions tests/testthat/_snaps/interpolate_path.md
View file
Original file line number Diff line number Diff line change
@@ -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

227 changes: 227 additions & 0 deletions tests/testthat/test-interpolate_path.R
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,227 @@
# Set up data from interpolate_path example 1
pos <- data.frame(
animal_id=1,
deploy_long=c(-87,-82.5, -78),
deploy_lat=c(44, 44.5, 43.5),
detection_timestamp_utc=as.POSIXct(
c("2000-01-01 00:00", "2000-02-01 00:00", "2000-03-01 00:00"),
tz = "UTC"
)
)




test_that("linear interpolation works", {
linear_interp <- interpolate_path(pos)
expect_snapshot(
linear_interp
)

expect_s3_class(
linear_interp,
'data.frame'
)

expect_named(
linear_interp,
c("animal_id", "bin_timestamp", "latitude", "longitude", "record_type")
)

# Retains actual detections
expect_equal(
nrow(
linear_interp[linear_interp$record_type == 'detection',]
),
nrow(pos)
)
})




test_that("Non-linear interpolation works", {
linear_interp <- interpolate_path(pos)
expect_message(
nonlinear_interp <- interpolate_path(pos, trans = greatLakesTrLayer),
'Calculating least-cost \\(non-linear\\) distances\\.\\.\\. \\(step 1 of 3\\)'
) |>
expect_output('|=*| 100%') |>
expect_message('Starting non-linear interpolation\\.\\.\\. \\(step 3 of 3\\)') |>
expect_message('Finalizing results\\.')

expect_false(
identical(
linear_interp,
nonlinear_interp
)
)

expect_snapshot(
nonlinear_interp
)

expect_s3_class(
nonlinear_interp,
'data.frame'
)

expect_named(
nonlinear_interp,
c("animal_id", "bin_timestamp", "latitude", "longitude", "record_type")
)

# Retains actual detections
expect_equal(
nrow(
nonlinear_interp[nonlinear_interp$record_type == 'detection',]
),
nrow(pos)
)
})



test_that("Forced linear interpolation works", {
linear_interp <- interpolate_path(pos)
nonlinear_interp <- suppressMessages(
interpolate_path(pos, trans = greatLakesTrLayer,
show_progress = FALSE)
)


forced_linear_interp <- interpolate_path(pos, trans = greatLakesTrLayer,
lnl_thresh = 0) |>
expect_no_message()


expect_false(
identical(
forced_linear_interp,
nonlinear_interp
)
)

expect_identical(
linear_interp,
forced_linear_interp
)

expect_s3_class(
forced_linear_interp,
'data.frame'
)

expect_named(
forced_linear_interp,
c("animal_id", "bin_timestamp", "latitude", "longitude", "record_type")
)

# Retains actual detections
expect_equal(
nrow(
forced_linear_interp[forced_linear_interp$record_type == 'detection',]
),
nrow(pos)
)
})



test_that("Progress bar can be suppressed", {
expect_output(
suppressMessages(
interpolate_path(pos, trans = greatLakesTrLayer,
show_progress = FALSE)
),
NA
)
})




test_that("Checks output class", {
# Error if wrong class
expect_error(
interpolate_path(pos, out_class = 'list'),
"out_class is not a \"data\\.table\" or \"tibble\""
)

# data.frame if NULL
expect_s3_class(
interpolate_path(pos, out_class = NULL),
'data.frame',
exact = TRUE
)

# data.table
expect_s3_class(
interpolate_path(pos, out_class = 'data.table'),
c('data.table', 'data.frame'),
exact = TRUE
)

# tibble
expect_s3_class(
interpolate_path(pos, out_class = 'tibble'),
c('tbl_df', 'tbl', 'data.frame'),
exact = TRUE
)
})



test_that("Checks trans is a transition layer or transition stack", {
suppressMessages(
trans <- make_transition3(great_lakes_polygon)
)

expect_error(
interpolate_path(pos, trans = trans),
"Supplied object for 'trans' argument is not class TransitionLayer or TransitionStack\\."
)
})



test_that("Checks that start_time was successfully coverted", {
expect_error(
interpolate_path(pos, start_time = NA),
"start_time cannot be coerced to 'POSIXct' or 'POSIXt' class"
)
})



test_that("Checks that start_time < largest timestamp in dataset", {
expect_error(
interpolate_path(pos, start_time = max(pos$detection_timestamp_utc) + 1),
"start_time is larger than last detection\\. No data to interpolate\\!"
)
})



test_that("Checks that fish have multiple observations", {
expect_error(
interpolate_path(pos[1,]),
"must have two observations to interpolate"
)
})



test_that("Errors and displays offending receivers if any receivers are on land", {
pos2 <- pos
pos2$deploy_long[1] <- -90

expect_error(
suppressMessages(
interpolate_path(pos2, trans = greatLakesTrLayer, show_progress = FALSE)
),
"Some coordinates are on land or beyond extent.
Interpolation impossible! Check receiver locations or extents of transition
layer:\n"
)
})

0 comments on commit 0750b57

Please sign in to comment.