Closed leilafouda closed 1 year ago
Just to note that when the package version from CRAN (0.1.7
) is used rather than the current development version from GitHub the random_steps()
function works but anything that was updated to use terra
rather than raster
has reverted to utilising raster
functions and features!
Thanks for reporting. I am preparing the new CRAN submission and will fix the problems you encounted.
That is great thank you @jmsigner! I look forward to it. Is there a rough timeline?
Hi @leilafouda, in the current Github version it worked for me, would you mind giving it an other try?
library(tidyverse)
library(amt)
#>
#> Attaching package: 'amt'
#> The following object is masked from 'package:stats':
#>
#> filter
data(sh)
tr2 <- sh %>% filter(complete.cases(.)) %>%
mutate(
ts = as.POSIXct(lubridate::ymd(day) + lubridate::hms(time)),
id = "Animal 1",
month = lubridate::month(ts)
) %>%
filter(!duplicated(ts)) %>%
make_track(x_epsg31467, y_epsg31467, ts, id = id, month = month,
crs = 'epsg:31467')
transform_coords(tr2, 'epsg:4326')
#> # A tibble: 1,493 × 5
#> x_ y_ t_ id month
#> * <dbl> <dbl> <dttm> <chr> <dbl>
#> 1 9.89 54.1 2008-03-30 00:01:47 Animal 1 3
#> 2 9.89 54.1 2008-03-30 06:00:54 Animal 1 3
#> 3 9.89 54.1 2008-03-30 12:01:47 Animal 1 3
#> 4 9.89 54.1 2008-03-30 18:01:24 Animal 1 3
#> 5 9.89 54.1 2008-03-30 18:25:56 Animal 1 3
#> 6 9.89 54.1 2008-03-30 18:26:05 Animal 1 3
#> 7 9.89 54.1 2008-03-30 18:26:14 Animal 1 3
#> 8 9.89 54.1 2008-03-30 18:26:24 Animal 1 3
#> 9 9.89 54.1 2008-03-30 18:26:33 Animal 1 3
#> 10 9.89 54.1 2008-03-30 18:38:01 Animal 1 3
#> # … with 1,483 more rows
tr2 <- tr2 %>% mutate(sl_ = step_lengths(.))
summary(tr2$sl_)
#> Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
#> 0.00 35.01 105.33 249.07 297.75 4727.86 1
summarize_sampling_rate(tr2)
#> # A tibble: 1 × 9
#> min q1 median mean q3 max sd n unit
#> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <chr>
#> 1 0.0025 2.00 2.01 6.34 6.00 3924. 102. 1492 hour
tr3 <- tr2 %>% track_resample(rate = hours(6), tolerance = minutes(20))
tr3_burst <- tr3 %>% steps_by_burst()
tr3_burst_ssf1 <- tr3_burst %>% random_steps(n_control = 20)
tr3_burst_ssf1
#> # A tibble: 15,939 × 12
#> burst_ x1_ x2_ y1_ y2_ sl_ ta_ t1_
#> * <dbl> <int> <dbl> <int> <dbl> <dbl> <dbl> <dttm>
#> 1 1 3558513 3558564 5999055 5999146 104. 3.00 2008-03-30 06:00:54
#> 2 1 3558513 3558670. 5999055 5999867. 827. -2.97 2008-03-30 06:00:54
#> 3 1 3558513 3558610. 5999055 5998970. 129. 1.22 2008-03-30 06:00:54
#> 4 1 3558513 3558675. 5999055 5999002. 170. 1.62 2008-03-30 06:00:54
#> 5 1 3558513 3558693. 5999055 5999112. 189. 2.24 2008-03-30 06:00:54
#> 6 1 3558513 3558280. 5999055 5998793. 350. -0.360 2008-03-30 06:00:54
#> 7 1 3558513 3558478. 5999055 5999003. 62.2 -0.223 2008-03-30 06:00:54
#> 8 1 3558513 3558302. 5999055 5998836. 304. -0.399 2008-03-30 06:00:54
#> 9 1 3558513 3559020. 5999055 6000316. 1359. 3.13 2008-03-30 06:00:54
#> 10 1 3558513 3558678. 5999055 5999176. 204. 2.57 2008-03-30 06:00:54
#> # … with 15,929 more rows, and 4 more variables: t2_ <dttm>, dt_ <drtn>,
#> # case_ <lgl>, step_id_ <int>
Created on 2023-02-12 with reprex v2.0.2
Hi @jmsigner, sorry for my delay in getting back to you. It is now working thank you so much for the update.
Hello!
I am trying to run the
random_steps()
function on individual animal movement tracks in UTM.I recently updated the package and am now getting two different errors:
Either:
Error: Expecting a single value: [extent=0].
orError in out[[1]] : subscript out of bounds
I tried to run the same process on the pre-loaded data from the amt vignette and Fieberg et al 2021
Vignette:
Fieberg et al 2021
With both above examples, I get:
Error: Expecting a single value: [extent=0].
I recently updated my packages:
install.packages(c("broom", "class", "codetools", "colorspace", "dplyr", "e1071", "effectsize", "fansi", "fontawesome", "forcats", "fs", "future", "gargle", "ggrepel", "gsl", "insight", "knitr", "lubridate", "markdown", "MASS", "nlme", "parameters", "Rcpp", "rmarkdown", "Rmpfr", "sass", "sourcetools", "spatial", "spatstat", "spatstat.explore", "spatstat.geom", "spatstat.linnet", "spatstat.model", "spatstat.random", "terra", "tidyr", "tinytex", "utf8", "vctrs", "vroom", "xfun", "yaml"))
and
amt
.The
Error in out[[1]] : subscript out of bounds
appeared when I played around with thetrack_resample
making it too long too short!Would you know the source and a fix for either of these errors?
Thank you for your time!