foieGras failure for Lotek

[marosteg]

Stipulating 'fG = T' works for Wildlife Computers but not Lotek tags. Tested on multiple of each. Lotek failure example below:

> df <- get_3d(etuff, series=ts, fG=T) ## existing functionality to add spatial/location information to your series data
[1] "No time zone specified. Detecting the time zone(s) from the tracking data: Etc/GMT+8."
[1] "No time zone specified. Detecting the time zone(s) from the tracking data: America/Tijuana."
[1] "No time zone specified. Detecting the time zone(s) from the tracking data: America/Los_Angeles."
[1] "No time zone specified. Detecting the time zone(s) from the tracking data: America/Phoenix."
[1] "No time zone specified. Detecting the time zone(s) from the tracking data: America/Mazatlan."
[1] "No time zone specified. Detecting the time zone(s) from the tracking data: America/Hermosillo."
[1] "No time zone specified. Detecting the time zone(s) from the tracking data: America/Boise."
[1] "No time zone specified. Detecting the time zone(s) from the tracking data: Etc/GMT+7; Etc/GMT+8."
[1] "No time zone specified. Detecting the time zone(s) from the tracking data: America/Iqaluit."

pre-filtering data...
Warning in prefilter(., vmax = vmax, ang = ang, distlim = distlim, spdf = spdf,  :

argosfilter::sdafilter produced an error on id 1 using argosfilter::vmask instead
Warning in prefilter(., vmax = vmax, ang = ang, distlim = distlim, spdf = spdf,  :

argosfilter::vmask also produced an error on id 1 can not apply speed filter prior to SSM filtering

fitting SSM...
Error: Problem with `mutate()` input `id`.
x $ operator is invalid for atomic vectors
ℹ Input `id` is `sapply(.$ssm, function(x) x$data$id[1])`.
Run `rlang::last_error()` to see where the error occurred.
In addition: Warning messages:
1: In tz_lookup_accurate.sf(ll_sf) :
  Some points are in areas with more than one time zone defined.These are often disputed areas and should be treated with care.
2: In lubridate::with_tz(tr$DateTime[i], tr$tz[i]) :
  Unrecognized time zone 'Etc/GMT+7; Etc/GMT+8'
3: In as.POSIXlt.POSIXct(x, tz = tz(x)) :
  unknown timezone 'Etc/GMT+7; Etc/GMT+8'
4: In lubridate::with_tz(tr$DateTime[i], tr$tz[i]) :
  Unrecognized time zone 'Etc/GMT+7; Etc/GMT+8'
5: In as.POSIXlt.POSIXct(x, tz = tz(x)) :
  unknown timezone 'Etc/GMT+7; Etc/GMT+8'
6: Problem with `mutate()` input `date`.
ℹ All formats failed to parse. No formats found.
ℹ Input `date` is `ymd_hms(date, tz = "GMT")`. 

[camrinbraun]

sessionInfo() ??

[marosteg]

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] trawllight_3.1.0  tags2etuff_1.0.0  data.table_1.12.8 dplyr_1.0.2      

loaded via a namespace (and not attached):
  [1] VGAM_1.1-1          minqa_1.2.4         colorspace_1.4-1    ellipsis_0.3.1     
  [5] class_7.3-15        rgdal_1.4-8         rprojroot_1.3-2     fs_1.3.1           
  [9] mc2d_0.1-21         rstudioapi_0.11     ICV_1.0             listenv_0.7.0      
 [13] furrr_0.1.0         farver_2.0.3        remotes_2.2.0       mvtnorm_1.0-11     
 [17] lubridate_1.7.9.2   codetools_0.2-16    splines_3.6.3       polyclip_1.10-0    
 [21] pkgload_1.1.0       spam_2.6-0          nloptr_1.2.1        foieGras_0.4.0     
 [25] ggforce_0.3.2       compiler_3.6.3      backports_1.1.8     assertthat_0.2.1   
 [29] Matrix_1.2-18       cli_2.3.1           tweenr_1.0.1        prettyunits_1.1.1  
 [33] tools_3.6.3         dotCall64_1.0-1     gtable_0.3.0        glue_1.4.2         
 [37] reshape2_1.4.4      maps_3.3.0          Rcpp_1.0.6          raster_3.4-5       
 [41] vctrs_0.3.6         nlme_3.1-150        argosfilter_0.63    stringr_1.4.0      
 [45] globals_0.12.4      ps_1.3.4            testthat_2.3.2      lme4_1.1-25        
 [49] lifecycle_1.0.0     fishmethods_1.11-2  devtools_2.3.2      statmod_1.4.32     
 [53] future_1.14.0       MASS_7.3-53         scales_1.1.1        parallel_3.6.3     
 [57] TMB_1.7.16          fields_11.6         memoise_1.1.0       gridExtra_2.3      
 [61] ggplot2_3.3.2       reshape_0.8.8       stringi_1.5.3       maptools_1.0-2     
 [65] desc_1.2.0          e1071_1.7-3         OSCV_1.0            boot_1.3-24        
 [69] pkgbuild_1.1.0      rlang_0.4.10        pkgconfig_2.0.3     moments_0.14       
 [73] pracma_2.2.9        lattice_0.20-41     purrr_0.3.4         sf_0.8-1           
 [77] labeling_0.3        kedd_1.0.3          processx_3.4.4      tidyselect_1.1.0   
 [81] fasttime_1.0-2      lutz_0.3.1          plyr_1.8.6          magrittr_2.0.1     
 [85] R6_2.5.0            generics_0.1.0      bootstrap_2019.6    DBI_1.1.0          
 [89] pillar_1.4.6        foreign_0.8-75      withr_2.3.0         mgcv_1.8-33        
 [93] units_0.6-5         sp_1.4-5            tibble_3.0.4        crayon_1.4.1       
 [97] KernSmooth_2.23-16  usethis_1.6.3       grid_3.6.3          callr_3.5.1        
[101] digest_0.6.27       classInt_0.4-2      tidyr_1.1.2         numDeriv_2016.8-1.1
[105] stats4_3.6.3        munsell_0.5.0       sessioninfo_1.1.1

[camrinbraun]

may not be the complete solution but you definitely should update foieGras to at least master if not dev. i'm running the current dev on my machine and working fine.

i'm sure the source of position info in the eTUFF files was also problematic (raw light) but those have almost all been replaced with HMMoce derived estimates

[marosteg]

I updated to master for foieGras, as well as another half dozen plus packages involved in this function call, and am down to these issues:

Error in validityMethod(object) : duplicated records within data
In addition: Warning message:
Problem with `mutate()` column `date`.
ℹ `date = ymd_hms(date, tz = "UTC")`.
ℹ All formats failed to parse. No formats found. 

Traceback below:

 Error in validityMethod(object) : duplicated records within data 
20.
stop("duplicated records within data") 
19.
validityMethod(object) 
18.
isTRUE(x) 
17.
anyStrings(validityMethod(object)) 
16.
validObject(.Object) 
15.
initialize(value, ...) 
14.
initialize(value, ...) 
13.
new("trip", obj, TORnames) 
12.
trip(d.tr, TORnames = c("date", "id"), correct_all = FALSE) 
11.
trip(d.tr, TORnames = c("date", "id"), correct_all = FALSE) 
10.
withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning")) 
9.
suppressWarnings(trip(d.tr, TORnames = c("date", "id"), correct_all = FALSE)) 
8.
prefilter(data = .x, vmax = vmax, ang = ang, distlim = distlim, 
    spdf = spdf, min.dt = min.dt, emf = emf) 
7.
.f(.x[[i]], ...) 
6.
map(., ~prefilter(data = .x, vmax = vmax, ang = ang, distlim = distlim, 
    spdf = spdf, min.dt = min.dt, emf = emf)) 
5.
d %>% split(., .$id) %>% map(~prefilter(data = .x, vmax = vmax, 
    ang = ang, distlim = distlim, spdf = spdf, min.dt = min.dt, 
    emf = emf)) 
4.
foieGras::fit_ssm(x, model = "crw", time.step = time_step, vmax = 10) at get_3d.r#35
3.
FUN(X[[i]], ...) 
2.
lapply(df.locs, function(x) foieGras::fit_ssm(x, model = "crw", 
    time.step = time_step, vmax = 10)) at get_3d.r#35
1.
get_3d(etuff, series = ts, fG = T)

[camrinbraun]

which tag does this occur on?

[marosteg]

Still Lotek-specific, I've been testing it on this fish: 172419_2003_A1246

[camrinbraun]

Working fine for me. Stop by later if you're able

.