Error in if (p.GL > 0.75) { : missing value where TRUE/FALSE needed about animotum

[jamesgrecian]

Hi Esther,

When using aniMotum to process GPS data you need to specify the location class as "G" in the data frame that you are passing to fit_ssm. Please check ?fit_ssm for more info.

I would just reformat your lc column as follows, and then the function should run.

Best,

James

require(tidyverse)
#> Loading required package: tidyverse
require(aniMotum)
#> Loading required package: aniMotum
#> The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
#> which was just loaded, will retire in October 2023.
#> Please refer to R-spatial evolution reports for details, especially
#> https://r-spatial.org/r/2023/05/15/evolution4.html.
#> It may be desirable to make the sf package available;
#> package maintainers should consider adding sf to Suggests:.
#> The sp package is now running under evolution status 2
#>      (status 2 uses the sf package in place of rgdal)
#> 
#> Attaching package: 'aniMotum'
#> The following object is masked from 'package:purrr':
#> 
#>     map

df <- read_csv("~/Downloads/Cleaned_GullTrackssubset.csv")
#> Rows: 10 Columns: 5
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> dbl  (4): id, lc, lon, lat
#> dttm (1): date
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
df <- df |> mutate(lc = "G")
df
#> # A tibble: 10 × 5
#>        id date                lc      lon   lat
#>     <dbl> <dttm>              <chr> <dbl> <dbl>
#>  1 211696 2021-05-25 04:03:28 G     -73.2  40.8
#>  2 211696 2021-05-25 04:18:27 G     -73.2  40.8
#>  3 211696 2021-05-25 04:33:31 G     -73.2  40.8
#>  4 211696 2021-05-25 04:48:29 G     -73.2  40.8
#>  5 211696 2021-05-25 05:03:28 G     -73.2  40.8
#>  6 211696 2021-05-25 05:18:34 G     -73.2  40.8
#>  7 211696 2021-05-25 05:34:05 G     -73.2  40.8
#>  8 211696 2021-05-25 05:48:34 G     -73.2  40.8
#>  9 211696 2021-05-25 06:03:42 G     -73.2  40.8
#> 10 211696 2021-05-25 06:18:31 G     -73.2  40.8

fit <- fit_ssm(df, model = "rw", time.step = 24)
#> fitting rw SSM to 1 tracks...
#>  pars:   -5.74965 -4.71341 1.91815 0 0 0

plot(fit)
#> $`211696`

^{Created on 2024-01-08 with reprex v2.0.2}

[enosazeogie]

Hi James, I appreciate your help. I've been able to fit the model. Regards, Esther

…

On Mon, Jan 8, 2024 at 4:29 AM James Grecian ***@***.***> wrote: Hi Esther, When using aniMotum to process GPS data you need to specify the location class as "G" in the data frame that you are passing to fit_ssm. Please check ?fit_ssm for more info. I would just reformat your lc column as follows, and then the function should run. Best, James require(tidyverse)#> Loading required package: tidyverse require(aniMotum)#> Loading required package: aniMotum#> The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,#> which was just loaded, will retire in October 2023.#> Please refer to R-spatial evolution reports for details, especially#> https://r-spatial.org/r/2023/05/15/evolution4.html.#> It may be desirable to make the sf package available;#> package maintainers should consider adding sf to Suggests:.#> The sp package is now running under evolution status 2#> (status 2 uses the sf package in place of rgdal)#> #> Attaching package: 'aniMotum'#> The following object is masked from 'package:purrr':#> #> map df <- read_csv("~/Downloads/Cleaned_GullTrackssubset.csv")#> Rows: 10 Columns: 5#> ── Column specification ────────────────────────────────────────────────────────#> Delimiter: ","#> dbl (4): id, lc, lon, lat#> dttm (1): date#> #> ℹ Use `spec()` to retrieve the full column specification for this data.#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. df <- df |> mutate(lc = "G")df#> # A tibble: 10 × 5#> id date lc lon lat#> <dbl> <dttm> <chr> <dbl> <dbl>#> 1 211696 2021-05-25 04:03:28 G -73.2 40.8#> 2 211696 2021-05-25 04:18:27 G -73.2 40.8#> 3 211696 2021-05-25 04:33:31 G -73.2 40.8#> 4 211696 2021-05-25 04:48:29 G -73.2 40.8#> 5 211696 2021-05-25 05:03:28 G -73.2 40.8#> 6 211696 2021-05-25 05:18:34 G -73.2 40.8#> 7 211696 2021-05-25 05:34:05 G -73.2 40.8#> 8 211696 2021-05-25 05:48:34 G -73.2 40.8#> 9 211696 2021-05-25 06:03:42 G -73.2 40.8#> 10 211696 2021-05-25 06:18:31 G -73.2 40.8 fit <- fit_ssm(df, model = "rw", time.step = 24)#> fitting rw SSM to 1 tracks...#> pars: -5.74965 -4.71341 1.91815 0 0 0 plot(fit)#> $`211696` <https://camo.githubusercontent.com/221edbda2ce5f505ad71749ca85fc760583d196d15a8d35f2c4a209d2019fc14/68747470733a2f2f692e696d6775722e636f6d2f4638643462426b2e706e67> Created on 2024-01-08 with reprex v2.0.2 <https://reprex.tidyverse.org> — Reply to this email directly, view it on GitHub <#49 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A5L4JKWSYFZQSYAHZBEB253YNO37HAVCNFSM6AAAAABBO6L7ECVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBQGY2DGOBSG4> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[enosazeogie]

Hi,

I downloaded more data, and I can't get the model to fit anymore.

For the full dataset (dat2), I keep getting this error:

glimpse(dat2)
Rows: 128,144
Columns: 5
$ id "211696", "211696", "211696", "211696", "211696", "211696", "211696", "211696", "211696", "211696", "211…
$ date 2021-05-25 04:03:28, 2021-05-25 04:18:27, 2021-05-25 04:33:31, 2021-05-25 04:48:29, 2021-05-25 05:03:28…
$ lc "G", "G", "G", "G", "G", "G", "G", "G", "G", "G", "G", "G", "G", "G", "G", "G", "G", "G", "G", "G", "G",…
$ lon -73.20768, -73.20767, -73.20747, -73.20747, -73.20737, -73.20757, -73.20767, -73.20756, -73.20740, -73.2…
$ lat 40.83309, 40.83319, 40.83356, 40.83337, 40.83317, 40.83350, 40.83343, 40.83396, 40.83349, 40.83374, 40.8…

fit_crw <- fit_ssm(dat2, model = "crw", time.step = 24)
fitting crw SSM to 9 tracks...
Error in seq.int(from, by = by, length.out = length.out) : 'length.out' must be a non-negative number

I tried this

fit_crw <- fit_ssm(dat2, model = "crw", time.step = NA)
fitting crw SSM to 9 tracks...
pars: 1 1 NA NA NA NA NA NA NA NA 0 0 NA 0 Error in nlminb(obj$par, ifelse(control$verbose == 1, myfn, obj$fn), obj$gr, :
NA/NaN gradient evaluation

Error in optimHess(par.fixed, obj$fn, obj$gr) :
non-finite value supplied by optim
Error in rep$pdHess : $ operator is invalid for atomic vectors

So I did a subset of the first 50 rows and I got this:

df=head(dat2, 50)
fit <- fit_ssm(df, model = "rw", time.step = 24)
fitting rw SSM to 1 tracks...
pars: 1.10021 1.46654 2.46752 1.95034 -0.46163 0.41839
Warning message: In sqrt(as.numeric(object$diag.cov.random)) : NaNs produced

And when I try to plot, I get this error (although type=1 plots fine)

plot(fit, what = "fitted", type = 2, ask = TRUE)##plots 2D
Error in FUN(X[[i]], ...) : !anyNA(x) is not TRUE

I kept increasing the subset. It fit the model for the first 100 rows, but for the first 1000 rows, it gave the same error as for the first 50 rows

Here's the subset of the first 50 rows.
Cleaned_GullTrackssubset2.csv

I checked and my animotum is the latest version, 1.2. I'm not sure what the problem is, and I'd appreciate your help.

Regards,
Esther

[jamesgrecian]

Hi Esther,

When running your data the correlated random walk seems to run fine, but not the random walk. I'm not sure why that would be @ianjonsen?

Could it be that time step is set to 24 hours when the example data frame spans less than 24 hours? This would result in aniMotum trying to generate only one location from the data?

Your example data has a location on average every 15 minutes, and so setting time.step = .25 seems sensible.

Best,

James

require(tidyverse)
#> Loading required package: tidyverse
require(aniMotum)
#> Loading required package: aniMotum
#> The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
#> which was just loaded, will retire in October 2023.
#> Please refer to R-spatial evolution reports for details, especially
#> https://r-spatial.org/r/2023/05/15/evolution4.html.
#> It may be desirable to make the sf package available;
#> package maintainers should consider adding sf to Suggests:.
#> The sp package is now running under evolution status 2
#>      (status 2 uses the sf package in place of rgdal)
#> 
#> Attaching package: 'aniMotum'
#> The following object is masked from 'package:purrr':
#> 
#>     map

df <- read_csv("~/Downloads/Cleaned_GullTrackssubset2.csv")
#> Rows: 50 Columns: 5
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr  (1): lc
#> dbl  (3): id, lon, lat
#> dttm (1): date
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

df |> summarise(interval = mean(difftime(date, lag(date)), na.rm = T))
#> # A tibble: 1 × 1
#>   interval     
#>   <drtn>       
#> 1 15.00578 mins

fit <- fit_ssm(df, model = "crw", time.step = .25)
#> fitting crw SSM to 1 tracks...
#>  pars:   0 0 0 0       pars:   0.65492 0.58628 0.41856 0.2284       pars:   0.65702 1.22032 1.18098 0.35766       pars:   -0.31006 2.70153 2.04332 0.82648       pars:   0.22062 2.2577 3.92804 1.07518       pars:   -0.05075 2.48466 2.96426 0.948       pars:   0.03115 2.3236 2.79494 1.90501       pars:   0.20592 2.5047 2.41912 2.78398       pars:   1.13183 2.42618 2.34409 2.63158       pars:   2.04353 2.36026 2.15319 2.95591       pars:   1.84063 2.446 2.31948 3.66558       pars:   1.99794 2.54114 2.39723 4.87055       pars:   2.16676 2.57425 2.39979 5.84701       pars:   2.02625 2.58376 2.46564 7       pars:   2.11117 2.53943 2.3937 7       pars:   2.11117 2.53943 2.3937 7

plot(fit)
#> $`211696`

^{Created on 2024-01-12 with reprex v2.0.2}

[ianjonsen]

@enosazeogie, as @jamesgrecian shows, the issues you have been getting are not aniMotum code issues they are likely due to unfortunate time.step choices. The best advice I can provide is to try to understand your data by plotting & summarizing (e.g., as @jamesgrecian did) BEFORE you try to fit models to the data! I remind myself to do this almost daily! I am happy to help you overcome issues using aniMotum but this thread is better placed in Discussions, so I'm moving it there.

Best, Ian