local_decoding - Githubissues

Hi there I am having good success exploring fitting various hmmSSF models, however one function local_decoding() - which works fine in the archived manuscript code lodged on zenodo - is throwing an error?

states <- viterbi_decoding(mod = mod4) # works fine head(states) [1] 2 2 2 2 2 2

local_decoding(mod4) # throws error Error: Not compatible with requested type: [type=NULL; target=double].

mod4 # hmmSSF object Negative log-likelihood: 29444 Convergence code: 0

SSF model: ~step + log(step) + cos(angle) + cov1 mle low upp step.S1 -0.386 -0.410 -0.362 log(step).S1 0.302 0.189 0.415 cos(angle).S1 -0.066 -0.116 -0.015 cov1.S1 -3.404 -6.219 -0.590 step.S2 -0.102 -0.112 -0.092 log(step).S2 1.043 0.715 1.371 cos(angle).S2 2.409 2.127 2.692 cov1.S2 -3.476 -7.482 0.530

TPM model: ~1 S1 S2 S1 0.962 0.038 S2 0.160 0.840

str(mod4) # model object structure List of 3 $ par :List of 2 ..$ ssf: num [1:4, 1:2] -0.3859 0.3021 -0.0656 -3.4043 -0.1021 ... .. ..- attr(, "dimnames")=List of 2 .. .. ..$ : chr [1:4] "step" "log(step)" "cos(angle)" "cov1" .. .. ..$ : chr [1:2] "S1" "S2" ..$ tpm: num [1, 1:2] -3.22 -1.66 .. ..- attr(, "dimnames")=List of 2 .. .. ..$ : chr "(Intercept)" .. .. ..$ : chr [1:2] "1>2" "2>1" $ fit :List of 6 ..$ par : num [1:10] -0.3859 0.3021 -0.0656 -3.4043 -0.1021 ... ..$ value : num 29444 ..$ counts : Named int [1:2] 1265 NA .. ..- attr(, "names")= chr [1:2] "function" "gradient" ..$ convergence: int 0 ..$ message : NULL ..$ hessian : num [1:10, 1:10] 44152.64 8004.6 -479.71 -8.33 -11244.11 ... $ args:List of 6 ..$ tpm_formula:Class 'formula' language ~1 .. .. ..- attr(, ".Environment")=<environment: 0x0000025b94777278> ..$ ssf_formula:Class 'formula' language ~step + log(step) + cos(angle) + cov1 .. .. ..- attr(*, ".Environment")= ..$ data :'data.frame': 134946 obs. of 11 variables: .. ..$ ID : chr [1:134946] "112724" "112724" "112724" "112724" ... .. ..$ stratum: Factor w/ 2646 levels "96382.2-3","96382.2-4",..: 65 65 65 65 65 65 65 65 65 65 ... .. ..$ obs : num [1:134946] 1 0 0 0 0 0 0 0 0 0 ... .. ..$ x : num [1:134946] -3111 -3165 -3130 -3157 -3125 ... .. ..$ y : num [1:134946] 598 658 636 647 644 ... .. ..$ time : POSIXct[1:134946], format: "2016-11-09 10:00:00" "2016-11-09 10:00:00" ... .. ..$ step : num [1:134946] 43.78 44.64 5.75 32.77 4.87 ... .. ..$ angle : num [1:134946] 0.00452 -2.30602 -1.34323 -2.11292 2.83458 ... .. ..$ w : num [1:134946] 2.43e-05 4.61e-06 1.20e-03 1.73e-05 7.26e-04 ... .. ..$ cov1 : num [1:134946] 1.14 1.2 1.18 1.2 1.18 ... .. ..$ doy_c2 : num [1:134946] 0.281 0.281 0.281 0.281 0.281 ... ..$ n_states : num 2 ..$ ssf_cov : chr [1:4] "step" "log(step)" "cos(angle)" "cov1" ..$ tpm_cov : chr "(Intercept)"

attr(*, "class")= chr [1:2] "hmmSSF" "list"

NJKlappstein / hmmSSF

local_decoding #5