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7b3c02a
Initial commit of occuRNMulti function
kenkellner Nov 30, 2023
731137d
Add occupancy support, model sp1-->sp3<--sp2 doesnt work
kenkellner Dec 1, 2023
3633e82
Fix bug with sp1 --> sp3 <-- sp2
kenkellner Dec 18, 2023
be9cc18
Merge branch 'master' into occuRNMulti
kenkellner Mar 4, 2024
359725e
Add sp1 --> sp2 --> sp3 & sp1 --> sp3 model cpp code
kenkellner Mar 30, 2024
51b0ffb
Merge branch 'master' into occuRNMulti
kenkellner Jul 10, 2024
a6171dc
Add predict method
kenkellner Jul 10, 2024
ff063b6
Fix cpp problem
kenkellner Jul 10, 2024
378e84a
Predict method works with occupancy species
kenkellner Jul 12, 2024
2d9f183
Fix some bugs in input processing
kenkellner Jul 15, 2024
65d627c
Easier specification of species to model occupancy for
kenkellner Jul 15, 2024
a29d698
Make sure K length is correct
kenkellner Jul 15, 2024
d41d5f0
Handle missing values in y
kenkellner Jul 15, 2024
ab39016
Handle missing values in covariates
kenkellner Jul 15, 2024
34e6544
For now, make sure detformulas are also in same order as y
kenkellner Jul 15, 2024
66ceeae
Handle out-of-order formula/data lists
kenkellner Jul 17, 2024
492d65f
Allow fixing dominant species abundance when predicting
kenkellner Jul 18, 2024
c0c6050
Swap lower/upper
kenkellner Jul 25, 2024
7b14ed7
Add detection prediction
kenkellner Jul 31, 2024
7aeac0f
Add getP, fitted, residuals, SSE methods
kenkellner Jul 31, 2024
87daab3
Add update, simulate, parboot methods
kenkellner Jul 31, 2024
e6cbed5
Add docs
kenkellner Jul 31, 2024
1f2b78b
Tests
kenkellner Jul 31, 2024
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1 change: 1 addition & 0 deletions DESCRIPTION
Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@ Collate: 'classes.R' 'unmarkedEstimate.R' 'mapInfo.R' 'unmarkedFrame.R'
'unmarkedCrossVal.R' 'piFun.R' 'vif.R' 'makePiFun.R' 'posteriorSamples.R'
'nmixTTD.R'
'gdistremoval.R'
'occuRNMulti.R'
'IDS.R'
'plotEffects.R'
'mixedModelTools.R'
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2 changes: 1 addition & 1 deletion NAMESPACE
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ importFrom(Rcpp, evalCpp)
export(occu, occuFP, occuRN, pcount, pcountOpen, multinomPois, distsamp,
colext, gmultmix, gdistsamp, gpcount, occuPEN, occuPEN_CV, occuMulti,
occuMS, computeMPLElambda, pcount.spHDS, occuTTD, distsampOpen,
multmixOpen, nmixTTD, gdistremoval, goccu, occuCOP, IDS)
multmixOpen, nmixTTD, gdistremoval, goccu, occuCOP, IDS, occuRNMulti)

export(removalPiFun, doublePiFun)
export(makeRemPiFun, makeCrPiFun, makeCrPiFunMb, makeCrPiFunMh)
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4 changes: 4 additions & 0 deletions R/RcppExports.R
Original file line number Diff line number Diff line change
Expand Up @@ -73,6 +73,10 @@ nll_occuRN <- function(beta, n_param, y, X, V, X_offset, V_offset, K, Kmin, thre
.Call(`_unmarked_nll_occuRN`, beta, n_param, y, X, V, X_offset, V_offset, K, Kmin, threads)
}

nll_occuRNMulti <- function(beta, state_ind, det_ind, S, modOcc, ylist, Xlist, Vlist, dep, K, Kmin, miss, site_miss, threads) {
.Call(`_unmarked_nll_occuRNMulti`, beta, state_ind, det_ind, S, modOcc, ylist, Xlist, Vlist, dep, K, Kmin, miss, site_miss, threads)
}

nll_occuTTD <- function(beta, y, delta, W, V, Xgam, Xeps, pind, dind, cind, eind, lpsi, tdist, N, T, J, naflag) {
.Call(`_unmarked_nll_occuTTD`, beta, y, delta, W, V, Xgam, Xeps, pind, dind, cind, eind, lpsi, tdist, N, T, J, naflag)
}
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