API for unmarked
Models for Data from Unmarked Animals

Global functions
.estimateInds	Source code
IDS	Man page Source code
IDS_convert_class	Source code
LRT	Man page
LRT,unmarkedFit,unmarkedFit-method	Man page
MesoCarnivores	Man page
RMSE_MAE	Source code
SE	Man page
SE,linCombOrBackTrans-method	Man page
SE,unmarkedEstimate-method	Man page
SE,unmarkedFit-method	Man page
SE,unmarkedFitList-method	Man page
SE,unmarkedModSel-method	Man page
SE-methods	Man page
SSE	Man page
SSE,unmarkedFit-method	Man page
SSE,unmarkedFitGDR-method	Man page
SSE,unmarkedFitIDS-method	Man page
SSE,unmarkedFitOccuComm-method	Man page
SSE,unmarkedFitOccuMulti-method	Man page
SSE-methods	Man page
Switzerland	Man page
[,unmarkedEstimateList,ANY,ANY,ANY-method	Man page
[,unmarkedFit,ANY,ANY,ANY-method	Man page
[,unmarkedFrame,missing,numericOrLogical,missing-method	Man page
[,unmarkedFrame,numericOrLogical,missing,missing-method	Man page
[,unmarkedFrame,numericOrLogical,numericOrLogical,missing-method	Man page
[,unmarkedPostSamples,ANY,ANY,ANY-method	Man page
[-methods	Man page
add_covariates	Source code
backTransform	Man page
backTransform,unmarkedEstimate-method	Man page
backTransform,unmarkedFit-method	Man page
backTransform,unmarkedLinComb-method	Man page
backTransform-methods	Man page
birds	Man page
bup	Man page
bup,unmarkedRanef-method	Man page
calculate_smooth	Source code
catbird	Man page
catbird.bin	Man page
check.integer	Source code
check_K_multinomial	Source code
check_coefs	Source code
check_formula	Source code
check_nested_formula_functions	Source code
check_no_support	Source code
check_predict_arguments	Source code
clean_up_covs	Source code
cloglog	Source code
cloglog.grad	Source code
cn	Source code
coef,linCombOrBackTrans-method	Man page
coef,unmarkedEstimate-method	Man page
coef,unmarkedFit-method	Man page
coef,unmarkedFitList-method	Man page
coef,unmarkedModSel-method	Man page
coef-methods	Man page
colext	Man page Source code
computeMPLElambda	Man page Source code
confint,unmarkedBackTrans-method	Man page
confint,unmarkedEstimate-method	Man page
confint,unmarkedFit-method	Man page
confint,unmarkedLinComb-method	Man page
confint,unmarkedRanef-method	Man page
confint-methods	Man page
covsToDF	Source code
crossVal	Man page
crossVal,unmarkedFit-method	Man page
crossVal,unmarkedFitList-method	Man page
crossVal-methods	Man page
crossbill	Man page
cruz	Man page
csvToUMF	Man page Source code
dateToObs	Source code
delaware_bfow_2001-2006	Man page
depDoublePiFun	Source code
detFuns	Man page
df_to_factor	Source code
diff_dir	Source code
distsamp	Man page Source code
distsampOpen	Man page Source code
doublePiFun	Man page Source code
drexp	Man page Source code
drhaz	Man page Source code
drhn	Man page Source code
drop_final_year	Source code
dxexp	Man page Source code
dxhaz	Man page Source code
dxhn	Man page Source code
dzip	Source code
fitList	Man page Source code
fit_TMB	Source code
fitted	Man page
fitted,unmarkedFit-method	Man page
form_has_correlated_effects	Source code
formatDelta	Source code
formatDistData	Man page
formatLong	Man page Source code
formatMult	Man page Source code
formatWide	Man page Source code
frog2001pcru	Man page
frog2001pfer	Man page
frogs	Man page
gdistremoval	Man page Source code
gdistsamp	Man page Source code
genFixedNLL	Source code
generate_random_effects	Source code
getB	Man page
getB,unmarkedFitOccuFP-method	Man page
getB-methods	Man page
getCombs	Source code
getData	Man page
getData,unmarkedFit-method	Man page
getDistCP	Source code
getFP	Man page
getFP,unmarkedFitOccuFP-method	Man page
getFP-methods	Man page
getL	Man page
getL,unmarkedFrameOccuCOP-method	Man page
getP	Man page
getP,unmarkedFit-method	Man page
getUA	Source code
getY	Man page
getY,unmarkedFit-method	Man page
getY,unmarkedFrame-method	Man page
getY,unmarkedFrameOccuMulti-method	Man page
get_Z	Source code
get_b_vector	Source code
get_base_newdata	Source code
get_coef_info	Source code
get_cov_seq	Source code
get_dist_prob	Source code
get_ds_area	Source code
get_ds_info	Source code
get_fit	Source code
get_fixed_names	Source code
get_group_vars	Source code
get_joint_cov	Source code
get_lik_trans	Source code
get_mlogit	Source code
get_model_matrix	Source code
get_nrandom	Source code
get_offset	Source code
get_randvar_info	Source code
get_ranef_inputs	Source code
get_reTrms	Source code
get_summary_df	Source code
get_xlev	Source code
gf	Man page
gf.data	Man page
gf.obs	Man page
gmultmix	Man page Source code
goccu	Man page Source code
gpcount	Man page Source code
grexp	Man page Source code
grhaz	Man page Source code
grhn	Man page Source code
gxexp	Man page Source code
gxhaz	Man page Source code
gxhn	Man page Source code
head,unmarkedFrame-method	Man page
hist,unmarkedFitDS-method	Man page
hist,unmarkedFitIDS-method	Man page
hist,unmarkedFrameDS-method	Man page
invertHessian	Source code
is_tmb_fit	Source code
issj	Man page
jay	Man page
lambda2psi	Man page Source code
lapply2	Source code
linearComb	Man page
linearComb,unmarkedEstimate,matrixOrVector-method	Man page
linearComb,unmarkedFit,matrixOrVector-method	Man page
linearComb-methods	Man page
linetran	Man page
logLik	Man page
logLik,unmarkedFit-method	Man page
logistic	Source code
logistic.grad	Source code
makeCrPiFun	Man page Source code
makeCrPiFunMb	Man page Source code
makeCrPiFunMh	Man page Source code
makePiFuns	Man page
makeRemPiFun	Man page Source code
make_mod_matrix	Source code
mallard	Man page
mallard.obs	Man page
mallard.site	Man page
mallard.y	Man page
masspcru	Man page
modSel	Man page
modSel,unmarkedFitList-method	Man page
multinomPois	Man page Source code
multispeciesFormula	Source code
multmixOpen	Man page Source code
nagR2	Source code
name_to_ind	Source code
names,unmarkedEstimateList-method	Man page
names,unmarkedFit-method	Man page
names,unmarkedFitIDS-method	Man page
newdata_from_raster	Source code
nll_distsamp	Source code
nll_distsampOpen	Source code
nll_gdistremoval	Source code
nll_gdistsamp	Source code
nll_gmultmix	Source code
nll_gpcount	Source code
nll_multinomPois	Source code
nll_multmixOpen	Source code
nll_nmixTTD	Source code
nll_occu	Source code
nll_occuCOP	Source code
nll_occuMS	Source code
nll_occuMulti	Source code
nll_occuMulti_loglik	Source code
nll_occuPEN	Source code
nll_occuRN	Source code
nll_occuTTD	Source code
nll_pcount	Source code
nll_pcountOpen	Source code
nmixTTD	Man page Source code
nonparboot	Man page
nonparboot,unmarkedFit-method	Man page
nonparboot-methods	Man page
numSites	Man page
numSites,unmarkedFrame-method	Man page
numY	Man page
numY,unmarkedFrame-method	Man page
obsCovs	Man page
obsCovs,unmarkedFrame-method	Man page
obsCovs<-	Man page
obsCovs<-,unmarkedFrame-method	Man page
obsNum	Man page
obsNum,unmarkedFrame-method	Man page
obsToY	Man page
obsToY,unmarkedFrame-method	Man page
obsToY<-	Man page
obsToY<-,unmarkedFrame-method	Man page
occu	Man page Source code
occuCOP	Man page Source code
occuComm	Man page Source code
occuFP	Man page Source code
occuMS	Man page Source code
occuMulti	Man page Source code
occuMultiLogLik	Source code
occuPEN	Man page Source code
occuPEN_CV	Man page Source code
occuRN	Man page Source code
occuTTD	Man page Source code
optimizePenalty	Man page
optimizePenalty,unmarkedFitOccuMulti-method	Man page
optimizePenalty-methods	Man page
ovendata	Man page
ovendata.list	Man page
pExp	Source code
pHalfnorm	Source code
pHazard	Source code
parboot	Man page
parboot,unmarkedFit-method	Man page
partitionHoldout	Source code
partitionKfold	Source code
partitionLeaveOneOut	Source code
pcount	Man page Source code
pcount.spHDS	Man page
pcountOpen	Man page Source code
pcru.bin	Man page
pcru.data	Man page
pcru.y	Man page
pfer.bin	Man page
pfer.data	Man page
pfer.y	Man page
piFuns	Man page
plot,parboot,missing-method	Man page
plot,profile,missing-method	Man page
plot,unmarkedFit,missing-method	Man page
plot,unmarkedFrame,missing-method	Man page
plot,unmarkedFrameOccuComm,missing-method	Man page
plot,unmarkedFrameOccuMulti,missing-method	Man page
plot,unmarkedFrameOccuTTD,missing-method	Man page
plot,unmarkedPower,missing-method	Man page
plot,unmarkedPowerList,ANY-method	Man page
plot,unmarkedPowerList_old,ANY-method	Man page
plot,unmarkedRanef,missing-method	Man page
plotEffects	Man page
plotEffects,unmarkedFit-method	Man page
plotEffects-methods	Man page
plotEffectsData	Man page
plotEffectsData,unmarkedFit-method	Man page
plotEffectsData-methods	Man page
plot_power	Source code
pointtran	Man page
posteriorSamples	Man page
posteriorSamples,unmarkedFit-method	Man page
posteriorSamples,unmarkedRanef-method	Man page
posteriorSamples-methods	Man page
powerAnalysis	Man page
powerAnalysis,list-method	Man page
powerAnalysis,unmarkedFit-method	Man page
powerAnalysis,unmarkedFrame-method	Man page
powerAnalysis_internal	Source code
predict	Man page
predict,unmarkedFit-method	Man page
predict,unmarkedFitList-method	Man page
predict,unmarkedFitOccuMS-method	Man page
predict,unmarkedFitOccuMulti-method	Man page
predict,unmarkedRanef-method	Man page
predict_inputs_from_umf	Source code
print.unmarkedPostSamples	Source code
print_randvar_info	Source code
process_multispecies_umf	Source code
process_obs_index	Source code
process_period_index	Source code
process_site_index	Source code
profile,unmarkedFit-method	Man page
profileCI	Source code
projected	Man page
projected,unmarkedFitColExt-method	Man page
randomTerms	Man page
randomTerms,unmarkedEstimate-method	Man page
randomTerms,unmarkedFit-method	Man page
randomTerms-methods	Man page
ranef	Man page
ranef,unmarkedFit-method	Man page
raster_from_predict	Source code
removalPiFun	Man page Source code
replace_estimates	Source code
residuals	Man page
residuals,unmarkedFit-method	Man page
richness	Man page
richness,unmarkedFitOccuComm-method	Man page
rmultinom2	Source code
rowProds	Source code
row_all_na	Source code
row_has_na	Source code
rzip	Source code
safeDeparse	Source code
sampleSize	Man page
sampleSize,unmarkedFit-method	Man page
sapply2	Source code
shinyPower	Man page Source code
show,parboot-method	Man page
show,unmarkedBackTrans-method	Man page
show,unmarkedCrossVal-method	Man page
show,unmarkedCrossValList-method	Man page
show,unmarkedEstimate-method	Man page
show,unmarkedEstimateList-method	Man page
show,unmarkedFrame-method	Man page
show,unmarkedFrameOccuCOP-method	Man page
show,unmarkedFrameOccuMulti-method	Man page
show,unmarkedFrameOccuTTD-method	Man page
show,unmarkedLinComb-method	Man page
show,unmarkedModSel-method	Man page
show,unmarkedMultFrame-method	Man page
show,unmarkedPostSamples-method	Man page
show,unmarkedPower-method	Man page
show,unmarkedPowerList-method	Man page
show,unmarkedPowerList_old-method	Man page
show,unmarkedPower_old-method	Man page
show,unmarkedRanef-method	Man page
sigma	Man page
sigma,unmarkedEstimate-method	Man page
sigma,unmarkedFit-method	Man page
sigma-methods	Man page
sigma_names	Source code
simOpenN	Source code
simulate	Man page
simulate,character-method	Man page
simulate,unmarkedFit-method	Man page
simulate,unmarkedFrame-method	Man page
siteCovs	Man page
siteCovs,unmarkedFrame-method	Man page
siteCovs<-	Man page
siteCovs<-,unmarkedFrame-method	Man page
smoothed	Man page
smoothed,unmarkedFitColExt-method	Man page
split_formula	Source code
summary,unmarkedEstimate-method	Man page
summary,unmarkedEstimateList-method	Man page
summary,unmarkedFit-method	Man page
summary,unmarkedFitList-method	Man page
summary,unmarkedFrame-method	Man page
summary,unmarkedFrameDS-method	Man page
summary,unmarkedFrameOccuCOP-method	Man page
summary,unmarkedFrameOccuComm-method	Man page
summary,unmarkedFrameOccuMulti-method	Man page
summary,unmarkedFrameOccuTTD-method	Man page
summary,unmarkedMultFrame-method	Man page
summary,unmarkedPower-method	Man page
summary,unmarkedPowerList-method	Man page
summary,unmarkedPowerList_old-method	Man page
summary,unmarkedPower_old-method	Man page
tmbfit_has_random	Source code
truncateToBinary	Source code
umf_to_factor	Source code
unmarked	Man page
unmarked-package	Man page
unmarkedCrossVal-class	Man page
unmarkedCrossValList-class	Man page
unmarkedEstimate	Man page Source code
unmarkedEstimate-class	Man page
unmarkedEstimateList	Source code
unmarkedEstimateList-class	Man page
unmarkedFit	Man page
unmarkedFit-class	Man page
unmarkedFrame	Man page Source code
unmarkedFrame-class	Man page
unmarkedFrameDS	Man page Source code
unmarkedFrameDSO	Man page Source code
unmarkedFrameGDR	Man page Source code
unmarkedFrameGDR-class	Man page
unmarkedFrameGDS	Man page Source code
unmarkedFrameGMM	Man page Source code
unmarkedFrameGOccu	Man page Source code
unmarkedFrameGPC	Man page Source code
unmarkedFrameMMO	Man page Source code
unmarkedFrameMPois	Man page Source code
unmarkedFrameOccu	Man page Source code
unmarkedFrameOccuCOP	Man page Source code
unmarkedFrameOccuComm	Man page Source code
unmarkedFrameOccuFP	Man page Source code
unmarkedFrameOccuMS	Man page Source code
unmarkedFrameOccuMulti	Man page Source code
unmarkedFrameOccuTTD	Man page Source code
unmarkedFramePCO	Man page Source code
unmarkedFramePCount	Man page Source code
unmarkedModSel-class	Man page
unmarkedMultFrame	Man page Source code
unmarkedPostSamples-class	Man page
unmarkedPower-class	Man page
unmarkedPower-methods	Man page
unmarkedPowerList	Man page
unmarkedPowerList,list-method	Man page
unmarkedPowerList,unmarkedFit-method	Man page
unmarkedPowerList,unmarkedPower-method	Man page
unmarkedPowerList-methods	Man page
unmarkedPowerList_old-class	Man page
unmarkedPower_old-class	Man page
unmarkedRanef-class	Man page
update,unmarkedFit-method	Man page
update,unmarkedPower-method	Man page
update,unmarkedPower_old-method	Man page
use_tmb_bootstrap	Source code
validunmarkedFrame	Source code
vcov,linCombOrBackTrans-method	Man page
vcov,unmarkedEstimate-method	Man page
vcov,unmarkedFit-method	Man page
vcov,unmarkedFitOccuMulti-method	Man page
vcov-methods	Man page
vcov_TMB	Source code
vif	Man page Source code
wald	Source code
woodthrush	Man page
woodthrush.bin	Man page
yearlySiteCovs	Man page
yearlySiteCovs,unmarkedMultFrame-method	Man page
yearlySiteCovs<-	Man page
yearlySiteCovs<-,unmarkedMultFrame-method	Man page