segclust2d-package |
segclust2d: tools for segmentation of animal GPS movement data |
add_covariates |
Covariate Calculations |
add_covariates.data.frame |
Covariate Calculations |
add_covariates.ltraj |
Covariate Calculations |
add_covariates.Move |
Covariate Calculations |
angular_speed |
Calculate angular speed along a path |
apply_rowSums |
apply_rowSums |
apply_subsampling |
Internal function for subsampling |
argcheck_diag.var |
Check for argument 'diag.var' |
argcheck_Kmax |
Check for argument 'Kmax' |
argcheck_lmin |
Check for argument 'lmin' |
argcheck_ncluster |
Check for argument 'ncluster' |
argcheck_order.var |
Check for argument 'order.var' |
argcheck_ordering |
Check for argument 'order' |
argcheck_scale.variable |
Check for argument 'scale.variable' |
argcheck_seg.var |
Check for argument 'seg.var' |
argcheck_segclust |
Check for argument 'ncluster' and 'nseg' |
argcheck_segmentation |
Check for argument 'nseg' |
argcheck_type_coord |
Check for deprecated 'type' and 'coord.names' argument |
arma_repmat |
arma_repmat |
augment |
Generic function for augment |
augment.segmentation |
segmentation class description |
BIC.segmentation |
segmentation class description |
bisig_plot |
bisig_plot draws the plots of the bivariate signal on the same plot (scale free) |
calc_BIC |
Calculate BIC |
calc_dist |
Calculate distance between locations |
calc_speed |
Calculate speed along a path |
calc_stat_states |
Calculate state statistics |
check_repetition |
Check for repetition in the series |
chooseseg_lavielle |
Internal Function for choosing optimal number of segment |
choose_kmax |
Finding best segmentation with a different threshold S |
colsums_sapply |
colsums_sapply |
cumsum_cpp |
cumsum_cpp |
DynProg |
DynProg computes the change points given a cost matrix matD and a maximum number of segments Kmax |
DynProg_algo_cpp |
DynProg_algo_cpp |
EM.algo_simultanee |
EM.algo_simultanee calculates the MLE of phi for given change-point instants |
EM.algo_simultanee_Cpp |
EM.algo_simultanee calculates the MLE of phi for given change-point instants and for a fixed number of clusters |
EM.init_simultanee |
EM.init_simultanee proposes an initial value for the EM algorithm based on a hierarchical clustering algorithm (ascending) |
Estep_simultanee |
Estep_simultanee computes posterior probabilities and incomplete-data log-likelihood for mixture models |
find_mu_sd |
Find mean and standard deviation of segments |
get_likelihood |
segmentation class description |
Gmean_simultanee |
Gmean_simultanee calculates the cost matrix for a segmentation model with changes in the mean and variance for all signals |
Gmixt_algo_cpp |
Gmixt_algo_cpp |
Gmixt_simultanee |
Gmixt_simultanee calculates the cost matrix for a segmentation/clustering model |
Gmixt_simultanee_fullcpp |
Gmixt_simultanee_fullcpp |
hybrid_simultanee |
'hybrid_simultanee' performs a simultaneous seg - clustering for bivariate signals. |
initialisePhi |
initialisePhi is the constructor for a set of parameters for a segclust model |
likelihood |
Generic function for likelihood |
likelihood.segmentation |
segmentation class description |
logdens_simultanee |
logdens_simultanee_cpp |
logdens_simultanee_cpp |
logdens_simultanee_cpp |
logLik.segmentation |
segmentation class description |
map_segm |
'plot_segm' plot segmented movement data on a map. |
matrixRupt |
matrixRupt transforms a vector of change point into a data.frame with start and end of every segment |
Mstep_simultanee |
Mstep_simultanee computes the MLE within the EM framework |
Mstep_simultanee_cpp |
Mstep_simultanee computes the MLE within the EM framework |
neighborsbis |
neighbors tests whether neighbors of point k,P can be used to re-initialize the EM algorithm and to improve the log-likelihood. |
plot.segmentation |
segmentation class description |
plot_BIC |
segmentation class description |
plot_likelihood |
segmentation class description |
plot_segm |
Plot segmentation on time-serie |
plot_states |
Plot states statistics |
prepare_HMM |
Prepare HMM output for proper comparison plots |
prepare_shiftfit |
Prepare shiftfit output for proper comparison plots |
prep_segm |
Find segment and states for a Picard model |
prep_segm_HMM |
Internal function for HMM |
prep_segm_shiftfit |
Internal function for HMM |
print.segmentation |
segmentation class description |
relabel_states |
Relabel states of a segmentation/clustering output |
repmat |
repmat repeats a matrix |
ruptAsMat |
ruptAsMat is an internal function to transform a vector giving the change point to matrix 2 columns matrix in which each line gives the beginning and the end of a segment |
segclust |
Segmentation/Clustering of movement data - Generic function |
segclust.data.frame |
Segmentation/Clustering of movement data - Generic function |
segclust.ltraj |
Segmentation/Clustering of movement data - Generic function |
segclust.Move |
Segmentation/Clustering of movement data - Generic function |
segclust2d |
segclust2d: tools for segmentation of animal GPS movement data |
segclust_internal |
Internal segmentation/clustering function |
segmap |
segmentation class description |
segmap_list |
'segmap_list' create maps with a list of object of 'segmentation' class |
segment |
segmentation class description |
segmentation |
Segmentation of movement data - Generic function |
segmentation-class |
segmentation class description |
segmentation.data.frame |
Segmentation of movement data - Generic function |
segmentation.ltraj |
Segmentation of movement data - Generic function |
segmentation.Move |
Segmentation of movement data - Generic function |
segmentation_internal |
Segmentation of movement data - Generic function |
simulmode |
Simulations of behavioural mode |
simulshift |
Simulations of home-range shift |
spatial_angle |
Calculate spatial angle along a path |
stateplot |
segmentation class description |
states |
segmentation class description |
stat_segm |
Calculate statistics on a given segmentation |
stat_segm_HMM |
Get segment statistic for HMM model |
stat_segm_shiftfit |
Get segment statistic for shiftfit model |
subsample_rename |
Internal function for subsampling |
test_data |
Test function generating fake data |
wrap_dynprog_cpp |
DynProg Rcpp DynProg computes the change points given a cost matrix matD and a maximum number of segments Kmax |