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This vignette outlines the code base for the LDATS package. It was constructed using LDATS version 0.3.0 on 2023-09-18.
To obtain the most recent version of LDATS, install the most recent version from GitHub:
install.packages("devtools")
::install_github("weecology/LDATS") devtools
The full LDATS analysis can be executed using the LDA_TS
function, which is the top-level of the coding pipeline’s hierarchy of
functions:
LDA_TS()
check_LDA_TS_inputs()
check_timename()
check_formulas()
check_nchangepoints()
check_weights()
check_control()
check_document_term_table()
check_document_covariate_table()
check_topics()
check_seeds()
LDA_set()
check_LDA_TS_inputs()
check_control()
check_document_term_table()
check_topics()
check_seeds()
prep_LDA_control()
LDA()
select_LDA()
measurer
and selector
functions supplied via LDA_controls_list()
TS_on_LDA()
check_LDA_TS_inputs()
check_LDA_models()
check_formulas()
check_nchangepoints()
check_timename()
check_control()
check_weights()
check_document_covariate_table()
expand_TS()
prep_TS_data()
TS()
check_TS_inputs()
check_formulas()
check_nchangepoints()
check_control()
check_weights()
est_changepoints()
prep_saves()
prep_ptMCMC_inputs()
prep_cpts()
multinom_TS()
prep_ids()
prep_pbar()
update_pbar()
step_chains()
propose_step()
proposed_step_mods()
multinom_TS()
eval_step()
take_step()
swap_chains()
update_saves()
update_cpts()
update_ids()
est_regressors()
multinom_TS()
mirror_vcov()
rmvnorm()
summarize_TS()
diagnose_ptMCMC()
count_trips()
summarize_rhos()
measure_rho_vcov()
summarize_etas()
measure_eta_vcov()
select_TS()
measurer
and selector
functions supplied via TS_controls_list()
package_LDA_TS()
Each component model’s function (LDA_set()
and
TS()
) can be run independently, as well.
To minimize the length of argument lists and facilitate simple
default usage throughout the pipeline, we implement an options/controls
list approach, where each of the main functions (LDA_TS
,
LDA_set
, and TS
) and its subfunctions have a
control
argument that takes a list
to replace
the defaults returned by its _control
function:
LDA_TS_control()
LDA_set_control()
TS_control()
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.