Man pages for npetraco/CRFutil
Handy Utility Functions for Use with CRF and gRbase packages
| adj2formula | Form pair-wise formula from adjacency matrix. XXXX |
| align.distributions | Align joint distributions in table form, to a reference joint... |
| compare_edges | XXXX |
| compare_edges_SAFEISH | Send in two or more models in the form of a list of crf... |
| complement.at.idx | Convenience function to complement a node in a configuration.... |
| compute.full.distribution | Compute the joint distribution, with just an input crf object |
| compute.model.matrix | Utility function to compute model matrix |
| conditional.config.energy | Energy function for energy of a conditional configuration of... |
| conditional.config.energy2 | Energy function for energy of a conditional configuration of... |
| conditional.config.energy.old | Older implementation of Energy function for energy of a... |
| conditional.energy.gradient | Gradient of a condtional energy for a node and a... |
| config.energy | Energy function for a configuration of states |
| config.potential | Product of potentials function over a configuration of states |
| copy.crf | (Deep) Copy and return a new independent crf object |
| count_row_matches | A quick and dirty function to find the frequency of a... |
| delta.alpha | Compute the delta-alpha matrix \boldsymbol \Delta_X_i=1 |
| distribution.calc | Compute the joint distribution, assuming a crf object is... |
| distribution.from.energies | Compute the joint distribution from the node and edge... |
| distribution.from.potentials | Compute the joint distribution from the node and edge... |
| dump.crf | Print out all contents of a crf object |
| edge.marginal | Compute an edge marginal |
| edges2adj | Form adjacency matrix from edge matrix. XXXX |
| Eone | One-body (node) energy function |
| Etwo | Two-body (edge) energy function |
| exp_list | Exp a bunch of stuff (vectors, matrices, etc) in a list |
| feature.means | Utility function to compute mean vector of unconditional... |
| fit_bayes_logistic | Joint distribution from bayes logistic regression fit of... |
| fit_bayes_loglinear | Joint distribution from bayes poisson regression fit of... |
| fit_bayes_loglinear2 | Joint distribution from bayes poisson regression fit of... |
| fit_bayes_zip | Joint distribution from bayes poisson regression fit of... |
| fit_empirical | Empirical joint distribution |
| fit_logistic | Joint distribution from logistic regression fit of parameters |
| fit_loglinear | Joint distribution from Poisson regression fit of parameters |
| fit_mle | Joint distribution from MLE fit of parameters for full MRF... |
| fit_mle_params | MLE fit of parameters ONLY for full MRF loglikelihood |
| fit_true | Joint distribution from true parameters for MRF |
| flatten.marginal.edge.beliefs | Flatten belief matrices output by marginal.edge.bels to make... |
| generate_brunner_lizards | Generate a little lizard data model from Brunner course for... |
| generate_gRbase_lizards | Generate a little lizard data model from the gRbase package... |
| generate_koller_misconception_model | Generate the original Koller-Friedman Misconception model... |
| generate_random_model | Generate a random model using Erdos Renyi game |
| generate_schmidt_small_model | Generate the original Schmidt small chain model used in Notes |
| generate_star_model | Generate the star model used in their book and the Notes |
| generate_tesseract_model | Generate the tesseract model used in their book and the Notes |
| generate_triangle_model | Generate the original triangle model used in Notes |
| get_configuration_frequencies | Get the frequencies of configurations |
| get.incoming.messages | Grab incoming messages from the neighboring nodes and put... |
| get.node.idxs | Utility function to convert a parameter index to the... |
| get.par.idx | Utility function to convert node and edge indices to the... |
| get.path | Get a (shortest) path between two nodes |
| get.root.paths | Get all paths from chosen root node to all leaf nodes |
| glmnet2graph_info | Pull info needed for a crf object out of a glmnet fit output |
| grad.negloglik | Utility function to compute gradient of log likelihood |
| grad.neglogpseudolik.config | Utility function to SEPARATELY compute gradient negative log... |
| grad.neglogpseudolik.FIXME | Gradient of sample negative log pseudo-likelihood |
| init.loopy.message.storage | Initialize an empty set of list containers to hold messages... |
| init.message.storage | Initialize an empty set of list containers to hold messages |
| KLD | Compute the Kullback-Leibler distance between two... |
| loglin2crf | Convert loglin, loglm or dModel (all really loglin) object to... |
| log_list | Take the log of stuff (vectors, matrices, etc) in a list |
| logsumexp | Log sum exp trick. From Brendon Brewer's DNest code: |
| logsumexp2 | Log sum exp trick. From Brendon Brewer's DNest code: |
| make.empty.field | Instantiate an empty field |
| make.f2v.msg | Make factor to variable (node) message |
| make.gRbase.beliefs | Decorate fit node and edge marginal beliefs to make... |
| make.gRbase.potentials | Decorate initalized mrf-object to make potentials compatible... |
| make.lattice | Quick generate a lattice graph |
| make.par.from.all.potentials | Make a new parameter vector from ALL of the potential values... |
| make.par.from.potentials | This version makes a parameter vector from the potentials... |
| make.pots | Make potentials from input parameter vector. |
| make.v2f.msg | Make factor to variable (node) message |
| marginal.edge.bayes.beleifs.indep.indic | marginal edge bayes independence indicators from beliefs |
| marginal.edge.bayes.bels.plot | marginal edge bayes posterior belief plots |
| marginal.edge.bayes.loglin | marginal edge fit using vanalla baysian poisson regression... |
| marginal.edge.bayes.plot | marginal edge plot for bayes posterior parameter output |
| marginal.edge.bayes.potentials.indep.indic | marginal edge bayes independence indicators |
| marginal.edge.bels | Marginal edge beliefs from parameter point estimates. |
| marginal.edge.bels.bayes | Marginal edge beliefs from bayes posterior sample |
| marginal.edge.emp.pr | Marginal edge empirical probs from a sample of data |
| marginal.edge.loglin | marginal edge fit using poisson regression glm |
| marginal.edge.mrf | marginal edge fit with MLE within the CRF framework |
| message.type | Get message type depending on name |
| mrf2pwfg | Convert Markov Random Field to pairwise (two-body) factor... |
| mrf.exact.nll | Work around for CRF bug evaluating nll for different... |
| mrf.glmnet.logistic.fit | Fit a MRF via cross-validation glmnet LASSO logistic... |
| mrf.junction.nll | Work around for CRF bug evaluating nll for different... |
| mrf.lbp.nll | Work around for CRF bug evaluating nll for different... |
| mrf.sample.plot | Plot a sample of states node-wise |
| mrf.standard.fit | Fit a MRF parameterized in the standard way |
| negloglik | Experiment: Modified Port of Schmidt UGM_MRF_NLL.m |
| neglogpseudolik | Sample negative log pseudo-likelihood |
| neglogpseudolik2 | Sample negative log pseudo-likelihood |
| neglogpseudolik.config | Utility function to compute negative log pseudo-likelihood.... |
| nex | Get all neighbors of start.node except end.node |
| node.marginal | Compute a node marginal |
| nodes2params.list | Function to find which nodes are associated with which... |
| nodes2params.list2 | Function to find which nodes are associated with which... |
| par2logpots | Reformat parameter vector to CRF object from node.pot and... |
| params2nodes.list | Function to find which parameters are associated with which... |
| pass.message | Pass a message over an edge on a factor graph |
| phi.component | Utility function to compute phi component CONDITIONED for... |
| phi.features | Utility function to compute unconditional features... |
| phi.features.explicit | Utility function to compute labeled explicit unconditional... |
| plot_crf | Plot a crf object |
| process.logistic.fit.JAGS | Process JAGS output for logistic fit |
| process.logistic.fit.stan | Process Stan output for logistic fit |
| pseudolikelihoods.from.energies | Compute the pseudolikelihoods from the node and edge... |
| pseudolikelihoods.from.energies2 | Revised: Compute the pseudolikelihoods from the node and edge... |
| reorder_configs | Spits out permutation to re-order configs in targ with... |
| row.match | Code from prodlim library to match a row in a matrix |
| shift.pots | Shift node potentials back to the originally fit parameter... |
| sim.field.random | Simulate an MRF with random unary (node) and pair (edge)... |
| sim.field.random.simplest | Simulate an MRF with random unary (node) and pair (edge)... |
| sim.ising.field.random | Simulate an MRF with random unary (node) and pair (edge)... |
| sim.random.field | Simulate an random MRF with random unary (node) and pair... |
| symbolic.conditional.energy | Spit out latex expression for E(Xi|X/Xi) given i, X and a... |
| UGM_MRF_computeSuffStat | Port of Schmidt UGM_MRF_computeSuffStat.m |
| UGM_MRF_makePotentials | Port of Schmidt UGM_MRF_makePotentials.m |
| UGM_MRF_NLL | Experiment: Port of Schmidt UGM_MRF_NLL.m |
| update_CRFutil | Easily update the CRFutil library by installing the current... |
