Man pages for sakrejda/stannis
Handles output from Stan (mc-stan.org)
| build_cmdstan | Build 'stanc' in the cmdstan directory. |
| build_registry | Build a registry |
| calculate_plist_reduction | Calculate Potential Scale Reduction Factor (PSRF) or other... |
| calculate_reduction | Calculate a per-parameter summary |
| check_key | Check that a key exists in the registry |
| compile_model | Return binary path to a compiled model, don't recompile if... |
| construct_cmdline | Create a flat string of CmdStan arguments based on a sub-tree... |
| copy_failed | Throw error when copying fails. |
| create_hash | create a pseudo-'secret', salted with project_id |
| extension | Retrieve just file extension from a string |
| finalize_args | Finalize an argument tree object by merging components that... |
| find | Find entry at a path in a list |
| find_ | Find entry at a path in a list |
| find_cmdstan | Find CmdStan installation |
| find_file | Find a full path to a file name, recursively |
| find_hash | Pick the hash out of a path |
| find_model | Based on an argument tree ('args' object) find a model and... |
| find_run_files | Find the components of a single run under a set of paths |
| flatten_array | Replace array dimensionality by explicit long-format data... |
| get_binary_dir | return binary dir for this project from an argument tree... |
| get_cmdstan | Get CmdStan from github.com/stan-dev/cmdstan |
| get_dimensions | Read the parameter dimensions of the binary rewrite |
| get_id | return project id from an argument tree ('args' object). |
| get_initial_number | Find number at the head of a string. |
| get_parameter | Read a specific parameter from the binary rewrite |
| get_parameter_names | Get names of parameters in set |
| hash_match | Check if two hashes match. |
| index_hashes | List all hashes under a target directory |
| insert_in | Add a key to a registry, with its arg-tree |
| install_cmdstan | Download CmdStan from github.com/stan-dev/cmdstan and build... |
| internal_parameters | Subset a vector of names to keep only sampler/internal... |
| is_directory | Check if a path exists and is a directory |
| is_empty_list | Check whether list elements are all zero. |
| is_named_data_frame | Check if input is a data frame with column names. |
| is_ragged_list | Check whether list elements have different lenghts. |
| last | Take last element of a vector. |
| list_max | Get the per-list-element max |
| list_sorted_heads | Get the per-list-element sorted head |
| list_sorted_tails | Get the per-list-element sorted tail |
| load_args | Load a Stannis run control list of arg-trees from a .yaml... |
| load_registry | Load a registry (or initialize if necessary). |
| merge_chains | Merge chains |
| merge_trees | Combine multiple arg-trees by merging matching sub-trees. |
| model_parameters | Subset a vector of names to keep only model parameters. |
| monitor | Monitor runs in a given root directory |
| normalize_margin_names | Normalize an array's labels. |
| not_null | Return an NA or the value |
| padded_sequence | Take a numeric sequence and force it to sort properly as a... |
| path_split | Normalizes a path and splits it on a path separator,... |
| pipe | re-export magrittr pipe operator |
| prepare_inputs | Prepare a single input tree by combining paths. |
| print.mcmc.monitor | Print output of stannis::monitor |
| process_diagnostics | Process sampling file Process diagnostics |
| process_key_value | Processes a strings data format (key[split]value) |
| push_adapt | Add sampler adaptation sub-arguments. |
| push_algorithm | Add algorithm sub-arguments. |
| push_arg | Basic method to return one CmdStan argument. |
| push_data | Add a data argument. |
| push_engine | Add HMC engine sub-arguments |
| push_fixed | Add fixed_param non-sampler arguments. |
| push_hmc | Add HMC algorithm sub-arguments |
| push_metric | Add HMC metric sub-arguments. |
| push_nuts | add nuts sampler sub-arguments. |
| push_output | Add output arguments. |
| push_random | Add a random init seed argument |
| push_sample | Add sampler sub-arguments |
| push_simple | Basic method to pull out arguments by name from a list. |
| push_static | add static HMC sub-arguments. |
| read_file_set | Read a set of Stan files and their metadata |
| read_run | Read a single Stannis run, rewrite to binary format, and... |
| read_stan_csv | Wrapper for C++ function wrapper. |
| register_run | Record that a run is being started |
| remove_failed_runs | Find and remove run directories with no output file. |
| remove_key | Remove a record from the registry |
| replicate_args | Replicate arg-tree and add replicate tag. |
| rewrite_stan_csv | Rewrite a Stan .csv output file. |
| run_cmdstan | Run a set of CmdStan runs based on a set of arg-trees in a... |
| run_model_cmd | Run a CmdStan model based on a single arg-tree. |
| save_registry | Save a registry |
| scatter | Scatter set |
| setup_runs | Set up a set of file to run examples. |
| split_rhat_rfun | rstan's split-r-hat implementation in R |
| std_estimates | Standard summary function. |
| substitutions | Substitute tags for the referenced file content. |
| summarize | Summarize iterations to estimates! |
| tag_file | File matching a tag. Replaces '::' separator with '-'... |
| tag_find | Find which items of a file read in as a character vector... |
| tag_pull | Extract the tag from file read in as a vector of text... |
| trim_comment_char | Trims comment char from the front of a string. |
| trim_warmup | Trim warmup |
| trim_whitespace | Trims whitespace from a string front and back. |
| uuid | Turn any vector of strings into a UUID |
| worst_psrf | Get the worst R-hat values per parameter. |
