Man pages for Giappo/jappe
Jap
| args_2_string | Convert list to string |
| branching_times | Extrapolate tidy branching times from phylogeny |
| build_description_file | Adds all require dependencies to the DESCRIPTION file |
| cat2 | cat2 |
| check_jobs | Check jobs on cluster |
| close_jobs | Close jobs on cluster |
| close_session | Close session |
| create_empty_phylo | Create an empty phylogeny |
| create_folder_structure | Create folder structure |
| create_singleton_phylo | Create an empty phylogeny |
| default_cluster_folder | Set the default cluster folder |
| default_drive_choice | Set the default drive choice |
| default_github_folder | Set the default github folder |
| default_home_dir | Fetch the os-dependent default home directory |
| default_my_email | Set the default email to receive results |
| default_params_doc | This function does nothing. It is intended to inherit is... |
| default_projects_folder | Set the default projects folder |
| delete_folder_structure | Delete folder structure |
| download_project_folder | Download the entire project folder |
| download_subfolder | Download the results to the results folder of the project |
| drive_dir.create | Create a directory on drive |
| drive_list.files | List drive files |
| edit_profile | Edit your profile function |
| file_path | Like file.path, but cooler |
| find_disks | Find name of disks on your machine |
| find_github_folder | Find github folder |
| fix_documentation | Fix End of Line documentation problem |
| fix_java | Fix Java (NOT WORKING YET) |
| folder_structure | Specify subfolder structure |
| get_cluster_address | Get peregrine cluster address |
| get_function_list | Get function list from the specified package |
| get_local_function_folder | Find local project folder |
| get_local_project_folder | Find local project folder |
| get_local_projects_folder | Find local projects folder |
| get_local_subfolder | Find local subfolder |
| get_remote_function_folder | Find remote function folder |
| get_remote_project_folder | Find remote project folder |
| get_remote_projects_folder | Find remote projects folder |
| get_remote_subfolder | Find remote subfolder |
| git_clone | Clone a repo |
| git_pull | Pull a repo |
| git_pull_request | Pull a repo |
| initialize_jap | Initialize Jap |
| install_package | Install and load a package |
| is_on_ci | Detect if it is called on continous integration |
| is_session_open | Check if session is open or not |
| list_githubs | Open github folder |
| list_projects | List all GitHub projects |
| my_try_catch | A better try catch |
| nee_params_doc | This function does nothing. It is intended to inherit is... |
| one_minus_pt | 1 - Pt |
| one_minus_ut | 1 - ut |
| open_file | Open a file |
| open_github_folder | Open github folder |
| open_github_project | Open github project |
| open_rlibrary | Open R library |
| open_session | Open session |
| pars_transform_back | Transform parameters back |
| pars_transform_forward | Transform parameters |
| path_2_file.path | Convert a path to the equivalent file.path call |
| plot_ltt | Ltt plot for a tree |
| plot_matrix | Just plot a matrix without rotating it |
| pn | Pn |
| pn_bar | Pn accounting for extinctions after the shifts |
| pocket_experiment | Run an experiment on cluster |
| print_from_global | Print a variable, but not from test environment |
| pt | Pt |
| read_phylo | Open tree file |
| read_phylo_node_bars | Open tree file to retrieve node bars info |
| remote_dir.create | Create a directory on cluster |
| remote_dir.exists | Check if folder exist on cluster |
| remote_dir.remove | Remove a directory |
| remote_file.exists | Check if file exist on cluster |
| remote_install.packages | Install packages for a given project |
| remote_list.files | List remote files |
| remove_package | Remove a package (and lock file) |
| run_function | run a function |
| run_function_from_file | run a function from file |
| run_on_cluster | Run a function on cluster |
| run_project_on_cluster | run pirouette example |
| upload_bash_scripts | Export cluster scripts |
| upload_cluster_scripts | Upload cluster scripts Upload '.sh' and '.bash' files from... |
| upload_jap_scripts | Export cluster scripts |
| ut | ut |
| your_account | Returns your peregrine account |
