Man pages for skgallagher/EpiCompare
A Pipeline to Analyze and Compare Infectious Disease Epidemics
| agent_array_to_df | Put agent_array into a data frame format |
| agent_array_to_mat | Put agent_array into a matrix format |
| agents_sims | agents_sims Example output from SIR simulations |
| agents_to_aggregate | generalized method to convert raw agent based data to... |
| agents_to_aggregate.data.frame | generalized function to convert raw agent based data to... |
| agents_to_aggregate.grouped_df | generalized function to convert raw agent based data to... |
| arrangeGrob | Arrange multiple grobs on a page ('ggtern' and 'ggplot2'... |
| as.matrix.tidy_dist_mat | convert 'tidy_dist_mat' to 'matrix' |
| cases_to_SIR | Impute Recovered counts for the SIR model |
| cases_to_SIR.data.frame | Impute Recovered counts for the SIR model |
| cases_to_SIR.grouped_df | Impute Recovered counts for the SIR model |
| check_character_percent | check if a character is a desirable percentage value |
| check_dist_params | checks the provided dist_params to make sure they are what is... |
| check_inside_elipsoid | assert if observation is inside elipsoid |
| check_inside_elipsoid_func | create a function assert if observations are inside elipsoid |
| check_min_max_time | min_max_time vector check |
| check_ordered | checks if states within data frame are ordered as inputted... |
| check_tidy_dist_mat_dimensions | check_tidy_dist_mat_dimensions |
| check_tidy_dist_names_distinct | check_tidy_dist_names_distinct |
| colnames-set-.tidy_dist_mat | assign colnames |
| compare_new_to_rest_via_distance | Title |
| contained | Method to check if a filament is completely contained in a... |
| convex_hull_compute_group_paths_to_points | convex hull function for compute_group ggplot object (for top... |
| create_convex_hull_structure | create the convex hull associated with points |
| create_delta_ball_structure | create the delta ball associated with points |
| delta_ball_compute_group_paths_to_points | delta ball function for compute_group ggplot object (for top... |
| delta_structure | Performs delta ball approach (2d approach) |
| dimnames-set-.tidy_dist_mat | assign dimnames for tidy_dist_mat |
| dimnames.tidy_dist_mat | return dimnames for tidy_dist_mat |
| dist_along_path_angle | Distance/angle between points along path relative to... |
| dist_along_path_direction | Distance/direction between points along path relative to... |
| distance_depth_function | Geenens & Nieto-Reyes functional distance-based depth |
| distance_psuedo_density_function | psuedo-density for objects with a distance between them |
| distanglepath_df | Distance/direction between points along path relative to... |
| dist_between_paths | Distance between points |
| distinct_time | select distinct rows (relative to time) |
| dist_matrix_innersq_2d | Calculates the distance matrix between a set of paths... |
| dist_matrix_innersq_direction | Calculates the distance matrix between a set of paths... |
| draws_to_states | Draw the transfer matrix |
| EpiCompare | EpiCompare: package overview |
| EpiModel_agg_bd | EpiModel_agg_bd Example output from the 'EpiModel' package... |
| EpiModel_det | EpiModel_det Example output from the 'EpiModel' package for a... |
| EpiModel_icm | EpiModel_icm Example output from the 'EpiModel' package for a... |
| equa_dist_points_angle | point compression (2d) |
| equa_dist_points_direction | point compression |
| equa_dist_points_listable_angle | List of compressions (2d) |
| equa_dist_points_listable_direction | List of compressions |
| expanding_info | expanding aggregate data to desirable format |
| extract_contour | Selection of specific contour level from KDE object |
| extract_icm_cols | Extract the icm class totals |
| filament_compression | Compress filaments to filaments with the same number of... |
| filament_distance_depth | Calculate filament depth (relative to distance depth) |
| fit_kde_object | Fit kernel density estimator (KDE) object |
| format.tidy_dist_mat | Format tidy_dist_mat for printing |
| fortify_aggregate | Take external aggregate data and put it in a format used in... |
| fortify_aggregate.data.frame | Takes in data from the R pomp package where the output is a... |
| fortify_aggregate.dcm | Take external aggregate data and put it in a format used in... |
| fortify_aggregate.epimodel_inner | Take EpiModel Data and format it |
| fortify_aggregate.icm | Take external aggregate data and put it in a format used in... |
| fortify_aggregate.list | Takes in data from the R pomp package where the output is a... |
| fortify_aggregate.netsim | Take external aggregate data and put it in a format used in... |
| fortify_aggregate.pomp | Takes in data from the R pomp package where the output is a... |
| fortify_aggregate.pomp_df | Takes in data from the R pomp package where the output is a... |
| fortify_aggregate.pomp_df_inner | Takes in data from the R pomp package where the output is a... |
| fortify_aggregate.pomp_list | Takes in data from the R pomp package where the output is a... |
| fortify_aggregate.pompList | Takes in data from the R pomp package where the output is a... |
| GeomPredBand | GeomPredBand |
| geom_prediction_band | The prediction_band geom/stat |
| GeomSirAggregate | GeomSirAggregate |
| get_closest | create a grid of points indicating near border or not (and... |
| get_closest_nn | create a grid of points indicating near border or not (and... |
| get_delta | Find delta for covering |
| get_delta_nn | calculate maxmin distance between points |
| get_epimodel_icm_states | Get the viable names for the states from an icm object |
| get_grid_elipsoid_containment | create a grid of points indicating whether in a set of 2d... |
| get_lines | Get edges within union of balls |
| get_previous_counts | Count number in each state |
| get_state_names | Get the state names fro the transition matrix |
| get_tri_matrix | Make triangle matrix |
| get_xy_coord | get xy ternary coordinates from xyz based data frame |
| grab_top_depth_filaments | Select a proportion of the top / most deep filaments |
| hagelloch_agents | Measles in Hagelloch, Germany, 1861 (agent format) |
| hagelloch_raw | Measles in Hagelloch, Germany, 1861 |
| hagelloch_sir | Measles in Hagelloch, Germany, 1861 (SIR format) |
| hausdorff_dist | Calculates the Hausdorff distance between 2 sets |
| head.tidy_dist_mat | Return the Last Parts of a 'tidy_dist_mat' (symmetric grab) |
| imports_hidden_from | import hidden function / variable from other package |
| initialize_agent_array | Initialize array for agent simulations |
| inner_compute_group_paths_to_points | inner function to compute points of top paths |
| inner_delta_ball_wrapper | Run delta ball analysis |
| is.tidy_dist_mat | checks if object is a tidy_dist_mat |
| is.wholenumber | Check for whole number values |
| kde_from_list | Contour of data points using Kernel Density Estimate. |
| l2filamentdist_df | inner l2 distance between filaments |
| local_distance_depth_function | Localized version of Geenens & Nieto-Reyes functional... |
| multinomial_updater | Multinomial draws to update states depending on past count |
| not | characterizes that we will subset by the indices *not* in... |
| pipe | Pipe operator |
| pomp_arr | Example SIR simulation output of class 'array' from the... |
| pomp_df | Example SIR simulation output of class ' data.frame' from the... |
| pomp_pomp | Example SIR simulation output of class ' pomp' from the... |
| pomp_sir | pomp_sir Example output from the 'pomp' package. |
| print.ggplot | Explicitly draw plot ('ggtern' and 'ggplot2' compatible) |
| print.tidy_dist_mat | print tidy_dist_mat objects |
| process_df_index | internal function to get the indices of the 'tidy_dist_mat'... |
| project_onto_simplex | Project onto a simplex where observations in the unit simplex... |
| project_to_simplex | project onto a standard 3d simplex. |
| quantile_curves_to_points | Pull top (1-alpha)% quantile percent of curves points. |
| remove_delta_off_line | Shorten line by delta on both sides |
| remove_incomplete_tri | Remove triangles with edges that need removal |
| reverse_not_df | removes the 'not'() operation (that makes a df a 'not_df') |
| r_new_interface | logic to check if R is >= 4 |
| rownames-set-.tidy_dist_mat | assign rownames for tidy_dist_mat |
| SEIR_to_SIR_E | Convert SEIR to XYZ coordinates fixed in a tetrahedron |
| SEIR_to_XYZ | Convert SEIR to XYZ coordinates fixed in a tetrahedron |
| sim_arr_to_df | Convert simulation output from simulate_SIR_agents to data... |
| simplex_project_mat | Create linear map to move simplex with p vertices to p-1... |
| simulate_agents | Simulate an agent-based model for given state-to-state... |
| simulate_SIR_agents | Simulate SIR data according to a chain Binomial |
| sirs_data | Example of SIRS model generated from the 'pomp' package. |
| sis_data | Example SIS model of class 'dcm' from the 'EpiModel' package. |
| sis_data_f | Example SIS model converted to aggregate format |
| stat_aggregate | aggregate SIR path visuals from agent data |
| StatAgregate | StatSirAggregate |
| state_change_inds | Determine which agents changed states |
| StatPredBandConvexHull | stat object for use in convex hull based stat_prediction_band... |
| StatPredBandDeltaBall | stat object for use in delta_ball based stat_prediction_band... |
| StatPredBandKDE | stat object for use in kde based stat_prediction_band and... |
| StatPredBandSpherical | stat object for use in spherical ball based... |
| step_along_angle | step along 2d path with angle |
| step_along_direction | step along path with direction |
| steps_along_2d_line | Create n equidistance points |
| sub-.tidy_dist_mat | Extract a part of a 'tidy_dist_mat' object |
| tail.tidy_dist_mat | Return the Last Parts of a 'tidy_dist_mat' (symmetric grab) |
| theme_sir | Add a portable theme for SIR ternary plots |
| tidy_dist_mat | tidy_dist_mat objects |
| to_lower_simplex | move df to simplex representation |
| top_curves_to_points | Pull the points from the top (1-alpha)% percent of curves. |
| top_curves_to_points.grouped_df | Pull the points from the top (1-alpha)% percent of curves... |
| top_curves_to_points.list | Pull the points from the top (1-alpha)% percent of curves... |
| trans_mat_to_D_fxn | Take a character formula transition matrix and turn it into a... |
| update_agents | Update agents based on Bernoulli draws |
| update_approved_layers | Updates approved layers of ggtern |
| which_index | find the index of a 'tidy_dist_mat' relative to a data.frame |
