Man pages for fmsan51/blvibmjp
Individual Based Model of Bovine Leukemia Virus Spread in a Dairy Herd in Japan
| add_1_to_month | Increment age and months_in_area in a cow table |
| add_newborns | Add newborns to a cow_table |
| areas | Setup of 'tie_stall_table' |
| area_table | A data.table to manage areas in a farm |
| assign_chambers | Assign chamber_id to cows allocated to tie-stall barns |
| assign_newborns | Assign 'chamber_id' to newborns |
| blvibmjp-package | blvibmjp: Simulation model of BLV infection in a Japanese... |
| calc_ai | Calculate the number of conducted AI |
| calc_infection_in_barns | Calculate infection in barns |
| calc_param | Calculate parameters necessary to the simulation. |
| calc_param_both | Calculate parameters used in both of prepare_data() and... |
| calc_param_pre | Calculate parameters necessary to prepare_data() |
| calc_prev | Calculate prevalence from 'cow_table' or a csv file |
| calculate_area_assignment | Make area_assignment list |
| causes_infected_in_exposed_chamber | Whether cows are infected in chambers next to infected cows... |
| change_area | Check and move cows between areas |
| change_infection_status | Check change of infection status of cows |
| change_stage | Change stage of cows accordinglly |
| check_removal | Check death and sale of current cows |
| classify_date_column | Check date_xxx columns whether they are numeric, date or... |
| cow_table | A data.table to store status of cows |
| cull_infected_cows | Cull infected cows |
| days_per_month | Days per month (365 / 12) |
| define_msg | Define plot title and labels |
| do_ai | Conduct AI and check chance of infection |
| do_test | Conduct BLV test |
| est_coef_inf_insects | Likelihood function of a coefficient for infection by insects |
| extract_owned_cows | Extract owned cows from a cow_table |
| format_date | Format and validate date columns |
| heat_cycle | Heat cycle |
| infect | Change infection status of new infected cows |
| integerize | Convert non-integer to integer |
| is_ai_started_heifer | Whether the first AIs for hifers are conducted |
| is_ai_started_milking | Whether the first AIs for milking cows are conducted |
| is_ai_succeeded | Whether a cow is concepted at the first or later AI |
| is_dried | Whether a cow is dried |
| is_ebl_detected | Whether a EBL cow is detected |
| is_heat_detected | Whether a heat is detected |
| is_infected_by_colostrum | Wheter newborns are infected by colostrum milk |
| is_infected_in_free_stall | Whether cows are infected in free pastures |
| is_infected_in_non_exposed_chamber | Whether cows are infected in chambers not next to infected... |
| is_infected_pasture | Whether cows are infected in a communal pasture |
| is_infected_rp | Whether cows are infected by rectal palpation |
| is_infected_vertical | Wheter newborns are infected vertically |
| is_replacement | Whether a newborn will be a replacement |
| is_stillbirth | Whether a delivery end up in stillbirth or abortion |
| is.wholenumbers | Test if a numeric vector is consisted of whole numbers or not |
| longevity | Expected age of death or slaugher |
| movement_table | A data.table to manage cows' movement between areas |
| n_month_to_progress | Calculate months to progress the disease |
| n_month_until_ebl_die | The number of months until EBL cows die |
| n_newborn_per_dam | The number of newborns per dam |
| param | Parameters about a simulation which should be set by users |
| plot_prev | Plot the change in prevalence |
| plot_route | Plot monthly infection routes nicely |
| prepare_area | Process raw area data to suitable form |
| prepare_cows | Process raw cow data to suitable form |
| prepare_data | Process raw data to suitable forms |
| prepare_movement | Process raw movement data to suitable form |
| process_param | Calculate parameters based on other parameters |
| q975 | 97.5% quantile of normal distribution |
| read_cows | Read cow information from simulation csvs |
| read_param | Read parameters from a txt file |
| redefine_route_levels | Redefine infection routes |
| remove_cows | Remove cows from a herd |
| remove_from_areas | Remove cows from areas |
| remove_na | Remove NA from a vector |
| replace_selected_cows | Replace selected cows |
| resample | sample() from x rather than 1:x |
| rp_table | A data.table to manage cow status related with rectal... |
| save_file | Export a cow_table or the list of parameters to a file. |
| set_i_month | Set the variable i_month in a cow_table |
| set_init_chamber_id | Initial assignment of 'chamber_id' |
| set_param | Overwrite default parameters with herd specific parameters |
| setup_area_table | Setup of 'area_table' |
| setup_cows | Setup of 'cow_table' |
| setup_movement_table | Setup of 'movement_table' |
| setup_newborn_table | Setup of 'newborn_table' |
| setup_rp_table | Setup of 'rp_table' |
| sex_newborns | Sex ratio of newborns |
| simulate_blv_spread | Simulate spread of BLV |
| simulate_once | Body of the simulation |
| susceptibility | Calculate susceptibility of newborns to the pathogen |
| table_route | Summarize infection routes |
| table_status | Summarize infection status |
| tether_roaming_cows | Assign cows roaming in a tie-stall to empty chambers |
| tie_stall_table | A data.table to store status of a tie-stall barn |
| translate_msg | Translate plot title and labels |
| validate_category | Validate that categorical columns contain valid categories... |
| validate_cow_table | Validate cow_table |
| validate_param | Validate parameters |
| warn_double_sep | Check whether input contains doublewidth separator |
| warn_invalid_col | Check whether input contains invalid column(s) |
