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) |
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