SimInf
A Framework for Data-Driven Stochastic Disease Spread Simulations

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Functions
356
Source code
74
Man pages
89
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SimInf: A Framework for Data-Driven Stochastic Disease Spread Simulations
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API

API for SimInf
A Framework for Data-Driven Stochastic Disease Spread Simulations

Global functions
.onUnload Source code
C_R_init Source code
C_calldef Source code
C_code Man page Source code
C_code_mparse Source code
C_define Source code
C_enum Source code
C_enumeration_constants Source code
C_heading Source code
C_include Source code
C_ptsFun Source code
C_run Source code
C_trFun Source code
C_variables Source code
G_label Source code
G_rownames Source code
KLIEP Source code
KLIEP_alpha Source code
KLIEP_density_ratio Source code
KLIEP_kernel Source code
KLIEP_learning Source code
Nc Source code
Nd Source code
SEIR Man page Source code
SEIR-class Man page
SIR Man page Source code
SIR-class Man page
SIS Man page Source code
SIS-class Man page
SISe Man page Source code
SISe-class Man page
SISe3 Man page Source code
SISe3-class Man page
SISe3_sp Man page Source code
SISe3_sp-class Man page
SISe_sp Man page Source code
SISe_sp-class Man page
SimInf Man page
SimInf-package Man page
SimInf_abc-class Man page
SimInf_events Man page Source code
SimInf_events-class Man page
SimInf_indiv_events-class Man page
SimInf_model Man page Source code
SimInf_model-class Man page
SimInf_pfilter-class Man page
abc Man page
abc,SimInf_model-method Man page
abc_accept Source code
abc_adaptive_tolerance Source code
abc_distance Source code
abc_first_epsilon Source code
abc_gdata Source code
abc_init_epsilon Source code
abc_init_generation Source code
abc_init_npart Source code
abc_init_particles Source code
abc_init_tolerance Source code
abc_init_weights Source code
abc_internal Source code
abc_ldata Source code
abc_n_particles Source code
abc_next_epsilon Source code
abc_particles Source code
abc_progress Source code
abc_proposal_covariance Source code
abc_weights Source code
as.data.frame.SimInf_abc Man page Source code
as.data.frame.SimInf_events Man page Source code
as.data.frame.SimInf_indiv_events Man page Source code
as_t_matrix Source code
boxplot,SimInf_model-method Man page
calculate_prevalence Source code
check_N Source code
check_age Source code
check_binomial_distribution Source code
check_compartments Source code
check_distance_matrix Source code
check_end_t_arg Source code
check_gamma_distribution Source code
check_gdata_arg Source code
check_hyperparameters Source code
check_indiv_events_event Source code
check_indiv_events_id Source code
check_indiv_events_nodes Source code
check_indiv_events_time Source code
check_infectious_pressure_arg Source code
check_integer_arg Source code
check_ldata_arg Source code
check_matched_data Source code
check_model_argument Source code
check_node_index_argument Source code
check_normal_distribution Source code
check_package_name Source code
check_poisson_distribution Source code
check_target Source code
check_u0 Source code
check_uniform_distribution Source code
check_v0 Source code
compartments_SEIR Source code
compartments_SIR Source code
compartments_SIS Source code
compartments_SISe Source code
compartments_SISe3 Source code
compartments_SISe3_sp Source code
compartments_SISe_sp Source code
compartments_has_lhs Source code
compile_model Source code
continue Man page
continue,SimInf_abc-method Man page
create_DESCRIPTION_file Source code
create_Makevars_files Source code
create_NAMESPACE_file Source code
create_model_C_file Source code
create_model_R_class Source code
create_model_R_file Source code
create_model_R_object Source code
create_model_R_object_E Source code
create_model_R_object_G Source code
create_model_R_object_N Source code
create_model_R_object_S Source code
create_model_R_object_function Source code
create_model_R_object_gdata Source code
create_model_R_object_ldata Source code
create_model_R_object_model Source code
create_model_R_object_roxygen Source code
create_model_R_object_u0 Source code
create_model_R_object_v0 Source code
create_model_R_timestamp Source code
create_model_class_man_file Source code
create_model_man_file Source code
create_model_run_fn Source code
create_model_run_man_file Source code
create_template Source code
create_valid_C_entry_point Source code
define_dot Source code
degree Source code
dependency_graph Source code
distance_matrix Man page Source code
do_is_trajectory_empty Source code
edge_properties_to_matrix Man page Source code
evaluate_condition Source code
events Man page
events,SimInf_model-method Man page
events_SEIR Man page Source code
events_SIR Man page Source code
events_SIS Man page Source code
events_SISe Man page Source code
events_SISe3 Man page
events_target Source code
events_to_tex Source code
gdata Man page
gdata,SimInf_model-method Man page
gdata<- Man page
gdata<-,SimInf_model-method Man page
get_individuals Man page
get_individuals,SimInf_indiv_events-method Man page
have_openmp Source code
indegree Man page Source code
indiv_events_time Source code
individual_events Man page Source code
init_C_code Source code
init_E Source code
init_data_matrix Source code
init_data_vector Source code
init_error Source code
init_events Source code
init_output_matrix Source code
init_plot_argv Source code
init_plot_color Source code
init_plot_line_type Source code
init_plot_node_index Source code
init_plot_prevalence_data Source code
init_plot_range Source code
init_plot_trajectory_data Source code
init_sparse_matrix Source code
init_tspan Source code
init_x0 Source code
inject_ageing_events Source code
is_variable Source code
is_wholenumber Source code
ldata Man page
ldata,SimInf_model-method Man page
logLik,SimInf_pfilter-method Man page
match_compartments Source code
match_priors Source code
model_dll_key Source code
mparse Man page Source code
n_generations Man page
n_generations,SimInf_abc-method Man page
n_nodes Man page
n_nodes,SimInf_model-method Man page
node_events Man page
node_events,SimInf_indiv_events-method Man page
nodes Man page
outdegree Man page Source code
package_skeleton Man page Source code
pairs,SimInf_model-method Man page
parse_compartments Source code
parse_distribution Source code
parse_formula Source code
parse_formula_item Source code
parse_hyperparameter_symbols Source code
parse_hyperparameters Source code
parse_priors Source code
parse_propensities Source code
parse_propensity Source code
parse_transitions Source code
parse_variable Source code
parse_variables Source code
pattern_variable Source code
pfilter Man page
pfilter,SimInf_model-method Man page
pfilter_data Source code
pfilter_events Source code
pfilter_multiple_nodes Source code
pfilter_npart Source code
pfilter_obs_process Source code
pfilter_single_node Source code
pfilter_tspan Source code
plot,SimInf_abc-method Man page
plot,SimInf_events-method Man page
plot,SimInf_indiv_events-method Man page
plot,SimInf_model-method Man page
plot,SimInf_pfilter-method Man page
plot_SimInf_events Source code
plot_data Source code
plot_density Source code
prevalence Man page
prevalence,SimInf_model-method Man page
prevalence,SimInf_pfilter-method Man page
print_title Source code
propensity_dependencies Source code
propensity_variables Source code
punchcard<- Man page
punchcard<-,SimInf_model-method Man page
remove_spaces Source code
replace_dot Source code
replicate_first_node Source code
rewrite_propensity Source code
rewrite_tokens Source code
run Man page
run,SEIR-method Man page
run,SIR-method Man page
run,SIS-method Man page
run,SISe-method Man page
run,SISe3-method Man page
run,SISe3_sp-method Man page
run,SISe_sp-method Man page
run,SimInf_abc-method Man page
run,SimInf_model-method Man page
select_compartments Source code
select_matrix Man page
select_matrix,SimInf_model-method Man page
select_matrix<- Man page
select_matrix<-,SimInf_model-method Man page
select_matrix_SEIR Source code
select_matrix_SIR Source code
select_matrix_SIS Source code
select_matrix_SISe Source code
select_matrix_SISe3 Source code
select_matrix_SISe3_sp Source code
select_matrix_SISe_sp Source code
set_num_threads Man page Source code
shift_matrix Man page
shift_matrix,SimInf_model-method Man page
shift_matrix<- Man page
shift_matrix<-,SimInf_model-method Man page
show,SimInf_abc-method Man page
show,SimInf_events-method Man page
show,SimInf_indiv_events-method Man page
show,SimInf_model-method Man page
show,SimInf_pfilter-method Man page
state_change_matrix Source code
stop_if_combined_data Source code
substitute_tokens Source code
sum_compartments Source code
summary,SimInf_abc-method Man page
summary,SimInf_events-method Man page
summary,SimInf_indiv_events-method Man page
summary,SimInf_model-method Man page
summary,SimInf_pfilter-method Man page
summary_data_matrix Source code
summary_events Source code
summary_gdata Source code
summary_matrix Source code
summary_output_matrix Source code
summary_particles Source code
summary_trajectory Source code
summary_transitions Source code
summary_vector Source code
tokenize Source code
topological_sort Source code
trajectory Man page
trajectory,SimInf_model-method Man page
trajectory,SimInf_pfilter-method Man page
trajectory_as_is Source code
trajectory_data Source code
transform_compartments Source code
u0 Man page
u0,SimInf_indiv_events-method Man page
u0,SimInf_model-method Man page
u0<- Man page
u0<-,SimInf_model-method Man page
u0_SEIR Man page Source code
u0_SIR Man page Source code
u0_SIS Man page Source code
u0_SISe Man page Source code
u0_SISe3 Man page
u0_target Source code
v0<- Man page
v0<-,SimInf_model-method Man page
valid_G Source code
valid_S Source code
valid_SimInf_abc_object Source code
valid_SimInf_events_object Source code
valid_SimInf_indiv_events Source code
valid_SimInf_model_object Source code
valid_U Source code
valid_V Source code
valid_events Source code
valid_gdata Source code
valid_ldata Source code
valid_tspan Source code
valid_u0 Source code
valid_v0 Source code
variable_names Source code
SimInf documentation built on June 22, 2024, 9:27 a.m.

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