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Running on a cluster
Documentation
Developer’s guide
Changelog
MetaWards
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Index
Index
_
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A
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B
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C
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D
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E
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F
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G
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H
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I
|
L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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X
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Y
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Z
_
__init__() (metawards.Disease method)
(metawards.Infections method)
(metawards.InputFiles method)
(metawards.Link method)
(metawards.Links method)
(metawards.Network method)
(metawards.Node method)
(metawards.Nodes method)
(metawards.OutputFiles method)
(metawards.Parameters method)
(metawards.Population method)
(metawards.Populations method)
(metawards.VariableSet method)
(metawards.VariableSets method)
(metawards.WardInfo method)
(metawards.WardInfos method)
(metawards.Workspace method)
(metawards.utils.NullProfiler method)
(metawards.utils.Profiler method)
A
add_distances() (metawards.Network method)
add_lookup() (in module metawards.utils)
add_seeds() (metawards.Parameters method)
add_wards_network_distance() (in module metawards.utils)
additional_seeds (metawards.Parameters attribute)
adjust() (metawards.VariableSet method)
adjustable_help() (metawards.VariableSet static method)
advance_additional() (in module metawards.iterators)
advance_additional_omp() (in module metawards.iterators)
advance_fixed() (in module metawards.iterators)
advance_fixed_omp() (in module metawards.iterators)
advance_foi() (in module metawards.iterators)
advance_foi_omp() (in module metawards.iterators)
advance_imports() (in module metawards.iterators)
advance_imports_omp() (in module metawards.iterators)
advance_infprob() (in module metawards.iterators)
advance_infprob_omp() (in module metawards.iterators)
advance_play() (in module metawards.iterators)
advance_play_omp() (in module metawards.iterators)
advance_recovery() (in module metawards.iterators)
advance_recovery_omp() (in module metawards.iterators)
allocate_vaccination() (in module metawards.utils)
alternate_codes (metawards.WardInfo attribute)
alternate_names (metawards.WardInfo attribute)
animate_plots() (in module metawards.analysis)
append() (metawards.Populations method)
(metawards.VariableSets method)
assert_not_null (metawards.Links attribute)
(metawards.Nodes attribute)
assert_sane() (metawards.Network method)
assert_sane_network() (in module metawards.utils)
assert_valid_index (metawards.Links attribute)
(metawards.Nodes attribute)
authority (metawards.WardInfo attribute)
authority_code (metawards.WardInfo attribute)
auto_bzip() (metawards.OutputFiles method)
B
begin_p (metawards.Node attribute)
begin_to (metawards.Node attribute)
begin_we (metawards.Node attribute)
beta (metawards.Disease attribute)
build() (metawards.Infections static method)
(metawards.Network static method)
(metawards.Workspace static method)
build_custom_iterator() (in module metawards.iterators)
build_play_matrix() (in module metawards.utils)
build_wards_network() (in module metawards.utils)
C
child_total() (metawards.utils.Profiler method)
clear() (metawards.Infections method)
clear_all_infections() (in module metawards.utils)
cli() (in module metawards.app)
close() (metawards.OutputFiles method)
code (metawards.WardInfo attribute)
contrib_foi (metawards.Disease attribute)
coordinates (metawards.InputFiles attribute)
create_average_plot() (in module metawards.analysis)
create_double_array() (in module metawards.utils)
create_fingerprint() (metawards.VariableSet static method)
create_int_array() (in module metawards.utils)
create_overview_plot() (in module metawards.analysis)
create_string_array() (in module metawards.utils)
create_thread_generators() (in module metawards.utils)
D
daily_imports (metawards.Parameters attribute)
date (metawards.Population attribute)
day (metawards.Population attribute)
delete_ran_binomial() (in module metawards.utils)
Disease (class in metawards)
disease_params (metawards.Parameters attribute)
E
end_p (metawards.Node attribute)
end_to (metawards.Node attribute)
extract() (in module metawards.utils)
extract_core() (in module metawards.extractors)
extract_custom() (in module metawards.extractors)
extract_default() (in module metawards.extractors)
extract_none() (in module metawards.extractors)
extract_small() (in module metawards.extractors)
extract_values() (metawards.VariableSet static method)
extractor_needs_setup() (in module metawards.extractors)
F
fill_in_gaps() (in module metawards.utils)
find() (metawards.WardInfos method)
fingerprint() (metawards.VariableSet method)
flush() (metawards.OutputFiles method)
G
get_available_num_threads() (in module metawards.utils)
get_cores_per_node() (in module metawards.app)
get_filename() (metawards.OutputFiles method)
get_hostfile() (in module metawards.app)
get_min_max_distances() (in module metawards.utils)
(metawards.Network method)
get_number_of_processes() (in module metawards.utils)
get_parallel_scheme() (in module metawards.app)
get_path() (metawards.OutputFiles method)
get_repository() (metawards.Parameters static method)
get_threads_per_task() (in module metawards.app)
get_version_string() (in module metawards)
,
[1]
H
how_many_vaccinated() (in module metawards.utils)
I
id (metawards.Node attribute)
identifier (metawards.InputFiles attribute)
identifier2 (metawards.InputFiles attribute)
import_animate_modules() (in module metawards.analysis)
import_graphics_modules() (in module metawards.analysis)
incidence (metawards.Workspace attribute)
inf_tot (metawards.Workspace attribute)
infecteds (metawards.Population attribute)
Infections (class in metawards)
info (metawards.Network attribute)
initial (metawards.Population attribute)
initial_inf (metawards.Parameters attribute)
initialise_infections() (in module metawards.utils)
(metawards.Network method)
initialise_play_infections() (in module metawards.utils)
input_files (metawards.Parameters attribute)
InputFiles (class in metawards)
is_closed() (metawards.OutputFiles method)
is_null (metawards.Links attribute)
(metawards.Nodes attribute)
is_null() (metawards.utils.Profiler method)
is_open() (metawards.OutputFiles method)
iterate() (in module metawards.utils)
iterate_custom() (in module metawards.iterators)
iterate_default() (in module metawards.iterators)
iterate_weekday() (in module metawards.iterators)
iterate_weekend() (in module metawards.iterators)
iterate_working_week() (in module metawards.iterators)
iterator_needs_setup() (in module metawards.iterators)
L
label (metawards.Node attribute)
latent (metawards.Population attribute)
length_day (metawards.Parameters attribute)
Link (class in metawards)
Links (class in metawards)
load() (metawards.Disease static method)
(metawards.InputFiles static method)
(metawards.Parameters static method)
lookup (metawards.InputFiles attribute)
lookup_columns (metawards.InputFiles attribute)
M
make_compatible_with() (metawards.VariableSet method)
max_links (metawards.Network attribute)
max_nodes (metawards.Network attribute)
metawards (module)
metawards.analysis (module)
metawards.app (module)
metawards.extractors (module)
metawards.iterators (module)
metawards.utils (module)
model_name() (metawards.InputFiles method)
model_path() (metawards.InputFiles method)
model_version() (metawards.InputFiles method)
move_from_play_to_work() (metawards.Network method)
move_population_from_play_to_work() (in module metawards.utils)
move_population_from_work_to_play() (in module metawards.utils)
mpi_supervisor() (in module metawards.app)
N
n_inf_classes (metawards.Workspace attribute)
N_INF_CLASSES() (metawards.Disease method)
n_inf_wards (metawards.Population attribute)
(metawards.Workspace attribute)
name (metawards.WardInfo attribute)
name() (metawards.utils.Profiler method)
Network (class in metawards)
nlinks (metawards.Network attribute)
nnodes (metawards.Network attribute)
(metawards.Workspace attribute)
Node (class in metawards)
Nodes (class in metawards)
nodes (metawards.Network attribute)
nodes_to_track (metawards.InputFiles attribute)
NullProfiler (class in metawards.utils)
O
open() (metawards.OutputFiles method)
open_subdir() (metawards.OutputFiles method)
output_basic() (in module metawards.extractors)
output_core() (in module metawards.extractors)
output_core_omp() (in module metawards.extractors)
output_core_serial() (in module metawards.extractors)
output_dir() (metawards.OutputFiles method)
output_dispersal() (in module metawards.extractors)
output_incidence() (in module metawards.extractors)
output_prevalence() (in module metawards.extractors)
OutputFiles (class in metawards)
P
Parameters (class in metawards)
params (metawards.Network attribute)
parse_args() (in module metawards.app)
pinf_tot (metawards.Workspace attribute)
play (metawards.Infections attribute)
(metawards.InputFiles attribute)
(metawards.Network attribute)
play_size (metawards.InputFiles attribute)
plength_day (metawards.Parameters attribute)
plinks (metawards.Network attribute)
Population (class in metawards)
population (metawards.Population attribute)
Populations (class in metawards)
position (metawards.InputFiles attribute)
prepare_worker() (in module metawards.utils)
Profiler (class in metawards.utils)
progress (metawards.Disease attribute)
R
ran_binomial() (in module metawards.utils)
ran_int() (in module metawards.utils)
ran_uniform() (in module metawards.utils)
read() (metawards.VariableSet static method)
(metawards.VariableSets static method)
read_done_file() (in module metawards.utils)
read_variables() (metawards.Parameters static method)
recalculate_play_denominator_day() (in module metawards.utils)
recalculate_work_denominator_day() (in module metawards.utils)
recovereds (metawards.Population attribute)
redirect_output() (in module metawards.utils)
region (metawards.WardInfo attribute)
region_code (metawards.WardInfo attribute)
remove() (metawards.OutputFiles static method)
repeat() (metawards.VariableSets method)
repeat_index() (metawards.VariableSet method)
rescale_play_matrix() (in module metawards.utils)
(metawards.Network method)
reset_everything() (in module metawards.utils)
(metawards.Network method)
reset_play_matrix() (in module metawards.utils)
reset_play_susceptibles() (in module metawards.utils)
reset_work_matrix() (in module metawards.utils)
resize (metawards.Links attribute)
(metawards.Nodes attribute)
resize_array() (in module metawards.utils)
run() (metawards.Network method)
run_model() (in module metawards.utils)
run_models() (in module metawards.utils)
run_worker() (in module metawards.utils)
S
save_summary_plots() (in module metawards.analysis)
scale_uv (metawards.Population attribute)
scoop_supervisor() (in module metawards.app)
seed (metawards.InputFiles attribute)
seed_ran_binomial() (in module metawards.utils)
set_disease() (metawards.Parameters method)
set_input_files() (metawards.Parameters method)
set_variables() (metawards.Parameters method)
setup_additional_seeds() (in module metawards.iterators)
setup_core() (in module metawards.extractors)
setup_seed_all_wards() (in module metawards.iterators)
setup_seed_specified_ward() (in module metawards.iterators)
setup_seed_wards() (in module metawards.iterators)
start() (metawards.utils.Profiler method)
start_symptom (metawards.Disease attribute)
stop() (metawards.utils.Profiler method)
string_to_ints() (in module metawards.utils)
susceptibles (metawards.Population attribute)
T
to_links (metawards.Network attribute)
to_seed (metawards.Network attribute)
too_ill_to_move (metawards.Disease attribute)
total (metawards.Population attribute)
total() (metawards.utils.Profiler method)
total_inf_ward (metawards.Workspace attribute)
total_new_inf_ward (metawards.Workspace attribute)
U
update() (metawards.Network method)
user_params (metawards.Parameters attribute)
uv (metawards.InputFiles attribute)
UV (metawards.Parameters attribute)
uv_filename (metawards.Parameters attribute)
V
vaccinate_same_id() (in module metawards.utils)
variable_names() (metawards.VariableSet method)
variable_values() (metawards.VariableSet method)
variables() (metawards.VariableSet method)
VariableSet (class in metawards)
VariableSets (class in metawards)
W
WardInfo (class in metawards)
WardInfos (class in metawards)
wards (metawards.WardInfos attribute)
weekend (metawards.InputFiles attribute)
(metawards.Network attribute)
work (metawards.Infections attribute)
(metawards.InputFiles attribute)
work_size (metawards.InputFiles attribute)
Workspace (class in metawards)
X
x (metawards.Node attribute)
Y
y (metawards.Node attribute)
Z
zero_all() (metawards.Workspace method)