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Expose xmit_work option #100

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merged 1 commit into from
Jan 29, 2025
Merged

Expose xmit_work option #100

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11 changes: 9 additions & 2 deletions cmake/GitVersion.cmake
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Original file line number Diff line number Diff line change
Expand Up @@ -25,8 +25,15 @@ function(get_version_from_git)
OUTPUT_STRIP_TRAILING_WHITESPACE
)

set(EXAEPI_VERSION "${GIT_TAG}-g${GIT_COMMIT_SHORT_HASH}")
set(EXAEPI_VERSION "${GIT_TAG}-g${GIT_COMMIT_SHORT_HASH}" PARENT_SCOPE)
execute_process(
COMMAND ${GIT_EXECUTABLE} branch --show-current
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
OUTPUT_VARIABLE GIT_BRANCH
OUTPUT_STRIP_TRAILING_WHITESPACE
)

set(EXAEPI_VERSION "${GIT_TAG}-g${GIT_COMMIT_SHORT_HASH} (${GIT_BRANCH})")
set(EXAEPI_VERSION "${GIT_TAG}-g${GIT_COMMIT_SHORT_HASH} (${GIT_BRANCH})" PARENT_SCOPE)

message(STATUS "Building version ${EXAEPI_VERSION}")
configure_file(${CMAKE_SOURCE_DIR}/src/version.h.in ${CMAKE_SOURCE_DIR}/src/version.h)
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2 changes: 2 additions & 0 deletions docs/source/usage/how_to_run.rst
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Expand Up @@ -158,6 +158,8 @@ The following inputs specify the disease parameters:
For a Gamma distribution, the mean is alpha*beta and the variance is alpha*beta^2.
* ``disease.hospitalization_days`` (`list of float`, default ``3.0 8.0 7.0``)
Number of hospitalization days for age groups: under 50, 50-64, 65 and over.
* ``disease.xmit_work`` (`float`, default ``0.0575``)
Transmission probability within a workgroup.
* ``disease.xmit_comm`` (`list of float`, default ``0.000018125 0.000054375 0.000145 0.000145 0.000145 0.0002175``)
Transmission probabilities at the community level, for both work and home locations,
given the age group of the susceptible agent (0-4, 5-17, 18-29, 30-49, 50-64).
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2 changes: 2 additions & 0 deletions examples/inputs.defaults
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Expand Up @@ -138,6 +138,8 @@ disease.xmit_school_a2c = 0 0.0315 0.0315 0.0375 0.0435 0.15
# Transmission probabilites within schools, where transmitter is a child and receiver is an adult,
# for school levels none, college, high, middle, elementary, daycare. Ignored for none.
disease.xmit_school_c2a = 0 0.0315 0.0315 0.0375 0.0435 0.15
# Transmission probability within workgroups
disease.xmit_wwork = 0.0575

# Probability of hospitalization when disease symptoms first appear, for age groups 0-4, 5-17, 18-29, 30-49, 50-64, 64+
disease.CHR = 0.0104 0.0104 0.070 0.28 0.28 1.0
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2 changes: 2 additions & 0 deletions src/DiseaseParm.cpp
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Expand Up @@ -63,6 +63,8 @@ void DiseaseParm::readInputs ( const std::string& a_pp_str /*!< Parmparse string
queryArray(pp, "xmit_school_a2c", xmit_school_a2c, SchoolType::total);
queryArray(pp, "xmit_school_c2a", xmit_school_c2a, SchoolType::total);

pp.query("xmit_work", xmit_work);

pp.query("p_trans", p_trans);
pp.query("p_asymp", p_asymp);
pp.query("asymp_relative_inf", asymp_relative_inf);
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