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Use multihost API with single host #186

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merged 12 commits into from
Dec 18, 2023
Merged

Use multihost API with single host #186

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3bec621
Use multihost API with single host
petrasovaa Nov 27, 2023
993ac34
small changes in API
petrasovaa Nov 29, 2023
4e97ffa
fix
petrasovaa Dec 1, 2023
b6f5d24
missing pest host table configuration
petrasovaa Dec 1, 2023
e659193
move code changing config before model is created
petrasovaa Dec 1, 2023
35889ac
update to latest pops-core
petrasovaa Dec 1, 2023
fb9604d
update to latest core with random number fix, remove left over file, …
petrasovaa Dec 14, 2023
558146f
sync to main pops-core
petrasovaa Dec 14, 2023
3c7cf63
Add check that hosts aren't greater than total populations when being…
ChrisJones687 Dec 15, 2023
6ba83d0
fixed hosts being drawn greater than total_populations
ChrisJones687 Dec 18, 2023
4602b87
update multihost test
ChrisJones687 Dec 18, 2023
cff1f13
don't change the test value
ChrisJones687 Dec 18, 2023
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9 changes: 9 additions & 0 deletions R/calibrate.R
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Original file line number Diff line number Diff line change
Expand Up @@ -327,7 +327,13 @@ calibrate <- function(infected_years_file,
random_seeds <- create_random_seeds(1)
if (config$use_initial_condition_uncertainty) {
config$infected <- matrix_norm_distribution(config$infected_mean, config$infected_sd)
while (any(config$infected < 0)) {
config$infected <- matrix_norm_distribution(config$infected_mean, config$infected_sd)
}
exposed2 <- matrix_norm_distribution(config$exposed_mean, config$exposed_sd)
while (any(exposed2 < 0)) {
exposed2 <- matrix_norm_distribution(config$infected_mean, config$infected_sd)
}
exposed <- config$exposed
exposed[[config$latency_period + 1]] <- exposed2
config$exposed <- exposed
Expand All @@ -341,6 +347,9 @@ calibrate <- function(infected_years_file,

if (config$use_host_uncertainty) {
config$host <- matrix_norm_distribution(config$host_mean, config$host_sd)
while (any(config$host > config$total_populations)) {
config$host <- matrix_norm_distribution(config$host_mean, config$host_sd)
}
} else {
config$host <- config$host_mean
}
Expand Down
2 changes: 1 addition & 1 deletion R/helpers.R
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Original file line number Diff line number Diff line change
Expand Up @@ -247,7 +247,7 @@ create_random_seeds <- function(n) {
matrix_norm_distribution <- function(mean_matrix, sd_matrix) {
new_matrix <-
round(matrix(mapply(function(x, y) {rnorm(x, y, n = 1)}, x = mean_matrix, y = sd_matrix),
nrow(mean_matrix), ncol(mean_matrix)))
nrow(mean_matrix), ncol(mean_matrix)), digits = 0)
new_matrix[is.na(new_matrix)] <- 0
new_matrix[new_matrix < 0] <- 0
return(new_matrix)
Expand Down
9 changes: 9 additions & 0 deletions R/pops.r
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Original file line number Diff line number Diff line change
Expand Up @@ -370,7 +370,13 @@ pops <- function(infected_file,

if (config$use_initial_condition_uncertainty) {
config$infected <- matrix_norm_distribution(config$infected_mean, config$infected_sd)
while (any(config$infected < 0)) {
config$infected <- matrix_norm_distribution(config$infected_mean, config$infected_sd)
}
exposed2 <- matrix_norm_distribution(config$exposed_mean, config$exposed_sd)
while (any(exposed2 < 0)) {
exposed2 <- matrix_norm_distribution(config$infected_mean, config$infected_sd)
}
exposed <- config$exposed
exposed[[config$latency_period + 1]] <- exposed2
config$exposed <- exposed
Expand All @@ -384,6 +390,9 @@ pops <- function(infected_file,

if (config$use_host_uncertainty) {
config$host <- matrix_norm_distribution(config$host_mean, config$host_sd)
while (any(config$host > config$total_populations)) {
config$host <- matrix_norm_distribution(config$host_mean, config$host_sd)
}
} else {
config$host <- config$host_mean
}
Expand Down
9 changes: 9 additions & 0 deletions R/pops_multirun.R
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Original file line number Diff line number Diff line change
Expand Up @@ -225,7 +225,13 @@ pops_multirun <- function(infected_file,

if (config$use_initial_condition_uncertainty) {
config$infected <- matrix_norm_distribution(config$infected_mean, config$infected_sd)
while (any(config$infected < 0)) {
config$infected <- matrix_norm_distribution(config$infected_mean, config$infected_sd)
}
exposed2 <- matrix_norm_distribution(config$exposed_mean, config$exposed_sd)
while (any(exposed2 < 0)) {
exposed2 <- matrix_norm_distribution(config$infected_mean, config$infected_sd)
}
exposed <- config$exposed
exposed[[config$latency_period + 1]] <- exposed2
config$exposed <- exposed
Expand All @@ -239,6 +245,9 @@ pops_multirun <- function(infected_file,

if (config$use_host_uncertainty) {
config$host <- matrix_norm_distribution(config$host_mean, config$host_sd)
while (any(config$host > config$total_populations)) {
config$host <- matrix_norm_distribution(config$host_mean, config$host_sd)
}
} else {
config$host <- config$host_mean
}
Expand Down
9 changes: 9 additions & 0 deletions R/validate.R
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Original file line number Diff line number Diff line change
Expand Up @@ -244,7 +244,13 @@ validate <- function(infected_years_file,

if (config$use_initial_condition_uncertainty) {
config$infected <- matrix_norm_distribution(config$infected_mean, config$infected_sd)
while (any(config$infected < 0)) {
config$infected <- matrix_norm_distribution(config$infected_mean, config$infected_sd)
}
exposed2 <- matrix_norm_distribution(config$exposed_mean, config$exposed_sd)
while (any(exposed2 < 0)) {
exposed2 <- matrix_norm_distribution(config$infected_mean, config$infected_sd)
}
exposed <- config$exposed
exposed[[config$latency_period + 1]] <- exposed2
config$exposed <- exposed
Expand All @@ -258,6 +264,9 @@ validate <- function(infected_years_file,

if (config$use_host_uncertainty) {
config$host <- matrix_norm_distribution(config$host_mean, config$host_sd)
while (any(config$host > config$total_populations)) {
config$host <- matrix_norm_distribution(config$host_mean, config$host_sd)
}
} else {
config$host <- config$host_mean
}
Expand Down
2 changes: 1 addition & 1 deletion inst/cpp/pops-core
Open in desktop
Submodule pops-core updated 47 files
+1 −1 .cppcheck_suppressions_cpp.txt
+11 −0 .cppcheck_suppressions_hpp.txt
+4 −3 .github/workflows/cppcheck.yml
+13 −0 .github/workflows/valgrind.yml
+11 −2 CMakeLists.txt
+4 −4 Doxyfile
+532 −0 include/pops/actions.hpp
+2 −0 include/pops/anthropogenic_kernel.hpp
+186 −0 include/pops/competency_table.hpp
+202 −1 include/pops/config.hpp
+4 −3 include/pops/date.hpp
+127 −6 include/pops/environment.hpp
+73 −0 include/pops/environment_interface.hpp
+0 −1 include/pops/gamma_kernel.hpp
+53 −31 include/pops/generator_provider.hpp
+1,171 −0 include/pops/host_pool.hpp
+52 −0 include/pops/host_pool_interface.hpp
+195 −125 include/pops/model.hpp
+63 −0 include/pops/model_type.hpp
+473 −0 include/pops/multi_host_pool.hpp
+2 −0 include/pops/natural_kernel.hpp
+0 −1 include/pops/network.hpp
+121 −0 include/pops/pest_host_table.hpp
+145 −0 include/pops/pest_pool.hpp
+14 −13 include/pops/quarantine.hpp
+436 −573 include/pops/simulation.hpp
+10 −4 include/pops/soils.hpp
+88 −92 include/pops/spread_rate.hpp
+84 −163 include/pops/treatments.hpp
+36 −2 include/pops/utils.hpp
+12 −6 tests/CMakeLists.txt
+151 −0 tests/test_competency_table.cpp
+28 −7 tests/test_environment.cpp
+3 −2 tests/test_generator_provider.cpp
+90 −102 tests/test_model.cpp
+76 −73 tests/test_movements.cpp
+1,571 −0 tests/test_multi_host_model.cpp
+2 −1 tests/test_network.cpp
+3 −6 tests/test_network_kernel.cpp
+5 −8 tests/test_overpopulation_movements.cpp
+44 −8 tests/test_quarantine.cpp
+71 −56 tests/test_simulation.cpp
+4 −14 tests/test_simulation_kernels.cpp
+92 −17 tests/test_soils.cpp
+40 −5 tests/test_spread_rate.cpp
+13 −12 tests/test_survival_rate.cpp
+307 −128 tests/test_treatments.cpp
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