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Competing hazards recovery infection resolution #300
Competing hazards recovery infection resolution #300
Commits on May 9, 2024
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competing_hazards.R: Giovanni designed two objects: CompetingOutcome …
…(containing an outcome following resolution and rates that that outcome occurs for each individual in the population) and CompetingHazard (contains all CompetingOutcomes and process function to resolve hazards). processes.R: create_biting_process now replaced with create_infection_rates_process and biting_process, that uses essentially the same functional pathway, but which stops when the rates of infection are generated, storing them in the infection_outcome object within human_infection.R Similarly, disease_progression_process(es) are replaced with new functions: create_recovery_rates_process and calculate_recovery_rates, that get the recovery rates for each individual based on disease state. We then add these processes to the process list, including the resolution function create_infection_recovery_hazard_process$resolve. This process (create_infection_recovery_hazard_process) contains infection_outcome and recovery_outcome. infection_outcome calls infection_process_resolved_hazard, which follows the rest of the infection pathway functions: assigning new infections to different human states. Note that this requires probability of infection which gets used in the incidence renderer function. recovery_outcome also updates human states and infectivities. I've adjusted some of the tests to reflect the changes in functions required to generate results. Removed white space deletions.
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Added a stash source_human function to the competing hazards function…
… for use in infection outcome.
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Commits on May 22, 2024
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competing_hazards.R: Giovanni designed two objects: CompetingOutcome …
…(containing an outcome following resolution and rates that that outcome occurs for each individual in the population) and CompetingHazard (contains all CompetingOutcomes and process function to resolve hazards). processes.R: create_biting_process now replaced with create_infection_rates_process and biting_process, that uses essentially the same functional pathway, but which stops when the rates of infection are generated, storing them in the infection_outcome object within human_infection.R Similarly, disease_progression_process(es) are replaced with new functions: create_recovery_rates_process and calculate_recovery_rates, that get the recovery rates for each individual based on disease state. We then add these processes to the process list, including the resolution function create_infection_recovery_hazard_process$resolve. This process (create_infection_recovery_hazard_process) contains infection_outcome and recovery_outcome. infection_outcome calls infection_process_resolved_hazard, which follows the rest of the infection pathway functions: assigning new infections to different human states. Note that this requires probability of infection which gets used in the incidence renderer function. recovery_outcome also updates human states and infectivities. I've adjusted some of the tests to reflect the changes in functions required to generate results. Removed white space deletions.
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Added a stash source_human function to the competing hazards function…
… for use in infection outcome.
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Commits on May 23, 2024
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To correctly render ages and incidence, given the competing hazards s…
…olution (any rendering in the infection outcome does not occur), I've split the incidence renderer into three functions: age rendering, n incidence rendering and p incidence rendering. This allows much more flexibility in when these are called in the code sequence. All age inputs are now consolidated and rendered in a single function. In addition, we intitate and populate these incidence columns with 0 when they are used.
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Removed "age" from age outputs in tests and vignettes.
Corrected dt variables recovery rate assignment when antimalarial resistance is modelled.
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Swap back to explicitly labelled age outputs.
Merge branch 'competing_hazards_recovery_infection_resolution' of https://github.com/mrc-ide/malariasimulation into competing_hazards_recovery_infection_resolution # Conflicts: # R/disease_progression.R # R/human_infection.R
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Commits on May 24, 2024
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Commits on Jun 24, 2024
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biting_process renamed as create_biting_process, where functionality …
…now occurs in biting_process.R. Similarly, create_recovery_rates_process functionality is now in disease_progression.R stash_source_humans in competing hazard resolution is now redundant and has been removed from infection processes. recovery rates are now assigned to a variable which is updated as infections, recoveries (via update_infection) and deaths occur. This also takes into account recovery time of treated due to slow parasite clearance and replaced the dt variable. I've also noticed (I think) that Tr->S and U->S recoveries can be done in a single step, so have attempted to combine these at risk of making the code more complicated! Added a metapopulation incidence rendering wrapper function for initialising multiple renderers. Rewrote create_age_group_renderer for clarity following feedback. Some tests have been adjusted to reflect these changes.
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competing_hazards.R: Giovanni designed two objects: CompetingOutcome …
…(containing an outcome following resolution and rates that that outcome occurs for each individual in the population) and CompetingHazard (contains all CompetingOutcomes and process function to resolve hazards). processes.R: create_biting_process now replaced with create_infection_rates_process and biting_process, that uses essentially the same functional pathway, but which stops when the rates of infection are generated, storing them in the infection_outcome object within human_infection.R Similarly, disease_progression_process(es) are replaced with new functions: create_recovery_rates_process and calculate_recovery_rates, that get the recovery rates for each individual based on disease state. We then add these processes to the process list, including the resolution function create_infection_recovery_hazard_process$resolve. This process (create_infection_recovery_hazard_process) contains infection_outcome and recovery_outcome. infection_outcome calls infection_process_resolved_hazard, which follows the rest of the infection pathway functions: assigning new infections to different human states. Note that this requires probability of infection which gets used in the incidence renderer function. recovery_outcome also updates human states and infectivities. I've adjusted some of the tests to reflect the changes in functions required to generate results. Removed white space deletions.
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Added a stash source_human function to the competing hazards function…
… for use in infection outcome.
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To correctly render ages and incidence, given the competing hazards s…
…olution (any rendering in the infection outcome does not occur), I've split the incidence renderer into three functions: age rendering, n incidence rendering and p incidence rendering. This allows much more flexibility in when these are called in the code sequence. All age inputs are now consolidated and rendered in a single function. In addition, we intitate and populate these incidence columns with 0 when they are used. Rebasing
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Removed "age" from age outputs in tests and vignettes.
Corrected dt variables recovery rate assignment when antimalarial resistance is modelled.
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competing_hazards.R: Giovanni designed two objects: CompetingOutcome …
…(containing an outcome following resolution and rates that that outcome occurs for each individual in the population) and CompetingHazard (contains all CompetingOutcomes and process function to resolve hazards). processes.R: create_biting_process now replaced with create_infection_rates_process and biting_process, that uses essentially the same functional pathway, but which stops when the rates of infection are generated, storing them in the infection_outcome object within human_infection.R Similarly, disease_progression_process(es) are replaced with new functions: create_recovery_rates_process and calculate_recovery_rates, that get the recovery rates for each individual based on disease state. We then add these processes to the process list, including the resolution function create_infection_recovery_hazard_process$resolve. This process (create_infection_recovery_hazard_process) contains infection_outcome and recovery_outcome. infection_outcome calls infection_process_resolved_hazard, which follows the rest of the infection pathway functions: assigning new infections to different human states. Note that this requires probability of infection which gets used in the incidence renderer function. recovery_outcome also updates human states and infectivities. I've adjusted some of the tests to reflect the changes in functions required to generate results. Removed white space deletions.
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Added a stash source_human function to the competing hazards function…
… for use in infection outcome.
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biting_process renamed as create_biting_process, where functionality …
…now occurs in biting_process.R. Similarly, create_recovery_rates_process functionality is now in disease_progression.R stash_source_humans in competing hazard resolution is now redundant and has been removed from infection processes. recovery rates are now assigned to a variable which is updated as infections, recoveries (via update_infection) and deaths occur. This also takes into account recovery time of treated due to slow parasite clearance and replaced the dt variable. I've also noticed (I think) that Tr->S and U->S recoveries can be done in a single step, so have attempted to combine these at risk of making the code more complicated! Added a metapopulation incidence rendering wrapper function for initialising multiple renderers. Rewrote create_age_group_renderer for clarity following feedback. Some tests have been adjusted to reflect these changes.
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Merge branch 'competing_hazards_recovery_infection_resolution' of htt…
…ps://github.com/mrc-ide/malariasimulation into competing_hazards_recovery_infection_resolution Rebased using dev.
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Commits on Jun 26, 2024
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Corrected age output names in Demography vignette to enable it to run…
… (e.g., n_age... rather than n_...)
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Commits on Jul 3, 2024
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Revert "Add print step to touchstone workflow"
This reverts commit 5fec286.
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Commits on Jul 4, 2024
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We only need to perform the selection for individuals that passed the occurs check, not the entire population.
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Commits on Jul 10, 2024
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Merge remote-tracking branch 'origin/dev' into competing_hazards_reco…
…very_infection_resolution
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Add a bitset_at implementation that works with a logical index.
Eventually this should go into individual.
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Commits on Jul 11, 2024
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Commits on Jul 12, 2024
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Commits on Jul 27, 2024
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Merge remote-tracking branch 'origin/dev' into competing_hazards_reco…
…very_infection_resolution
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