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Bitset index2 everywhere#12

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plietar wants to merge 36 commits intodevplietar/malariasimulation:devfrom bitset_index2_everywhereplietar/malariasimulation:bitset_index2_everywhereCopy head branch name to clipboard

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Commits on May 9, 2024

• 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 Compet…

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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

• 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 Compet…

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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

• To correctly render ages and incidence, given the competing hazards solution (any rendering in the infection outcome does not occur), I've split the incidence renderer into three functions: age ren…

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• Removed "age" from age outputs in tests and vignettes.

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• Swap back to explicitly labelled age outputs.

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Commits on May 24, 2024

• Merge branch 'dev' into competing_hazards_recovery_infection_resolution

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• Removed missed merge commit line.

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• Correcting rendering tests (merging error).

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Commits on Jun 24, 2024

• 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

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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 Compet…

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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 solution (any rendering in the infection outcome does not occur), I've split the incidence renderer into three functions: age ren…

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• Removed "age" from age outputs in tests and vignettes.

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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 Compet…

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• Added a stash source_human function to the competing hazards function for use in infection outcome.

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• Removed missed merge commit line.

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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

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• Re-added "age" to age outputs.

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• Merge branch 'competing_hazards_recovery_infection_resolution' of https://github.com/mrc-ide/malariasimulation into competing_hazards_recovery_infection_resolution

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Commits on Jun 26, 2024

• 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

• Removed redundant commented lines.

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• Add print step to touchstone workflow

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• Revert "Add print step to touchstone workflow"

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Commits on Jul 4, 2024

• Improve cumsum performance

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• Remove outlining of function

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• Optimize competing hazards.

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• Fix empty occurs case.

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Commits on Jul 10, 2024

• Simplify competing hazards as a single random draw.

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• Try to optimize competing hazards

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• All all states but S to create_recovery_rates_process

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• Merge remote-tracking branch 'origin/dev' into competing_hazards_recovery_infection_resolution

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• Add a bitset_at implementation that works with a logical index.

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• WIP

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• WIP

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