epinowcast - Flexible Hierarchical Nowcasting

Tools to enable flexible and efficient hierarchical nowcasting of right-truncated epidemiological time-series using a semi-mechanistic Bayesian model with support for a range of reporting and generative processes. Nowcasting, in this context, is gaining situational awareness using currently available observations and the reporting patterns of historical observations. This can be useful when tracking the spread of infectious disease in real-time: without nowcasting, changes in trends can be obfuscated by partial reporting or their detection may be delayed due to the use of simpler methods like truncation. While the package has been designed with epidemiological applications in mind, it could be applied to any set of right-truncated time-series count data.

Last updated 11 months ago

cmdstanreffective-reproduction-number-estimationepidemiologyinfectious-disease-surveillancenowcastingoutbreak-analysispandemic-preparednessreal-time-infectious-disease-modellingstan

8.09 score 60 stars 71 scripts

epinowcast - Flexible Hierarchical Nowcasting

Tools to enable flexible and efficient hierarchical nowcasting of right-truncated epidemiological time-series using a semi-mechanistic Bayesian model with support for a range of reporting and generative processes. Nowcasting, in this context, is gaining situational awareness using currently available observations and the reporting patterns of historical observations. This can be useful when tracking the spread of infectious disease in real-time: without nowcasting, changes in trends can be obfuscated by partial reporting or their detection may be delayed due to the use of simpler methods like truncation. While the package has been designed with epidemiological applications in mind, it could be applied to any set of right-truncated time-series count data.

Last updated 11 months ago

cmdstanreffective-reproduction-number-estimationepidemiologyinfectious-disease-surveillancenowcastingoutbreak-analysispandemic-preparednessreal-time-infectious-disease-modellingstan

7.88 score 61 stars 65 scripts

primarycensored - Primary Event Censored Distributions

Provides functions for working with primary event censored distributions and 'Stan' implementations for use in Bayesian modeling. Primary event censored distributions are useful for modeling delayed reporting scenarios in epidemiology and other fields (Charniga et al. (2024) <doi:10.48550/arXiv.2405.08841>). It also provides support for arbitrary delay distributions, a range of common primary distributions, and allows for truncation and secondary event censoring to be accounted for (Park et al. (2024) <doi:10.1101/2024.01.12.24301247>). A subset of common distributions also have analytical solutions implemented, allowing for faster computation. In addition, it provides multiple methods for fitting primary event censored distributions to data via optional dependencies.

Last updated 12 days ago

censoringdistributionsmc-stantruncation

7.69 score 8 stars 1 dependents 16 scripts 519 downloads

epidist - Estimate Epidemiological Delay Distributions With brms

Understanding and accurately estimating epidemiological delay distributions is important for public health policy. These estimates influence epidemic situational awareness, control strategies, and resource allocation. This package provides methods to address the key challenges in estimating these distributions, including truncation, interval censoring, and dynamical biases. These issues are frequently overlooked, resulting in biased conclusions.

Last updated 10 days ago

6.10 score 14 stars 7 scripts

hashprng - Hash-Based Matching Pseudo-Random Number Generation

Provides helper functions for use of hash-based matching (HBM) for pseudo-random number generation (PRNG) in stochastic simulations. HBM-PRNG is an approach to simplify matching synthetic experiment samples, which ensures that matched runs different only in the focal parameters, not in their chance events.

Last updated 2 years ago

stochastic-simulationcpp

3.30 score 2 stars 5 scripts