scholarly journals Statistical Estimation of the Reproductive Number From Case Notification Data

2020 ◽  
Author(s):  
Laura F White ◽  
Carlee B Moser ◽  
Robin N Thompson ◽  
Marcello Pagano
Keyword(s):  
Statistical Estimation ◽  
Reproduction Number ◽  
Large Body ◽  
Real Data ◽  
Reproductive Number ◽  
Tremendous Progress ◽  
Notification Data ◽  
Infectious Disease Dynamics ◽  
Case Notification ◽  
Insight Into

Abstract The reproductive number, or reproduction number, is a valuable metric in understanding infectious disease dynamics. There is a large body of literature related to its use and estimation. In the last 15 years, there has been tremendous progress in statistically estimating this number using case notification data. These approaches are appealing because they are relevant in an ongoing outbreak (e.g., for assessing the effectiveness of interventions) and do not require substantial modelling expertise to be implemented. In this review, we describe these methods and the extensions that have been developed. We provide insight into the distinct interpretations of the estimators proposed and provide real data examples to illustrate how they are implemented. Finally we conclude with a discussion of available software and opportunities for future development.

scholarly journals Modelling the dynamics of dengue real epidemics

2010 ◽  
Vol 368 (1933) ◽  
pp. 5679-5693 ◽  
Author(s):  
S. T. R. Pinho ◽  
C. P. Ferreira ◽  
L. Esteva ◽  
F. R. Barreto ◽  
V. C. Morato e Silva ◽  
...  
Keyword(s):  
Mosquito Control ◽  
Adult Stage ◽  
Reproduction Number ◽  
Real Data ◽  
Basic Reproductive Number ◽  
Reproductive Number ◽  
Adult Mosquito ◽  
Force Of Infection ◽  
Dengue Transmission ◽  
Suitable Measure

In this work, we use a mathematical model for dengue transmission with the aim of analysing and comparing two dengue epidemics that occurred in Salvador, Brazil, in 1995–1996 and 2002. Using real data, we obtain the force of infection, Λ , and the basic reproductive number, R 0 , for both epidemics. We also obtain the time evolution of the effective reproduction number, R ( t ), which results in a very suitable measure to compare the patterns of both epidemics. Based on the analysis of the behaviour of R 0 and R ( t ) in relation to the adult mosquito control parameter of the model, we show that the control applied only to the adult stage of the mosquito population is not sufficient to stop dengue transmission, emphasizing the importance of applying the control to the aquatic phase of the mosquito.

Estimation of Instant Fatality Rate of COVID-19 in Wuhan and Hubei Based on Daily Case Notification Data

2020 ◽  
Author(s):  
Lei Cao ◽  
Ting-ting Huang ◽  
Jun-xia Zhang ◽  
Qi Qin ◽  
Si-yu Liu ◽  
...  
Keyword(s):  
Fatality Rate ◽  
Notification Data ◽  
Case Notification

COVID-19: Time-Dependent Effective Reproduction Number and Sub-notification Effect Estimation Modeling (Preprint)

2020 ◽  
Author(s):  
Eduardo Atem De Carvalho ◽  
Rogerio Atem De Carvalho
Keyword(s):  
New York ◽  
Reproduction Number ◽  
Moving Average ◽  
Real Data ◽  
Time Dependent ◽  
Initial Value ◽  
Health Authorities ◽  
Reproduction Numbers ◽  
Effect Estimation ◽  
The Impact

BACKGROUND Since the beginning of the COVID-19 pandemic, researchers and health authorities have sought to identify the different parameters that govern their infection and death cycles, in order to be able to make better decisions. In particular, a series of reproduction number estimation models have been presented, with different practical results. OBJECTIVE This article aims to present an effective and efficient model for estimating the Reproduction Number and to discuss the impacts of sub-notification on these calculations. METHODS The concept of Moving Average Method with Initial value (MAMI) is used, as well as a model for Rt, the Reproduction Number, is derived from experimental data. The models are applied to real data and their performance is presented. RESULTS Analyses on Rt and sub-notification effects for Germany, Italy, Sweden, United Kingdom, South Korea, and the State of New York are presented to show the performance of the methods here introduced. CONCLUSIONS We show that, with relatively simple mathematical tools, it is possible to obtain reliable values for time-dependent, incubation period-independent Reproduction Numbers (Rt). We also demonstrate that the impact of sub-notification is relatively low, after the initial phase of the epidemic cycle has passed.

scholarly journals Comparison study in statistical estimation of gene effects based on a real data set

2021 ◽  
Vol 1978 (1) ◽  
pp. 012047
Author(s):  
Xiaona Sheng ◽  
Yuqiu Ma ◽  
Jiabin Zhou ◽  
Jingjing Zhou
Keyword(s):  
Statistical Estimation ◽  
Real Data ◽  
Comparison Study ◽  
Data Set ◽  
Gene Effects

MODELING THE IMPACT OF VOLUNTARY TESTING AND TREATMENT ON TUBERCULOSIS TRANSMISSION DYNAMICS

2012 ◽  
Vol 05 (04) ◽  
pp. 1250029 ◽  
Author(s):  
S. MUSHAYABASA ◽  
C. P. BHUNU
Keyword(s):  
Deterministic Model ◽  
Reproduction Number ◽  
Positive Impact ◽  
Transmission Dynamics ◽  
Effective Control ◽  
Reproductive Number ◽  
Voluntary Testing ◽  
Manifold Theory ◽  
The Impact ◽  
Disease Free

A deterministic model for evaluating the impact of voluntary testing and treatment on the transmission dynamics of tuberculosis is formulated and analyzed. The epidemiological threshold, known as the reproduction number is derived and qualitatively used to investigate the existence and stability of the associated equilibrium of the model system. The disease-free equilibrium is shown to be locally-asymptotically stable when the reproductive number is less than unity, and unstable if this threshold parameter exceeds unity. It is shown, using the Centre Manifold theory, that the model undergoes the phenomenon of backward bifurcation where the stable disease-free equilibrium co-exists with a stable endemic equilibrium when the associated reproduction number is less than unity. The analysis of the reproduction number suggests that voluntary tuberculosis testing and treatment may lead to effective control of tuberculosis. Furthermore, numerical simulations support the fact that an increase voluntary tuberculosis testing and treatment have a positive impact in controlling the spread of tuberculosis in the community.

scholarly journals Effect of daily periodic human movement on dengue dynamics: the case of the 2010 outbreak in Hermosillo, Mexico

2020 ◽  
Author(s):  
Mayra R. Tocto-Erazo ◽  
Daniel Olmos-Liceaga ◽  
José A. Montoya
Keyword(s):  
Real Data ◽  
Human Movement ◽  
Basic Reproductive Number ◽  
Reproductive Number ◽  
The South ◽  
South Side ◽  
Transmission Rates ◽  
The North ◽  
Local Properties ◽  
The City

AbstractThe human movement plays an important rol in the spread of infectious diseases. On an urban scale, people move daily to workplaces, schools, among others. Here, we are interested in exploring the effect of the daily local stay on the variations of some characteristics of dengue dynamics such as the transmission rates and local basic reproductive numbers. For this, we use a two-patch mathematical model that explicitly considers that daily mobility of people and real data from the 2010 dengue outbreak in Hermosillo, Mexico. Based on a preliminary cluster analysis, we divide the city into two regions, the south and north sides, which determine each patch of the model. We use a Bayesian approach to estimate the transmission rates and local basic reproductive numbers of some urban mobility scenarios where residents of each patch spend daily the 100% (no human movement between patches), 75% and 50% of their day at their place of residence. For the north side, estimates of transmission rates do not vary and it is more likely that the local basic reproductive number to be greater than one for all three different scenarios. On the contrary, tranmission rates of the south side have more weight in lower values when consider the human movement between patches compared to the uncoupled case. In fact, local basic reproductive numbers less than 1 are not negligible for the south side. If information about commuting is known, this work might be useful to obtain better estimates of some contagion local properties of a patch, such as the basic reproductive number.

scholarly journals Quantifying TB transmission: a systematic review of reproduction number and serial interval estimates for tuberculosis

2018 ◽  
Vol 146 (12) ◽  
pp. 1478-1494 ◽  
Author(s):  
Y. Ma ◽  
C. R. Horsburgh ◽  
L. F. White ◽  
H. E. Jenkins
Keyword(s):  
Systematic Review ◽  
Parameter Estimation ◽  
The Netherlands ◽  
Cause Of Death ◽  
Reproduction Number ◽  
Reproductive Number ◽  
Interval Estimates ◽  
Transmission Parameters ◽  
Serial Interval ◽  
Number Of Publications

AbstractTuberculosis (TB) is the leading global infectious cause of death. Understanding TB transmission is critical to creating policies and monitoring the disease with the end goal of TB elimination. To our knowledge, there has been no systematic review of key transmission parameters for TB. We carried out a systematic review of the published literature to identify studies estimating either of the two key TB transmission parameters: the serial interval (SI) and the reproductive number. We identified five publications that estimated the SI and 56 publications that estimated the reproductive number. The SI estimates from four studies were: 0.57, 1.42, 1.44 and 1.65 years; the fifth paper presented age-specific estimates ranging from 20 to 30 years (for infants <1 year old) to <5 years (for adults). The reproductive number estimates ranged from 0.24 in the Netherlands (during 1933–2007) to 4.3 in China in 2012. We found a limited number of publications and many high TB burden settings were not represented. Certain features of TB dynamics, such as slow transmission, complicated parameter estimation, require novel methods. Additional efforts to estimate these parameters for TB are needed so that we can monitor and evaluate interventions designed to achieve TB elimination.

#59: Children as Sentinels for Active Transmission of Tuberculosis: Disease Mapping Modeling of Programmatic Data in a High-Burden Setting

2021 ◽  
Vol 10 (Supplement_1) ◽  
pp. S16-S17
Author(s):  
Gunasekera Kenneth ◽  
Warren Joshua ◽  
Cohen Ted
Keyword(s):  
Census Data ◽  
Disease Mapping ◽  
Population Data ◽  
Grid Cells ◽  
High Burden ◽  
Individual Level ◽  
Tuberculosis Transmission ◽  
Subsequent Investigation ◽  
Notification Data ◽  
Case Notification

Abstract Background To meet the transmission reduction goals of the End TB strategy, there is a growing interest in identifying and targeting case-finding efforts to tuberculosis“hotspots,” geographic regions of active transmission. Collecting and interpreting spatial and pathogenic genetic information, the most reliable evidence of active transmission, is prohibitively resource-intensive under routine conditions in high-burden settings. Many countries maintain case-notification registers under routine conditions, representing an attractive source of data to investigate for transmission. However, notification data are imperfect. Areas of high incidence may reflect other underlying patterns, and individual-level covariate information and other information that may aid in its interpretation, such as baseline census data or other healthcare utilization data, is often unavailable. Despite imperfections, the accessibility of notification data demands further investigation. We examined notification data from 2005 to 2007 in a South American, high-burden setting where the household address of each case was geocoded. Subsequent investigation of notification data in the same setting from 2009 to 2012 additionally provided pathogen genetic evidence from all culture-positive cases suggesting regions of active transmission of tuberculosis. We investigated a disease mapping modeling approach leveraging only age-specified tuberculosis notification data to suggest hotspots of active tuberculosis transmission. Methods Given the absence of baseline population data at a comparable spatial resolution, we aggregated the point-referenced cases reported to the Peruvian National Tuberculosis Program from 2005 to 2007 within two of Lima’s four health districts into a grid with 400 m × 400 m cells. We used Bayesian hierarchical spatial modeling methodology to model the proportion of children cases of the total number of adult and child cases in each cell. Where the modeled proportion of child cases is higher than expected, we suggest that case notification is driven primarily by active transmission. Results This method identified several grid cells in which the proportion of child cases is higher than expected. The location of these grid cells was found to approximate the location of active transmission evidenced by a later genotyping study. Conclusions This evidence suggests that age-specified notification data, with all its limitations, may be sufficient to suggest hotspots of active transmission of tuberculosis. We additionally provide the first spatial evidence to support the long-cited belief that with respect to tuberculosis transmission, childhood cases may truly be “the canary in the coal mine.”

Missing Data Estimation Using Rough Sets

2010 ◽  
pp. 94-116
Author(s):  
Tshilidzi Marwala
Keyword(s):  
Missing Data ◽  
Rough Set ◽  
Rough Sets ◽  
Real Data ◽  
Valuable Insight ◽  
Lower And Upper Approximations ◽  
Decision Tables ◽  
Missing Data Estimation ◽  
Data Estimation ◽  
Insight Into

A number of techniques for handling missing data have been presented and implemented. Most of these proposed techniques are unnecessarily complex and, therefore, difficult to use. This chapter investigates a hot-deck data imputation method, based on rough set computations. In this chapter, characteristic relations are introduced that describe incompletely specified decision tables and then these are used for missing data estimation. It has been shown that the basic rough set idea of lower and upper approximations for incompletely specified decision tables may be defined in a variety of different ways. Empirical results obtained using real data are given and they provide a valuable insight into the problem of missing data. Missing data are predicted with an accuracy of up to 99%.

Exploring hate crime amongst a cohort of Scottish prisoners: an exploratory study

2019 ◽  
Vol 5 (1) ◽  
pp. 39-49
Author(s):  
Kirsty Penrice ◽  
Philip Birch ◽  
Stephan McAlpine
Keyword(s):  
Emotional Regulation ◽  
Hate Crime ◽  
Large Body ◽  
Exploratory Research ◽  
Structured Interviews ◽  
Environmental Implications ◽  
Prison Violence ◽  
Content Type ◽  
Prison Environment ◽  
Insight Into

Purpose The purpose of this paper is to explore the motives a person adopts in order to engage in hate-related behaviours within a prison setting. A subsidiary aim of the study was to compare this cohort of prisoners with prisoners who have been convicted for aggravated racism in the community. Design/methodology/approach In order to gather data, an exploratory research design was adopted, utilising the method of semi-structured interviews. In total, a number of nine interviews were conducted. Qualitative analysis was then employed allowing for an examination of meaning in relation to the motives behind the commission of hate crimes to occur. Findings The findings revealed the presence of racist beliefs and attitudes in both groups involved in the study. Further similarities between the two groups included the perception of inequality and beliefs about racism. The differences between the two groups included poor emotional regulation and an inability to manage beliefs and subsequent behaviours about people from different ethnic groups, with those in custody seeming to be more reactive. Practical implications The findings provide a preliminary insight into enhancing inmate safety. The environmental implications begin to reveal the complexity of hate-related behaviours in custody. There are differences between the context of hate crime committed in a prison environment compared to that committed in the community that require different solutions for addressing such behaviour. Further implications are considered in the final section of the paper. Originality/value A large body of research has been conducted on prison violence, seldom does this research examine this issue within the context of hate crime. This preliminary study offers an insight into prison-based hate crime.

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