The Calculus of M-estimation in R with geex

M-estimation, or estimating equation, methods are widely applicable for point estimation and asymptotic inference. In this paper, we present an R package that can find roots and compute the empirical sandwich variance estimator for any set of user-specified, unbiased estimating equations. Examples from the M-estimation primer by Stefanski and Boos (2002) demonstrate use of the software. The package also includes a framework for finite sample variance corrections and a website with an extensive collection of tutorials

Advanced study of coastal zone oceanographic requirements for ERTS E and F

Earth Resources Technology Satellites E and F orbits and remote sensor instruments for coastal oceanographic data collectio

Exploring content and psychometric validity of newly developed assessment tools for itch and skin pain in atopic dermatitis.

BackgroundAtopic dermatitis (AD) is a common skin disorder characterized by chronic inflammation, altered skin barrier function, and inflammatory cell skin infiltration that decreases health-related quality of life (HRQoL). The study objective was to understand the patient perspective of AD burden and determine suitable patient-reported outcome (PRO) measures.MethodsThis mixed methods study involved the collection of qualitative and quantitative information from adults (≥ 18 years old) and adolescents (12 - 17 years old) with clinician-confirmed AD regarding their experiences of AD symptoms and its impact on HRQoL. The first part of the study included three stages: in-person concept elicitation (CE) interviews, a 2-week daily electronic diary (eDiary) study, and in-person cognitive debriefing (CD) interviews. An Itch numeric rating scale (NRS) (v1.0) and a Skin Pain NRS (v1.0) evaluation during CD interviews required participants to think about their 'worst' itch and 'worst' skin pain in the past 24 h. Other PRO measures allowed for psychometric testing. The second part of the study involved telephone-depth interviews (TDIs) and qualitative feedback from participants who had not participated in the CD interviews. Qualitative data were thematically analyzed. Psychometric evaluation of NRS measures was performed using eDiary data.ResultsIn the CE interviews, itch and/or itching and skin pain were the most prevalent symptoms consistently discussed by participants. Both NRS measures demonstrated strong psychometric reliability and were applicable across ages with suitable concurrent validity. During the CD interviews, some participants focused their answers on their 'average' itch/itching in the past 24 h, rather than their 'worst' itch. Some participants answered the Skin Pain NRS thinking about general pain or other types of pain, rather than skin pain specifically. Consequently, modifications to both measures addressed these issues and re-tested as paper-and-pen versions in subsequent TDIs. Itch NRS (v2.0) modifications helped participants focus on their worst itching. Most participants preferred Skin Pain NRS v2.0b, which included skin pain descriptors.ConclusionsItching and skin pain are the most important and relevant AD symptoms. The Itch NRS (v2.0) and Skin Pain NRS (v2.0b) appear to be appropriate endpoints for the assessment of itching and skin pain severity for clinical trials with adults and adolescents with AD

Genética de la conservación para la recuperación de especies animales en peligro de extinción: revisión de los planes de recuperación de especies en peligro de extinción de Estados Unidos (1977–1998)

The utility of genetic data in conservation efforts, particularly in comparison to demographic information, is the subject of ongoing debate. Using a database of information surveyed from 181 US endangered and threatened species recovery plans, we addressed the following questions concerning the use of genetic information in animal recovery plans: I. What is the relative prominence of genetic vs. demographic data in recovery plan development? and, II. When are genetic factors viewed as a threat, and how do plans respond to genetic threats? In general, genetics appear to play a minor and relatively ill–defined part in the recovery planning process; demographic data are both more abundant and more requested in recovery plans, and tasks are more frequently assigned to the collection / monitoring of demographic rather than genetic information. Nonetheless, genetic threats to species persistence and recovery are identified in a substantial minority (22 %) of recovery plans, although there is little uniform response to these perceived threats in the form of specific proposed recovery or management tasks. Results indicate that better guidelines are needed to identify how and when genetic information is most useful for species recovery; we highlight specific contexts in which genetics may provide unique management information, beyond that provided by other kinds of data.La utilidad de los datos genéticos en los esfuerzos conservacionistas, en particular en comparación con la información demográfica, es objeto de un continuo debate. Utilizando una base de datos con información sobre los 181 planes de recuperación de especies amenazadas y en peligro de extinción de Estados Unidos, hemos estudiado las siguientes cuestiones referentes al uso de la información genética en los planes de recuperación de especies animales: I ¿Cuál es la importancia relativa de los datos genéticos en comparación con los demográficos en el desarrollo de los planes de recuperación? y II ¿Cuándo se considera que los factores genéticos constituyen una amenaza, y cómo responden los planes a esas amenazas genéticas? En general, parece que la genética sólo desempeña un papel menor y relativamente mal definido en el proceso de planificación de la recuperación de especies; los datos demográficos son más abundantes y más solicitados para la elaboración de planes de recuperación, y las acciones que se llevan a cabo con frecuencia se enfocan más a las recopilación/observación de los datos demográficos que a la obtención de información genética. No obstante, las amenazas genéticas para la supervivencia y recuperación de especies se indican como un importante factor minoritario (22 %) en los planes de recuperación, si bien la respuesta a esas amenazas mediante medidas de gestión o recuperación específicas es poco uniforme. Los resultados apuntan a que se necesitan unas directrices más claras para determinar cómo y cuándo resulta más útil la información genética para la recuperación de especies; hemos resaltado contextos concretos en los que la genética puede proporcionar una valiosísima fuente de información para la gestión de esas cuestiones, superior a la que se pueda obtener a partir de otros datos

A Recipe for inferference: Start with Causal Inference. Add Interference. Mix Well with R.

In causal inference, interference occurs when the treatment of one subject affects the outcome of other subjects. Interference can distort research conclusions about causal effects when not accounted for properly. In the absence of interference, inverse probability weighted (IPW) estimators are commonly used to estimate causal effects from observational data. Recently, IPW estimators have been extended to handle interference. Tchetgen Tchetgen and VanderWeele (2012) proposed IPW methods to estimate direct and indirect (or spillover) effects that allow for interference between individuals within groups. In this paper, we present inferference, an R package that computes these IPW causal effect estimates when interference may be present within groups. We illustrate use of the package with examples from political science and infectious disease

Timing and predictors of severe rotavirus gastroenteritis among unvaccinated infants in low- and middle-income countries

Delays in rotavirus vaccine schedule could improve performance in low- and middle-income countries (LMICs). However, delaying the first dose could be detrimental if infants experience severe rotavirus gastroenteritis (RVGE) early in life. Our objective was to describe the timing and predictors of severe RVGE in unvaccinated children in LMICs. We analysed the placebo arms from two clinical trials (cohort 1: NCT00241644; cohort 2: NCT00362648). We estimated the rate, cumulative incidence (per 1000 infants) and age distribution of severe RVGE episodes. Cox proportional hazards models were used to estimate hazard ratios and 95% confidence intervals (CI) for the association between baseline factors and severe RVGE. Cumulative incidence at 6 months of age was 23/1000 (95% CI 15-30) in cohort 1 and 6/1000 (95% CI 3-8) in cohort 2. Early antibiotic use (compared with no use) was associated with 2.03 (95% CI 1.18-3.48) and 1.41 (95% CI 0.80-2.51) times the rate of severe RVGE in cohorts 1 and 2, respectively. The cumulative incidence of severe RVGE was low at 6 months of age, suggesting that a 4-week delay in the vaccination schedule may not result in a large number of severe RVGE episodes prior to vaccine receipt. Copyright © Cambridge University Press 2018

Electronic Dose Monitoring Device Patterns in Youth Living With HIV Enrolled in an Adherence Intervention Clinical Trial

INTRODUCTION: Youth living with HIV in the US have low rates of viral suppression, in part because of challenges with antiretroviral therapy adherence. METHODS: Daily dosing in the Adolescent Medicine Trials Network for HIV/AIDS Interventions 152 study, a randomized controlled trial of a 12-week adherence intervention (triggered escalating real-time adherence intervention) for viremic youth, compared with standard of care (SOC), was measured by electronic dose monitoring (EDM) throughout 48 weeks of follow-up. EDM data collected over the first 24 weeks were used to characterize patterns of antiretroviral therapy adherence with group-based trajectory models. RESULTS: Four trajectory groups were identified among the 85 participants included in the analysis during the intervention phase of the study: (Worst) no interaction with EDM, (Declining) initially moderate EDM-based adherence followed by steep declines, (Good) initially high EDM-based adherence with modest declines, and (Best) consistently high EDM-based adherence. Being in the SOC arm, not being in school, higher evasiveness and panic decision-making scores, and lower adherence motivation were associated with higher odds of being in a worse trajectory group ( P < 0.05). A general decline in dosing was observed in the 12 weeks postintervention, when all participants were managed using SOC. CONCLUSIONS: Use of group-based trajectory models allowed a more nuanced understanding of EDM-based adherence over time compared with collapsed summary measures. In addition to the study intervention, other factors influencing EDM-based adherence included being in school, decision-making styles, and adherence-related motivation. This information can be used to design better intervention services for youth living with HIV

Timing of HIV Seroreversion Among HIV-Exposed, Breastfed Infants in Malawi: Type of HIV Rapid Test Matters

Introduction Rapid HIV serological tests are a cost-effective, point-of-care test among HIV exposed infants but cannot distinguish between maternal and infant antibodies. The lack of data on the timing of decay of maternal antibodies in young infants hinders the potential use of rapid tests in exposed infants. We aimed to determine the time to seroreversion for two commonly used rapid tests in a prospective cohort of HIV-exposed breastfeeding infants ages 3-18 months of life. Methods We collected data on the performance of two commonly used rapid tests (Determine and Unigold) in Malawi between 2008 and 2012 or at the University of North Carolina between 2014 and 2015. Time to seroreversion was estimated for both rapid tests using the Kaplan-Meier product limit estimator which allows for interval censored data. Results At 3 months of age, 3 % of infants had seroreverted according to Determine and 7 % had seroreverted according to Unigold. About one in four infants had achieved seroreversion by 4 months using Unigold, but only about one in twelve infants by 4 months when using Determine. More than 95 % of all infants had seroverted by 7 months according to Unigold and by 12 months according to the Determine assay. Discussion We show that the time of seroreversion depends greatly on the type of test used. Our results highlight the need for recommendations to specify the timing and type of test used in the context of infant HIV detection in resource-poor settings, and base the interpretation of test result on knowledge of time to seroreversion of the selected test