gems: An R Package for Simulating from Disease Progression Models

Mathematical models of disease progression predict disease outcomes and are useful epidemiological tools for planners and evaluators of health interventions. The R package gems is a tool that simulates disease progression in patients and predicts the effect of different interventions on patient outcome. Disease progression is represented by a series of events (e.g., diagnosis, treatment and death), displayed in a directed acyclic graph. The vertices correspond to disease states and the directed edges represent events. The package gems allows simulations based on a generalized multistate model that can be described by a directed acyclic graph with continuous transition-specific hazard functions. The user can specify an arbitrary hazard function and its parameters. The model includes parameter uncertainty, does not need to be a Markov model, and may take the history of previous events into account. Applications are not limited to the medical field and extend to other areas where multistate simulation is of interest. We provide a technical explanation of the multistate models used by gems, explain the functions of gems and their arguments, and show a sample application.

The Blinder-Oaxaca decomposition for linear regression models

The counterfactual decomposition technique popularized by Blinder (1973, Journal of Human Resources, 436–455) and Oaxaca (1973, International Economic Review, 693–709) is widely used to study mean outcome differences between groups. For example, the technique is often used to analyze wage gaps by sex or race. This article summarizes the technique and addresses several complications, such as the identification of effects of categorical predictors in the detailed decomposition or the estimation of standard errors. A new command called oaxaca is introduced, and examples illustrating its usage are given.

Cultural capital and smoking in young adults: applying new indicators to explore social inequalities in health behaviour.

BACKGROUND Associations between social status and health behaviours are well documented, but the mechanisms involved are less understood. Cultural capital theory may contribute to a better understanding by expanding the scope of inequality indicators to include individuals' knowledge, skills, beliefs and material goods to examine how these indicators impact individuals' health lifestyles. We explore the structure and applicability of a set of cultural capital indicators in the empirical exploration of smoking behaviour among young male adults. METHODS We analysed data from the Swiss Federal Survey of Adolescents (CH-X) 2010-11 panel of young Swiss males (n = 10 736). A set of nine theoretically relevant variables (including incorporated, institutionalized and objectified cultural capital) were investigated using exploratory factor analysis. Regression models were run to observe the association between factor scores and smoking outcomes. Outcome measures consisted of daily smoking status and the number of cigarettes smoked by daily smokers. RESULTS Cultural capital indicators aggregated in a three-factor solution representing 'health values', 'education and knowledge' and 'family resources'. Each factor score predicted the smoking outcomes. In young males, scoring low on health values, education and knowledge and family resources was associated with a higher risk of being a daily smoker and of smoking more cigarettes daily. CONCLUSION Cultural capital measures that include, but go beyond, educational attainment can improve prediction models of smoking in young male adults. New measures of cultural capital may thus contribute to our understanding of the social status-based resources that individuals can use towards health behaviours.

Disclosure attitudes and social acknowledgement as predictors of posttraumatic stress disorder symptom severity in Chinese and German crime victims

Objective: Only rare data exist comparing cross-cultural aspects of civilian traumatization. We compared prevalence rates of posttraumatic stress disorder (PTSD) in German and Chinese crime victims, and investigated the cross-cultural effect of 2 interpersonal predictors. Method: German (n = 151) and Chinese (n = 144) adult crime victims were assessed several months postcrime. The parallel questionnaire set assessed PTSD symptom severity, disclosure attitudes, social acknowledgement, and demographic and crime characteristics. Results: German and Chinese participants differed significantly in their PTSD symptom severity. However, in both samples, disclosure attitudes and social acknowledgement predicted PTSD symptom severity with a similar strength, in addition to the effects of other PTSD predictors. Conclusions: The results suggest that interpersonal variables are predictors of PTSD symptom severity in both cultures and should be included in etiologic models of PTSD.

Childhood Trauma and Complex Posttraumatic Stress Disorder Symptoms in Older Adults: A Study of Direct Effects and Social-Interpersonal Factors as Potential Mediators

Childhood traumatic events may lead to long-lasting psychological effects and contribute to the development of complex posttraumatic sequelae. These might be captured by the diagnostic concept of complex posttraumatic stress disorder (CPTSD) as an alternative to classic posttraumatic stress disorder (PTSD). CPTSD comprises a further set of symptoms in addition to those of PTSD, namely, changes in affect, self, and interpersonal relationships. Previous empirical research on CPTSD has focused on middle-aged adults but not on older adults. Moreover, predictor models of CPTSD are still rare. The current study investigated the association between traumatic events in childhood and complex posttraumatic stress symptoms in older adults. The mediation of this association by 2 social-interpersonal factors (social acknowledgment as a survivor and dysfunctional disclosure) was investigated. These 2 factors focus on the perception of acknowledgment by others and either the inability to disclose traumatic experiences or the ability to do so only with negative emotional reactions. A total of 116 older individuals (age range = 59–98 years) who had experienced childhood traumatic events completed standardized self-report questionnaires indexing childhood trauma, complex trauma sequelae, social acknowledgment, and dysfunctional disclosure of trauma. The results showed that traumatic events during childhood were associated with later posttraumatic stress symptoms but with classic rather than complex symptoms. Social acknowledgment and dysfunctional disclosure partially mediated this relationship. These findings suggest that childhood traumatic stress impacts individuals across the life span and may be associated with particular adverse psychopathological consequences.

Sample size considerations using mathematical models: an example with Chlamydia trachomatis infection and its sequelae pelvic inflammatory disease.

BACKGROUND The success of an intervention to prevent the complications of an infection is influenced by the natural history of the infection. Assumptions about the temporal relationship between infection and the development of sequelae can affect the predicted effect size of an intervention and the sample size calculation. This study investigates how a mathematical model can be used to inform sample size calculations for a randomised controlled trial (RCT) using the example of Chlamydia trachomatis infection and pelvic inflammatory disease (PID). METHODS We used a compartmental model to imitate the structure of a published RCT. We considered three different processes for the timing of PID development, in relation to the initial C. trachomatis infection: immediate, constant throughout, or at the end of the infectious period. For each process we assumed that, of all women infected, the same fraction would develop PID in the absence of an intervention. We examined two sets of assumptions used to calculate the sample size in a published RCT that investigated the effect of chlamydia screening on PID incidence. We also investigated the influence of the natural history parameters of chlamydia on the required sample size. RESULTS The assumed event rates and effect sizes used for the sample size calculation implicitly determined the temporal relationship between chlamydia infection and PID in the model. Even small changes in the assumed PID incidence and relative risk (RR) led to considerable differences in the hypothesised mechanism of PID development. The RR and the sample size needed per group also depend on the natural history parameters of chlamydia. CONCLUSIONS Mathematical modelling helps to understand the temporal relationship between an infection and its sequelae and can show how uncertainties about natural history parameters affect sample size calculations when planning a RCT.

A common mechanism underlying food choice and social decisions

People make numerous decisions every day including perceptual decisions such as walking through a crowd, decisions over primary rewards such as what to eat, and social decisions that require balancing own and others’ benefits. The unifying principles behind choices in various domains are, however, still not well understood. Mathematical models that describe choice behavior in specific contexts have provided important insights into the computations that may underlie decision making in the brain. However, a critical and largely unanswered question is whether these models generalize from one choice context to another. Here we show that a model adapted from the perceptual decision-making domain and estimated on choices over food rewards accurately predicts choices and reaction times in four independent sets of subjects making social decisions. The robustness of the model across domains provides behavioral evidence for a common decision-making process in perceptual, primary reward, and social decision making.

Detecting outlying studies in meta-regression models using a forward search algorithm.

When considering data from many trials, it is likely that some of them present a markedly different intervention effect or exert an undue influence on the summary results. We develop a forward search algorithm for identifying outlying and influential studies in meta-analysis models. The forward search algorithm starts by fitting the hypothesized model to a small subset of likely outlier-free studies and proceeds by adding studies into the set one-by-one that are determined to be closest to the fitted model of the existing set. As each study is added to the set, plots of estimated parameters and measures of fit are monitored to identify outliers by sharp changes in the forward plots. We apply the proposed outlier detection method to two real data sets; a meta-analysis of 26 studies that examines the effect of writing-to-learn interventions on academic achievement adjusting for three possible effect modifiers, and a meta-analysis of 70 studies that compares a fluoride toothpaste treatment to placebo for preventing dental caries in children. A simple simulated example is used to illustrate the steps of the proposed methodology, and a small-scale simulation study is conducted to evaluate the performance of the proposed method. Copyright © 2016 John Wiley & Sons, Ltd.

Code-switching: a touchstone of models of bilingual language production

The goal of the present thesis was to investigate the production of code-switched utterances in bilinguals’ speech production. This study investigates the availability of grammatical-category information during bilingual language processing. The specific aim is to examine the processes involved in the production of Persian-English bilingual compound verbs (BCVs). A bilingual compound verb is formed when the nominal constituent of a compound verb is replaced by an item from the other language. In the present cases of BCVs the nominal constituents are replaced by a verb from the other language. The main question addressed is how a lexical element corresponding to a verb node can be placed in a slot that corresponds to a noun lemma. This study also investigates how the production of BCVs might be captured within a model of BCVs and how such a model may be integrated within incremental network models of speech production. In the present study, both naturalistic and experimental data were used to investigate the processes involved in the production of BCVs. In the first part of the present study, I collected 2298 minutes of a popular Iranian TV program and found 962 code-switched utterances. In 83 (8%) of the switched cases, insertions occurred within the Persian compound verb structure, hence, resulting in BCVs. As to the second part of my work, a picture-word interference experiment was conducted. This study addressed whether in the case of the production of Persian-English BCVs, English verbs compete with the corresponding Persian compound verbs as a whole, or whether English verbs compete with the nominal constituents of Persian compound verbs only. Persian-English bilinguals named pictures depicting actions in 4 conditions in Persian (L1). In condition 1, participants named pictures of action using the whole Persian compound verb in the context of its English equivalent distractor verb. In condition 2, only the nominal constituent was produced in the presence of the light verb of the target Persian compound verb and in the context of a semantically closely related English distractor verb. In condition 3, the whole Persian compound verb was produced in the context of a semantically unrelated English distractor verb. In condition 4, only the nominal constituent was produced in the presence of the light verb of the target Persian compound verb and in the context of a semantically unrelated English distractor verb. The main effect of linguistic unit was significant by participants and items. Naming latencies were longer in the nominal linguistic unit compared to the compound verb (CV) linguistic unit. That is, participants were slower to produce the nominal constituent of compound verbs in the context of a semantically closely related English distractor verb compared to producing the whole compound verbs in the context of a semantically closely related English distractor verb. The three-way interaction between version of the experiment (CV and nominal versions), linguistic unit (nominal and CV linguistic units), and relation (semantically related and unrelated distractor words) was significant by participants. In both versions, naming latencies were longer in the semantically related nominal linguistic unit compared to the response latencies in the semantically related CV linguistic unit. In both versions, naming latencies were longer in the semantically related nominal linguistic unit compared to response latencies in the semantically unrelated nominal linguistic unit. Both the analysis of the naturalistic data and the results of the experiment revealed that in the case of the production of the nominal constituent of BCVs, a verb from the other language may compete with a noun from the base language, suggesting that grammatical category does not necessarily provide a constraint on lexical access during the production of the nominal constituent of BCVs. There was a minimal context in condition 2 (the nominal linguistic unit) in which the nominal constituent was produced in the presence of its corresponding light verb. The results suggest that generating words within a context may not guarantee that the effect of grammatical class becomes available. A model is proposed in order to characterize the processes involved in the production of BCVs. Implications for models of bilingual language production are discussed.

Family Models of In(ter)dependence: Cultural Change and the Question of Universal Needs

I will start by discussing some aspects of Kagitcibasi’s Theory of Family Change: its current empirical status and, more importantly, its focus on universal human needs and the consequences of this focus. Family Change Theory’s focus on the universality of the basic human needs of autonomy and relatedness and its culture-level emphasis on cultural norms and family values as reflecting a culture’s capacity for fulfilling its members’ respective needs shows that the theory advocates balanced cultural norms of independence and interdependence. As a normative theory it therefore postulates the necessity of a synthetic family model of emotional interdependence as an alternative to extreme models of total independence and total interdependence. Generalizing from this I will sketch a theoretical model where a dynamic and dialectical process of the fit between individual and culture and between culture and universal human needs and related social practices is central. I will discuss this model using a recent cross-cultural project on implicit theories of self/world and primary/secondary control orientations as an example. Implications for migrating families and acculturating individuals are also discussed.