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The use of open-source programming languages, such as R, in health decision sciences is growing and has the potential to facilitate model transparency, reproducibility, and shareability. However, realizing this potential can be challenging. Models are complex and primarily built to answer a research question, with model sharing and transparency relegated to being secondary goals. Consequently, code is often neither well documented nor systematically organized in a comprehensible and shareable approach. Moreover, many decision modelers are not formally trained in computer programming and may lack good coding practices, further compounding the problem of model transparency. To address these challenges, we propose a high-level framework for model-based decision and cost-effectiveness analyses (CEA) in R. The proposed framework consists of a conceptual, modular structure and coding recommendations for the implementation of model-based decision analyses in R. This framework defines a set of common decision model elements divided into five components: (1) model inputs, (2) decision model implementation, (3) model calibration, (4) model validation, and (5) analysis. The first four components form the model development phase. The analysis component is the application of the fully developed decision model to answer the policy or the research question of interest, assess decision uncertainty, and/or to determine the value of future research through value of information (VOI) analysis. In this framework, we also make recommendations for good coding practices specific to decision modeling, such as file organization and variable naming conventions. We showcase the framework through a fully functional, testbed decision model, which is hosted on GitHub for free download and easy adaptation to other applications. The use of this framework in decision modeling will improve code readability and model sharing, paving the way to an ideal, open-source world.

Clinical trials require participation of numerous patients, enormous research resources and substantial public funding. Time-consuming trials lead to delayed implementation of beneficial interventions and to reduced benefit to patients. This manuscript discusses two methods for the allocation of research resources and reviews a framework for prioritisation and design of clinical trials. The traditional error-driven approach of clinical trial design controls for type I and II errors. However, controlling for those statistical errors has limited relevance to policy makers. Therefore, this error-driven approach can be inefficient, waste research resources and lead to research with limited impact on daily practice. The novel value-driven approach assesses the currently available evidence and focuses on designing clinical trials that directly inform policy and treatment decisions. Estimating the net value of collecting further information, prior to undertaking a trial, informs a decision maker whether a clinical or health policy decision can be made with current information or if collection of extra evidence is justified. Additionally, estimating the net value of new information guides study design, data collection choices, and sample size estimation. The value-driven approach ensures the efficient use of research resources, reduces unnecessary burden to trial participants, and accelerates implementation of beneficial healthcare interventions.

PurposeDecision models can be used to support allocation of scarce surgical resources. These models incorporate health-related quality of life (HRQoL) values that can be determined using physician panels. The predominant opinion is that one should use values obtained from citizens. We investigated whether physicians give different HRQoL values to citizens and evaluate whether such differences impact decision model outcomes.MethodsA two-round Delphi study was conducted. Citizens estimated HRQoL of pre- and post-operative health states for ten surgeries using a visual analogue scale. These values were compared using Bland–Altman analysis with HRQoL values previously obtained from physicians. Impact on decision model outcomes was evaluated by calculating the correlation between the rankings of surgeries established using the physicians’ and the citizens’ values.ResultsA total of 71 citizens estimated HRQoL. Citizens’ values on the VAS scale were − 0.07 points (95% CI − 0.12 to − 0.01) lower than the physicians’ values. The correlation between the rankings of surgeries based on citizens’ and physicians’ values was 0.96 (p < 0.001).ConclusionPhysicians put higher values on health states than citizens. However, these differences only result in switches between adjacent entries in the ranking. It would seem that HRQoL values obtained from physicians are adequate to inform decision models during crises.

Objectives A previously developed decision model to prioritize surgical procedures in times of scarce surgical capacity used quality of life (QoL) primarily derived from experts in one center. These estimates are key input of the model, and might be more context-dependent than the other input parameters (age, survival). The aim of this study was to validate our model by replicating these QoL estimates. Methods The original study estimated QoL of patients in need of commonly performed procedures in live expert-panel meetings. This study replicated this procedure using a web-based Delphi approach in a different hospital. The new QoL scores were compared with the original scores using mixed effects linear regression. The ranking of surgical procedures based on combined QoL values from the validation and original study was compared to the ranking based solely on the original QoL values. Results The overall mean difference in QoL estimates between the validation study and the original study was − 0.11 (95% CI:  -0.12 - -0.10). The model output (DALY/month delay) based on QoL data from both studies was similar to the model output based on the original data only: The Spearman’s correlation coefficient between the ranking of all procedures before and after including the new QoL estimates was 0.988. Discussion Even though the new QoL estimates were systematically lower than the values from the original study, the ranking for urgency based on health loss per unit of time delay of procedures was consistent. This underscores the robustness and generalizability of the decision model for prioritization of surgical procedures.

Background The burden of the COVID-19 pandemic resulted in a reduction of available health care capacity for regular care. To guide prioritisation of semielective surgery in times of scarcity, we previously developed a decision model to quantify the expected health loss due to delay of surgery, in an academic hospital setting. The aim of this study is to validate our decision model in a nonacademic setting and include additional elective surgical procedures. Methods In this study, we used the previously published three-state cohort state-transition model, to evaluate the health effects of surgery postponement for 28 surgical procedures commonly performed in nonacademic hospitals. Scientific literature and national registries yielded nearly all input parameters, except for the quality of life (QoL) estimates which were obtained from experts using the Delphi method. Two expert panels, one from a single nonacademic hospital and one from different nonacademic hospitals in the Netherlands, were invited to estimate QoL weights. We compared estimated model results (disability adjusted life years (DALY)/month of surgical delay) based on the QoL estimates from the two panels by calculating the mean difference and the correlation between the ranks of the different surgical procedures. The eventual model was based on the combined QoL estimates from both panels. Results Pacemaker implantation was associated with the most DALY/month of surgical delay (0.054 DALY/month, 95% CI: 0.025–0.103) and hemithyreoidectomy with the least DALY/month (0.006 DALY/month, 95% CI: 0.002–0.009). The overall mean difference of QoL estimates between the two panels was 0.005 (95% CI -0.014–0.004). The correlation between ranks was 0.983 ( p  < 0.001). Conclusions Our study provides an overview of incurred health loss due to surgical delay for surgeries frequently performed in nonacademic hospitals. The quality of life estimates currently used in our model are robust and validate towards a different group of experts. These results enrich our earlier published results on academic surgeries and contribute to prioritising a more complete set of surgeries.

PurposeThe objective of this study was to compare the cost-effectiveness of preoperative octreotide therapy followed by surgery versus the standard treatment modality for growth-hormone secreting pituitary adenomas, direct surgery (that is, surgery without preoperative treatment) from a public third-party payer perspective. MethodsWe developed an individual-level state-transition microsimulation model to simulate costs and outcomes associated with preoperative octreotide therapy followed by surgery and direct surgery for patients with growth-hormone secreting pituitary adenomas. Transition probabilities, utilities, and costs were estimated from recent published data and discounted by 3% annually over a lifetime time horizon. Model outcomes included lifetime costs [2020 United States (US) Dollars], quality-adjusted life-years (QALYs) and incremental cost-effectiveness ratios (ICERs).ResultsUnder base case assumptions, direct surgery was found to be the dominant strategy as it yielded lower costs and greater health effects (QALYs) compared to preoperative octreotide strategy in the second-order Monte Carlo microsimulation. The ICER was most sensitive to probability of remission following primary therapy and duration of preoperative octreotide therapy. Accounting for joint parameter uncertainty, direct surgery had a higher probability of demonstrating a cost-effective profile compared to preoperative octreotide treatment at 77% compared to 23%, respectively.ConclusionsUsing standard benchmarks for cost-effectiveness in the US ($100,000/QALY), preoperative octreotide therapy followed by surgery may not be cost-effective compared to direct surgery for patients with growth-hormone secreting pituitary adenomas but the result is highly sensitive to initial treatment failure and duration of preoperative treatment.

Cost-effectiveness analyses often rely on cohort state-transition models (cSTMs). The cohort trace is the primary outcome of cSTMs, which captures the proportion of the cohort in each health state over time (state occupancy). However, the cohort trace is an aggregated measure that does not capture the information about the specific transitions among the health states (transition dynamics). In practice, these transition dynamics are crucial in many applications, such as incorporating transition rewards or computing various epidemiological outcomes that could be used for model calibration and validation (e.g. disease incidence and lifetime risk). In this manuscript we propose modifying the transitional cSTMs cohort trace computation to compute and store cSTMs dynamics that capture both state occupancy and transition dynamics. This approach produces a multidimensional matrix from which both the state occupancy and the transition dynamics can be recovered. We highlight the advantages and potential applications of this approach with an example coded in R to facilitate the implementation of our method. Footnotes * The code of the reward matrix. * https://github.com/DARTH-git/state-transition-model-dynamics

In an introductory tutorial, we illustrated building cohort state-transition models (cSTMs) in R, where the state transitions probabilities were constant over time. However, in practice, many cSTMs require transitions, rewards, or both to vary over time (time-dependent). This tutorial illustrates adding two types of time-dependency using a previously published cost-effectiveness analysis of multiple strategies as an example. The first is simulation-time dependence, which allows for the transition probabilities to vary as a function of time as measured since the start of the simulation (e.g., varying probability of death as the cohort ages). The second is state-residence time dependence, allowing for history by tracking the time spent in any particular health state using tunnel states. We use these time-dependent cSTMs to conduct cost-effectiveness and probabilistic sensitivity analyses. We also obtain various epidemiological outcomes of interest from the outputs generated from the cSTM, such as survival probability and disease prevalence, often used for model calibration and validation. We present the mathematical notation first, followed by the R code to execute the calculations. The full R code is provided in a public code repository for broader implementation.

Decision models can combine information from different sources to simulate the long-term consequences of alternative strategies in the presence of uncertainty. A cohort state-transition model (cSTM) is a decision model commonly used in medical decision-making to simulate the transitions of a hypothetical cohort among various health states over time. This tutorial focuses on time-independent cSTM, where transition probabilities among health states remain constant over time. We implement time-independent cSTM in R, an open-source mathematical and statistical programming language. We illustrate time-independent cSTMs using a previously published decision model, calculate costs and effectiveness outcomes, conduct a cost-effectiveness analysis of multiple strategies, including a probabilistic sensitivity analysis. We provide open-source code in R to facilitate wider adoption. In a second, more advanced tutorial, we illustrate time-dependent cSTMs.

This tutorial shows how to implement time-dependent cohort state-transition models (cSTMs) to conduct cost-effectiveness analyses (CEA) in R, where transition probabilities and rewards vary by time. We account for two types of time dependency: time since the start of the simulation (simulation-time dependency) and time spent in a health state (state residence dependency). We illustrate how to conduct a CEA of multiple strategies based on a time-dependent cSTM using a previously published cSTM, including probabilistic sensitivity analyses. We also demonstrate how to compute various epidemiological outcomes of interest from the outputs generated from the cSTM, such as survival probability and disease prevalence. We present both the mathematical notation and the R code to execute the calculations. This tutorial builds upon an introductory tutorial that introduces time-independent cSTMs using a CEA example in R. We provide an up-to-date public code repository for broader implementation.