R and Shiny for Cost-Effectiveness Analyses: Why and When? A Hypothetical Case Study

INTRODUCTION

Health economics models are typically built in Microsoft Excel^® owing to its wide familiarity, accessibility and perceived transparency. However, given the increasingly rapid and analytically complex decision-making needs of both the pharmaceutical industry and the field of health economics and outcomes research (HEOR), the demands of cost-effectiveness analyses may be better met by the programming language R.

OBJECTIVE

This case study provides an explicit comparison between Excel and R for contemporary cost-effectiveness analysis.

METHODS

We constructed duplicate cost-effectiveness models using Excel and R (with a user interface built using the Shiny package) to address a hypothetical case study typical of contemporary health technology assessment.

RESULTS

We compared R and Excel versions of the same model design to determine the advantages and limitations of the modelling platforms in terms of (i) analytical capability, (ii) data safety, (iii) building considerations, (iv) usability for technical and non-technical users and (v) model adaptability.

CONCLUSIONS

The findings of this explicit comparison are used to produce recommendations for when R might be more suitable than Excel in contemporary cost-effectiveness analyses. We conclude that selection of appropriate modelling software needs to consider case-by-case modelling requirements, particularly (i) intended audience, (ii) complexity of analysis, (iii) nature and frequency of updates and (iv) anticipated model run time.

Toward health technology assessment of whole-genome sequencing diagnostic tests: challenges and solutions

Whole-genome sequencing (WGS) is being applied within research settings across Europe to develop genomic WGS-based diagnostic tests. The focus of this perspective paper is to describe if, and how, current approaches of health technology assessment could be applied to WGS-based diagnostic tests. This perspective draws on the collective view from a trans-European multidisciplinary consortium of methodologists, clinicians and scientists. Specific challenges can be described by using the PICO (population, intervention, comparator, outcome) framework to inform health technology assessment. Practical solutions are suggested which require joined-up, multidisciplinary working across healthcare systems using existing expert networks so that emergent issues for the health technology assessment of WGS can be met in a timely fashion.

True hermaphroditism: first evidence of an ovotestis in a cetacean species

An immature unilateral hermaphrodite common dolphin (Delphinus delphis) was found stranded on the southwest coast of the UK. The external phenotype was that of a female, but internally there was one ovotestis, containing both ovarian follicles and testicular tubular elements, and a contralateral ovary. Ovarian portions of the ovotestis appeared normal and demonstrated follicular development, whereas the testicular tissue exhibited hypoplasia and degeneration. This is the first reported case of an ovotestis in a cetacean species.

Postmortem evidence of interactions of bottlenose dolphins (Tursiops truncatus) with other dolphin species in south-west England

Reports of violent interactions between bottlenose dolphins (Tursiops truncatus) and harbour porpoises (Phocoena phocoena) in the coastal waters of the UK are well documented. Examination of stranded cetaceans by the Cornwall Wildlife Trust Marine Strandings Network and the UK Cetacean Strandings Investigation Programme has indicated that seven animals, of four other species, found stranded in south-west England, had pathology consistent with bottlenose dolphin interaction, including two juvenile and two adult common dolphins (Delphinus delphis), one juvenile pilot whale (Globicephala melas), one juvenile Risso's dolphin (Grampus griseus) and one adult striped dolphin (Stenella coeruleoalba). Although recorded traumatic lesions were often not as severe as those found in harbour porpoises, it is probable that the interactions did contribute to stranding and/or death in all four of the juvenile animals examined. Furthermore, analysis of photographs taken before establishment of the Marine Strandings Network revealed rake (teeth) marks consistent with bottlenose dolphin interaction on one stranded common dolphin in 1992. A number of causes have been suggested for these interactions in harbour porpoises stranded in the UK and it is possible that any combination of these factors may also be implicated in the cases described in this report.

Hepatozoon species infection in wild red squirrels (Sciurus vulgaris) on the Isle of Wight

Postmortem examinations of 49 red squirrels (Sciurus vulgaris) found dead on the Isle of Wight revealed the presence of a Hepatozoon species in 18 of them (37 per cent). The prevalence of infection was highest in subadult animals and no juveniles were infected. The prevalence was higher in the squirrels dying from natural causes (nine of 12) than in squirrels killed in road accidents (seven of 27). The weight of infection varied, and there were heavy infections in squirrels dying from toxoplasmosis and bacterial pneumonia. A PCR-based assay was used to identify the presence of Hepatozoon species DNA in the lungs, and immunoperoxidase staining was used to confirm the identity of schizonts observed in histological sections. The nucleotide base sequence of the PCR products indicated that the organism was a novel species closely related to, but distinct from, Hepatozoon erhardovae of bank voles (Clethrionomys glareolus).

Mechanical dysfunction of the left atrium and the left atrial appendage following cardioversion of atrial fibrillation and its relation to total electrical energy used for cardioversion

In 39 patients undergoing electrical cardioversion for atrial fibrillation (AF), we examined the effect of total electrical energy used for cardioversion on postcardioversion peak left atrial (LA) rapid filling velocity (A) and the atrial emptying fraction, and recovery of LA effective mechanical atrial function (defined as peak A velocity > or = 0.50 m/s), as assessed by transthoracic echocardiography. In a subset of 27 patients who underwent pre- and postcardioversion transesophageal echocardiography, we assessed the relation between total electrical energy and LA appendage filling and emptying velocities and spontaneous echo contrast. Patients were randomized to receive an initial shock of 1.5 J/kg based on body weight, or 2.5, 3.5, 5 J/kg, or 360 J, followed sequentially by higher shock intensities until sinus rhythm was achieved. Patients were classified into 4 groups based on quartiles of total energy delivered for cardioversion. Conversion to sinus rhythm was associated with a significant decrease in the LA appendage filling velocities (0.42 +/- 0.20 m/s vs 0.29 +/- 0.14 m/s; p = 0.002) and LA appendage emptying velocities (0.40 +/- 0.22 m/s vs 0.29 +/- 0.18 m/s; p = 0.03), but no change in the incidence of spontaneous echo contrast (61% vs 70%, p = 0.08). The 4 groups of patients did not differ with respect to postcardioversion LA appendage filling velocities, LA appendage emptying velocities, incidence of spontaneous echo contrast, or worsening of spontaneous echo contrast. Similarly, the change in LA appendage filling and emptying velocities associated with cardioversion was not different between the groups. Furthermore, postcardioversion peak A velocity and atrial emptying fraction and recovery of effective mechanical atrial function were similar between the 4 groups. These results suggest that in patients undergoing electrical cardioversion for AF, the total electrical energy used for cardioversion has no effect on the mechanical function of the left atrium or LA appendage following cardioversion.

Sensitivity and care: vital tools for skill-mix review

The issue of skill mix has become linked in the minds of many nurses with 'skill dilution'. This paper discusses the ideas used in a skill-mix review and looks at the essential differences between skill mix and grade mix. The authors have examined the literature and draw some important lessons, providing pointers for anybody who is charged with, or whose unit is subject to, a skill-mix review.

Screening elderly people in primary care: a randomized controlled trial

A randomized controlled trial was carried out to test the effectiveness of a screening programme carried out by nurses for elderly people aged 75 years and over in a general practice. A total of 151 people were randomly allocated to the test group and 145 to the control group. The test group received a home visit from a nurse at which an assessment lasting 45 minutes was made of: activities of daily living, social functioning, sensory functions, mental and emotional problems, current medical problems, blood pressure, urinalysis, haemoglobin level and compliance with medication. Both groups completed a selection of items from four health indices before and 20 months after the intervention. At follow up, the test group scored significantly better than the control group on a morale scale. However, this trial provided no evidence for better resolution of physical problems or finding activities of daily living easier in the test group compared with the control group. It is suggested that the main benefit of such a screening process is that the special attention and education provided improves adaptation to old age and awareness of the support systems available. The government has proposed an annual review of elderly people in their own home and this study suggests that the objectives of this scheme should be clarified.