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Revised

whoishRisk – an R package to calculate WHO/ISH cardiovascular risk scores for all epidemiological subregions of the world

[version 2; peer review: 3 approved]
Previously titled: Simple and adaptable R implementation of WHO/ISH cardiovascular risk charts for all epidemiological subregions of the world
PUBLISHED 08 Mar 2017
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OPEN PEER REVIEW
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This article is included in the RPackage gateway.

Abstract

The World Health Organisation and International Society of Hypertension (WHO/ISH) cardiovascular disease (CVD) risk assessment charts have been implemented in many low- and middle-income countries as part of the WHO Package of Essential Non-Communicable Disease (PEN) Interventions for Primary Health Care in Low-Resource settings. Evaluation of the WHO/ISH cardiovascular risk charts and their use is a key priority and since they only existed in paper or PDF formats, we developed an R implementation of the charts for all epidemiological subregions of the world. The main strengths of this implementation are that it is built in a free, open-source, coding language with simple syntax, can be downloaded from github as a package (“whoishRisk”), and can be used with a standard computer.

Keywords

WHO/ISH, Cardiovascular Risk Charts, Risk Score, R

Revised Amendments from Version 1

The main update of this version is the development of an R package using the previously reported R code. The package, called whoishRisk, can be downloaded directly from github as described in the paper. The benefit of this is that users now do not need to load the R code or any dependency files in the work space; instead they must download the whoishRisk package and load it from the library.

The major update to the code itself is the addition of warning messages when parameters passed to the WHO_ISH_Risk() function appear out of range.

The title was changed accordingly to reflect the development of the whoishRisk package. Figure 1 was removed as it was no longer relevant, and table 2 was added to show the new WHO/ISH Risk warning messages.

See the authors' detailed response to the review by Raivo Kolde
See the authors' detailed response to the review by Maria Suarez-Diez
See the authors' detailed response to the review by Scott A. Chamberlain

Introduction

Cardiovascular disease (CVD) is the leading cause of death worldwide, including in many low-and-middle income countries (LMIC)1,2. Preventing CVD is therefore a worldwide priority and the World Health Organisation (WHO) is coordinating a global strategy for LMIC to systematically prevent CVD in primary care3.

In 2007 the WHO and the International Society of Hypertension (ISH) published the WHO/ISH CVD risk charts for all WHO epidemiological subregions of the world4. These charts are to be used as part of the WHO’s Package of Essential NCD (PEN) Interventions for Primary Health Care in Low-Resource Settings in jurisdictions that do not have their own population-derived risk assessment algorithms. While these charts are a good resource for many health systems, little is known about their validity5. Therefore, it is important that jurisdictions that implement these charts conduct operational research and attempt to validate and optimise them for their setting.

Two paper-based versions of WHO/ISH charts are available for each subregion: one that requires measured total cholesterol and one that does not. The latter was made available for use in settings with limited access to laboratory testing or where the cost of cholesterol testing is prohibitive. Both charts require information on age, gender, diabetes status, smoking status, and systolic blood pressure to stratify people into one of five risk categories of 10-year risk of a fatal or non-fatal CVD event. Further instructions for their use have been published, including the definition and classification of the fourteen epidemiological sub-regions3.

Through our experience collaborating with LMIC with the implementation of WHO PEN, we identified a common need for an open-source tool to facilitate the implementation of WHO/ISH risk charts and operational research of WHO PEN at a population level. We therefore developed an R package called whoishRisk, which we describe here and make available to researchers in LMIC. R is a statistical computing language and environment which is open source and freely available to anyone6.

Methods

Extraction of WHO/ISH cardiovascular risk charts

We extracted all versions of the paper-based WHO/ISH CVD risk charts by hand into a standardized Microsoft Excel template, independently and in duplicate. We compared the duplicate extractions and calculated Cohen’s kappa coefficient for inter-rater reliability, using the irr package in R7. Discrepancies were reviewed by the same two extractors and resolved by referring to the original paper chart.

Development of the WHO/ISH risk function

One author wrote the initial code for the WHO/ISH risk function in R and created the whoishRisk package (DC). This was reviewed and adapted by a second author experienced in the R language (CK). Two additional authors (JL, NB), new to the R language, reviewed the code to ensure the syntax was comprehensible.

Validation

A MatLab implementation of WHO/ISH risk charts for epidemiological subregion SEAR D had been previously reported8. We used Octave (www.gnu.org/software/octave/) version 8.3.2 to calculate the SEAR D WHO/ISH risk score for every possible combination of risk factors using the previously reported MatLab implementation, and compared the percent agreement to the risk scores generated by our R package, whoishRisk.

Results

whoishRisk Package

The whoishRisk package can be downloaded and installed directly from github using the install_github() command in the devtools package, with the argument “DylanRJCollins/whoishRisk”9. The package contains a single function, WHO_ISH_Risk(), which calculates the WHO/ISH CVD risk score for any epidemiological subregion of the world based on the parameter values passed to it.

Extraction of WHO/ISH cardiovascular risk charts

All WHO/ISH risk charts were extracted by hand into a single comma delimited file (Dataset 1). The first six columns specify the risk factor values, and the last 14 columns specify the corresponding risk category for a given subregion. whoishRisk uses these data internally to calculate the WHO/ISH risk score. Cohen’s kappa for initial agreement between the independent extractors was 0.97, indicating excellent agreement. All remaining discrepancies were resolved by consensus.

dmgdrsmkagesbpchlrefvAFR_DAFR_EAMR_AAMR_BAMR_DEMR_BEMR_DEUR_AEUR_BEUR_CSEAR_BSEAR_DWPR_BWPR_A
101401204400111204<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
101401205400111205<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
101401206400111206<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
101401207400111207<10%<10%10% to <20%<10%<10%<10%<10%<10%<10%<10%10% to <20%10% to <20%<10%<10%
10140120840011120810% to <20%10% to <20%20% to <30%10% to <20%10% to <20%<10%<10%<10%10% to <20%<10%20% to <30%30% to <40%<10%<10%
101401404400111404<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
101401405400111405<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%10% to <20%<10%<10%<10%
101401406400111406<10%<10%10% to <20%10% to <20%10% to <20%<10%<10%<10%<10%<10%10% to <20%10% to <20%<10%<10%
10140140740011140710% to <20%20% to <30%20% to <30%20% to <30%10% to <20%<10%10% to <20%<10%10% to <20%<10%30% to <40%30% to <40%10% to <20%10% to <20%
10140140840011140820% to <30%20% to <30%>=40%30% to <40%30% to <40%10% to <20%20% to <30%10% to <20%30% to <40%20% to <30%>=40%>=40%30% to <40%10% to <20%
101401604400111604<10%<10%10% to <20%10% to <20%10% to <20%<10%<10%<10%<10%<10%10% to <20%20% to <30%<10%<10%
10140160540011160510% to <20%10% to <20%20% to <30%20% to <30%20% to <30%10% to <20%10% to <20%<10%10% to <20%<10%30% to <40%20% to <30%20% to <30%10% to <20%
10140160640011160620% to <30%20% to <30%30% to <40%>=40%30% to <40%20% to <30%20% to <30%<10%20% to <30%10% to <20%>=40%>=40%20% to <30%20% to <30%
101401607400111607>=40%>=40%>=40%>=40%>=40%30% to <40%30% to <40%10% to <20%>=40%20% to <30%>=40%>=40%>=40%30% to <40%
101401608400111608>=40%>=40%>=40%>=40%>=40%>=40%>=40%20% to <30%>=40%>=40%>=40%>=40%>=40%>=40%
10140180440011180430% to <40%30% to <40%>=40%>=40%>=40%30% to <40%30% to <40%10% to <20%30% to <40%20% to <30%>=40%>=40%>=40%30% to <40%
101401805400111805>=40%30% to <40%>=40%>=40%>=40%>=40%>=40%20% to <30%>=40%30% to <40%>=40%>=40%>=40%>=40%
101401806400111806>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
101401807400111807>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
101401808400111808>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
101501204500111204<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
101501205500111205<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
101501206500111206<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%10% to <20%10% to <20%<10%<10%
101501207500111207<10%<10%10% to <20%10% to <20%10% to <20%<10%<10%<10%<10%<10%10% to <20%20% to <30%<10%<10%
10150120850011120810% to <20%10% to <20%20% to <30%20% to <30%10% to <20%10% to <20%10% to <20%<10%10% to <20%10% to <20%20% to <30%>=40%10% to <20%<10%
101501404500111404<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%10% to <20%<10%<10%
101501405500111405<10%<10%10% to <20%10% to <20%10% to <20%<10%<10%<10%<10%<10%10% to <20%10% to <20%<10%<10%
10150140650011140610% to <20%10% to <20%10% to <20%10% to <20%10% to <20%10% to <20%10% to <20%<10%10% to <20%<10%20% to <30%30% to <40%10% to <20%<10%
10150140750011140720% to <30%20% to <30%30% to <40%20% to <30%20% to <30%10% to <20%20% to <30%<10%20% to <30%10% to <20%30% to <40%>=40%20% to <30%10% to <20%
10150140850011140820% to <30%20% to <30%>=40%30% to <40%>=40%30% to <40%30% to <40%10% to <20%30% to <40%30% to <40%>=40%>=40%30% to <40%20% to <30%
10150160450011160410% to <20%10% to <20%10% to <20%20% to <30%10% to <20%10% to <20%10% to <20%<10%10% to <20%<10%20% to <30%20% to <30%10% to <20%10% to <20%
10150160550011160510% to <20%10% to <20%20% to <30%20% to <30%20% to <30%20% to <30%20% to <30%<10%10% to <20%10% to <20%30% to <40%30% to <40%20% to <30%10% to <20%
10150160650011160620% to <30%20% to <30%>=40%>=40%30% to <40%30% to <40%30% to <40%10% to <20%20% to <30%10% to <20%>=40%>=40%30% to <40%20% to <30%
101501607500111607>=40%>=40%>=40%>=40%>=40%>=40%>=40%20% to <30%>=40%30% to <40%>=40%>=40%>=40%30% to <40%
101501608500111608>=40%>=40%>=40%>=40%>=40%>=40%>=40%30% to <40%>=40%>=40%>=40%>=40%>=40%>=40%
10150180450011180430% to <40%30% to <40%>=40%>=40%>=40%>=40%>=40%20% to <30%>=40%30% to <40%>=40%>=40%>=40%30% to <40%
101501805500111805>=40%>=40%>=40%>=40%>=40%>=40%>=40%30% to <40%>=40%>=40%>=40%>=40%>=40%>=40%
101501806500111806>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
101501807500111807>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
101501808500111808>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
101601204600111204<10%<10%<10%<10%<10%10% to <20%10% to <20%<10%<10%<10%<10%10% to <20%<10%<10%
10160120560011120510% to <20%<10%<10%<10%<10%20% to <30%10% to <20%<10%<10%<10%10% to <20%20% to <30%<10%<10%
10160120660011120610% to <20%10% to <20%10% to <20%<10%10% to <20%20% to <30%20% to <30%<10%10% to <20%<10%20% to <30%30% to <40%10% to <20%<10%
10160120760011120720% to <30%10% to <20%10% to <20%10% to <20%10% to <20%30% to <40%30% to <40%<10%10% to <20%10% to <20%30% to <40%>=40%10% to <20%10% to <20%
10160120860011120830% to <40%10% to <20%20% to <30%20% to <30%30% to <40%>=40%>=40%10% to <20%20% to <30%20% to <30%30% to <40%>=40%20% to <30%10% to <20%
10160140460011140410% to <20%10% to <20%10% to <20%10% to <20%10% to <20%20% to <30%10% to <20%<10%10% to <20%<10%10% to <20%30% to <40%10% to <20%<10%
10160140560011140510% to <20%10% to <20%10% to <20%10% to <20%10% to <20%30% to <40%20% to <30%<10%10% to <20%10% to <20%20% to <30%>=40%10% to <20%10% to <20%
10160140660011140620% to <30%20% to <30%20% to <30%10% to <20%20% to <30%>=40%30% to <40%10% to <20%20% to <30%10% to <20%30% to <40%>=40%20% to <30%10% to <20%
10160140760011140730% to <40%20% to <30%30% to <40%20% to <30%30% to <40%>=40%>=40%10% to <20%20% to <30%20% to <30%>=40%>=40%20% to <30%10% to <20%
10160140860011140830% to <40%20% to <30%>=40%30% to <40%>=40%>=40%>=40%20% to <30%>=40%30% to <40%>=40%>=40%>=40%20% to <30%
10160160460011160420% to <30%10% to <20%20% to <30%20% to <30%20% to <30%>=40%30% to <40%10% to <20%10% to <20%10% to <20%30% to <40%>=40%20% to <30%10% to <20%
10160160560011160530% to <40%20% to <30%30% to <40%20% to <30%30% to <40%>=40%>=40%10% to <20%20% to <30%20% to <30%>=40%>=40%30% to <40%20% to <30%
101601606600111606>=40%30% to <40%>=40%>=40%>=40%>=40%>=40%20% to <30%30% to <40%20% to <30%>=40%>=40%>=40%20% to <30%
101601607600111607>=40%>=40%>=40%>=40%>=40%>=40%>=40%20% to <30%>=40%30% to <40%>=40%>=40%>=40%30% to <40%
101601608600111608>=40%>=40%>=40%>=40%>=40%>=40%>=40%30% to <40%>=40%>=40%>=40%>=40%>=40%>=40%
101601804600111804>=40%>=40%>=40%>=40%>=40%>=40%>=40%30% to <40%>=40%>=40%>=40%>=40%>=40%>=40%
101601805600111805>=40%>=40%>=40%>=40%>=40%>=40%>=40%30% to <40%>=40%>=40%>=40%>=40%>=40%>=40%
101601806600111806>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
101601807600111807>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
101601808600111808>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
10170120470011120410% to <20%10% to <20%10% to <20%10% to <20%10% to <20%20% to <30%10% to <20%10% to <20%10% to <20%10% to <20%10% to <20%20% to <30%10% to <20%10% to <20%
10170120570011120510% to <20%10% to <20%20% to <30%10% to <20%10% to <20%30% to <40%20% to <30%10% to <20%10% to <20%10% to <20%10% to <20%30% to <40%10% to <20%10% to <20%
10170120670011120620% to <30%10% to <20%20% to <30%20% to <30%20% to <30%30% to <40%30% to <40%10% to <20%10% to <20%20% to <30%20% to <30%>=40%20% to <30%10% to <20%
10170120770011120720% to <30%10% to <20%30% to <40%20% to <30%30% to <40%>=40%>=40%20% to <30%20% to <30%20% to <30%30% to <40%>=40%20% to <30%20% to <30%
10170120870011120830% to <40%30% to <40%30% to <40%30% to <40%30% to <40%>=40%>=40%20% to <30%30% to <40%30% to <40%30% to <40%>=40%20% to <30%20% to <30%
10170140470011140420% to <30%10% to <20%20% to <30%20% to <30%20% to <30%30% to <40%20% to <30%10% to <20%10% to <20%20% to <30%20% to <30%>=40%20% to <30%10% to <20%
10170140570011140520% to <30%20% to <30%30% to <40%20% to <30%30% to <40%>=40%30% to <40%20% to <30%20% to <30%20% to <30%30% to <40%>=40%20% to <30%20% to <30%
10170140670011140630% to <40%20% to <30%30% to <40%30% to <40%30% to <40%>=40%>=40%20% to <30%30% to <40%30% to <40%30% to <40%>=40%30% to <40%20% to <30%
101701407700111407>=40%30% to <40%>=40%>=40%>=40%>=40%>=40%30% to <40%30% to <40%30% to <40%>=40%>=40%>=40%30% to <40%
101701408700111408>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
10170160470011160430% to <40%20% to <30%30% to <40%30% to <40%>=40%>=40%>=40%30% to <40%20% to <30%30% to <40%30% to <40%>=40%30% to <40%20% to <30%
101701605700111605>=40%30% to <40%>=40%>=40%>=40%>=40%>=40%30% to <40%30% to <40%30% to <40%>=40%>=40%>=40%30% to <40%
101701606700111606>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
101701607700111607>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
101701608700111608>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
101701804700111804>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
101701805700111805>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
101701806700111806>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
101701807700111807>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
101701808700111808>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
100401204400101204<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
100401205400101205<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
100401206400101206<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
100401207400101207<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
100401208400101208<10%<10%10% to <20%<10%<10%<10%<10%<10%<10%<10%20% to <30%20% to <30%<10%<10%
100401404400101404<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
100401405400101405<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
100401406400101406<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%10% to <20%<10%<10%<10%
100401407400101407<10%<10%10% to <20%10% to <20%<10%<10%<10%<10%<10%<10%20% to <30%10% to <20%<10%<10%
10040140840010140820% to <30%10% to <20%30% to <40%30% to <40%20% to <30%10% to <20%10% to <20%<10%20% to <30%10% to <20%20% to <30%>=40%20% to <30%10% to <20%
100401604400101604<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
100401605400101605<10%<10%10% to <20%10% to <20%10% to <20%<10%<10%<10%<10%<10%10% to <20%10% to <20%<10%<10%
10040160640010160610% to <20%10% to <20%20% to <30%20% to <30%10% to <20%<10%10% to <20%<10%10% to <20%<10%30% to <40%20% to <30%10% to <20%<10%
10040160740010160720% to <30%20% to <30%30% to <40%30% to <40%20% to <30%10% to <20%10% to <20%<10%20% to <30%10% to <20%>=40%>=40%20% to <30%10% to <20%
100401608400101608>=40%>=40%>=40%>=40%>=40%20% to <30%30% to <40%10% to <20%>=40%20% to <30%>=40%>=40%>=40%30% to <40%
10040180440010180410% to <20%20% to <30%20% to <30%30% to <40%20% to <30%10% to <20%20% to <30%<10%20% to <30%10% to <20%30% to <40%30% to <40%20% to <30%10% to <20%
10040180540010180520% to <30%30% to <40%30% to <40%>=40%30% to <40%20% to <30%30% to <40%10% to <20%30% to <40%20% to <30%>=40%>=40%>=40%20% to <30%
100401806400101806>=40%>=40%>=40%>=40%>=40%30% to <40%>=40%10% to <20%>=40%30% to <40%>=40%>=40%>=40%30% to <40%
100401807400101807>=40%>=40%>=40%>=40%>=40%>=40%>=40%30% to <40%>=40%>=40%>=40%>=40%>=40%>=40%
100401808400101808>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
100501204500101204<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
100501205500101205<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
100501206500101206<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
100501207500101207<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%10% to <20%10% to <20%<10%<10%
100501208500101208<10%10% to <20%10% to <20%10% to <20%10% to <20%<10%<10%<10%10% to <20%<10%20% to <30%20% to <30%<10%<10%
100501404500101404<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
100501405500101405<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
100501406500101406<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%10% to <20%10% to <20%<10%<10%
10050140750010140710% to <20%10% to <20%10% to <20%10% to <20%10% to <20%10% to <20%10% to <20%<10%10% to <20%<10%20% to <30%20% to <30%10% to <20%<10%
10050140850010140820% to <30%20% to <30%30% to <40%30% to <40%20% to <30%20% to <30%20% to <30%10% to <20%20% to <30%10% to <20%30% to <40%>=40%20% to <30%10% to <20%
100501604500101604<10%<10%<10%10% to <20%<10%<10%<10%<10%<10%<10%10% to <20%10% to <20%<10%<10%
100501605500101605<10%<10%10% to <20%10% to <20%10% to <20%10% to <20%10% to <20%<10%10% to <20%<10%10% to <20%20% to <30%10% to <20%<10%
10050160650010160610% to <20%10% to <20%20% to <30%20% to <30%10% to <20%10% to <20%10% to <20%<10%10% to <20%10% to <20%30% to <40%30% to <40%10% to <20%10% to <20%
10050160750010160720% to <30%20% to <30%30% to <40%30% to <40%20% to <30%20% to <30%20% to <30%10% to <20%20% to <30%10% to <20%>=40%>=40%20% to <30%10% to <20%
100501608500101608>=40%>=40%>=40%>=40%>=40%>=40%>=40%20% to <30%>=40%30% to <40%>=40%>=40%>=40%30% to <40%
10050180450010180420% to <30%20% to <30%20% to <30%30% to <40%30% to <40%20% to <30%20% to <30%10% to <20%20% to <30%20% to <30%30% to <40%30% to <40%30% to <40%20% to <30%
10050180550010180530% to <40%30% to <40%30% to <40%>=40%>=40%30% to <40%>=40%10% to <20%30% to <40%20% to <30%>=40%>=40%>=40%20% to <30%
100501806500101806>=40%>=40%>=40%>=40%>=40%>=40%>=40%20% to <30%>=40%30% to <40%>=40%>=40%>=40%30% to <40%
100501807500101807>=40%>=40%>=40%>=40%>=40%>=40%>=40%30% to <40%>=40%>=40%>=40%>=40%>=40%>=40%
100501808500101808>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
100601204600101204<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
100601205600101205<10%<10%10% to <20%<10%<10%<10%10% to <20%<10%<10%<10%<10%10% to <20%<10%<10%
100601206600101206<10%<10%10% to <20%<10%<10%10% to <20%10% to <20%<10%<10%10% to <20%<10%10% to <20%<10%<10%
10060120760010120710% to <20%10% to <20%20% to <30%10% to <20%10% to <20%10% to <20%20% to <30%<10%10% to <20%10% to <20%10% to <20%20% to <30%10% to <20%<10%
10060120860010120820% to <30%20% to <30%20% to <30%10% to <20%10% to <20%30% to <40%30% to <40%10% to <20%10% to <20%20% to <30%20% to <30%30% to <40%10% to <20%10% to <20%
100601404600101404<10%<10%10% to <20%<10%<10%10% to <20%10% to <20%<10%<10%10% to <20%<10%10% to <20%10% to <20%<10%
10060140560010140510% to <20%10% to <20%10% to <20%10% to <20%10% to <20%10% to <20%20% to <30%<10%10% to <20%10% to <20%10% to <20%20% to <30%10% to <20%10% to <20%
10060140660010140610% to <20%10% to <20%20% to <30%10% to <20%10% to <20%20% to <30%20% to <30%10% to <20%10% to <20%20% to <30%10% to <20%30% to <40%10% to <20%10% to <20%
10060140760010140720% to <30%20% to <30%30% to <40%20% to <30%20% to <30%30% to <40%30% to <40%10% to <20%20% to <30%20% to <30%20% to <30%>=40%20% to <30%10% to <20%
10060140860010140830% to <40%20% to <30%>=40%30% to <40%30% to <40%>=40%>=40%20% to <30%30% to <40%30% to <40%30% to <40%>=40%30% to <40%20% to <30%
10060160460010160410% to <20%10% to <20%20% to <30%20% to <30%10% to <20%20% to <30%20% to <30%10% to <20%10% to <20%20% to <30%10% to <20%20% to <30%20% to <30%10% to <20%
10060160560010160520% to <30%10% to <20%30% to <40%20% to <30%20% to <30%30% to <40%30% to <40%10% to <20%20% to <30%20% to <30%20% to <30%30% to <40%20% to <30%20% to <30%
10060160660010160620% to <30%20% to <30%>=40%30% to <40%20% to <30%>=40%>=40%20% to <30%20% to <30%30% to <40%30% to <40%>=40%30% to <40%20% to <30%
10060160760010160730% to <40%30% to <40%>=40%>=40%30% to <40%>=40%>=40%20% to <30%30% to <40%30% to <40%>=40%>=40%>=40%30% to <40%
100601608600101608>=40%>=40%>=40%>=40%>=40%>=40%>=40%30% to <40%>=40%>=40%>=40%>=40%>=40%>=40%
100601804600101804>=40%30% to <40%>=40%>=40%30% to <40%>=40%>=40%20% to <30%>=40%>=40%30% to <40%>=40%>=40%30% to <40%
100601805600101805>=40%>=40%>=40%>=40%>=40%>=40%>=40%30% to <40%>=40%>=40%>=40%>=40%>=40%>=40%
100601806600101806>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
100601807600101807>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
100601808600101808>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
100701204700101204<10%<10%10% to <20%<10%<10%10% to <20%10% to <20%<10%<10%<10%<10%10% to <20%<10%<10%
10070120570010120510% to <20%<10%10% to <20%10% to <20%10% to <20%10% to <20%10% to <20%<10%<10%<10%10% to <20%20% to <30%<10%<10%
10070120670010120610% to <20%10% to <20%10% to <20%10% to <20%10% to <20%20% to <30%20% to <30%10% to <20%10% to <20%10% to <20%10% to <20%20% to <30%10% to <20%10% to <20%
10070120770010120710% to <20%10% to <20%20% to <30%10% to <20%10% to <20%30% to <40%20% to <30%10% to <20%10% to <20%10% to <20%20% to <30%30% to <40%10% to <20%10% to <20%
10070120870010120820% to <30%20% to <30%20% to <30%20% to <30%10% to <20%>=40%30% to <40%10% to <20%20% to <30%20% to <30%20% to <30%>=40%10% to <20%10% to <20%
10070140470010140410% to <20%10% to <20%10% to <20%10% to <20%10% to <20%20% to <30%10% to <20%10% to <20%10% to <20%10% to <20%10% to <20%20% to <30%10% to <20%10% to <20%
10070140570010140510% to <20%10% to <20%20% to <30%10% to <20%10% to <20%20% to <30%20% to <30%10% to <20%10% to <20%10% to <20%20% to <30%30% to <40%10% to <20%10% to <20%
10070140670010140620% to <30%10% to <20%20% to <30%20% to <30%20% to <30%30% to <40%20% to <30%10% to <20%10% to <20%20% to <30%20% to <30%30% to <40%20% to <30%10% to <20%
10070140770010140720% to <30%20% to <30%30% to <40%20% to <30%30% to <40%>=40%30% to <40%20% to <30%20% to <30%20% to <30%30% to <40%>=40%20% to <30%20% to <30%
10070140870010140830% to <40%30% to <40%>=40%30% to <40%30% to <40%>=40%>=40%20% to <30%30% to <40%30% to <40%>=40%>=40%30% to <40%20% to <30%
10070160470010160420% to <30%10% to <20%20% to <30%20% to <30%20% to <30%30% to <40%20% to <30%10% to <20%10% to <20%20% to <30%20% to <30%30% to <40%20% to <30%10% to <20%
10070160570010160520% to <30%20% to <30%30% to <40%20% to <30%30% to <40%>=40%30% to <40%20% to <30%20% to <30%20% to <30%30% to <40%>=40%20% to <30%20% to <30%
10070160670010160630% to <40%20% to <30%>=40%30% to <40%30% to <40%>=40%>=40%20% to <30%20% to <30%30% to <40%30% to <40%>=40%30% to <40%20% to <30%
100701607700101607>=40%30% to <40%>=40%>=40%30% to <40%>=40%>=40%30% to <40%30% to <40%30% to <40%>=40%>=40%>=40%30% to <40%
100701608700101608>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
100701804700101804>=40%30% to <40%>=40%>=40%>=40%>=40%>=40%30% to <40%>=40%>=40%>=40%>=40%>=40%30% to <40%
100701805700101805>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
100701806700101806>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
100701807700101807>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
100701808700101808>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
111401204401111204<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
111401205401111205<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
111401206401111206<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
111401207401111207<10%<10%10% to <20%<10%<10%<10%<10%<10%<10%<10%<10%10% to <20%<10%<10%
11140120840111120810% to <20%10% to <20%30% to <40%20% to <30%<10%<10%10% to <20%<10%10% to <20%10% to <20%20% to <30%30% to <40%10% to <20%10% to <20%
111401404401111404<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
111401405401111405<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
11140140640111140610% to <20%10% to <20%10% to <20%10% to <20%<10%<10%<10%<10%<10%<10%<10%10% to <20%<10%<10%
11140140740111140710% to <20%20% to <30%30% to <40%10% to <20%<10%<10%10% to <20%<10%10% to <20%10% to <20%10% to <20%30% to <40%10% to <20%10% to <20%
11140140840111140820% to <30%>=40%>=40%>=40%20% to <30%10% to <20%20% to <30%10% to <20%30% to <40%30% to <40%>=40%>=40%20% to <30%20% to <30%
11140160440111160410% to <20%10% to <20%10% to <20%10% to <20%<10%<10%10% to <20%<10%<10%<10%10% to <20%10% to <20%10% to <20%<10%
11140160540111160510% to <20%20% to <30%20% to <30%20% to <30%10% to <20%10% to <20%10% to <20%<10%10% to <20%10% to <20%10% to <20%20% to <30%20% to <30%10% to <20%
11140160640111160630% to <40%>=40%30% to <40%30% to <40%20% to <30%10% to <20%20% to <30%<10%20% to <30%10% to <20%20% to <30%>=40%30% to <40%20% to <30%
111401607401111607>=40%>=40%>=40%>=40%30% to <40%20% to <30%30% to <40%10% to <20%30% to <40%30% to <40%>=40%>=40%30% to <40%30% to <40%
111401608401111608>=40%>=40%>=40%>=40%>=40%>=40%>=40%30% to <40%>=40%>=40%>=40%>=40%>=40%>=40%
111401804401111804>=40%>=40%30% to <40%>=40%>=40%30% to <40%>=40%10% to <20%30% to <40%30% to <40%>=40%>=40%>=40%30% to <40%
111401805401111805>=40%>=40%>=40%>=40%>=40%>=40%>=40%10% to <20%>=40%>=40%>=40%>=40%>=40%>=40%
111401806401111806>=40%>=40%>=40%>=40%>=40%>=40%>=40%30% to <40%>=40%>=40%>=40%>=40%>=40%>=40%
111401807401111807>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
111401808401111808>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
111501204501111204<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
111501205501111205<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
111501206501111206<10%<10%10% to <20%<10%<10%<10%<10%<10%<10%<10%<10%10% to <20%<10%<10%
11150120750111120710% to <20%10% to <20%20% to <30%10% to <20%<10%<10%10% to <20%<10%<10%<10%10% to <20%20% to <30%<10%<10%
11150120850111120820% to <30%10% to <20%>=40%20% to <30%10% to <20%10% to <20%20% to <30%<10%20% to <30%20% to <30%20% to <30%>=40%10% to <20%10% to <20%
111501404501111404<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%<10%
11150140550111140510% to <20%10% to <20%10% to <20%10% to <20%<10%<10%10% to <20%<10%<10%<10%<10%10% to <20%10% to <20%<10%
11150140650111140610% to <20%20% to <30%20% to <30%10% to <20%10% to <20%10% to <20%10% to <20%<10%10% to <20%10% to <20%10% to <20%20% to <30%10% to <20%10% to <20%
11150140750111140720% to <30%30% to <40%>=40%20% to <30%10% to <20%10% to <20%20% to <30%<10%20% to <30%20% to <30%20% to <30%>=40%20% to <30%10% to <20%
11150140850111140830% to <40%>=40%>=40%>=40%30% to <40%30% to <40%>=40%20% to <30%>=40%>=40%>=40%>=40%30% to <40%30% to <40%
11150160450111160410% to <20%10% to <20%20% to <30%20% to <30%10% to <20%10% to <20%20% to <30%<10%10% to <20%10% to <20%10% to <20%20% to <30%20% to <30%10% to <20%
11150160550111160520% to <30%30% to <40%30% to <40%30% to <40%20% to <30%20% to <30%30% to <40%10% to <20%20% to <30%20% to <30%20% to <30%30% to <40%30% to <40%20% to <30%
11150160650111160630% to <40%>=40%>=40%>=40%30% to <40%30% to <40%>=40%10% to <20%30% to <40%30% to <40%30% to <40%>=40%>=40%30% to <40%
111501607501111607>=40%>=40%>=40%>=40%>=40%>=40%>=40%20% to <30%>=40%>=40%>=40%>=40%>=40%>=40%
111501608501111608>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
111501804501111804>=40%>=40%>=40%>=40%>=40%>=40%>=40%20% to <30%>=40%>=40%>=40%>=40%>=40%>=40%
111501805501111805>=40%>=40%>=40%>=40%>=40%>=40%>=40%30% to <40%>=40%>=40%>=40%>=40%>=40%>=40%
111501806501111806>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
111501807501111807>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%>=40%
This is a portion of the data; to view all the data, please download the file.
Dataset 1.WHO_ISH_Scores.csv.
CSV file of all parameter combinations and corresponding WHO/ISH risk scores used internally by WHO_ISH_Risk() to match parameter values passed to it to their respective risk score.

Development of the WHO_ISH_Risk() Function

whoishRisk contains a single function, called WHO_ISH_Risk(), which calculates the WHO/ISH risk score for any epidemiological subregion. The function code is reported herein (Dataset 2).

Dataset 2.R code for the WHO_ISH_Risk() function of the whoishRisk package.

WHO_ISH_Risk() requires seven parameters: age, gender, smoking status, diabetes status, systolic blood pressure, total cholesterol, and the appropriate WHO epidemiological subregion. The function format in the workspace is: WHO_ISH_Risk(age, gdr, smk, sbp, dm, chl, subregion). These parameters and their abbreviations are summarised in Table 1. No default values are specified for any parameter.

Table 1. Description of the WHO_ISH_Risk() function parameters.

Function
parameter
Full parameter
name
Parameter
class
Parameter values
ageAgenumericContinuous (years)
gdrGendernumericDichotomous
(0=female; 1=male)
smkSmokingnumericDichotomous
(0=non-smoker;
1=smoker)
sbpSystolic blood
pressure
numericContinuous (mmHg)
dmDiabetes
mellitus status
numericDichotomous
(0=not diabetic;
1=diabetic)
chlTotal cholesterolnumericContinuous (mmol/
L); 0=unknown
cholesterol
subregionWHO
epidemiological
subregion
character“AFR_D”, “AFR_E”,
“AMR_A”, “AMR_B”,
“AMR_D”,“EMR_B”,
“EMR_D”, “EUR_A”,
“EUR_B”, EUR_C”,
“SEAR_B”, “SEAR_
D”, “WPR_A”,
“WPR_B”

Internally, WHO_ISH_Risk() requires access to the comma delimited file named “WHO_ISH_Scores.csv”, which it calls automatically from within the package but is also included herein (Dataset 1).

The WHO_ISH_Risk() function creates an internal data frame of the risk factor values passed to it. Parameters can be single values or vectors of equal length. It then categorises the continuous parameters age, systolic blood pressure, and total cholesterol. Age and systolic blood pressure were categorised according to WHO guidance10. Total cholesterol was categorised into one of the five possible categories (<=4,5,6,7 and >=8 mmol/L) according to common clinical practice, rounding up from 0.5 to the nearest integer.

Internally, a unique identification code is generated corresponding to the combinations of risk factors for each individual. This code is matched to a reference code from the “WHO_ISH_Scores.csv” file. The function stores the risk scores in a data frame that includes the risk factors, and ultimately returns a vector containing the risk scores. The output of the function is one of five different character strings, corresponding to the five different WHO/ISH risk categories: “<10%”, “10 to <20%”, “20 to <30%”, “30 to <40%”, >=40%”.

Warning messages are included when parameters appear out of range. These messages, their conditions, and their intended interpretation are described in Table 2. Out of range continuous parameters (age, systolic blood pressure, total cholesterol) are non-fatal and a risk score will be generated with a warning message. Out of range dichotomous variables (gender, smoking status, diabetes status) are fatal errors and the output (NA) will be generated with a warning.

Table 2. WHO_ISH_Risk() warning messages, their conditions, and intended interpretation.

Condition
of Warning
Warning MessageInterpretation of Warning
age < 19"At least one age is 18 or younger"WHO/ISH risk scores are meant for use in
adults. At least one age value is equal to 18
or younger. Check for errors in age values.
age >100"At least one age is greater than 100"Age values greater than 100 may indicate a
data error. Check to ensure age values over
100 are correct.
gdr > 1"Gender must be equal to 0 or 1"A value for gender other than 0 or 1 is
included. Check gender values.
smk > 1"Smoking must be equal to 0 or 1"A value for smoking other than 0 or 1 is
included. Check smoking values.
sbp < 90"At least one systolic blood pressure
is below 90 mmHg"
SBP values below 90 mmHg may indicate a
data error. Check to ensure values under
90 mmHg are correct.
sbp > 250"At least one systolic blood pressure
is over 250 mmHg"
SBP values over 250 mmHg may indicate a
data error. Check to ensure values over 250
are correct.
dm > 1"Diabetes status must be equal to 0
or 1"
A value for diabetes status other than 0 or 1
is included. Check diabetes status values.
tc > 10"At least one total cholesterol is
greater than 10 mmol/L. Ensure all
values are in units of mmol/L"
Total cholesterol values over 10 mmol/L
may indicate a data error. Check to ensure
values over 10 mmol/L are correct and in
units of mmol/L.

Worked example

whoishRisk can be installed in one step using install_github() from the devtools package9. We have included a worked example of how to install whoishRisk and use the WHO_ISH_Risk() function to calculate the risk score for five individuals.

  • #Step 1: Install whoishRisk package

  • > library(devtools)

  • > install_github("DylanRJCollins/whoishRisk")

  • #Step 2: Load whoishRisk package into workspace

  • > library(whoishRisk)

  • #Step 3: Load risk factor data

  • > Age <- c(40, 87, 65, 53, 71) #Age in years

  • > Gender <- c(0,0,0,1,1) #0=female, 1=male

  • > Smoking <- c(1,1,0,1,0) #0=non-smoker 1=smoker

  • > Systolic_Blood_Pressure <- c(129, 157, 134, 189, 141) #SBP in mmHg

  • > Diabetes <- c(1,1,1,0,1) #0=not diabetic 1=diabetic

  • > Total_Cholesterol <- c(0, 5.1, 4.5, 0, 8.3) #Total cholesterol (mmol/L, 0=unknown cholesterol)

  • #Step 4: Pass the risk factor vectors to the WHO_ISH_Risk() function, and set subregion equal to the name of the appropriate epidemiological subregion (e.g. “EMR_B”). This will return a vector of WHO/ISH risk scores.

  • > WHO_ISH_Risk(Age, Gender, Smoking, Systolic_Blood_Pressure, Diabetes, Total_Cholesterol,"EMR_B")

  • [1] "<10%" ">=40%" "<10%" ">=40%" ">=40%"

Validation

Comparison with the published MatLab implementation of the SEAR D risk charts8 showed 100% agreement with our R implementation, for all possible combinations of risk factors.

Discussion

To our knowledge, this is the first publically available R implementation of WHO/ISH CVD risk charts for all WHO epidemiological subregions of the world. Our package, whoishRisk, may be used for analysis of cardiovascular risk when electronic patient data is available. The code will automatically apply WHO/ISH risk scores to patients based on age, gender, systolic blood pressure, smoking status, diabetes status, total cholesterol, and epidemiological subregion. This code could be used, for example, during a pilot implementation of WHO PEN to audit the accuracy of risk assessment by comparing documented risk scores to actual risk scores calculated using this tool. We have provided a complete worked example.

While WHO PEN guidance specifies the range of systolic blood pressure values for each systolic blood pressure category, it provides no such guidance for categorising total cholesterol. Based on our opinion and clinical experience, and on a previously published implementation in MatLab8, we chose to categorise total cholesterol by rounding up at 0.5 to the next integer.

The “WHO_ISH_Scores.csv” file is provided herein for transparency and to promote collaboration and cross validation. While the risk score values it stores are returned to the workspace as characters (e.g. “10 to <20%”), a user could simply convert these to class numeric or factor. We chose to return them as character strings that are identical to the patient charts in order to produce a literal implementation of the risk charts.

Conclusion

We created an R package called whoishRisk to be used for the calculation of WHO/ISH CVD risk charts for all WHO epidemiological subregions of the world. It contains a single function, WHO_ISH_Risk(), that requires seven parameters: age, gender, systolic blood pressure, smoking status, diabetes status, total cholesterol, and epidemiological subregion. whoishRisk can be used to quickly calculate WHO/ISH risk scores from routinely collected electronic patient data and therefore aid in the implementation and evaluation of these risk charts in low-resource settings.

Data and software availability

F1000Research: Dataset 1. CSV file of all parameter combinations and corresponding WHO/ISH risk scores used internally by WHO_ISH_Risk() to match parameter values passed to it to their respective risk score 10.5256/f1000research.9742.d15337511

F1000Research: Dataset 2. R code for the WHO_ISH_Risk() function of the whoishRisk package, 10.5256/f1000research.9742.d15337612

Comments on this article Comments (2)

Version 2
VERSION 2 PUBLISHED 08 Mar 2017
Revised
Version 1
VERSION 1 PUBLISHED 14 Oct 2016
Discussion is closed on this version, please comment on the latest version above.
  • Author Response 20 Oct 2016
    Dylan Collins, University of British Columbia, Canada
    20 Oct 2016
    Author Response
    Dear Rajarshi Guha, 

    Thank you for reading our work. I've created a plain text format version of Dataset 2 which is the dataset that contains the R code and ... Continue reading
  • Reader Comment 18 Oct 2016
    Rajarshi Guha, National Institutes of Health, USA
    18 Oct 2016
    Reader Comment
    Please make the R code available in plain text format.
    Competing Interests: No competing interests were disclosed.
  • Discussion is closed on this version, please comment on the latest version above.
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Collins D, Lee J, Bobrovitz N et al. whoishRisk – an R package to calculate WHO/ISH cardiovascular risk scores for all epidemiological subregions of the world [version 2; peer review: 3 approved]. F1000Research 2017, 5:2522 (https://doi.org/10.12688/f1000research.9742.2)
NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article.
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Open Peer Review

Current Reviewer Status: ?
Key to Reviewer Statuses VIEW
ApprovedThe paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approvedFundamental flaws in the paper seriously undermine the findings and conclusions
Version 2
VERSION 2
PUBLISHED 08 Mar 2017
Revised
Views
23
Cite
Reviewer Report 14 Mar 2017
Scott A. Chamberlain, rOpenSci project, University of California, Berkeley, Berkeley, CA, USA 
Approved
VIEWS 23
I'm mostly satisfied with the author's changes, with a few minor changes. 

Thank you for making an R package. I downloaded, and checked the package, with a few observations:
  • In the package use
... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Chamberlain SA. Reviewer Report For: whoishRisk – an R package to calculate WHO/ISH cardiovascular risk scores for all epidemiological subregions of the world [version 2; peer review: 3 approved]. F1000Research 2017, 5:2522 (https://doi.org/10.5256/f1000research.11940.r20822)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
Views
19
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Reviewer Report 10 Mar 2017
Maria Suarez-Diez, Laboratory of Systems and Synthetic Biology, Wageningen University and Research (WUR), Wageningen, The Netherlands 
Approved
VIEWS 19
My main concerns have been addressed in this new version of the manuscript.

I think the developed package represents a useful addition to the field. I was able to install and run the package and indeed the ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Suarez-Diez M. Reviewer Report For: whoishRisk – an R package to calculate WHO/ISH cardiovascular risk scores for all epidemiological subregions of the world [version 2; peer review: 3 approved]. F1000Research 2017, 5:2522 (https://doi.org/10.5256/f1000research.11940.r20821)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
Views
23
Cite
Reviewer Report 09 Mar 2017
Raivo Kolde, Philips Research North America, Cambridge, MA, USA 
Approved
VIEWS 23
All my main concerns were satisfied with the update. I was able to install and run the package. I guess ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Kolde R. Reviewer Report For: whoishRisk – an R package to calculate WHO/ISH cardiovascular risk scores for all epidemiological subregions of the world [version 2; peer review: 3 approved]. F1000Research 2017, 5:2522 (https://doi.org/10.5256/f1000research.11940.r20823)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
Version 1
VERSION 1
PUBLISHED 14 Oct 2016
Views
37
Cite
Reviewer Report 28 Oct 2016
Maria Suarez-Diez, Laboratory of Systems and Synthetic Biology, Wageningen University and Research (WUR), Wageningen, The Netherlands 
Approved with Reservations
VIEWS 37
The authors present an R script and an additional datafile to calculate cardiovascular risk using the Who/ISH risk assessment charts. Previous implementations required the use of MatLab and I believe an R implementation can be an useful addition to the ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Suarez-Diez M. Reviewer Report For: whoishRisk – an R package to calculate WHO/ISH cardiovascular risk scores for all epidemiological subregions of the world [version 2; peer review: 3 approved]. F1000Research 2017, 5:2522 (https://doi.org/10.5256/f1000research.10503.r17004)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
  • Author Response 08 Mar 2017
    Dylan Collins, University of British Columbia, Canada
    08 Mar 2017
    Author Response
    Dear Maria Suarez-Diez,

    Thank you for your valuable comments. In response we have made the following changes:
    • We created an R package including all documentation files which
    ... Continue reading
COMMENTS ON THIS REPORT
  • Author Response 08 Mar 2017
    Dylan Collins, University of British Columbia, Canada
    08 Mar 2017
    Author Response
    Dear Maria Suarez-Diez,

    Thank you for your valuable comments. In response we have made the following changes:
    • We created an R package including all documentation files which
    ... Continue reading
Views
34
Cite
Reviewer Report 25 Oct 2016
Scott A. Chamberlain, rOpenSci project, University of California, Berkeley, Berkeley, CA, USA 
Approved with Reservations
VIEWS 34
The authors describe some R code for helping to calculate cardiovascular risk scores. I think the code needs significant work.  
  • The code is in an .rtf file. This is very bad software practice. The authors
... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Chamberlain SA. Reviewer Report For: whoishRisk – an R package to calculate WHO/ISH cardiovascular risk scores for all epidemiological subregions of the world [version 2; peer review: 3 approved]. F1000Research 2017, 5:2522 (https://doi.org/10.5256/f1000research.10503.r17006)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
  • Author Response 08 Mar 2017
    Dylan Collins, University of British Columbia, Canada
    08 Mar 2017
    Author Response
    Dear Scott A. Chamberlain,

    Thank you for your thoughtful and considered feedback. We have responded in the updated version as detailed below.
    • We have created an R
    ... Continue reading
COMMENTS ON THIS REPORT
  • Author Response 08 Mar 2017
    Dylan Collins, University of British Columbia, Canada
    08 Mar 2017
    Author Response
    Dear Scott A. Chamberlain,

    Thank you for your thoughtful and considered feedback. We have responded in the updated version as detailed below.
    • We have created an R
    ... Continue reading
Views
41
Cite
Reviewer Report 20 Oct 2016
Raivo Kolde, Philips Research North America, Cambridge, MA, USA 
Approved with Reservations
VIEWS 41
The paper describes a software tool for calculation of WHO/ISH cardiovascular risk scores for different epidemiological subregions of the world. This could be a useful piece of software for researchers working with cardiovascular epidemiological data and make the practices for ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Kolde R. Reviewer Report For: whoishRisk – an R package to calculate WHO/ISH cardiovascular risk scores for all epidemiological subregions of the world [version 2; peer review: 3 approved]. F1000Research 2017, 5:2522 (https://doi.org/10.5256/f1000research.10503.r17007)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
  • Author Response 08 Mar 2017
    Dylan Collins, University of British Columbia, Canada
    08 Mar 2017
    Author Response
    Dear Raivo Kolde,

    Thank you for your insightful review and comments. In response we have made the following changes:
    • As suggested, we created an R package which
    ... Continue reading
COMMENTS ON THIS REPORT
  • Author Response 08 Mar 2017
    Dylan Collins, University of British Columbia, Canada
    08 Mar 2017
    Author Response
    Dear Raivo Kolde,

    Thank you for your insightful review and comments. In response we have made the following changes:
    • As suggested, we created an R package which
    ... Continue reading

Comments on this article Comments (2)

Version 2
VERSION 2 PUBLISHED 08 Mar 2017
Revised
Version 1
VERSION 1 PUBLISHED 14 Oct 2016
Discussion is closed on this version, please comment on the latest version above.
  • Author Response 20 Oct 2016
    Dylan Collins, University of British Columbia, Canada
    20 Oct 2016
    Author Response
    Dear Rajarshi Guha, 

    Thank you for reading our work. I've created a plain text format version of Dataset 2 which is the dataset that contains the R code and ... Continue reading
  • Reader Comment 18 Oct 2016
    Rajarshi Guha, National Institutes of Health, USA
    18 Oct 2016
    Reader Comment
    Please make the R code available in plain text format.
    Competing Interests: No competing interests were disclosed.
  • Discussion is closed on this version, please comment on the latest version above.
Alongside their report, reviewers assign a status to the article:
Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approved - fundamental flaws in the paper seriously undermine the findings and conclusions
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