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Addresses the remaining State of the Field items in openjournals/joss-reviews#10489. 1. Rename the bolded 'State of the field.' subsection inside Statement of need to 'Limitations of traditional assessment.' The material is about the limitations of traditional instruments, which is need framing rather than a survey of the field, so the label was simply wrong. This resolves the duplicate heading. 2. Remove the sentence claiming Forest 'appears to be the only open-source library for the analysis of raw, high-throughput smartphone data.' Cortex and RAPIDS are both open source, both analyze raw mobile data, and both predate this draft, so the claim is not accurate. Removing it also resolves the 'only' versus 'few' inconsistency, since the surviving statement is the defensible one. 3. Add a paragraph to State of the Field contrasting Forest with Cortex and RAPIDS, and stating why Forest was developed rather than contributed to an existing project. Adds three references for the tools discussed. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
The previous version of this paragraph distinguished Forest on the grounds that it models missingness while Cortex and RAPIDS summarize it. That is not accurate and would not have survived scrutiny. RAPIDS ships a port of Barnett and Onnela 2020 as its BARNETT provider for phone locations, including the imputation step, and cites that paper directly. Cortex exposes impute() and impute_bins(). Both were verified against their source rather than their abstracts. The paragraph now acknowledges the overlap and rests the distinction on scope and provenance instead: Forest is maintained by the authors of the methods it implements, spans five method domains rather than one, and tracks the literature as it develops, providing Liu and Onnela 2021 alongside the earlier method. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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…e-of-field Includes changes from update to CONTRIBUTING.md, so that it is present.
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Three edits to the State of the Field section. Stacked on #337, so that one goes first.
The bolded "State of the field." subsection inside Statement of need is renamed to "Limitations of traditional assessment." The material there is about the limitations of instruments like the ALSFRS-R, which belongs to the need argument rather than to a survey of the field. That resolves the duplicate heading.
The sentence claiming Forest "appears to be the only open-source library for the analysis of raw, high-throughput smartphone data" is removed. Cortex and RAPIDS are both open source, both analyze raw mobile data, and both predate this draft. Removing it also resolves the only versus few inconsistency.
A paragraph is added to State of the Field covering both tools. It closes by saying why Forest was developed rather than contributed to an existing project, which the JOSS checklist asks for and the paper did not answer anywhere.
Worth knowing for that paragraph. RAPIDS ships a port of the mobility measures from Barnett & Onnela 2020, imputation included, and cites that paper directly. Its docs note the feature descriptions are adapted from the Beiwe Summary Statistics wiki. Cortex exposes impute() and impute_bins(). So the paragraph acknowledges the overlap rather than claiming methodological distinctiveness. It rests on scope and provenance instead. Forest is maintained by the authors of the methods it implements. It spans mobility, accelerometry, communication logs, survey processing and simulation rather than a single domain. It provides the sparse online Gaussian process approach from Liu & Onnela 2021 alongside the earlier method.
Adds vega2021rapids, burns2024cortex and vaidyam2022lamp.
JP, the second edit is the one to weigh in on. It drops a claim the paper has carried since the first draft. The alternative is narrowing it to a defensible scope rather than deleting it.
mora2017edaravone becomes uncited after the ALSFRS-R fix in #337 and can be dropped from paper.bib.