ttime: an R Package for Translating the Timing of Brain Development Across Mammalian Species
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ttime: an R Package for Translating the Timing of Brain Development Across Mammalian Species Radhakrishnan Nagarajan & Richard B. Darlington & Barbara L. Finlay & Barbara Clancy
Published online: 8 September 2010 # Springer Science+Business Media, LLC 2010
Abstract Understanding relationships between the sequence and timing of brain developmental events across a given set of mammalian species can provide information about both neural development and evolution. Yet neurodevelopmental event timing data available from the published literature are incomplete, particularly for humans. Experimental documentation of unknown event timings requires considerable effort that can be expensive, time consuming, and for humans, often impossible. Application of suitable statistical models for translating neurodevelopmental event timings across mammalian species is essential. The present study implements an established statistical model and related functions as an open-source R package (ttime, translating time). The model incorporated into ttime allows predictions of unknown neurodevelopmental timings and explorations of phylogenetic relationships. The opensource package will enable transparency and reproducibility while minimizing redundancy. Sustainability and widespread dissemination will be guaranteed by the active CRAN (Comprehensive R Archive Network) community. The package updates the web-service (Clancy et al. 2007b) www.translatingtime.net by permitting predictions based on R. Nagarajan (*) Division of Biomedical Informatics, University of Arkansas for Medical Sciences, COPH/UAMS, Room 3234, 4301W Markham, Slot 781, Little Rock, AR 72205-7199, USA e-mail: [email protected] R. B. Darlington : B. L. Finlay Department of Psychology, Cornell University, Ithaca, NY, USA B. Clancy Department of Biology, University of Central Arkansas, ConWay, AR, USA
curated event timing databases which may include species not yet incorporated in the current model. The R package can be integrated into complex workflows that use the event predictions in their analyses. The package ttime is publicly available and can be downloaded from http://cran. r-project.org/web/packages/ttime/index.html. Keywords Open-source . R package . Cross-species modeling . Cross-species comparisons . Neurodevelopment
Introduction Understanding similarities and variations in the sequence of neurodevelopmental events across mammalian species can provide critical insight into brain development and evolution (Finlay et al. 1998; Finlay et al. 2001). However, the distribution of empirically derived data across the various species is skewed. While many neurodevelopmental events are documented for certain species (e.g. rats, mice, macaques), less information is available for others (e.g. rabbits, cats, humans). Experimental documentation demands expensive, dedicated efforts, and for humans the ethical constraints are considerable. A solution to this challenge is to translate the neurodevelopmental timing data from species in which they were empirically derived to
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