Data and code for: Feeding, mating, and animal wellbeing: New insights from Phylogenetic Comparative Methods

Some species tend to thrive in captivity, while others risk health and reproductive problems. This enables the use of Phylogenetic Comparative Methods (PCMs) to identify aspects of natural biology that predispose species to faring poorly or well. Risk factors can then suggest new ways to improve animal care. A steady trickle of studies has applied PCMs to animal welfare over the last two decades, Lewis et al. (1) providing the latest. Here we contextualise this new work and suggest further research it might inspire.
Provided here are the data and R code for Figure 1 provided in a commentary on: (1) Lewis, K., M.O. Parker, L. Proops, and S.D. McBride, Risk factors for stereotypic behaviour in captive ungulates. Proceedings of the Royal Society B: Biological Sciences, 2022. 289(1983): p. 20221311., Data on stereotypic behaviour came from Lewis et al. [1]. Values for (sex-specific) relative lifespan and species-typical percentage grass in the natural diet came from Müller et al. [2]. Following Müller et al. [2], we calculated relative lifespans (sexes pooled) using data from Moorad et al. [3]. Values for digestive health problems came from Gattiker et al. [4].
[1] Lewis, K., M.O. Parker, L. Proops, and S.D. McBride, Risk factors for stereotypic behaviour in captive ungulates. Proceedings of the Royal Society B: Biological Sciences, 2022. 289(1983): p. 20221311.
[2] Müller, D.W.H., L.B. Lackey, W.J. Streich, J. Fickel, J.-M. Hatt, and M. Clauss, Mating system, feeding type and ex situ conservation effort determine life expectancy in captive ruminants. Proceedings of the Royal Society B: Biological Sciences, 2011. 278(1714): p. 2076-2080.
[3] Moorad, J.A., D.E.L. Promislow, N. Flesness, and R.A. Miller, A comparative assessment of univariate longevity measures using zoological animal..., Data and code for: Feeding, mating, and animal wellbeing: New insights from Phylogenetic Comparative Methods
Provided here are the data and R code for Figure 1 provided in a commentary on: Lewis, K., M.O. Parker, L. Proops, and S.D. McBride, Risk factors for stereotypic behaviour in captive ungulates. Proceedings of the Royal Society B: Biological Sciences, 2022. 289(1983): p. 20221311.
Suitable for use in Excel and/or R.
Missing values indicated with 'NA'.
 
Metadata:

Species: species names as per Upham et al. [1]
PRA_percent_Gattiker: % of animals found to have parakeratosis, rumenitis, and/or ruminal acidosis at death from Gattiker et al. [2]
Teeth_probs_percent_Gattiker: % of animals found to have abnormally worn teeth at death
Abn_stomach_contents_percent_Gattiker: % of animals found to have abnormal stomach contents at death
Poor_BC_percent_Gattiker: % of animals in poor body condition at death 
SB_reported_Lewis: if stereotypic behaviour has been reported (yes v no) from Lewis e...