Data and scripts to assess mammals in plantations using occupancy, species richness and activity patterns analyses

Conservation efforts includes plantations of non-native and some native timber species. Whether these plantations are suitable as habitat or corridors for wildlife remains unclear due to limited empirical evidence. Here, we archived data from ground-dwelling vertebrates' surveys, using camera trap during one-year of sampling in five types of plantations in Central Panama. We deployed camera traps in random points to estimate community composition and occupancy for each plantation type. Additionally, we assessed activity for species of interest. We found that the plantations harbored few mammals in comparison with surveys from protected lowland Panamanian forests, and mostly short-lived species. Teak (Tectona grandis) plantations, which covered the largest area in the study, had the lowest estimated richness and occupancy. Two diurnal frugivores, Central American Agouti (Dasyprocta punctata) and White-nosed Coati (Nasua narica) were more nocturnal in the plantations than in natural forests. Our findings suggest that plantations – especially Teak plantations – have limited conservation value as habitat or corridors for ground-dwelling mammals. The archived data includes: A CSV file called "argos_observations_2019-03-11_22-26-52" for the occupancy and species richness analyses, a CSV file for the accumulation curves, and all text files needed for the activity pattern estimates. There is a R file for each analyses and within each script, there description on how the data was managed, as well as a step by step analyses processing. Also, there is a jags file which is required for the occupancy analysis and it's called from the R occupancy script.人工造林实践常涉及外来树种与部分本土用材树种的种植。由于相关实证证据匮乏，此类人工林是否可作为野生动物的栖息地或连通廊道，目前尚无定论。本研究归档了巴拿马中部5种人工林为期一年的地面栖息脊椎动物调查数据，调查采用红外相机陷阱（camera trap）开展。我们在随机布设的位点部署红外相机，以估算每种人工林类型的群落组成与物种占用率，并针对目标物种的活动节律进行分析。 研究结果显示，与巴拿马受保护低地森林的调查数据相比，此类人工林所承载的哺乳动物类群较少，且多为短命物种。本研究中面积占比最大的柚木（Tectona grandis）人工林，其估算物种丰富度与占用率均为最低。两种昼行性食果动物——中美刺豚鼠（Dasyprocta punctata）与白鼻浣熊（Nasua narica），在人工林内的活动节律相较于天然森林更偏向夜行性。本研究结果表明，人工林——尤其是柚木人工林——作为地面栖息哺乳动物的栖息地或连通廊道，其保护价值十分有限。 本研究归档的数据包含：用于物种占用率与物种丰富度分析的CSV文件"argos_observations_2019-03-11_22-26-52"、用于物种累积曲线分析的CSV文件，以及所有用于活动节律估算的文本文件。每项分析均配有对应的R脚本文件，脚本内详细说明了数据管理流程与逐步分析处理步骤。此外，物种占用率分析所需的JAGS脚本文件可通过R语言占用率分析脚本调用。