Occupancy of two Colombian endemic birds (Habia gutturalis) and White-Mantled Barbet (Capito hypoleucus) in fragmented forests of the Central Andes in Colombia

The Sooty Ant-Tanager (Habia gutturalis) and White-mantled Barbet (Capito hypoleucus) are endangered and endemic birds of Colombia. Both species have small geographic ranges and presumably low population sizes possibly due to habitat destruction and fragmentation. In order to estimate the effects of landscape features on the occupancy of both species, we sampled a variety of landscape configurations within the buffer zones of two hydroelectric impoundments in the Central Andes of Colombia and applied occupancy models to estimate the proportion of area occupied as a function of these covariates. We surveyed 35 point-counts in each hydroelectric impoundment, between June and July of 2014 and 2015. We used single-season models to estimate occupancy while recognizing imperfect detection. Mean occupancy estimates in the study area were similar for both species (0.61 SD=0.33 for the Sooty Ant-Tanager and 0.63 SD=0.25 for the White-mantled). Nonetheless, occupancy probability within the study ..., Study Area
The study was conducted in fragmented secondary forests within the buffer zones of two hydroelectric power plants located in the department of Antioquia in the Central Andes of Colombia: one in the municipality of San Carlos (Punchiná), and the other in the municipalities of San Rafael, Alejandría, Santo Domingo and San Roque (San Lorenzo). These protected areas encompass ~80 km2 (ISAGEN 2008) of transitional forest from premontane to tropical wet forests (Holdridge 1947), a key elevation band (580-1420 m) characterized by high levels of fragmentation (Cardona et al. 2011).
Sampling
Our sampling units were point counts defined as circles of 125 m radius, within which birds were registered during 30 minutes. We defined the maximum radius, as the longest distance at which there was a record of any of the two species. Point counts were distributed along transects of ~1 km each. Transects were located near trails and separated by more than 2 km from each other. Each transect cons..., Dataset contains the following files (detailed information about each in the README section:
Detection_histories.csv: Detection histories for Capito hypoleucus and Habia gutturalis. Numbers refer to number of individuals detected. Notice that we use only presence/absence in our manuscript.
Detection_covariates.csv: Detection covariates for both species. 
Occupancy_covariates.csv: Site covariates for both species. 
Point_counts.csv: Geographic coordinates (WGS84) for each site. 
CH_single_season.R: R script to run occupancy analyses for Capito hypoleucus.
HG_single_season.R: R script to run occupancy analyses for Habia gutturalis., # Occupancy of two Colombian endemic birds (Habia gutturalis) and White-Mantled Barbet (Capito hypoleucus) in fragmented forests of the Central Andes in Colombia

[https://doi.org/10.5061/dryad.w9ghx3fmc](https://doi.org/10.5061/dryad.w9ghx3fmc)

## Description of the data and file structure

Dataset contains the following files necessary to run the two R scripts (also included) to run occupancy models for two species *Habia gutturalis* and *Capito hypoleucos*:

**Detection_histories.csv**: Detection histories for *Capito hypoleucus* and *Habia gutturalis*. Five columns: Species name, and four columns that refer to the number of individuals detected each repetition (2014-1, 2014-2, 2015-1, 2015-2). Notice that we use only presence/absence in our manuscript.

**Detection_covariates.csv**: Detection covariates for both species. Columns refer to:

*   covariate*: name of the covariate. Three covariates were used in analyses. We included original time format in the table: time of the survey...

乌喉蚁唐纳雀（Sooty Ant-Tanager, *Habia gutturalis*）与白须拟鴷（White-mantled Barbet, *Capito hypoleucus*）是哥伦比亚特有且濒危的鸟类。两个物种种群的地理分布范围狭窄，种群规模推测偏低，潜在成因或为栖息地破坏与片段化。为评估景观特征对这两个物种种群占据情况的影响，我们在哥伦比亚中部安第斯山脉两座水电水库的缓冲区范围内布设了多种景观配置样地，并应用占据模型（occupancy models），以这些协变量为解释变量，估算物种占据的面积比例。

2014年与2015年的6-7月期间，我们在每座水电水库内布设了35个点状计数样点（point counts）。我们采用单季占据模型估算种群占据率，同时考虑到检测不完全性。研究区域内两个物种的平均占据估计值相近：乌喉蚁唐纳雀为0.61，标准差(SD)=0.33；白须拟鴷为0.63，SD=0.25。不过，研究区域内的占据概率……[研究区域]

## 研究区域
本研究在哥伦比亚中部安第斯山脉安蒂奥基亚省两座水电站的缓冲区破碎次生林内开展：一座位于圣卡洛斯市（蓬奇纳），另一座位于圣拉斐尔、亚历杭德里亚、圣多明各与圣罗克市境内（圣洛伦索）。这些保护区域涵盖约80平方千米的过渡林（从山麓预林到热带湿林，Holdridge 1947），处于580-1420米的关键海拔带，该区域存在高度的栖息地片段化（Cardona et al. 2011），相关数据由ISAGEN（2008）提供。

## 采样方案
我们的采样单元为点状计数样点（point counts），即以125米为半径的圆形区域，在此区域内开展30分钟的鸟类观测记录。该最大半径的设定依据为两种鸟类的已知最远观测记录。点状计数样点沿每条长约1千米的样线布设，样线临近步道且彼此间距大于2千米。每条样线……

## 数据集文件说明（详细信息见README章节）
本数据集包含以下文件：
1. `Detection_histories.csv`：白须拟鴷（*Capito hypoleucus*）与乌喉蚁唐纳雀（*Habia gutturalis*）的检测历史文件，数值代表单次调查中检测到的个体数量。请注意本文仅使用存在/缺失数据开展分析。
2. `Detection_covariates.csv`：两个物种的检测协变量文件。
3. `Occupancy_covariates.csv`：两个物种的样点协变量文件。
4. `Point_counts.csv`：每个样点的地理坐标（WGS84坐标系）。
5. `CH_single_season.R`：用于开展白须拟鴷单季占据分析的R脚本。
6. `HG_single_season.R`：用于开展乌喉蚁唐纳雀单季占据分析的R脚本。

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# 哥伦比亚中部安第斯山脉破碎林生境中两种哥伦比亚特有鸟类的种群占据情况
[https://doi.org/10.5061/dryad.w9ghx3fmc](https://doi.org/10.5061/dryad.w9ghx3fmc)

## 数据与文件结构描述
本数据集包含运行两个R脚本所需的全部文件（脚本亦包含于本数据集中），用于开展两个物种（乌喉蚁唐纳雀*Habia gutturalis*与白须拟鴷*Capito hypoleucos*）的占据模型分析：

**`Detection_histories.csv`**：白须拟鴷与乌喉蚁唐纳雀的检测历史文件，共5列：物种名称，以及4列分别代表四次重复调查中检测到的个体数量（2014-1、2014-2、2015-1、2015-2）。请注意本文仅使用存在/缺失数据开展分析。

**`Detection_covariates.csv`**：两个物种的检测协变量文件，各列信息如下：
* `covariate`：协变量名称。本分析中共使用3种协变量，表格中保留了原始调查时间格式：调查时间……