Old habits die hard: homing pigeons maintain their route fidelity but change flight altitude when exposed to a raptor-like robot

Dataset and R code used for the analyses presented in manuscript. ########################## the file "calculate_relative_directions.R" contains the code of custom function used to calculate the relative position and orientation of pigeon in respect of RobotFalcon position. The final output is an angle in degrees from 0° to 180° which indicates if the pigeon is located in front of the RobotFalcon (0°) or at the back (180°). The function is called in the main script the file "DataAnalysis_Paper_Pigeons_RobotFalcon_Landscape.R" contains the code used for the analyses. ########################## Explanation of variables contained in files (txt or csv) to be used in the .R file: - "Deployment_information.csv": contains all the information on pigeon releases. the columns represent: group = color band of the pigeon that was used to divide into different groups the birds and facilitate idenitification od treatment individuals at release site (groups N, GrNGr and GNG include only experimental subjects); id = bird id; gps_ID = id of gps used; type = generic classification of releases, not used in the analysis (E = training, C = pre-exposure and post-exposure , F = exposure); type2 = flags each release as E (training), PRE (pre-exposure), F (exposure) and POST (post-exposure); release_site = name of release site; release = name of release; release_date and release_time = date and time of release; no_data = flags if gps collected (1) or not (0) locations. -"CleanData_pigeons.txt" is a dataframe of the cleaned GPS data collected for the experimental pigeon during the procedure (pre-exposure, exposure and post-exposure flights). The data was cleaned to remove locations collected during pigeon transportation from the loft to the release site and to retain only the parts of the route when the pigeon was flying (speed > 5 km/h). The data contains only the segment of the route considered for the analyses from 750m up to 1680m from release site. The columns indicate: id = pigeon id; Latitude; Longitude; release = name of release; type2 = flags each release as PRE (pre-exposure), F (exposure) and POST (post-exposure); release_type = flags each release to identify 1st and 2nd pre-exposure (PRE1 and PRE2), 1st, 2nd and 3rd exposure (F1, F2 and F3) and post-exposure (POST1) flights; Datetime_UTC; Altitude(m) = altitude collected by the GPS; Rel.Altitude = corrected altitude collected by the GPS; Speed(km/h) = speed collected by the GPS; dist_from_home = distance in metres of the location from the home loft; dist_from_RS = distance in metres of the location from the release site; idfix = unique identifier of location; no_data = always 1, corresponds at "no_data" column in Deployment_information file. -"Clean_RobotFalcon.txt" is a dataframe of the cleaned RobotFalcon GPS data. The data was cleaned to remove locations collected during drone transportation loft area-release site and back. Moreover the data was downsampled to have a sample rate of 1Hz (comparable to the sampling rate of pigeons). From the locations it was calculated the speed, turning angle and acceleration. The columns indicate: falco_id = name of the gps used to track RobotFalcon route; falco_long = longitude; falco_lat = latitude; Datetime_UTC = timestamp in UTC; falco_height = altitude collected by the GPS; falco_speed_ms = speed estimated from coordinates and timestamps; falco_turn_angle = estimated turning angles; falco_acc_ms2 = acceleration. - "Fidelity_Index_df.txt" is the dataframe containing the Fidelity Index values estimated per id and release type (exposure and post-expodure flights). Columns indicate: id = pigeon id; release = name of release; release type = type of release (1st, 2nd, 3rd exposure or post-exposure flight); FI = Fidelity Index for the release type; FI_base = Fidelity Index of the last pre-exposure flight (individually specific).本手稿中呈现的分析所使用的数据集与R代码。 文件`calculate_relative_directions.R`包含用于计算鸽子相对于RobotFalcon位置的相对方位与姿态的自定义函数代码。最终输出为0°至180°的角度值，用于指示鸽子位于RobotFalcon前方（0°）还是后方（180°）。该函数将在主脚本中被调用。 文件`DataAnalysis_Paper_Pigeons_RobotFalcon_Landscape.R`包含本次分析所使用的代码。 以下为将在.R文件中使用的txt或csv格式数据文件的变量说明： - `Deployment_information.csv`：包含所有鸽子放归相关信息。各列含义如下： group：用于将鸽子划分为不同组别并便于在放归位点识别试验个体的鸽子彩色脚环（组别N、GrNGr和GNG仅包含试验对象）； id：鸽子个体编号； gps_ID：所使用GPS的编号； type：放归的通用分类，本次分析未使用该字段（E=训练放归，C=预暴露与后暴露放归，F=暴露放归）； type2：标记每一次放归的类型，包括E（训练）、PRE（预暴露）、F（暴露）与POST（后暴露）； release_site：放归位点名称； release：放归事件名称； release_date和release_time：放归的日期与时间； no_data：标记是否收集到GPS位置数据（1=未收集，0=已收集）。 - `CleanData_pigeons.txt`：为试验鸽子在整个试验流程（预暴露、暴露与后暴露飞行）中采集的经清洗后的GPS数据框。该数据已完成清洗，移除了从鸽舍到放归位点的运输阶段采集的位置数据，仅保留鸽子飞行阶段（速度>5km/h）的有效数据。本次分析仅使用放归位点750m至1680m范围内的航路段数据。各列含义如下： id：鸽子个体编号； Latitude：纬度； Longitude：经度； release：放归事件名称； type2：标记每一次放归的类型，包括PRE（预暴露）、F（暴露）与POST（后暴露）； release_type：标记每一次放归以区分首次、第二次预暴露飞行（PRE1、PRE2），首次、第二次、第三次暴露飞行（F1、F2、F3）以及首次后暴露飞行（POST1）； Datetime_UTC：协调世界时下的日期时间； Altitude(m)：GPS采集的海拔高度； Rel.Altitude：GPS采集的校正后海拔高度； Speed(km/h)：GPS采集的飞行速度； dist_from_home：当前位置至鸽舍的距离（单位：米）； dist_from_RS：当前位置至放归位点的距离（单位：米）； idfix：位置数据的唯一标识符； no_data：固定为1，与`Deployment_information`文件中的`no_data`字段对应。 - `Clean_RobotFalcon.txt`：为经清洗后的RobotFalcon的GPS数据框。该数据已完成清洗，移除了无人机在鸽舍-放归位点往返运输阶段采集的位置数据，同时下采样至1Hz采样率以匹配鸽子的GPS采样频率。基于该位置数据可计算得到飞行速度、转弯角度与加速度。各列含义如下： falco_id：用于追踪RobotFalcon航迹的GPS编号； falco_long：经度； falco_lat：纬度； Datetime_UTC：协调世界时下的时间戳； falco_height：GPS采集的海拔高度； falco_speed_ms：基于坐标与时间戳估算的飞行速度（单位：米/秒）； falco_turn_angle：估算得到的转弯角度； falco_acc_ms2：加速度（单位：米/秒²）。 - `Fidelity_Index_df.txt`：包含按鸽子个体编号与放归类型（暴露与后暴露飞行）估算的归巢保真度指数（Fidelity Index）数据框。各列含义如下： id：鸽子个体编号； release：放归事件名称； release type：放归类型（首次、第二次、第三次暴露飞行或后暴露飞行）； FI：对应放归类型的归巢保真度指数； FI_base：对应鸽子个体的末次预暴露飞行的归巢保真度指数。