Data from: Interplay of cooperative breeding and predation risk on egg allocation and reproductive output

# Data from: Interplay of cooperative breeding and predation risk on egg allocation and reproductive output [https://doi.org/10.5061/dryad.rjdfn2zkk](https://doi.org/10.5061/dryad.rjdfn2zkk) These datasets contain results of an experiment aimed at increasing perceived predator presence, by playing back calls of a predator of adults, to test how this affects maternal allocation — clutch size, egg mass, yolk mass and yolk corticosterone — and reproductive output — hatching and fledging success. The study was conducted on the colonial cooperatively breeding sociable weaver (*Philetairus socius*), with the aim of assessing how breeding group sizes may modulate maternal allocation responses to predation risk. This repository includes six datasets (see below), one R script that runs all analyses and produces figures included in the manuscript, called "open_code_models.R"; one file citing file sources and credits for calls used to build the playback tracks called "XENOCANTO_Ref_GABAR_GOSHAWK_CALLS"; one README file. ## Description of the data and file structure Please read Methods in the manuscript for details on how data was collected and processed. "cs_dat2.txt" - used to test effects on clutch size; includes the following columns, by order of appearance: col_nest_code (nest identity); NestCode (clutch identity); colony (colony identity); clutch_size (nr of eggs laid); treatment (1 for predator, 0 for control); incubation_group_size (nr of birds visiting the nest - includes breeders and helpers) "emass_dat2.txt" - used to test effects on egg mass; includes the following columns, by order of appearance: col_nest_code (nest identity); NestCode (clutch identity); colony (colony identity); mass_egg (egg mass in grams); treatment (1 for predator, 0 for control); incubation_group_size (nr of birds visiting the nest - includes breeders and helpers); clutch_size (nr of eggs laid) "dat_yolkmass_cort2.txt" - used to test effects on yolk mass and corticosterone concentration; includes the following columns, by order of appearance: Sample_ID (yolk sample identity); corticosterone_pg_mg (concentratio of yolk corticosterone in pg/mg); mass_yolk_mg (yolk mass in mg); col_nest_code (nest identity); NestCode (clutch identity); colony (colony identity); mass_egg (egg mass in grams); treatment (1 for predator, 0 for control); incubation_group_size (nr of birds visiting the nest - includes breeders and helpers) "hatched_dat.txt" - used to test effects on hatching success; includes the following columns, by order of appearance: col_nest_code (nest identity); NestCode (clutch identity); colony (colony identity); treatment (1 for predator, 0 for control); incubation_group_size (nr of birds visiting the nest - includes breeders and helpers); hatched (0 for no, 1 for yes: at the egg level); clutch_size (nr of eggs laid) "fledged_dat.txt" - used to test effects on fledging success from hatching; includes the following columns, by order of appearance: col_nest_code (nest identity); NestCode (clutch identity); colony (colony identity); treatment (1 for predator, 0 for control); incubation_group_size (nr of birds visiting the nest - includes breeders and helpers); fledged(0 for no, 1 for yes: at the chick level); clutch_size (nr of eggs laid); hatched (0 for no, 1 for yes --- only hatched chicks included here) "incubation_dat2.txt" - used to test effects on Nest visit rate during incubation; includes the following columns, by order of appearance: NestCode (clutch identity); NestCode_dchicks (day of recording for each clutch ID); Total_visits (nr of visits to the nest): Total_time (total time nest was recorded); col_nest_code (nest identity); colony (colony identity); treatment (1 for predator, 0 for control); incubation_group_size (nr of birds visiting the nest - includes breeders and helpers); day_video (days_2_4 for videos recorded between days 2 and 4 of incubation: days_8_10 for videos recorded between days 8 and 10 of incubation); birdID (dummy identity for each bird visiting the nests). ## Code/Software R script to run all analyses and produce figures included in the manuscript: "open_code_models.R". To run the R script, please follow instructions in the R code. All analyses were conducted using the R software v.4.0.4 (R Core Team, 2022).

# 数据来源：合作繁殖与捕食风险对产卵分配及繁殖产出的交互影响 [https://doi.org/10.5061/dryad.rjdfn2zkk](https://doi.org/10.5061/dryad.rjdfn2zkk)
本数据集包含一项实验的相关结果：该实验通过回放成虫捕食者的鸣叫声，提升实验对象对捕食风险的感知水平，以此检验该处理如何影响母体繁殖分配指标——包括窝卵数、卵重、卵黄重及卵黄皮质酮浓度——与繁殖产出指标——包括孵化成功率与出飞成功率。本研究以群居合作繁殖的群居织巢鸟（*Philetairus socius*）为研究对象，旨在评估繁殖群体规模如何调节母体对捕食风险的繁殖分配响应。本数据集仓库包含六个数据集、一份用于运行所有分析并生成论文配图的R脚本"open_code_models.R"、一份标注回放鸣叫声来源与引用信息的文件"XENOCANTO_Ref_GABAR_GOSHAWK_CALLS"，以及一份README文件。

## 数据与文件结构说明
请参阅论文的方法部分，以了解数据收集与处理的详细流程。
1. "cs_dat2.txt"：用于检验对窝卵数的影响，按列出现顺序包含以下字段：col_nest_code（巢群标识）、NestCode（窝卵标识）、colony（种群标识）、clutch_size（产卵总数）、treatment（处理组：1为捕食风险组，0为对照组）、incubation_group_size（到访巢穴的鸟类数量，包含繁殖亲鸟与协助繁殖者）
2. "emass_dat2.txt"：用于检验对卵重的影响，按列出现顺序包含以下字段：col_nest_code（巢群标识）、NestCode（窝卵标识）、colony（种群标识）、mass_egg（卵重，单位：克）、treatment（处理组：1为捕食风险组，0为对照组）、incubation_group_size（到访巢穴的鸟类数量，包含繁殖亲鸟与协助繁殖者）、clutch_size（产卵总数）
3. "dat_yolkmass_cort2.txt"：用于检验对卵黄重与皮质酮浓度的影响，按列出现顺序包含以下字段：Sample_ID（卵黄样本标识）、corticosterone_pg_mg（卵黄皮质酮浓度，单位：pg/mg）、mass_yolk_mg（卵黄重，单位：毫克）、col_nest_code（巢群标识）、NestCode（窝卵标识）、colony（种群标识）、mass_egg（卵重，单位：克）、treatment（处理组：1为捕食风险组，0为对照组）、incubation_group_size（到访巢穴的鸟类数量，包含繁殖亲鸟与协助繁殖者）
4. "hatched_dat.txt"：用于检验对孵化成功率的影响，按列出现顺序包含以下字段：col_nest_code（巢群标识）、NestCode（窝卵标识）、colony（种群标识）、treatment（处理组：1为捕食风险组，0为对照组）、incubation_group_size（到访巢穴的鸟类数量，包含繁殖亲鸟与协助繁殖者）、hatched（卵级结果：0为未孵化，1为已孵化）、clutch_size（产卵总数）
5. "fledged_dat.txt"：用于检验从孵化到出飞的成功率影响，按列出现顺序包含以下字段：col_nest_code（巢群标识）、NestCode（窝卵标识）、colony（种群标识）、treatment（处理组：1为捕食风险组，0为对照组）、incubation_group_size（到访巢穴的鸟类数量，包含繁殖亲鸟与协助繁殖者）、fledged（雏鸟级结果：0为未出飞，1为已出飞；仅纳入已孵化的雏鸟）、clutch_size（产卵总数）、hatched（卵级结果：0为未孵化，1为已孵化；此处仅包含已孵化雏鸟）
6. "incubation_dat2.txt"：用于检验孵化期间的巢穴到访率影响，按列出现顺序包含以下字段：NestCode（窝卵标识）、NestCode_dchicks（对应每窝卵的录制日期）、Total_visits（巢穴到访总次数）、Total_time（巢穴录制总时长）、col_nest_code（巢群标识）、colony（种群标识）、treatment（处理组：1为捕食风险组，0为对照组）、incubation_group_size（到访巢穴的鸟类数量，包含繁殖亲鸟与协助繁殖者）、day_video（录制时段：days_2_4表示孵化第2至4天录制的视频，days_8_10表示孵化第8至10天录制的视频）、birdID（到访巢穴的每只鸟类的虚拟标识）

## 代码与软件
用于运行所有分析并生成论文配图的R脚本为"open_code_models.R"，运行该脚本请遵循代码内的说明。所有分析均使用R软件v.4.0.4（R核心团队，2022）完成。