Heatwaves cause relative fitness decline in aquatic insects by altering life history and host-pathogen relationships - Data and R scripts

Data and r scripts related to the paper.InfectTempDataStored -Daily data from saprolegnia experimental heatwave experiment 2021. Data includes egg mass identification and the related infection, hatching and dead eggs for each day until the completion of the experiment.column namesDate - Date of observationDay - Numbered day of experiment on given dateTemps - Temperature name given to each treatment. 22.5 = High, 12.5 = Low and Spike = SpikePersonnel - Initials of individuals taking observations on given day/dateRo_ID - Identification number of rockCl_ID - identification number of clusters of egg masses on a given rockEM_ID - identification number ofegg masses within a cluster on a given rockIsEdge - y/n as to whether an egg mass is on the outside of a cluster or entirely surrounded by other egg massesRiffle - Location where the rock was collected fromInfect% - estimated percent of infected eggs on given day/dateHatch% - estimated percent of hatched eggs on a given dat/date from healthy eggs. infected eggs not includedD_Eggs - presence of dead eggs which are not infected 1 = yes, 0 = no. infected eggs not includednotes - notes for individual egg massesEgg_count - number of egg in each egg massNeonate_count - number of neonates counted for each rock, only labelled in one egg mass per rock as they are counted at the rock scale. changed to neonates per rock in rStudioInfectTempScript.r -r script analysing above dataFirst5DaysScript.r -same data set as above script but filter to only the first 5 daysfungusHelpers.r -functions used in previous two scriptsPopulationModelScript.r -script where the population modelling occurs.maxtempsurvivalmodelpreds + sustainestemphatchmodelpreds are used in this script after being created in the InfectTempScriptLOW, SPIKE and HIGH life table .xlxs are also used in this scriptTempLoggers.r -Script where the temp loggers from the lab experiment are uploaded and cut to the right date/time for visualisation

本数据集及配套R脚本均与本论文相关。其中，`InfectTempDataStored` 存储了2021年绵霉（Saprolegnia）实验性热浪胁迫实验的每日观测数据，涵盖实验全程每日的卵块标识、对应感染、孵化及死亡卵粒记录。

各字段的具体含义如下：
- `Date`：观测日期
- `Day`：对应观测日期的实验天数编号
- `Temps`：各实验处理组的温度标识，其中22.5代表高温组，12.5代表低温组，`Spike`代表热浪冲击组
- `Personnel`：当日开展观测的人员姓名首字母
- `Ro_ID`：单块岩石的唯一标识编号
- `Cl_ID`：单块岩石上卵块集群的唯一标识编号
- `EM_ID`：单块岩石单卵块集群内单个卵块的唯一标识编号
- `IsEdge`：卵块位置标识，用于说明卵块是否处于集群外侧，取值为y（是）或n（否），即卵块是否完全被其他卵块包围
- `Riffle`：采集该岩石的浅滩生境位置
- `Infect%`：当日观测时感染卵粒的估算百分比
- `Hatch%`：当日观测时健康卵粒的估算孵化率（未纳入感染卵粒进行统计）
- `D_Eggs`：非感染性死卵的存在标识，1代表存在该类死卵，0代表不存在（未纳入感染卵粒进行统计）
- `notes`：单个卵块的备注信息
- `Egg_count`：单个卵块内的卵粒总数
- `Neonate_count`：单块岩石的幼体计数，因幼体以岩石为统计单位，故仅在单块岩石的一个卵块条目中标注该值，该字段在RStudio中已调整为“单块岩石幼体总数”

配套的R脚本说明如下：
1. `InfectTempScript.r`：用于分析上述数据集的核心分析脚本
2. `First5DaysScript.r`：使用与上述脚本相同的数据集，但仅筛选实验前5天的数据进行分析的脚本
3. `fungusHelpers.r`：为上述两个分析脚本提供自定义函数支持的工具脚本
4. `PopulationModelScript.r`：用于开展种群建模的脚本，该脚本需调用在`InfectTempScript.r`中生成的`maxtempsurvivalmodelpreds`与`sustainestemphatchmodelpreds`文件，同时还需使用`LOW`、`SPIKE`和`HIGH`生命表`.xlxs`文件
5. `TempLoggers.r`：用于上传实验室实验中的温度记录仪数据，并将数据裁剪至对应观测日期与时间以用于可视化的脚本