Repository containing all the code and data to simulate different microclimates for Reyes-Puig et al. 2026 Physiology-microhabitat matching may help organisms cope with the thermal and hydric challenges under climate change: a tale of two lizards (Ecography)
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This repository contains all the code and data to simulate different microclimates. We simulate different microclimates in Castro São Paio using NicheMapR. The weather data comes from Modivas (https://www.wunderground.com/dashboard/pws/IMODIV1). Repository structure /code/ aux_functions.R: helpful functions to handle data readLoggers: reads and cleans datalogger data given the logger name and timeperiod. read.logger: reads the data from iButton csv files. Internal of readLoggers. clean.logger: cleans datalogger data, and formats dates. Internal of readLoggers. clean.logger2: same as clean.logger but for a different time format. Internal of readLoggers. prepare.weather: adds logger data to the weather station data. Internal of run.microclimate. retrieve.output: retrieves output of the microclimate model. Internal of run.microclimate. run.microclimate: runs the model, if needed it prepares the weather data, and finally retrieves the data from the model. plot.predictions: plot simulation predictions and datalogger observations. site.info: get coordinates, elevation, slope and aspect for each site from the datalogger table. micro_custom.R: Function to prepare the input for NicheMapR microclimate model and run the model. microclimate_hourly_Castro.R: example script that shows how to use hourly data from weather stations as input for the NicheMapR microclimate model. prepare_rasters.R: script used to compute the slope and aspect in the study area, and save the files in the terrain folder. prepare_weather.R: script used to download and prepare the weather data from Modivas station, which is then saved in the weather folder. The script can download data from any station, if you supply its code in wunderground. read_dataLoggers.R: example script to read and plot datalogger data (Old). /dataloggers_Castro/ datalogger data on temperature and humidity. /terrain/ marrisk-2019-02-20-dsm.tif: digital elevation model of Castro Saõ Paio. marrisk-2019-02-20-dsmshd.tif: digital elevation model (shade). marrisk-2019-02-20-orto.tif: ortophoto. slope.tif: slope for the area where dataloggers where placed. aspect.tif: aspect for the area where dataloggers where placed. /weather/ weather data from Modiva station, downloaded from wunderground. microclimates_CastroSampaio.Rmd: Run simulations for different microhabitats and compare to the data recorded by iButtons placed in those microclimates.
本仓库包含用于模拟不同微气候的全部代码与数据。 我们借助NicheMapR（NicheMapR）在卡斯特罗·圣帕尤（Castro São Paio）地区开展不同微气候的模拟实验。所用气象数据来源于Modivas站（https://www.wunderground.com/dashboard/pws/IMODIV1）。 ### 仓库目录结构 #### /code/ 目录 - `aux_functions.R`：用于数据处理的辅助工具函数 - `readLoggers`：根据数据记录仪名称与时间段读取并清理数据记录仪数据 - `read.logger`：从iButton（纽扣式数据记录仪）CSV文件中读取数据，为`readLoggers`的内部子函数 - `clean.logger`：清理数据记录仪数据并格式化日期，为`readLoggers`的内部子函数 - `clean.logger2`：功能与`clean.logger`一致，但适配不同的时间格式，为`readLoggers`的内部子函数 - `prepare.weather`：将数据记录仪数据整合至气象站数据中，为`run.microclimate`的内部子函数 - `retrieve.output`：获取微气候模型的输出结果，为`run.microclimate`的内部子函数 - `run.microclimate`：运行微气候模型，若有必要则先预处理气象数据，最终提取模型输出数据 - `plot.predictions`：绘制微气候模拟预测结果与数据记录仪观测值的对比图 - `site.info`：从数据记录仪数据表中提取各监测点的坐标、海拔、坡度与坡向信息 - `micro_custom.R`：用于为NicheMapR微气候模型准备输入数据并运行模型的函数 - `microclimate_hourly_Castro.R`：示例脚本，演示如何将气象站逐小时数据作为NicheMapR微气候模型的输入 - `prepare_rasters.R`：用于计算研究区域内坡度与坡向，并将结果保存至`terrain`（地形）文件夹的脚本 - `prepare_weather.R`：用于从Modivas站下载并预处理气象数据，随后将数据保存至`weather`（气象）文件夹的脚本；若提供Wunderground平台上的其他气象站代码，该脚本可支持下载任意站点的气象数据 - `read_dataLoggers.R`：用于读取并绘制数据记录仪数据的示例脚本（旧版） #### /dataloggers_Castro/ 目录 存放卡斯特罗·圣帕尤（Castro São Paio）地区的温度与湿度数据记录仪监测数据 #### /terrain/ 目录 - `marrisk-2019-02-20-dsm.tif`：卡斯特罗·圣帕尤（Castro Saõ Paio）地区的数字高程模型（DSM） - `marrisk-2019-02-20-dsmshd.tif`：带阴影的数字高程模型 - `marrisk-2019-02-20-orto.tif`：正射影像图 - `slope.tif`：数据记录仪部署区域的坡度栅格数据 - `aspect.tif`：数据记录仪部署区域的坡向栅格数据 #### /weather/ 目录 存放从Wunderground平台下载的Modivas站气象数据 `microclimates_CastroSampaio.Rmd`：用于针对不同微生境运行微气候模拟，并与部署在对应微气候环境中的iButton记录仪所采集的数据进行对比分析的文档
