The R Language as a Tool for Biometeorological Research
Abstract
:1. Introduction: The Biometeorology in the New Research Era
2. Methods and Tools in Biometeorology
2.1. The Classic Research Workflow
2.1.1. Data Acquisition
2.1.2. Data Handling
2.1.3. Data Analysis
2.1.4. Results Dissemination
2.2. Reproducibility or Why We Use Code in Research
3. The R Biometeorological Research Workflow
3.1. R’s main Characteristics
3.2. Data Acquisition with R
3.3. Data Handling with R
3.4. Biometeorological Data Analysis with R
3.5. Results Dissemination with R
3.6. A Reproducible Research Example with the R Language
4. Conclusions
Supplementary Materials
Funding
Conflicts of Interest
References
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Package Name | Short Description | |
---|---|---|
Manual (local) input | readr | Fast and friendly way to read rectangular data (like csv, tsv, and fwf). |
xlxs | Provides tools to read and write xlsx files and control the appearance of the spreadsheet files. | |
foreign | Reading and writing data stored by some versions of ‘Epi Info’, ‘Minitab’, ‘S’, ‘SAS’, ‘SPSS’, ‘Stata’, ‘Systat’, ‘Weka’ and ‘dBase’ files. | |
haven | Reading and writing data stored by of ‘SAS’, ‘SPSS’, ‘Stata’. | |
feather | Read and write in an easy-to-use binary file format (feather) for storing data frames. | |
Web database acquisition | rnoaa | Is an R wrapper to many NOAA APIs. Select and download each type of data |
nasapower | Making quick and easy to automate downloading from NASA POWER global meteorology, surface solar energy and climatology data. | |
MODIS | Downloading and processing functionalities for the Moderate Resolution Imaging Spectroradiometer (MODIS). | |
Copernicus | Downloading data from the COPERNICUS data portal through the fast HTTP access. | |
rWBclimate | Download model predictions from 15 different global circulation models in 20-year intervals from the World Bank. Access historical data and create maps at 2 different spatial scales. | |
cmsaf | Provides satellite-based climate data records of essential climate variables of the energy budget and water cycle. The data records are generally distributed in NetCDF format. | |
NASAaccess | Can generate gridded ASCII tables of climate (CIMP5) and weather data (GPM, TRMM, GLDAS) needed to drive various hydrological models (e.g., SWAT, VIC, RHESSys). |
Package Name | Short Description |
---|---|
data.table | Integrated and quick data handling. |
dplyr | A powerful package with a noticeably clear syntax to transform, summarise and do calculation into and between tabular data frames. |
reshape2 | Is dedicated to the transformation processes between wide and long data frame format. |
lubridate | Providing functions to deal with date and time formats and time spans. |
Package Name | Short Description |
---|---|
comf | Calculates various common and less common thermal comfort indices, convert physical variables and evaluate the performance of thermal comfort indices. |
ClimInd | Computes 138 standard climate indices at monthly, seasonal and annual resolution. |
rBiometeo | Human thermal comfort and many biometeorological indices used in Institute of Biometeorology in Florence. Biometeorological indices used in Institute of Biometeorology in Florence |
climate | Automized downloading of meteorological and hydrological data from publicly available repositories. |
RNCEP | Contains functions to retrieve, organise and visualise weather data from the NCEP/NCAR Reanalysis and NCEP/DOE Reanalysis II datasets. |
weathermetrics | Conversions between primary weather metrics. |
Package Name | Short Description | |
---|---|---|
Visualisation | lattice | High-level data visualisation system, with an emphasis on multivariate data. |
ggplot2 | A system for ‘declaratively’ creating graphics, based on “The Grammar of Graphics”. | |
plotly | An all-in-one interactive graphics package (3D and animated). | |
Communication | rmarkdown | Writing functional reports with embedded code and its results in .doc, .pdf, HTML format. |
blogdown | Publishing web pages created with rmarkdown. | |
bookdown | Facilitating writing ebooks, ready to print books, long articles and reports. | |
shiny | Building interactive web applications focused on data sharing. |
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Charalampopoulos, I. The R Language as a Tool for Biometeorological Research. Atmosphere 2020, 11, 682. https://doi.org/10.3390/atmos11070682
Charalampopoulos I. The R Language as a Tool for Biometeorological Research. Atmosphere. 2020; 11(7):682. https://doi.org/10.3390/atmos11070682
Chicago/Turabian StyleCharalampopoulos, Ioannis. 2020. "The R Language as a Tool for Biometeorological Research" Atmosphere 11, no. 7: 682. https://doi.org/10.3390/atmos11070682