This report discusses some problems that can arise when attempting to import PostScript images into R, when the PostScript image contains coordinate transformations that skew the image. There is a description of some new features in the ‘grImport’ package for R that allow these sorts of images to be imported into R successfully.

Taking place at the Leeds Institute for Data Analytics on April 27th as part of the Leeds Digital Festival, the aim of the Vision Zero Innovation Lab is to explore ways to reduce the number of road casualties to zero in Leeds. If you would like to get involved or find out more, check out the event on eventbrite.Student Data Labs runs data-driven Innovation Labs for university students to learn practical data skills whilst working on civic problems. In the past, we have held Labs that tackle Type 2 Diabetes and health inequalities in Leeds. Student Data Labs works with an interdisciplinary team of students, data scientists, designers, researchers and software developers. We also aim to connect our Data Lab Volunteers with local employers who may be interested in employing them upon graduation. Visit our website, Twitter or Facebook for more info.The Vision Zero Innovation Lab is split into two sections - a Learning Lab and a Innovation Lab. The Learning Lab helps students learn real-world data skills - getting them up and running with tools like R as well as common data science problems as part of a team. The Innovation Lab is more experimental, where the aim is to develop ideas and data-driven tools to take on wicked problems.

This is a repository for codes and datasets for the open-access paper in Linguistik Indonesia, the flagship journal for the Linguistic Society of Indonesia (Masyarakat Linguistik Indonesia [MLI]) (cf. the link in the references below).

Dataset

This dataset was created by Manohar Reddy

Contents

This child page contains a zipped folder which contains all files necessary to run trend models and produce results published in U.S. Geological Scientific Investigations Report 2020–5079 [Nustad, R.A., and Vecchia, A.V., 2020, Water-quality trends for selected sites and constituents in the international Red River of the North Basin, Minnesota and North Dakota, United States, and Manitoba, Canada, 1970–2017: U.S. Geological Survey Scientific Investigations Report 2020–5079, 75 p., https://doi.org/10.3133/sir20205079]. The folder contains: six files required to run the R–QWTREND trend analysis tool; a readme.txt file; an alldata.RData file; a siteinfo_appendix.txt: and a folder called "scripts". R–QWTREND is a software package for analyzing trends in stream-water quality. The package is a collection of functions written in R (R Development Core Team, 2019), an open source language and a general environment for statistical computing and graphics. The following system requirements are necessary for using R–QWTREND: • Windows 10 operating system • R (version 3.4 or later; 64 bit recommended) • RStudio (version 1.1.456 or later). An accompanying report (Vecchia and Nustad, 2020) serves as the formal documentation for R–QWTREND. Vecchia, A.V., and Nustad, R.A., 2020, Time-series model, statistical methods, and software documentation for R–QWTREND—An R package for analyzing trends in stream-water quality: U.S. Geological Survey Open-File Report 2020–1014, 51 p., https://doi.org/10.3133/ofr20201014 R Development Core Team, 2019, R—A language and environment for statistical computing: Vienna, Austria, R Foundation for Statistical Computing, accessed June 12, 2019, at https://www.r-project.org.

This folder contains datasets to be downloaded from students for their practices with R and Python

Online Supplemental Material 2 (OSM 2) contains the data and code necessary to generate Figures 3-6, 8-9, S1 and S5-S6 presented in Sinensky et al. (2022). The R Markdown document (OSM 2.0) will render these figures using the data provided in OSM 2.1-2.6.

Categorical scatterplots with R for biologists: a step-by-step guide

Benjamin Petre1, Aurore Coince2, Sophien Kamoun1

1 The Sainsbury Laboratory, Norwich, UK; 2 Earlham Institute, Norwich, UK

Weissgerber and colleagues (2015) recently stated that ‘as scientists, we urgently need to change our practices for presenting continuous data in small sample size studies’. They called for more scatterplot and boxplot representations in scientific papers, which ‘allow readers to critically evaluate continuous data’ (Weissgerber et al., 2015). In the Kamoun Lab at The Sainsbury Laboratory, we recently implemented a protocol to generate categorical scatterplots (Petre et al., 2016; Dagdas et al., 2016). Here we describe the three steps of this protocol: 1) formatting of the data set in a .csv file, 2) execution of the R script to generate the graph, and 3) export of the graph as a .pdf file.

Protocol

• Step 1: format the data set as a .csv file. Store the data in a three-column excel file as shown in Powerpoint slide. The first column ‘Replicate’ indicates the biological replicates. In the example, the month and year during which the replicate was performed is indicated. The second column ‘Condition’ indicates the conditions of the experiment (in the example, a wild type and two mutants called A and B). The third column ‘Value’ contains continuous values. Save the Excel file as a .csv file (File -> Save as -> in ‘File Format’, select .csv). This .csv file is the input file to import in R.

• Step 2: execute the R script (see Notes 1 and 2). Copy the script shown in Powerpoint slide and paste it in the R console. Execute the script. In the dialog box, select the input .csv file from step 1. The categorical scatterplot will appear in a separate window. Dots represent the values for each sample; colors indicate replicates. Boxplots are superimposed; black dots indicate outliers.

• Step 3: save the graph as a .pdf file. Shape the window at your convenience and save the graph as a .pdf file (File -> Save as). See Powerpoint slide for an example.

Notes

• Note 1: install the ggplot2 package. The R script requires the package ‘ggplot2’ to be installed. To install it, Packages & Data -> Package Installer -> enter ‘ggplot2’ in the Package Search space and click on ‘Get List’. Select ‘ggplot2’ in the Package column and click on ‘Install Selected’. Install all dependencies as well.

• Note 2: use a log scale for the y-axis. To use a log scale for the y-axis of the graph, use the command line below in place of command line #7 in the script.

7 Display the graph in a separate window. Dot colors indicate

replicates

graph + geom_boxplot(outlier.colour='black', colour='black') + geom_jitter(aes(col=Replicate)) + scale_y_log10() + theme_bw()

References

Dagdas YF, Belhaj K, Maqbool A, Chaparro-Garcia A, Pandey P, Petre B, et al. (2016) An effector of the Irish potato famine pathogen antagonizes a host autophagy cargo receptor. eLife 5:e10856.

Petre B, Saunders DGO, Sklenar J, Lorrain C, Krasileva KV, Win J, et al. (2016) Heterologous Expression Screens in Nicotiana benthamiana Identify a Candidate Effector of the Wheat Yellow Rust Pathogen that Associates with Processing Bodies. PLoS ONE 11(2):e0149035

Weissgerber TL, Milic NM, Winham SJ, Garovic VD (2015) Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm. PLoS Biol 13(4):e1002128

https://cran.r-project.org/

http://ggplot2.org/

### Information for replicating the analysis for "Reining in the Rascals: Challenger Parties' Path to Power" ### The Journal of Politics ### ### Frederik Hjorth, Jacob Nyrup & Martin Vinæs Larsen ###### All code to replicate the analysis is written in R. 14 files in total are used to replicate the analysis in the article: 5 r-scripts and 9 datafiles. The scripts use the R package "pacman" to install and load relevant packages, which is handled by the function pacman::p_load(). To make sure the function runs, the replicator should have "pacman" installed. The scripts use the R package "here" to automatically set the working directory to the replication folder. If "here" fails to locate the appropriate folder, simply set the working directory to the folder containing scripts and data using setwd(). When running the analysis it is important that 00-helperfunctions.R is loaded into R. This file contains a list of extra functions used throughout the analysis. ### List of r-scripts 00-helperfunctions.R 01-comparativeanalysis.R 02-mainanalysis.R 03-mechanismanalysis.R 04-appendix.R ### List of datasets df_comparative.xlsx df_main.rds df_mainretroactive.rds dkvaa13txtdf.rds dkvaa17txtdf.rds dkvaa2013.xlsx dkvaa2017.xlsx irtposbyparty.rds municodelist.txt

A major objective of biometrical genetics is to explore the nature of gene action in determining quantitative traits. This also includes determination of the number of major genetic factors or genes responsible for the traits. Diallel Mating Designs have been designed to deal with the type of genetic experiments that help assess variability in observed quantitative traits arising from genetic factors, environmental factors, and their interactions. Some Diallel Mating Designs are North Carolina Designs, Line by Tester Designs and Diallel designs. AGD-R is a set of R programs that performs statistical analyses to calculate Diallel, Line by Tester, North Carolina. AGD-R contains a graphical JAVA interface that helps the user to easily choose input files, which analysis to implement, and which variables to analyze.

An implementation of Quantitative Fatty Acid Signature Analysis (QFASA) in R. QFASA is a method of estimating the diet composition of predators. The fundamental unit of information in QFASA is a fatty acid signature (signature), which is a vector of proportions describing the fatty acid composition of adipose tissue. Signature data from at least one predator and from samples of all potential prey types are required. Calibration coefficients, which adjust for the differential metabolism of individual fatty acids by predators, are also required. Given those data inputs, a predator signature is modeled as a mixture of potential prey signatures and its diet estimate is obtained as the mixture that minimizes a measure of distance between the observed and modeled signatures. A variety of estimation options, goodness-of-fit diagnostic procedures to assess the suitability of estimates, and simulation capabilities are implemented. Please refer to the package vignette and the documentation files for individual functions for details and references.

Here you can find the R Markdown Notebook, dataset, and other materials for an open-access paper (in Indonesian) on Linguistik Indonesia, the journal of the Linguistic Society of Indonesia (Masyarakat Linguistik Indonesia [MLI]) (cf. further below for how to run them in R):Paper citation:Rajeg, G. P. W., & Rajeg, I. M. (2019). Pemahaman kuantitatif dasar dan penerapannya dalam mengkaji keterkaitan antara bentuk dan makna. Linguistik Indonesia, 37(1), 13–31. http://ojs.linguistik-indonesia.org/index.php/linguistik_indonesia/article/view/87/83The post-print version after peer-review (without the journal's layout and paginating) is available at INA-Rxiv. This figshare repository is imported from its GitHub repo (see the Release page for versioning of the repo).If you use data and codes from this repository, please cite this repository via the dark pink Cite button. The default citation style is "DataCite".The paper introduces the basics of chi-square test as a significance test of independence with application on the study of form-meaning relationship in the lexical field for the word "hot" (i.e. panas) in Indonesian.To run the codes in the R Notebook, you need to have the latest version of R and RStudio installed. The codes in the Notebook also use the tidyverse and vcd R packages. To render the notebook into MS Word document, we use the bookdown package. So make sure these packages are installed in R.How to run the codes in the R Notebook1. Download this repository by clicking the Download button next to the Cite button.2. Unzip the file if it is not automatically unzipped. For macOS, the file is automatically unzipped into a folder that begins with gederajeg-pemahaman_kuantitatif_...3. Go to this folder and double-click the file with .Rproj extension (i.e. 2018 Oct - PANAS.Rproj). This will open up an RStudio session whose working directory is associated with the contents of this folder.4. Then, double-click on the panas_paper.Rmd that will be open in the RStudio session. This .Rmd file contains the main text and R codes of the published paper.5. Next, you can run all the codes in the file using shortcut ALT+Ctrl/Cmd+R. 6. After running all the codes, you can preview in RStudio the rendered filed as R Notebook, which is an html document. To do this, click the dropdown arrow within the Knit button in the open .Rmd file, select Preview Notebook, then click the Preview button.

This Resource serves to explain and contain the methodology, R codes, and results of the PRISM freshwater supply key indicator analysis for my thesis. For more information, see my thesis at the USU Digital Commons.

Freshwater availability in the state can be summarized using streamflow, reservoir level, precipitation, and temperature data. Climate data for this study have a period of record greater than 30 years, preferably extending beyond 1950, and are representative of natural conditions at the county-level.

Oregon State University, Northwest Alliance for Computational Science and Engineering PRISM precipitation and temperature gridded data are representative of statewide, to county-level, from 1895-2015. These data are available online from the PRISM Climate Group. Using the R ‘prism’ package, monthly PRISM 4km raster grids were downloaded. Boundary shapefiles of Utah state, and each county, were obtained online from the Utah Geospatial Resource Center webpage. Using the R ‘rgdal’ and ‘sp’ packages, these shapefiles were transformed from their native World Geodetic System 1984 coordinate system to match the PRISM BIL raster’s native North American Datum 1983 coordinate system. Using the R ‘raster’ package, medians of PRISM precipitation grids at each spatial area of interest were calculated and summed for water years and seasons. Medians were also calculated for PRISM temperature grids and averaged over water years and seasons. For analysis of single months, the median results were used for all PRISM indicators. Seasons were analyzed for the calendar year which they are in, Winter being the first season of each year. Freshwater availability key indicators were non-parametrically separated per temporal/spatial delineation into quintiles representing Very Wet/Very High/Hot (top 20% of values), Wet/High/Hot (60-80%), Moderate/Mid-level (40-60%), Dry/Low/Cool (20-40%), to Very Dry/Very Low/Cool (bottom 20%). Each quintile bin was assigned a rank value 1-5, with ‘5’ being the value of the top quintile, in preparation for the Kendall Tau-b correlation analysis. These results, along with USGS irrigation withdrawal and acreage data, were loaded into R. State-level quintile results were matched according to USGS report year. County quintile results were matched with corresponding USGS irrigation withdrawal and acreage county-level data per report year for all other areas of interest. Using the base R function cor(), with the “kendall” method selected (which is, by default, the Kendall Tau-b calculation), relationship correlation matrices were produced for all areas of interest. The USGS irrigation withdrawal and acreage data correlation analysis matrices were created using the R ‘corrplot’ package for all areas of interest.

See Word file for an Example PRISM Analysis, made by Alan Butler at the United States Bureau of Reclamation, which was used as a guide for this analysis.

Free Introduction to R Course at DataCamp

As high-throughput methods become more common, training undergraduates to analyze data must include having them generate informative summaries of large datasets. This flexible case study provides an opportunity for undergraduate students to become familiar with the capabilities of R programming in the context of high-throughput evolutionary data collected using macroarrays. The story line introduces a recent graduate hired at a biotech firm and tasked with analysis and visualization of changes in gene expression from 20,000 generations of the Lenski Lab’s Long-Term Evolution Experiment (LTEE). Our main character is not familiar with R and is guided by a coworker to learn about this platform. Initially this involves a step-by-step analysis of the small Iris dataset built into R which includes sepal and petal length of three species of irises. Practice calculating summary statistics and correlations, and making histograms and scatter plots, prepares the protagonist to perform similar analyses with the LTEE dataset. In the LTEE module, students analyze gene expression data from the long-term evolutionary experiments, developing their skills in manipulating and interpreting large scientific datasets through visualizations and statistical analysis. Prerequisite knowledge is basic statistics, the Central Dogma, and basic evolutionary principles. The Iris module provides hands-on experience using R programming to explore and visualize a simple dataset; it can be used independently as an introduction to R for biological data or skipped if students already have some experience with R. Both modules emphasize understanding the utility of R, rather than creation of original code. Pilot testing showed the case study was well-received by students and faculty, who described it as a clear introduction to R and appreciated the value of R for visualizing and analyzing large datasets.

About this course Machine Learning (ML) is a new way to program computers to solve real world problems. It has gained popularity over the last few years by achieving tremendous success in tasks that we believed only humans could solve, from recognising images to self-driving cars. In this course, we will explore the fundamentals of Machine Learning from a practical perspective with the help of the R programming language and its scientific computing packages. Learning Outcomes Understand the difference between supervised and unsupervised Machine Learning. Understand the fundamentals of Machine Learning. Comprehensive introduction to Machine Learning models and techniques such as Linear Regression and Model Training. Understand the Machine Learning modelling workflows. Use R and and its relevant packages to process real datasets, train and apply Machine Learning models Prerequisites Either Learn to Program: R and Data Manipulation in R or Learn to Program: R and Data Manipulation and Visualisation in R needed to attend this course. If you already have experience with programming, please check the topics covered in the Learn to Program: R, Data Manipulation in R and Data Manipulation and Visualisation in R courses to ensure that you are familiar with the knowledge needed for this course, such as good understanding of R syntax and basic programming concepts and familiarity with dplyr, tidyr and ggplot2 packages. Maths knowledge is not required. There are only a few Math formula that you are going to see in this course, however references to Mathematics required for learning about Machine Learning will be provided. Having an understanding of the Mathematics behind each Machine Learning algorithms is going to make you appreciate the behaviour of the model and know its pros/cons when using them. Why do this course? Useful for anyone who wants to learn about Machine Learning but are overwhelmed with the tremendous amount of resources. It does not go in depth into mathematical concepts and formula, however formal intuitions and references are provided to guide the participants for further learning. We do have applications on real datasets! Machine Learning models are introduced in this course together with important feature engineering techniques that are guaranteed to be useful in your own projects. Give you enough background to kickstart your own Machine Learning journey, or transition yourself into Deep Learning. For a better and more complete understanding of the most popular Machine Learning models and techniques please consider attending all three Introduction to Machine Learning using R workshops: Introduction to Machine Learning using R: Introduction & Linear Regression Introduction to Machine Learning using R: Classification Introduction to Machine Learning using R: SVM & Unsupervised Learning Licence Copyright © 2021 Intersect Australia Ltd. All rights reserved.

This dataset tracks annual distribution of students across grade levels in R Brown Mcallister Elementary School

A collection of 204 brain maps. Each brain map is a 3D array of values representing properties of the brain at different locations.

Collection description

This collection corresponds to the two sets of the atlas of white matter function (original A and replication B) derived from the brain disconnection of 1333 stroke participants. (O to R terms)

This dataset represents a modeling effort intended to explore the impacts of oiling on migratory birds. The purpose of this model is to provide a first principles approach to predict potential biological impacts of altered energetics dynamics in north American migratory birds due to oiling of feathers. This data includes predicted theoretical impacts on migration timing, wintering latitude, starvation rates, and increased food uptake. This data was generated through model implementation in R (R Core Team 2020; Version 4.0.4).

Languages change over time, driven by creation of new words and cultural pressure to optimise communication. Programming languages resemble written language but communicate primarily with computer hardware rather than a human audience. I tested for changes over time in use of R, a mature, open-source programming language used for scientific computing. Across 393,142 GitHub repositories published between 2014 and 2021, I extracted 143,409,288 R functions, programming "verbs", and paired linguistic and ecological approaches to estimate change in the diversity and composition of function use over time. I found that the number of R functions in use increased and underwent substantial change, driven primarily by the popularity of the "tidyverse" collection of community-written extensions. I provide evidence that users can directly change the nature of programming languages, with patterns that match known processes from natural languages and genetic evolution. In the case of R, patterns suggested there are selective pressures for increased analytic complexity and R functions in decline but not extinct ("extinction debts"). R's evolution towards the tidyverse may also represent the start of a division into two distinct dialects, which may impact the readability and continuity of analytic and scientific inquiries codified in R, as well as the language's future.