The GAPs Data Repository provides a comprehensive overview of available qualitative and quantitative data on national return regimes, now accessible through an advanced web interface at https://data.returnmigration.eu/.

This updated guideline outlines the complete process, starting from the initial data collection for the return migration data repository to the development of a comprehensive web-based platform. Through iterative development, participatory approaches, and rigorous quality checks, we have ensured a systematic representation of return migration data at both national and comparative levels.

The Repository organizes data into five main categories, covering diverse aspects and offering a holistic view of return regimes: country profiles, legislation, infrastructure, international cooperation, and descriptive statistics. These categories, further divided into subcategories, are based on insights from a literature review, existing datasets, and empirical data collection from 14 countries. The selection of categories prioritizes relevance for understanding return and readmission policies and practices, data accessibility, reliability, clarity, and comparability. Raw data is meticulously collected by the national experts.

The transition to a web-based interface builds upon the Repository’s original structure, which was initially developed using REDCap (Research Electronic Data Capture). It is a secure web application for building and managing online surveys and databases.The REDCAP ensures systematic data entries and store them on Uppsala University’s servers while significantly improving accessibility and usability as well as data security. It also enables users to export any or all data from the Project when granted full data export privileges. Data can be exported in various ways and formats, including Microsoft Excel, SAS, Stata, R, or SPSS for analysis. At this stage, the Data Repository design team also converted tailored records of available data into public reports accessible to anyone with a unique URL, without the need to log in to REDCap or obtain permission to access the GAPs Project Data Repository. Public reports can be used to share information with stakeholders or external partners without granting them access to the Project or requiring them to set up a personal account. Currently, all public report links inserted in this report are also available on the Repository’s webpage, allowing users to export original data.

This report also includes a detailed codebook to help users understand the structure, variables, and methodologies used in data collection and organization. This addition ensures transparency and provides a comprehensive framework for researchers and practitioners to effectively interpret the data.

The GAPs Data Repository is committed to providing accessible, well-organized, and reliable data by moving to a centralized web platform and incorporating advanced visuals. This Repository aims to contribute inputs for research, policy analysis, and evidence-based decision-making in the return and readmission field.

Explore the GAPs Data Repository at https://data.returnmigration.eu/.

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/

This dataset reflects reported incidents of crime (with the exception of murders where data exists for each victim) that occurred in the City of Chicago from 2001 to present, minus the most recent seven days. Data is extracted from the Chicago Police Department's CLEAR (Citizen Law Enforcement Analysis and Reporting) system. In order to protect the privacy of crime victims, addresses are shown at the block level only and specific locations are not identified. Should you have questions about this dataset, you may contact the Research & Development Division of the Chicago Police Department at 312.745.6071 or RandD@chicagopolice.org. Disclaimer: These crimes may be based upon preliminary information supplied to the Police Department by the reporting parties that have not been verified. The preliminary crime classifications may be changed at a later date based upon additional investigation and there is always the possibility of mechanical or human error. Therefore, the Chicago Police Department does not guarantee (either expressed or implied) the accuracy, completeness, timeliness, or correct sequencing of the information and the information should not be used for comparison purposes over time. The Chicago Police Department will not be responsible for any error or omission, or for the use of, or the results obtained from the use of this information. All data visualizations on maps should be considered approximate and attempts to derive specific addresses are strictly prohibited. The Chicago Police Department is not responsible for the content of any off-site pages that are referenced by or that reference this web page other than an official City of Chicago or Chicago Police Department web page. The user specifically acknowledges that the Chicago Police Department is not responsible for any defamatory, offensive, misleading, or illegal conduct of other users, links, or third parties and that the risk of injury from the foregoing rests entirely with the user. The unauthorized use of the words "Chicago Police Department," "Chicago Police," or any colorable imitation of these words or the unauthorized use of the Chicago Police Department logo is unlawful. This web page does not, in any way, authorize such use. Data is updated daily Tuesday through Sunday. The dataset contains more than 65,000 records/rows of data and cannot be viewed in full in Microsoft Excel. Therefore, when downloading the file, select CSV from the Export menu. Open the file in an ASCII text editor, such as Wordpad, to view and search. To access a list of Chicago Police Department - Illinois Uniform Crime Reporting (IUCR) codes, go to http://data.cityofchicago.org/Public-Safety/Chicago-Police-Department-Illinois-Uniform-Crime-R/c7ck-438e

The “Final_matrices” excel file contains research output related to the paper “From exports to value added to income: Accounting for bilateral income transfers”. Details on how the data are assembled can be found in the paper and in its online appendix. Replication files (R-files and Matlab-codes) as well as the raw data needed for replication of all empirical results in the paper are available upon request from the author.

A routine was developed in R ('bathy_plots.R') to plot bathymetry data over time during individual CEAMARC events. This is so we can analyse benthic data in relation to habitat, ie. did we trawl over a slope or was the sea floor relatively flat. Note that the depth range in the plots is autoscaled to the data, so a small range in depths appears as a scatetring of points. As long as you look at the depth scale though interpretation will be ok.

 The R files need a file of bathymetry data in '200708V3_one_minute.csv' which is a file containing a data export from the underway PostgreSQL ship database and 'events.csv' which is a stripped down version of the events export from the ship board events database export. If you wish to run the code again you may need to change the pathnames in the R script to relevant locations. If you have opened the csv files in excel at any stage and the R script gets an error you may need to format the date/time columns as yyyy-mm-dd hh;mm:ss, save and close the file as csv without opening it again and then run the R script.

 However, all output files are here for every CEAMARC event. Filenames contain a referenec to CEAMARC event id. Files are in eps format and can be viewed using Ghostview which is available as a free download on the internet.

This repository contains two key components:

• Dataset: Export data on fresh grapes from Mexico, Chile, and Peru, focusing on the U.S. and global markets.
• R Scripts: Code for performing Constant Market Share (CMS) and Revealed Comparative Advantage (RCA) analyses based on the dataset.
  The dataset is provided in Excel format, and the R scripts include detailed comments to ensure reproducibility. This work supports the article: "Competitive Dynamics of Mexican Fresh Grapes in the U.S. Market".

Data for corresponding project/publication "Testing sample selection criteria and loss of biomarkers during cleaning of archaeological unglazed pottery to maximize organic residue yield". Raw GC-MS (ChemStation and MassHunter) and GC-MSMS (MassHunter) outputs, as well as data processing (OpenChrom) and quantitation (R, Excel). R data import and export commands will not reference the paths in this data file but the paths on the PC originally used.

Using Web of Science and Unpaywall data, we here provide an update of Open Access (OA) levels of Dutch universities, for 2016 and 2017.

Our previous analysis (10.5281/zenodo.1133759 and 10.7287/peerj.preprints.3520v1) looked at OA classification as included in Web of Science (gold and green OA, based on Unpaywall data), and supplemented that with a breakdown of gold OA into pure gold, hybrid and bronze, taken from Unpaywall data (formerly OADOI) directly. Here, we improve on this by running all DOIs retrieved from WoS through Unpaywall data (using their web interface that allows batch checking of up to 10,000 DOIs at a time). Unlike WoS, Unpaywall data itself includes author-submitted versions in their green OA classification, resulting in more complete green OA levels.

In addition, since our initial analysis of December 2017, Unpaywall data has considerably expanded its coverage of institutional repositories (IRs) (see https://unpaywall.org/sources). This now includes coverage of the IRs from all Dutch universities.

Taken together, the current data show higher levels of green open access, including author-submitted versions, compared to our previous analysis.

In this update, we include output (articles and reviews) from 2016 and 2017 for all 14 universities in the Netherlands.

The following categories are distinguished (description taken from Piwowar at al., 2018, doi: 10.7717/peerj.4375)

Pure gold: Published in an open-access journal (as defined by the DOAJ)

Hybrid: Free under an open license in a toll-access journal

Bronze: Free to read on the publisher page, but without a license

Green: Available from an institutional or disciplinary repository (including PubMedCentral)

Data for Dutch universities were collected from Web of Science using the organization-enhanced field. Only articles and reviews were included. DOIs were extracted from the Web of Science export, run through the Unpaywall data Simple Query Tool. From the resulting data from Unpaywall, OA classification was done using a simple formula in Excel (to be replaced by an R script in a future update). The Excel template used is included in this dataset, as is the OADOI API output for each Dutch university's article subset, and the lists of DOIs derived from Web of Science. The dataset also includes summarized data and three charts generated from these data, showing levels of different types of OA for 2016, 2017 and the two years compared.