This book is written for statisticians, data analysts, programmers, researchers, teachers, students, professionals, and general consumers on how to perform different types of statistical data analysis for research purposes using the R programming language. R is an open-source software and object-oriented programming language with a development environment (IDE) called RStudio for computing statistics and graphical displays through data manipulation, modelling, and calculation. R packages and supported libraries provides a wide range of functions for programming and analyzing of data. Unlike many of the existing statistical softwares, R has the added benefit of allowing the users to write more efficient codes by using command-line scripting and vectors. It has several built-in functions and libraries that are extensible and allows the users to define their own (customized) functions on how they expect the program to behave while handling the data, which can also be stored in the simple object system.For all intents and purposes, this book serves as both textbook and manual for R statistics particularly in academic research, data analytics, and computer programming targeted to help inform and guide the work of the R users or statisticians. It provides information about different types of statistical data analysis and methods, and the best scenarios for use of each case in R. It gives a hands-on step-by-step practical guide on how to identify and conduct the different parametric and non-parametric procedures. This includes a description of the different conditions or assumptions that are necessary for performing the various statistical methods or tests, and how to understand the results of the methods. The book also covers the different data formats and sources, and how to test for reliability and validity of the available datasets. Different research experiments, case scenarios and examples are explained in this book. It is the first book to provide a comprehensive description and step-by-step practical hands-on guide to carrying out the different types of statistical analysis in R particularly for research purposes with examples. Ranging from how to import and store datasets in R as Objects, how to code and call the methods or functions for manipulating the datasets or objects, factorization, and vectorization, to better reasoning, interpretation, and storage of the results for future use, and graphical visualizations and representations. Thus, congruence of Statistics and Computer programming for Research.

This module series covers how to import, manipulate, format and plot time series data stored in .csv format in R. Originally designed to teach researchers to use NEON plant phenology and air temperature data; has been used in undergraduate classrooms.

This dataset includes all the data and R code needed to reproduce the analyses in a forthcoming manuscript:Copes, W. E., Q. D. Read, and B. J. Smith. Environmental influences on drying rate of spray applied disinfestants from horticultural production services. PhytoFrontiers, DOI pending.Study description: Instructions for disinfestants typically specify a dose and a contact time to kill plant pathogens on production surfaces. A problem occurs when disinfestants are applied to large production areas where the evaporation rate is affected by weather conditions. The common contact time recommendation of 10 min may not be achieved under hot, sunny conditions that promote fast drying. This study is an investigation into how the evaporation rates of six commercial disinfestants vary when applied to six types of substrate materials under cool to hot and cloudy to sunny weather conditions. Initially, disinfestants with low surface tension spread out to provide 100% coverage and disinfestants with high surface tension beaded up to provide about 60% coverage when applied to hard smooth surfaces. Disinfestants applied to porous materials were quickly absorbed into the body of the material, such as wood and concrete. Even though disinfestants evaporated faster under hot sunny conditions than under cool cloudy conditions, coverage was reduced considerably in the first 2.5 min under most weather conditions and reduced to less than or equal to 50% coverage by 5 min. Dataset contents: This dataset includes R code to import the data and fit Bayesian statistical models using the model fitting software CmdStan, interfaced with R using the packages brms and cmdstanr. The models (one for 2022 and one for 2023) compare how quickly different spray-applied disinfestants dry, depending on what chemical was sprayed, what surface material it was sprayed onto, and what the weather conditions were at the time. Next, the statistical models are used to generate predictions and compare mean drying rates between the disinfestants, surface materials, and weather conditions. Finally, tables and figures are created. These files are included:Drying2022.csv: drying rate data for the 2022 experimental runWeather2022.csv: weather data for the 2022 experimental runDrying2023.csv: drying rate data for the 2023 experimental runWeather2023.csv: weather data for the 2023 experimental rundisinfestant_drying_analysis.Rmd: RMarkdown notebook with all data processing, analysis, and table creation codedisinfestant_drying_analysis.html: rendered output of notebookMS_figures.R: additional R code to create figures formatted for journal requirementsfit2022_discretetime_weather_solar.rds: fitted brms model object for 2022. This will allow users to reproduce the model prediction results without having to refit the model, which was originally fit on a high-performance computing clusterfit2023_discretetime_weather_solar.rds: fitted brms model object for 2023data_dictionary.xlsx: descriptions of each column in the CSV data files

analyze the health and retirement study (hrs) with r the hrs is the one and only longitudinal survey of american seniors. with a panel starting its third decade, the current pool of respondents includes older folks who have been interviewed every two years as far back as 1992. unlike cross-sectional or shorter panel surveys, respondents keep responding until, well, death d o us part. paid for by the national institute on aging and administered by the university of michigan's institute for social research, if you apply for an interviewer job with them, i hope you like werther's original. figuring out how to analyze this data set might trigger your fight-or-flight synapses if you just start clicking arou nd on michigan's website. instead, read pages numbered 10-17 (pdf pages 12-19) of this introduction pdf and don't touch the data until you understand figure a-3 on that last page. if you start enjoying yourself, here's the whole book. after that, it's time to register for access to the (free) data. keep your username and password handy, you'll need it for the top of the download automation r script. next, look at this data flowchart to get an idea of why the data download page is such a righteous jungle. but wait, good news: umich recently farmed out its data management to the rand corporation, who promptly constructed a giant consolidated file with one record per respondent across the whole panel. oh so beautiful. the rand hrs files make much of the older data and syntax examples obsolete, so when you come across stuff like instructions on how to merge years, you can happily ignore them - rand has done it for you. the health and retirement study only includes noninstitutionalized adults when new respondents get added to the panel (as they were in 1992, 1993, 1998, 2004, and 2010) but once they're in, they're in - respondents have a weight of zero for interview waves when they were nursing home residents; but they're still responding and will continue to contribute to your statistics so long as you're generalizing about a population from a previous wave (for example: it's possible to compute "among all americans who were 50+ years old in 1998, x% lived in nursing homes by 2010"). my source for that 411? page 13 of the design doc. wicked. this new github repository contains five scripts: 1992 - 2010 download HRS microdata.R loop through every year and every file, download, then unzip everything in one big party impor t longitudinal RAND contributed files.R create a SQLite database (.db) on the local disk load the rand, rand-cams, and both rand-family files into the database (.db) in chunks (to prevent overloading ram) longitudinal RAND - analysis examples.R connect to the sql database created by the 'import longitudinal RAND contributed files' program create tw o database-backed complex sample survey object, using a taylor-series linearization design perform a mountain of analysis examples with wave weights from two different points in the panel import example HRS file.R load a fixed-width file using only the sas importation script directly into ram with < a href="http://blog.revolutionanalytics.com/2012/07/importing-public-data-with-sas-instructions-into-r.html">SAScii parse through the IF block at the bottom of the sas importation script, blank out a number of variables save the file as an R data file (.rda) for fast loading later replicate 2002 regression.R connect to the sql database created by the 'import longitudinal RAND contributed files' program create a database-backed complex sample survey object, using a taylor-series linearization design exactly match the final regression shown in this document provided by analysts at RAND as an update of the regression on pdf page B76 of this document . click here to view these five scripts for more detail about the health and retirement study (hrs), visit: michigan's hrs homepage rand's hrs homepage the hrs wikipedia page a running list of publications using hrs notes: exemplary work making it this far. as a reward, here's the detailed codebook for the main rand hrs file. note that rand also creates 'flat files' for every survey wave, but really, most every analysis you c an think of is possible using just the four files imported with the rand importation script above. if you must work with the non-rand files, there's an example of how to import a single hrs (umich-created) file, but if you wish to import more than one, you'll have to write some for loops yourself. confidential to sas, spss, stata, and sudaan users: a tidal wave is coming. you can get water up your nose and be dragged out to sea, or you can grab a surf board. time to transition to r. :D

analyze the current population survey (cps) annual social and economic supplement (asec) with r the annual march cps-asec has been supplying the statistics for the census bureau's report on income, poverty, and health insurance coverage since 1948. wow. the us census bureau and the bureau of labor statistics ( bls) tag-team on this one. until the american community survey (acs) hit the scene in the early aughts (2000s), the current population survey had the largest sample size of all the annual general demographic data sets outside of the decennial census - about two hundred thousand respondents. this provides enough sample to conduct state- and a few large metro area-level analyses. your sample size will vanish if you start investigating subgroups b y state - consider pooling multiple years. county-level is a no-no. despite the american community survey's larger size, the cps-asec contains many more variables related to employment, sources of income, and insurance - and can be trended back to harry truman's presidency. aside from questions specifically asked about an annual experience (like income), many of the questions in this march data set should be t reated as point-in-time statistics. cps-asec generalizes to the united states non-institutional, non-active duty military population. the national bureau of economic research (nber) provides sas, spss, and stata importation scripts to create a rectangular file (rectangular data means only person-level records; household- and family-level information gets attached to each person). to import these files into r, the parse.SAScii function uses nber's sas code to determine how to import the fixed-width file, then RSQLite to put everything into a schnazzy database. you can try reading through the nber march 2012 sas importation code yourself, but it's a bit of a proc freak show. this new github repository contains three scripts: 2005-2012 asec - download all microdata.R down load the fixed-width file containing household, family, and person records import by separating this file into three tables, then merge 'em together at the person-level download the fixed-width file containing the person-level replicate weights merge the rectangular person-level file with the replicate weights, then store it in a sql database create a new variable - one - in the data table 2012 asec - analysis examples.R connect to the sql database created by the 'download all microdata' progr am create the complex sample survey object, using the replicate weights perform a boatload of analysis examples replicate census estimates - 2011.R connect to the sql database created by the 'download all microdata' program create the complex sample survey object, using the replicate weights match the sas output shown in the png file below 2011 asec replicate weight sas output.png statistic and standard error generated from the replicate-weighted example sas script contained in this census-provided person replicate weights usage instructions document. click here to view these three scripts for more detail about the current population survey - annual social and economic supplement (cps-asec), visit: the census bureau's current population survey page the bureau of labor statistics' current population survey page the current population survey's wikipedia article notes: interviews are conducted in march about experiences during the previous year. the file labeled 2012 includes information (income, work experience, health insurance) pertaining to 2011. when you use the current populat ion survey to talk about america, subract a year from the data file name. as of the 2010 file (the interview focusing on america during 2009), the cps-asec contains exciting new medical out-of-pocket spending variables most useful for supplemental (medical spending-adjusted) poverty research. confidential to sas, spss, stata, sudaan users: why are you still rubbing two sticks together after we've invented the butane lighter? time to transition to r. :D

a MOCK dataset used to show how to import Qualtrics metadata into the codebook R package

Table of variables

This table contains variable names, labels, and number of missing values. See the complete codebook for more.

Note

This dataset was automatically described using the codebook R package (version 0.9.5).

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/

Abstract \r

\r This dataset was derived by the Bioregional Assessment Programme from multiple source datasets. The source datasets are identified in the Lineage field in this metadata statement.\r \r The processes undertaken to produce this derived dataset are described in the History field in this metadata statement.\r \r \r \r The Groundwater (GW) quantiles are extracted from the Groundwater modelling outputs. Dataset prepared for import into the Impact and Risk Analysis Database.\r \r

Dataset History \r

\r Drawdown percentile and exceedance probability values was extracted from groundwater model outputs. This was performed using a GIS routine to extract groundwater model raster values using the assessment units (as points) attributed with the regional water table aquifer layer and assigning the model value from the corresponding layer to each assessment unit.\r \r

Dataset Citation \r

\r XXXX XXX (2017) GAL GW Quantile Interpolation 20161013. Bioregional Assessment Derived Dataset. Viewed 12 December 2018, http://data.bioregionalassessments.gov.au/dataset/49f20390-3340-4b08-b1dc-370fb919d34c.\r \r

Dataset Ancestors \r

\r * Derived From Surface Geology of Australia, 1:2 500 000 scale, 2012 edition\r \r * Derived From Galilee Drawdown Rasters\r \r * Derived From Galilee model HRV receptors gdb\r \r * Derived From Queensland petroleum exploration data - QPED\r \r * Derived From Galilee groundwater numerical modelling AEM models\r \r * Derived From Galilee drawdown grids\r \r * Derived From Three-dimensional visualisation of the Great Artesian Basin - GABWRA\r \r * Derived From Geoscience Australia GEODATA TOPO series - 1:1 Million to 1:10 Million scale\r \r * Derived From Phanerozoic OZ SEEBASE v2 GIS\r \r * Derived From Galilee Hydrological Response Variable (HRV) model\r \r * Derived From QLD Department of Natural Resources and Mines Groundwater Database Extract 20142808\r \r * Derived From GAL Assessment Units 1000m 20160522 v01\r \r * Derived From Galilee Groundwater Model, Hydrogeological Formation Extents v01\r \r * Derived From BA ALL Assessment Units 1000m Reference 20160516_v01\r \r * Derived From GAL Aquifer Formation Extents v01\r \r * Derived From Queensland Geological Digital Data - Detailed state extent, regional. November 2012\r \r * Derived From BA ALL Assessment Units 1000m 'super set' 20160516_v01\r \r * Derived From GAL Aquifer Formation Extents v02\r \r

Dataset

This dataset was created by rpsantosa_kaggle

Contents

Objective: To develop a clinical informatics pipeline designed to capture large-scale structured EHR data for a national patient registry.

Materials and Methods: The EHR-R-REDCap pipeline is implemented using R-statistical software to remap and import structured EHR data into the REDCap-based multi-institutional Merkel Cell Carcinoma (MCC) Patient Registry using an adaptable data dictionary.

Results: Clinical laboratory data were extracted from EPIC Clarity across several participating institutions. Labs were transformed, remapped and imported into the MCC registry using the EHR labs abstraction (eLAB) pipeline. Forty-nine clinical tests encompassing 482,450 results were imported into the registry for 1,109 enrolled MCC patients. Data-quality assessment revealed highly accurate, valid labs. Univariate modeling was performed for labs at baseline on overall survival (N=176) using this clinical informatics pipeline.

Conclusion: We demonstrate feasibility of the facile eLAB workflow. EHR data is successfully transformed, and bulk-loaded/imported into a REDCap-based national registry to execute real-world data analysis and interoperability.

Methods eLAB Development and Source Code (R statistical software):

eLAB is written in R (version 4.0.3), and utilizes the following packages for processing: DescTools, REDCapR, reshape2, splitstackshape, readxl, survival, survminer, and tidyverse. Source code for eLAB can be downloaded directly (https://github.com/TheMillerLab/eLAB).

eLAB reformats EHR data abstracted for an identified population of patients (e.g. medical record numbers (MRN)/name list) under an Institutional Review Board (IRB)-approved protocol. The MCCPR does not host MRNs/names and eLAB converts these to MCCPR assigned record identification numbers (record_id) before import for de-identification.

Functions were written to remap EHR bulk lab data pulls/queries from several sources including Clarity/Crystal reports or institutional EDW including Research Patient Data Registry (RPDR) at MGB. The input, a csv/delimited file of labs for user-defined patients, may vary. Thus, users may need to adapt the initial data wrangling script based on the data input format. However, the downstream transformation, code-lab lookup tables, outcomes analysis, and LOINC remapping are standard for use with the provided REDCap Data Dictionary, DataDictionary_eLAB.csv. The available R-markdown ((https://github.com/TheMillerLab/eLAB) provides suggestions and instructions on where or when upfront script modifications may be necessary to accommodate input variability.

The eLAB pipeline takes several inputs. For example, the input for use with the ‘ehr_format(dt)’ single-line command is non-tabular data assigned as R object ‘dt’ with 4 columns: 1) Patient Name (MRN), 2) Collection Date, 3) Collection Time, and 4) Lab Results wherein several lab panels are in one data frame cell. A mock dataset in this ‘untidy-format’ is provided for demonstration purposes (https://github.com/TheMillerLab/eLAB).

Bulk lab data pulls often result in subtypes of the same lab. For example, potassium labs are reported as “Potassium,” “Potassium-External,” “Potassium(POC),” “Potassium,whole-bld,” “Potassium-Level-External,” “Potassium,venous,” and “Potassium-whole-bld/plasma.” eLAB utilizes a key-value lookup table with ~300 lab subtypes for remapping labs to the Data Dictionary (DD) code. eLAB reformats/accepts only those lab units pre-defined by the registry DD. The lab lookup table is provided for direct use or may be re-configured/updated to meet end-user specifications. eLAB is designed to remap, transform, and filter/adjust value units of semi-structured/structured bulk laboratory values data pulls from the EHR to align with the pre-defined code of the DD.

Data Dictionary (DD)

EHR clinical laboratory data is captured in REDCap using the ‘Labs’ repeating instrument (Supplemental Figures 1-2). The DD is provided for use by researchers at REDCap-participating institutions and is optimized to accommodate the same lab-type captured more than once on the same day for the same patient. The instrument captures 35 clinical lab types. The DD serves several major purposes in the eLAB pipeline. First, it defines every lab type of interest and associated lab unit of interest with a set field/variable name. It also restricts/defines the type of data allowed for entry for each data field, such as a string or numerics. The DD is uploaded into REDCap by every participating site/collaborator and ensures each site collects and codes the data the same way. Automation pipelines, such as eLAB, are designed to remap/clean and reformat data/units utilizing key-value look-up tables that filter and select only the labs/units of interest. eLAB ensures the data pulled from the EHR contains the correct unit and format pre-configured by the DD. The use of the same DD at every participating site ensures that the data field code, format, and relationships in the database are uniform across each site to allow for the simple aggregation of the multi-site data. For example, since every site in the MCCPR uses the same DD, aggregation is efficient and different site csv files are simply combined.

Study Cohort

This study was approved by the MGB IRB. Search of the EHR was performed to identify patients diagnosed with MCC between 1975-2021 (N=1,109) for inclusion in the MCCPR. Subjects diagnosed with primary cutaneous MCC between 2016-2019 (N= 176) were included in the test cohort for exploratory studies of lab result associations with overall survival (OS) using eLAB.

Statistical Analysis

OS is defined as the time from date of MCC diagnosis to date of death. Data was censored at the date of the last follow-up visit if no death event occurred. Univariable Cox proportional hazard modeling was performed among all lab predictors. Due to the hypothesis-generating nature of the work, p-values were exploratory and Bonferroni corrections were not applied.

Dataset Information

This dataset presents long-term term indoor solar harvesting traces and jointly monitored with the ambient conditions. The data is recorded at 6 indoor positions with diverse characteristics at our institute at ETH Zurich in Zurich, Switzerland.

The data is collected with a measurement platform [3] consisting of a solar panel (AM-5412) connected to a bq25505 energy harvesting chip that stores the harvested energy in a virtual battery circuit. Two TSL45315 light sensors placed on opposite sides of the solar panel monitor the illuminance level and a BME280 sensor logs ambient conditions like temperature, humidity and air pressure.

The dataset contains the measurement of the energy flow at the input and the output of the bq25505 harvesting circuit, as well as the illuminance, temperature, humidity and air pressure measurements of the ambient sensors. The following timestamped data columns are available in the raw measurement format, as well as preprocessed and filtered HDF5 datasets:

V_in - Converter input/solar panel output voltage, in volt

I_in - Converter input/solar panel output current, in ampere

V_bat - Battery voltage (emulated through circuit), in volt

I_bat - Net Battery current, in/out flowing current, in ampere

Ev_left - Illuminance left of solar panel, in lux

Ev_right - Illuminance left of solar panel, in lux

P_amb - Ambient air pressure, in pascal

RH_amb - Ambient relative humidity, unit-less between 0 and 1

T_amb - Ambient temperature, in centigrade Celsius

The following publication presents and overview of the dataset and more details on the deployment used for data collection. A copy of the abstract is included in this dataset, see the file abstract.pdf.

L. Sigrist, A. Gomez, and L. Thiele. "Dataset: Tracing Indoor Solar Harvesting." In Proceedings of the 2nd Workshop on Data Acquisition To Analysis (DATA '19), 2019.

Folder Structure and Files

processed/ - This folder holds the imported, merged and filtered datasets of the power and sensor measurements. The datasets are stored in HDF5 format and split by measurement position posXX and and power and ambient sensor measurements. The files belonging to this folder are contained in archives named yyyy_mm_processed.tar, where yyyy and mm represent the year and month the data was published. A separate file lists the exact content of each archive (see below).

raw/ - This folder holds the raw measurement files recorded with the RocketLogger [1, 2] and using the measurement platform available at [3]. The files belonging to this folder are contained in archives named yyyy_mm_raw.tar, where yyyy and mmrepresent the year and month the data was published. A separate file lists the exact content of each archive (see below).

LICENSE - License information for the dataset.

README.md - The README file containing this information.

abstract.pdf - A copy of the above mentioned abstract submitted to the DATA '19 Workshop, introducing this dataset and the deployment used to collect it.

raw_import.ipynb [open in nbviewer] - Jupyter Python notebook to import, merge, and filter the raw dataset from the raw/ folder. This is the exact code used to generate the processed dataset and store it in the HDF5 format in the processed/folder.

raw_preview.ipynb [open in nbviewer] - This Jupyter Python notebook imports the raw dataset directly and plots a preview of the full power trace for all measurement positions.

processing_python.ipynb [open in nbviewer] - Jupyter Python notebook demonstrating the import and use of the processed dataset in Python. Calculates column-wise statistics, includes more detailed power plots and the simple energy predictor performance comparison included in the abstract.

processing_r.ipynb [open in nbviewer] - Jupyter R notebook demonstrating the import and use of the processed dataset in R. Calculates column-wise statistics and extracts and plots the energy harvesting conversion efficiency included in the abstract. Furthermore, the harvested power is analyzed as a function of the ambient light level.

Dataset File Lists

Processed Dataset Files

The list of the processed datasets included in the yyyy_mm_processed.tar archive is provided in yyyy_mm_processed.files.md. The markdown formatted table lists the name of all files, their size in bytes, as well as the SHA-256 sums.

Raw Dataset Files

A list of the raw measurement files included in the yyyy_mm_raw.tar archive(s) is provided in yyyy_mm_raw.files.md. The markdown formatted table lists the name of all files, their size in bytes, as well as the SHA-256 sums.

Dataset Revisions

v1.0 (2019-08-03)

Initial release. Includes the data collected from 2017-07-27 to 2019-08-01. The dataset archive files related to this revision are 2019_08_raw.tar and 2019_08_processed.tar. For position pos06, the measurements from 2018-01-06 00:00:00 to 2018-01-10 00:00:00 are filtered (data inconsistency in file indoor1_p27.rld).

v1.1 (2019-09-09)

Revision of the processed dataset v1.0 and addition of the final dataset abstract. Updated processing scripts reduce the timestamp drift in the processed dataset, the archive 2019_08_processed.tar has been replaced. For position pos06, the measurements from 2018-01-06 16:00:00 to 2018-01-10 00:00:00 are filtered (indoor1_p27.rld data inconsistency).

v2.0 (2020-03-20)

Addition of new data. Includes the raw data collected from 2019-08-01 to 2019-03-16. The processed data is updated with full coverage from 2017-07-27 to 2019-03-16. The dataset archive files related to this revision are 2020_03_raw.tar and 2020_03_processed.tar.

Dataset Authors, Copyright and License

Authors: Lukas Sigrist, Andres Gomez, and Lothar Thiele

Contact: Lukas Sigrist (lukas.sigrist@tik.ee.ethz.ch)

Copyright: (c) 2017-2019, ETH Zurich, Computer Engineering Group

License: Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/)

References

[1] L. Sigrist, A. Gomez, R. Lim, S. Lippuner, M. Leubin, and L. Thiele. Measurement and validation of energy harvesting IoT devices. In Design, Automation & Test in Europe Conference & Exhibition (DATE), 2017.

[2] ETH Zurich, Computer Engineering Group. RocketLogger Project Website, https://rocketlogger.ethz.ch/.

[3] L. Sigrist. Solar Harvesting and Ambient Tracing Platform, 2019. https://gitlab.ethz.ch/tec/public/employees/sigristl/harvesting_tracing

README 2025-09-10 Introduction The peatland mid infrared database (pmird) stores data from peat, vegetation, litter, and dissolved organic matter samples, in particular mid infrared spectra and other variables, from previously published and unpublished data sources. The majority of samples in the database are peat samples from northern bogs. Currently, the database contains entries from 26 studies, 11216 samples, and 3877 mid infrared spectra. The aim is to provide a harmonized data source that can be useful to re-analyse existing data, analyze peat chemistry, develop and test spectral prediction models, and provide data on various peat properties. Usage notes Download and Setup The peatland mid infrared database can be downloaded from https://doi.org/10.5281/zenodo.17092587. The publication contains the following files and folders: pmird-backup-2025-09-10.sql: A mysqldump backup of the pmird database. pmird_prepared_data: A folder that contains: Folders like c00001-2020-08-17-Hodgkins with the raw spectra for samples from each dataset in the pmird database (see below for how to import the spectra). Files like pmird_prepare_data_c00001-2020-08-17-Hodgkins.Rmd that contain the R code used to process and import the data from each dataset into the database. Corresponding html files contain the compiled scripts. pmird_prepare_data.Rmd: An Rmarkdown script that was used to run the scripts that created the database (the top level script). mysql_scripts: A folder that contains: pmird_mysql_initialization.sql: MariaDB script to initialize the database. 001-db-initialize.Rmd: Rmarkdown script that executes pmird_mysql_initialization.sql and populated dataset-independent tables. add-citations.Rmd: Rmarkdown script that adds information on references to the database. add-licenses.Rmd: Rmarkdown script that adds information on licenses to the database. add-mir-metadata-quality.Rmd Rmarkdown script that adds information on the quality of the infrared spectra to the database. Dockerfile: A Dockerfile that defines the computing environment used to create the database. renv.lock A renv.lock file that lists the R packages used to create the database. The database can be set up as follows: The downloaded database needs to be imported in a running MariaDB instance. In a linux terminal, the downloaded sql file can be imported like so: mysql -u

Explanation/Overview: Corresponding dataset for the analyses and results achieved in the CS Track project in the research line on participation analyses, which is also reported in the publication "Does Volunteer Engagement Pay Off? An Analysis of User Participation in Online Citizen Science Projects", a conference paper for the conference CollabTech 2022: Collaboration Technologies and Social Computing and published as part of the Lecture Notes in Computer Science book series (LNCS,volume 13632) here. The usernames have been anonymised. Purpose: The purpose of this dataset is to provide the basis to reproduce the results reported in the associated deliverable, and in the above-mentioned publication. As such, it does not represent raw data, but rather files that already include certain analysis steps (like calculated degrees or other SNA-related measures), ready for analysis, visualisation and interpretation with R. Relatedness: The data of the different projects was derived from the forums of 7 Zooniverse projects based on similar discussion board features. The projects are: 'Galaxy Zoo', 'Gravity Spy', 'Seabirdwatch', 'Snapshot Wisconsin', 'Wildwatch Kenya', 'Galaxy Nurseries', 'Penguin Watch'. Content: In this Zenodo entry, several files can be found. The structure is as follows (files and folders and descriptions). corresponding_calculations.html Quarto-notebook to view in browser corresponding_calculations.qmd Quarto-notebook to view in RStudio assets data annotations annotations.csv List of annotations made per day for each of the analysed projects comments comments.csv Total list of comments with several data fields (i.e., comment id, text, reply_user_id) rolechanges 478_rolechanges.csv List of roles per user to determine number of role changes 1104_rolechanges.csv ... ... totalnetworkdata Edges 478_edges.csv Network data (edge set) for the given projects (without time slices) 1104_edges.csv ... ... Nodes 478_nodes.csv Network data (node set) for the given projects (without time slices) 1104_nodes.csv ... ... trajectories Network data (edge and node sets) for the given projects and all time slices (Q1 2016 - Q4 2021) 478 Edges edges_4782016_q1.csv edges_4782016_q2.csv edges_4782016_q3.csv edges_4782016_q4.csv ... Nodes nodes_4782016_q1.csv nodes_4782016_q4.csv nodes_4782016_q3.csv nodes_4782016_q2.csv ... 1104 Edges ... Nodes ... ... scripts datavizfuncs.R script for the data visualisation functions, automatically executed from within corresponding_calculations.qmd import.R script for the import of data, automatically executed from within corresponding_calculations.qmd corresponding_calculations_files files for the html/qmd view in the browser/RStudio Grouping: The data is grouped according to given criteria (e.g., project_title or time). Accordingly, the respective files can be found in the data structure

all-recipes-xs (500)

All Recipes dataset (extra small). from datasets import load_dataset

Load the dataset

dataset = load_dataset("AWeirdDev/all-recipes-xs")

Alternatively, load with pickle from _frozen.pkl: import pickle import requests

r = requests.get("https://huggingface.co/datasets/AWeirdDev/all-recipes-xs/resolve/main/_frozen.pkl") dataset = pickle.loads(r.content)

  Features

Note: Empty values are presented as "unknown" instead of None (normally, unless… See the full description on the dataset page: https://huggingface.co/datasets/AWeirdDev/all-recipes-xs.

Helios-R-6M

Helios-R-6M is a high-quality, compact reasoning dataset designed to strengthen multi-step problem solving across mathematics, computer science, and scientific inquiry. While the dataset covers a range of disciplines, math constitutes the largest share of examples and drives the reasoning complexity.

  Quick Start with Hugging Face Datasets🤗

pip install -U datasets

from datasets import load_dataset

dataset = load_dataset("prithivMLmods/Helios-R-6M"… See the full description on the dataset page: https://huggingface.co/datasets/prithivMLmods/Helios-R-6M.

The Russian Financial Statements Database (RFSD) is an open, harmonized collection of annual unconsolidated financial statements of the universe of Russian firms:

• 🔓 First open data set with information on every active firm in Russia.

• 🗂️ First open financial statements data set that includes non-filing firms.

• 🏛️ Sourced from two official data providers: the Rosstat and the Federal Tax Service.

• 📅 Covers 2011-2023 initially, will be continuously updated.

• 🏗️ Restores as much data as possible through non-invasive data imputation, statement articulation, and harmonization.

The RFSD is hosted on 🤗 Hugging Face and Zenodo and is stored in a structured, column-oriented, compressed binary format Apache Parquet with yearly partitioning scheme, enabling end-users to query only variables of interest at scale.

The accompanying paper provides internal and external validation of the data: http://arxiv.org/abs/2501.05841.

Here we present the instructions for importing the data in R or Python environment. Please consult with the project repository for more information: http://github.com/irlcode/RFSD.

Importing The Data

You have two options to ingest the data: download the .parquet files manually from Hugging Face or Zenodo or rely on 🤗 Hugging Face Datasets library.

Python

🤗 Hugging Face Datasets

It is as easy as:

from datasets import load_dataset import polars as pl

This line will download 6.6GB+ of all RFSD data and store it in a 🤗 cache folder

RFSD = load_dataset('irlspbru/RFSD')

Alternatively, this will download ~540MB with all financial statements for 2023# to a Polars DataFrame (requires about 8GB of RAM)

RFSD_2023 = pl.read_parquet('hf://datasets/irlspbru/RFSD/RFSD/year=2023/*.parquet')

Please note that the data is not shuffled within year, meaning that streaming first n rows will not yield a random sample.

Local File Import

Importing in Python requires pyarrow package installed.

import pyarrow.dataset as ds import polars as pl

Read RFSD metadata from local file

RFSD = ds.dataset("local/path/to/RFSD")

Use RFSD_dataset.schema to glimpse the data structure and columns' classes

print(RFSD.schema)

Load full dataset into memory

RFSD_full = pl.from_arrow(RFSD.to_table())

Load only 2019 data into memory

RFSD_2019 = pl.from_arrow(RFSD.to_table(filter=ds.field('year') == 2019))

Load only revenue for firms in 2019, identified by taxpayer id

RFSD_2019_revenue = pl.from_arrow( RFSD.to_table( filter=ds.field('year') == 2019, columns=['inn', 'line_2110'] ) )

Give suggested descriptive names to variables

renaming_df = pl.read_csv('local/path/to/descriptive_names_dict.csv') RFSD_full = RFSD_full.rename({item[0]: item[1] for item in zip(renaming_df['original'], renaming_df['descriptive'])})

R

Local File Import

Importing in R requires arrow package installed.

library(arrow) library(data.table)

Read RFSD metadata from local file

RFSD <- open_dataset("local/path/to/RFSD")

Use schema() to glimpse into the data structure and column classes

schema(RFSD)

Load full dataset into memory

scanner <- Scanner$create(RFSD) RFSD_full <- as.data.table(scanner$ToTable())

Load only 2019 data into memory

scan_builder <- RFSD$NewScan() scan_builder$Filter(Expression$field_ref("year") == 2019) scanner <- scan_builder$Finish() RFSD_2019 <- as.data.table(scanner$ToTable())

Load only revenue for firms in 2019, identified by taxpayer id

scan_builder <- RFSD$NewScan() scan_builder$Filter(Expression$field_ref("year") == 2019) scan_builder$Project(cols = c("inn", "line_2110")) scanner <- scan_builder$Finish() RFSD_2019_revenue <- as.data.table(scanner$ToTable())

Give suggested descriptive names to variables

renaming_dt <- fread("local/path/to/descriptive_names_dict.csv") setnames(RFSD_full, old = renaming_dt$original, new = renaming_dt$descriptive)

Use Cases

🌍 For macroeconomists: Replication of a Bank of Russia study of the cost channel of monetary policy in Russia by Mogiliat et al. (2024) — interest_payments.md

🏭 For IO: Replication of the total factor productivity estimation by Kaukin and Zhemkova (2023) — tfp.md

🗺️ For economic geographers: A novel model-less house-level GDP spatialization that capitalizes on geocoding of firm addresses — spatialization.md

FAQ

Why should I use this data instead of Interfax's SPARK, Moody's Ruslana, or Kontur's Focus?hat is the data period?

To the best of our knowledge, the RFSD is the only open data set with up-to-date financial statements of Russian companies published under a permissive licence. Apart from being free-to-use, the RFSD benefits from data harmonization and error detection procedures unavailable in commercial sources. Finally, the data can be easily ingested in any statistical package with minimal effort.

What is the data period?

We provide financials for Russian firms in 2011-2023. We will add the data for 2024 by July, 2025 (see Version and Update Policy below).

Why are there no data for firm X in year Y?

Although the RFSD strives to be an all-encompassing database of financial statements, end users will encounter data gaps:

We do not include financials for firms that we considered ineligible to submit financial statements to the Rosstat/Federal Tax Service by law: financial, religious, or state organizations (state-owned commercial firms are still in the data).

Eligible firms may enjoy the right not to disclose under certain conditions. For instance, Gazprom did not file in 2022 and we had to impute its 2022 data from 2023 filings. Sibur filed only in 2023, Novatek — in 2020 and 2021. Commercial data providers such as Interfax's SPARK enjoy dedicated access to the Federal Tax Service data and therefore are able source this information elsewhere.

Firm may have submitted its annual statement but, according to the Uniform State Register of Legal Entities (EGRUL), it was not active in this year. We remove those filings.

Why is the geolocation of firm X incorrect?

We use Nominatim to geocode structured addresses of incorporation of legal entities from the EGRUL. There may be errors in the original addresses that prevent us from geocoding firms to a particular house. Gazprom, for instance, is geocoded up to a house level in 2014 and 2021-2023, but only at street level for 2015-2020 due to improper handling of the house number by Nominatim. In that case we have fallen back to street-level geocoding. Additionally, streets in different districts of one city may share identical names. We have ignored those problems in our geocoding and invite your submissions. Finally, address of incorporation may not correspond with plant locations. For instance, Rosneft has 62 field offices in addition to the central office in Moscow. We ignore the location of such offices in our geocoding, but subsidiaries set up as separate legal entities are still geocoded.

Why is the data for firm X different from https://bo.nalog.ru/?

Many firms submit correcting statements after the initial filing. While we have downloaded the data way past the April, 2024 deadline for 2023 filings, firms may have kept submitting the correcting statements. We will capture them in the future releases.

Why is the data for firm X unrealistic?

We provide the source data as is, with minimal changes. Consider a relatively unknown LLC Banknota. It reported 3.7 trillion rubles in revenue in 2023, or 2% of Russia's GDP. This is obviously an outlier firm with unrealistic financials. We manually reviewed the data and flagged such firms for user consideration (variable outlier), keeping the source data intact.

Why is the data for groups of companies different from their IFRS statements?

We should stress that we provide unconsolidated financial statements filed according to the Russian accounting standards, meaning that it would be wrong to infer financials for corporate groups with this data. Gazprom, for instance, had over 800 affiliated entities and to study this corporate group in its entirety it is not enough to consider financials of the parent company.

Why is the data not in CSV?

The data is provided in Apache Parquet format. This is a structured, column-oriented, compressed binary format allowing for conditional subsetting of columns and rows. In other words, you can easily query financials of companies of interest, keeping only variables of interest in memory, greatly reducing data footprint.

Version and Update Policy

Version (SemVer): 1.0.0.

We intend to update the RFSD annualy as the data becomes available, in other words when most of the firms have their statements filed with the Federal Tax Service. The official deadline for filing of previous year statements is April, 1. However, every year a portion of firms either fails to meet the deadline or submits corrections afterwards. Filing continues up to the very end of the year but after the end of April this stream quickly thins out. Nevertheless, there is obviously a trade-off between minimization of data completeness and version availability. We find it a reasonable compromise to query new data in early June, since on average by the end of May 96.7% statements are already filed, including 86.4% of all the correcting filings. We plan to make a new version of RFSD available by July.

Licence

Creative Commons License Attribution 4.0 International (CC BY 4.0).

Copyright © the respective contributors.

Citation

Please cite as:

@unpublished{bondarkov2025rfsd, title={{R}ussian {F}inancial {S}tatements {D}atabase}, author={Bondarkov, Sergey and Ledenev, Victor and Skougarevskiy, Dmitriy}, note={arXiv preprint arXiv:2501.05841}, doi={https://doi.org/10.48550/arXiv.2501.05841}, year={2025}}

Acknowledgments and Contacts

Data collection and processing: Sergey Bondarkov, sbondarkov@eu.spb.ru, Viktor Ledenev, vledenev@eu.spb.ru

Project conception, data validation, and use cases: Dmitriy Skougarevskiy, Ph.D.,

ImageNet-R

This repo is made to facilitate the evaluation of various pretraining models. It's constructed from the source file provided by official implementation.

  Usage

from datasets import load_dataset

dataset = load_dataset('axiong/imagenet-r')

  Dataset Summary

ImageNet-R(endition) contains art, cartoons, deviantart, graffiti, embroidery, graphics, origami, paintings, patterns, plastic objects, plush objects, sculptures, sketches, tattoos, toys, and video… See the full description on the dataset page: https://huggingface.co/datasets/axiong/imagenet-r.

Shakespeare Complete Works Dataset

This dataset contains the complete works of William Shakespeare, including:

The Sonnets (154 sonnets) Plays (Tragedies, Comedies, Histories) Poems

  Dataset Structure

Each entry contains:

work: The title of the work section: Specific section (e.g., "Sonnet 1") if applicable text: The actual text content type: Type of work (sonnet, play, poem) id: Unique identifier

  Usage

from datasets import load_dataset

dataset =… See the full description on the dataset page: https://huggingface.co/datasets/r-three/shakespeare-complete-works.

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.

Overview Supplementary materials for the paper "Comparing Internet experiences and prosociality in Amazon Mechanical Turk and population-based survey samples" by Eszter Hargittai and Aaron Shaw published in Socius in 2020 (https://doi.org/10.1177/2378023119889834). License The materials provided here are issued under the same (Creative Commons Attribution Non-Commercial 4.0) license as the paper. Details and a copy of the license are available at: http://creativecommons.org/licenses/by-nc/4.0/. Manifest The files included are: Hargittai-Shaw-AMT-NORC-2019.rds and Hargittai-Shaw-AMT-NORC-2019.tsv: Two (identical) versions the dataset used for the analysis. The tsv file is provided to facilitate import into software other than R. R analysis code files: 01-import.R - Imports dataset. Creates a mapping of dependent variables and variable names used elsewhere in the figure and analysis. 02-gen_figure.R - Generates Figure 1 in PDF and PNG formats and saves them in the "figures" directory. 03-gendescriptivestats.R - Generates results reported in Table 1. 04-gen_models.R - Fits models reported in Tables 2-4. 05-alternative_specifications.R - Fits models using log-transformed version of the income variable. Makefile: Executes all of the R files in sequence, produces corresponding .log files in the "log" directory that contain the full R session from each file as well as separate error log files (also in the "log" directory) that capture any error messages and warnings generated by R along the way. HargittaiShaw2019Socius-Instrument.pdf: The questions distributed to both the NORC and AMT survey participants used in the analysis reported in this paper. How to reproduce the analysis presented in the paper Depending on your computing environment, reproducing the analysis presented in the paper may be as easy as invoking "make all" or "make" in the directory containing this file on a system that has the appropriate software installed. Once compilation is complete, you can review the log files in a text editor. See below for more on software and dependencies. If calling the makefile fails, the individual R scripts can also be run interactively or in batch mode. Software and dependencies The R and compilation materials provided here were created and tested on a 64-bit laptop pc running Ubuntu 18.04.3 LTS, R version 3.6.1, ggplot2 version 3.2.1, reshape2 version 1.4.3, forcats version 0.4.0, pscl version 1.5.2, and stargazer version 5.2.2 (these last five are R packages called in specific .R files). As with all software, your mileage may vary and the authors provide no warranties. Codebook The dataset consists of 36 variables (columns) and 2,716 participants (rows). The variable names and brief descriptions follow below. Additional details of measurement are provided in the paper and survey instrument. All dichotomous indicators are coded 0/1 where 1 is the affirmative response implied by the variable name: id: Index to identify individual units (participants). svy_raked_wgt: Raked survey weights provided by NORC. amtsample: Data source coded 0 (NORC) or 1 (AMT). age: Participant age in years. female: Participant selected "female" gender. incomecont: Income in USD (continuous) coded from center-points of categories reported in the instruments. incomediv: Income in $1,000s USD (=incomecont/1000). incomesqrt: Square-root of incomecont. lincome: Natural logarithm of incomecont. rural: Participant resides in a rural area. employed: Participant is fully or partially employed. eduhsorless: Highest education level is high school or less. edusc: Highest education level is completed some college. edubaormore: Highest education level is BA or more. white: Race = white. black: Race = black. nativeam: Race = native american. hispanic: Ethnicity = hispanic. asian: Race = asian. raceother: Race = other. skillsmean: Internet use skills index (described in paper). accesssum: Internet use autonomy (described in paper). webweekhrs: Internet use frequency (described in paper). do_sum: Participatory online activities (described in paper). snssumcompare: Social network site activities (described in paper). altru_scale: Generous behaviors (described in paper). trust_scale: Trust scale score (described in paper). pts_give: Points donated in unilateral dictator game (described in paper). std_accesssum: Standardized (z-score) version of accesssum. std_webweekhrs: Standardized (z-score) version of webweekhrs. std_skillsmean: Standardized (z-score) version of skillsmean. std_do_sum: Standardized (z-score) version of do_sum. std_snssumcompare: Standardized (z-score) version of snssumcompare. std_trust_scale: Standardized (z-score) version of trust_scale. std_altru_scale: Standardized (z-score) version of altru_scale. std_pts_give: Standardized (z-score) version of pts_give.