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.

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.

Replication pack, FSE2018 submission #164:
------------------------------------------

**Working title:** Ecosystem-Level Factors Affecting the Survival of Open-Source Projects: 
A Case Study of the PyPI Ecosystem

**Note:** link to data artifacts is already included in the paper. 
Link to the code will be included in the Camera Ready version as well.


Content description
===================

- **ghd-0.1.0.zip** - the code archive. This code produces the dataset files 
 described below
- **settings.py** - settings template for the code archive.
- **dataset_minimal_Jan_2018.zip** - the minimally sufficient version of the dataset.
 This dataset only includes stats aggregated by the ecosystem (PyPI)
- **dataset_full_Jan_2018.tgz** - full version of the dataset, including project-level
 statistics. It is ~34Gb unpacked. This dataset still doesn't include PyPI packages
 themselves, which take around 2TB.
- **build_model.r, helpers.r** - R files to process the survival data 
  (`survival_data.csv` in **dataset_minimal_Jan_2018.zip**, 
  `common.cache/survival_data.pypi_2008_2017-12_6.csv` in 
  **dataset_full_Jan_2018.tgz**)
- **Interview protocol.pdf** - approximate protocol used for semistructured interviews.
- LICENSE - text of GPL v3, under which this dataset is published
- INSTALL.md - replication guide (~2 pages)

Replication guide
=================

Step 0 - prerequisites
----------------------

- Unix-compatible OS (Linux or OS X)
- Python interpreter (2.7 was used; Python 3 compatibility is highly likely)
- R 3.4 or higher (3.4.4 was used, 3.2 is known to be incompatible)

Depending on detalization level (see Step 2 for more details):
- up to 2Tb of disk space (see Step 2 detalization levels)
- at least 16Gb of RAM (64 preferable)
- few hours to few month of processing time

Step 1 - software
----------------

- unpack **ghd-0.1.0.zip**, or clone from gitlab:

   git clone https://gitlab.com/user2589/ghd.git
   git checkout 0.1.0
 
 `cd` into the extracted folder. 
 All commands below assume it as a current directory.
  
- copy `settings.py` into the extracted folder. Edit the file:
  * set `DATASET_PATH` to some newly created folder path
  * add at least one GitHub API token to `SCRAPER_GITHUB_API_TOKENS` 
- install docker. For Ubuntu Linux, the command is 
  `sudo apt-get install docker-compose`
- install libarchive and headers: `sudo apt-get install libarchive-dev`
- (optional) to replicate on NPM, install yajl: `sudo apt-get install yajl-tools`
 Without this dependency, you might get an error on the next step, 
 but it's safe to ignore.
- install Python libraries: `pip install --user -r requirements.txt` . 
- disable all APIs except GitHub (Bitbucket and Gitlab support were
 not yet implemented when this study was in progress): edit
 `scraper/init.py`, comment out everything except GitHub support
 in `PROVIDERS`.

Step 2 - obtaining the dataset
-----------------------------

The ultimate goal of this step is to get output of the Python function 
`common.utils.survival_data()` and save it into a CSV file:

  # copy and paste into a Python console
  from common import utils
  survival_data = utils.survival_data('pypi', '2008', smoothing=6)
  survival_data.to_csv('survival_data.csv')

Since full replication will take several months, here are some ways to speedup
the process:

####Option 2.a, difficulty level: easiest

Just use the precomputed data. Step 1 is not necessary under this scenario.

- extract **dataset_minimal_Jan_2018.zip**
- get `survival_data.csv`, go to the next step

####Option 2.b, difficulty level: easy

Use precomputed longitudinal feature values to build the final table.
The whole process will take 15..30 minutes.

- create a folder `

The data represent web-scraping of hyperlinks from a selection of environmental stewardship organizations that were identified in the 2017 NYC Stewardship Mapping and Assessment Project (STEW-MAP) (USDA 2017). There are two data sets: 1) the original scrape containing all hyperlinks within the websites and associated attribute values (see "README" file); 2) a cleaned and reduced dataset formatted for network analysis. For dataset 1: Organizations were selected from from the 2017 NYC Stewardship Mapping and Assessment Project (STEW-MAP) (USDA 2017), a publicly available, spatial data set about environmental stewardship organizations working in New York City, USA (N = 719). To create a smaller and more manageable sample to analyze, all organizations that intersected (i.e., worked entirely within or overlapped) the NYC borough of Staten Island were selected for a geographically bounded sample. Only organizations with working websites and that the web scraper could access were retained for the study (n = 78). The websites were scraped between 09 and 17 June 2020 to a maximum search depth of ten using the snaWeb package (version 1.0.1, Stockton 2020) in the R computational language environment (R Core Team 2020). For dataset 2: The complete scrape results were cleaned, reduced, and formatted as a standard edge-array (node1, node2, edge attribute) for network analysis. See "READ ME" file for further details. References: R Core Team. (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/. Version 4.0.3. Stockton, T. (2020). snaWeb Package: An R package for finding and building social networks for a website, version 1.0.1. USDA Forest Service. (2017). Stewardship Mapping and Assessment Project (STEW-MAP). New York City Data Set. Available online at https://www.nrs.fs.fed.us/STEW-MAP/data/. This dataset is associated with the following publication: Sayles, J., R. Furey, and M. Ten Brink. How deep to dig: effects of web-scraping search depth on hyperlink network analysis of environmental stewardship organizations. Applied Network Science. Springer Nature, New York, NY, 7: 36, (2022).

This dataset contains files reconstructing single-cell data presented in 'Reference transcriptomics of porcine peripheral immune cells created through bulk and single-cell RNA sequencing' by Herrera-Uribe & Wiarda et al. 2021. Samples of peripheral blood mononuclear cells (PBMCs) were collected from seven pigs and processed for single-cell RNA sequencing (scRNA-seq) in order to provide a reference annotation of porcine immune cell transcriptomics at enhanced, single-cell resolution. Analysis of single-cell data allowed identification of 36 cell clusters that were further classified into 13 cell types, including monocytes, dendritic cells, B cells, antibody-secreting cells, numerous populations of T cells, NK cells, and erythrocytes. Files may be used to reconstruct the data as presented in the manuscript, allowing for individual query by other users. Scripts for original data analysis are available at https://github.com/USDA-FSEPRU/PorcinePBMCs_bulkRNAseq_scRNAseq. Raw data are available at https://www.ebi.ac.uk/ena/browser/view/PRJEB43826. Funding for this dataset was also provided by NRSP8: National Animal Genome Research Program (https://www.nimss.org/projects/view/mrp/outline/18464). Resources in this dataset:Resource Title: Herrera-Uribe & Wiarda et al. PBMCs - All Cells 10X Format. File Name: PBMC7_AllCells.zipResource Description: Zipped folder containing PBMC counts matrix, gene names, and cell IDs. Files are as follows: matrix of gene counts* (matrix.mtx.gx) gene names (features.tsv.gz) cell IDs (barcodes.tsv.gz) *The ‘raw’ count matrix is actually gene counts obtained following ambient RNA removal. During ambient RNA removal, we specified to calculate non-integer count estimations, so most gene counts are actually non-integer values in this matrix but should still be treated as raw/unnormalized data that requires further normalization/transformation. Data can be read into R using the function Read10X().Resource Title: Herrera-Uribe & Wiarda et al. PBMCs - All Cells Metadata. File Name: PBMC7_AllCells_meta.csvResource Description: .csv file containing metadata for cells included in the final dataset. Metadata columns include: nCount_RNA = the number of transcripts detected in a cell nFeature_RNA = the number of genes detected in a cell Loupe = cell barcodes; correspond to the cell IDs found in the .h5Seurat and 10X formatted objects for all cells prcntMito = percent mitochondrial reads in a cell Scrublet = doublet probability score assigned to a cell seurat_clusters = cluster ID assigned to a cell PaperIDs = sample ID for a cell celltypes = cell type ID assigned to a cellResource Title: Herrera-Uribe & Wiarda et al. PBMCs - All Cells PCA Coordinates. File Name: PBMC7_AllCells_PCAcoord.csvResource Description: .csv file containing first 100 PCA coordinates for cells. Resource Title: Herrera-Uribe & Wiarda et al. PBMCs - All Cells t-SNE Coordinates. File Name: PBMC7_AllCells_tSNEcoord.csvResource Description: .csv file containing t-SNE coordinates for all cells.Resource Title: Herrera-Uribe & Wiarda et al. PBMCs - All Cells UMAP Coordinates. File Name: PBMC7_AllCells_UMAPcoord.csvResource Description: .csv file containing UMAP coordinates for all cells.Resource Title: Herrera-Uribe & Wiarda et al. PBMCs - CD4 T Cells t-SNE Coordinates. File Name: PBMC7_CD4only_tSNEcoord.csvResource Description: .csv file containing t-SNE coordinates for only CD4 T cells (clusters 0, 3, 4, 28). A dataset of only CD4 T cells can be re-created from the PBMC7_AllCells.h5Seurat, and t-SNE coordinates used in publication can be re-assigned using this .csv file.Resource Title: Herrera-Uribe & Wiarda et al. PBMCs - CD4 T Cells UMAP Coordinates. File Name: PBMC7_CD4only_UMAPcoord.csvResource Description: .csv file containing UMAP coordinates for only CD4 T cells (clusters 0, 3, 4, 28). A dataset of only CD4 T cells can be re-created from the PBMC7_AllCells.h5Seurat, and UMAP coordinates used in publication can be re-assigned using this .csv file.Resource Title: Herrera-Uribe & Wiarda et al. PBMCs - Gamma Delta T Cells UMAP Coordinates. File Name: PBMC7_GDonly_UMAPcoord.csvResource Description: .csv file containing UMAP coordinates for only gamma delta T cells (clusters 6, 21, 24, 31). A dataset of only gamma delta T cells can be re-created from the PBMC7_AllCells.h5Seurat, and UMAP coordinates used in publication can be re-assigned using this .csv file.Resource Title: Herrera-Uribe & Wiarda et al. PBMCs - Gamma Delta T Cells t-SNE Coordinates. File Name: PBMC7_GDonly_tSNEcoord.csvResource Description: .csv file containing t-SNE coordinates for only gamma delta T cells (clusters 6, 21, 24, 31). A dataset of only gamma delta T cells can be re-created from the PBMC7_AllCells.h5Seurat, and t-SNE coordinates used in publication can be re-assigned using this .csv file.Resource Title: Herrera-Uribe & Wiarda et al. PBMCs - Gene Annotation Information. File Name: UnfilteredGeneInfo.txtResource Description: .txt file containing gene nomenclature information used to assign gene names in the dataset. 'Name' column corresponds to the name assigned to a feature in the dataset.Resource Title: Herrera-Uribe & Wiarda et al. PBMCs - All Cells H5Seurat. File Name: PBMC7.tarResource Description: .h5Seurat object of all cells in PBMC dataset. File needs to be untarred, then read into R using function LoadH5Seurat().

The goal of this lesson is to learn how to import datasets into R, understand variable types, make adjustments to variables, perform basic calculations, and begin data visualization. The exercise uses an over 100 year time series of climate data.

For any questions about this data please email me at jacob@crimedatatool.com. If you use this data, please cite it.Version 3 release notes:Adds data in the following formats: Excel.Changes project name to avoid confusing this data for the ones done by NACJD.Version 2 release notes:Adds data for 2017.Adds a "number_of_months_reported" variable which says how many months of the year the agency reported data.Property Stolen and Recovered is a Uniform Crime Reporting (UCR) Program data set with information on the number of offenses (crimes included are murder, rape, robbery, burglary, theft/larceny, and motor vehicle theft), the value of the offense, and subcategories of the offense (e.g. for robbery it is broken down into subcategories including highway robbery, bank robbery, gas station robbery). The majority of the data relates to theft. Theft is divided into subcategories of theft such as shoplifting, theft of bicycle, theft from building, and purse snatching. For a number of items stolen (e.g. money, jewelry and previous metals, guns), the value of property stolen and and the value for property recovered is provided. This data set is also referred to as the Supplement to Return A (Offenses Known and Reported). All the data was received directly from the FBI as text or .DTA files. I created a setup file based on the documentation provided by the FBI and read the data into R using the package asciiSetupReader. All work to clean the data and save it in various file formats was also done in R. For the R code used to clean this data, see here: https://github.com/jacobkap/crime_data. The Word document file available for download is the guidebook the FBI provided with the raw data which I used to create the setup file to read in data.There may be inaccuracies in the data, particularly in the group of columns starting with "auto." To reduce (but certainly not eliminate) data errors, I replaced the following values with NA for the group of columns beginning with "offenses" or "auto" as they are common data entry error values (e.g. are larger than the agency's population, are much larger than other crimes or months in same agency): 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000, 20000, 30000, 40000, 50000, 60000, 70000, 80000, 90000, 100000, 99942. This cleaning was NOT done on the columns starting with "value."For every numeric column I replaced negative indicator values (e.g. "j" for -1) with the negative number they are supposed to be. These negative number indicators are not included in the FBI's codebook for this data but are present in the data. I used the values in the FBI's codebook for the Offenses Known and Clearances by Arrest data.To make it easier to merge with other data, I merged this data with the Law Enforcement Agency Identifiers Crosswalk (LEAIC) data. The data from the LEAIC add FIPS (state, county, and place) and agency type/subtype. If an agency has used a different FIPS code in the past, check to make sure the FIPS code is the same as in this data.

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

For any questions about this data please email me at jacob@crimedatatool.com. If you use this data, please cite it.Version 4 release notes:Adds data for 2018Version 3 release notes:Adds data in the following formats: Excel.Changes project name to avoid confusing this data for the ones done by NACJD.Version 2 release notes:Adds data for 2017.Adds a "number_of_months_reported" variable which says how many months of the year the agency reported data.Property Stolen and Recovered is a Uniform Crime Reporting (UCR) Program data set with information on the number of offenses (crimes included are murder, rape, robbery, burglary, theft/larceny, and motor vehicle theft), the value of the offense, and subcategories of the offense (e.g. for robbery it is broken down into subcategories including highway robbery, bank robbery, gas station robbery). The majority of the data relates to theft. Theft is divided into subcategories of theft such as shoplifting, theft of bicycle, theft from building, and purse snatching. For a number of items stolen (e.g. money, jewelry and previous metals, guns), the value of property stolen and and the value for property recovered is provided. This data set is also referred to as the Supplement to Return A (Offenses Known and Reported). All the data was received directly from the FBI as text or .DTA files. I created a setup file based on the documentation provided by the FBI and read the data into R using the package asciiSetupReader. All work to clean the data and save it in various file formats was also done in R. For the R code used to clean this data, see here: https://github.com/jacobkap/crime_data. The Word document file available for download is the guidebook the FBI provided with the raw data which I used to create the setup file to read in data.There may be inaccuracies in the data, particularly in the group of columns starting with "auto." To reduce (but certainly not eliminate) data errors, I replaced the following values with NA for the group of columns beginning with "offenses" or "auto" as they are common data entry error values (e.g. are larger than the agency's population, are much larger than other crimes or months in same agency): 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000, 20000, 30000, 40000, 50000, 60000, 70000, 80000, 90000, 100000, 99942. This cleaning was NOT done on the columns starting with "value."For every numeric column I replaced negative indicator values (e.g. "j" for -1) with the negative number they are supposed to be. These negative number indicators are not included in the FBI's codebook for this data but are present in the data. I used the values in the FBI's codebook for the Offenses Known and Clearances by Arrest data.To make it easier to merge with other data, I merged this data with the Law Enforcement Agency Identifiers Crosswalk (LEAIC) data. The data from the LEAIC add FIPS (state, county, and place) and agency type/subtype. If an agency has used a different FIPS code in the past, check to make sure the FIPS code is the same as in this data.

R is a very powerful language for statistical computing in many disciplines of research and has a steep learning curve. The software is open source, freely available and has a thriving community. This crash course provides an overview of Base-R concepts for beginners and covers the topics 1) introduction into R, 2) reading, saving, and viewing data, 3) selecting and changing objects in R, and 4) descriptive statistics.This course was held by Lisa Spitzer on September 3, 2021, as a precursor to the R tidyverse Workshop by Aurélien Ginolhac and Roland Krause (September 8 - 10, 2021). This entry features the slides, exercises/results, and chat messages of the crash course. Related to this entry are the recordings of the course, and the r tidyverse workshop materials. Click on "related PsychArchives objects" to view or download the recordings of the workshop.:

ABSTRACT: The World Soil Information Service (WoSIS) provides quality-assessed and standardized soil profile data to support digital soil mapping and environmental applications at broad scale levels. Since the release of the ‘WoSIS snapshot 2019’ many new soil data were shared with us, registered in the ISRIC data repository, and subsequently standardized in accordance with the licenses specified by the data providers. The source data were contributed by a wide range of data providers, therefore special attention was paid to the standardization of soil property definitions, soil analytical procedures and soil property values (and units of measurement). We presently consider the following soil chemical properties (organic carbon, total carbon, total carbonate equivalent, total Nitrogen, Phosphorus (extractable-P, total-P, and P-retention), soil pH, cation exchange capacity, and electrical conductivity) and physical properties (soil texture (sand, silt, and clay), bulk density, coarse fragments, and water retention), grouped according to analytical procedures (aggregates) that are operationally comparable. For each profile we provide the original soil classification (FAO, WRB, USDA, and version) and horizon designations as far as these have been specified in the source databases. Three measures for 'fitness-for-intended-use' are provided: positional uncertainty (for site locations), time of sampling/description, and a first approximation for the uncertainty associated with the operationally defined analytical methods. These measures should be considered during digital soil mapping and subsequent earth system modelling that use the present set of soil data. DATA SET DESCRIPTION: The 'WoSIS 2023 snapshot' comprises data for 228k profiles from 217k geo-referenced sites that originate from 174 countries. The profiles represent over 900k soil layers (or horizons) and over 6 million records. The actual number of measurements for each property varies (greatly) between profiles and with depth, this generally depending on the objectives of the initial soil sampling programmes. The data are provided in TSV (tab separated values) format and as GeoPackage. The zip-file (446 Mb) contains the following files: - Readme_WoSIS_202312_v2.pdf: Provides a short description of the dataset, file structure, column names, units and category values (this file is also available directly under 'online resources'). The pdf includes links to tutorials for downloading the TSV files into R respectively Excel. See also 'HOW TO READ TSV FILES INTO R AND PYTHON' in the next section. - wosis_202312_observations.tsv: This file lists the four to six letter codes for each observation, whether the observation is for a site/profile or layer (horizon), the unit of measurement and the number of profiles respectively layers represented in the snapshot. It also provides an estimate for the inferred accuracy for the laboratory measurements. - wosis_202312_sites.tsv: This file characterizes the site location where profiles were sampled. - wosis_2023112_profiles: Presents the unique profile ID (i.e. primary key), site_id, source of the data, country ISO code and name, positional uncertainty, latitude and longitude (WGS 1984), maximum depth of soil described and sampled, as well as information on the soil classification system and edition. Depending on the soil classification system used, the number of fields will vary . - wosis_202312_layers: This file characterises the layers (or horizons) per profile, and lists their upper and lower depths (cm). - wosis_202312_xxxx.tsv : This type of file presents results for each observation (e.g. “xxxx” = “BDFIOD” ), as defined under “code” in file wosis_202312_observation.tsv. (e.g. wosis_202311_bdfiod.tsv). - wosis_202312.gpkg: Contains the above datafiles in GeoPackage format (which stores the files within an SQLite database). HOW TO READ TSV FILES INTO R AND PYTHON: A) To read the data in R, please uncompress the ZIP file and specify the uncompressed folder. setwd("/YourFolder/WoSIS_2023_December/") ## For example: setwd('D:/WoSIS_2023_December/') Then use read_tsv to read the TSV files, specifying the data types for each column (c = character, i = integer, n = number, d = double, l = logical, f = factor, D = date, T = date time, t = time). observations = readr::read_tsv('wosis_202312_observations.tsv', col_types='cccciid') observations ## show columns and first 10 rows sites = readr::read_tsv('wosis_202312_sites.tsv', col_types='iddcccc') sites profiles = readr::read_tsv('wosis_202312_profiles.tsv', col_types='icciccddcccccciccccicccci') profiles layers = readr::read_tsv('wosis_202312_layers.tsv', col_types='iiciciiilcc') layers ## Do this for each observation 'XXXX', e.g. file 'Wosis_202312_orgc.tsv': orgc = readr::read_tsv('wosis_202312_orgc.tsv', col_types='... Visit https://dataone.org/datasets/sha256%3Aae94fefb74f928a3d482eee20abf33cf04d988555ef2beef2977eba7d5504bd7 for complete metadata about this dataset.

This data package is associated with the publication “Investigating the impacts of solid phase extraction on dissolved organic matter optical signatures and the pairing with high-resolution mass spectrometry data in a freshwater system” submitted to “Limnology and Oceanography: Methods.” This data is an extension of the River Corridor and Watershed Biogeochemistry SFA’s Spatial Study 2021 (https://doi.org/10.15485/1898914). Other associated data and field metadata can be found at the link provided. The goal of this manuscript is to assess the impact of solid phase extraction (SPE) on the ability to pair ultra-high resolution mass spectrometry data collected from SPE extracts with optical properties collected on ambient stream samples. Forty-seven samples collected from within the Yakima River Basin, Washington were analyzed dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC), absorbance, and fluorescence. Samples were subsequently concentrated with SPE and reanalyzed for each measurement. The extraction efficiency for the DOC and common optical indices were calculated. In addition, SPE samples were subject to ultra-high resolution mass spectrometry and compared with the ambient and SPE generated optical data. Finally, in addition to this cross-platform inter-comparison, we further performed and intra-comparison among the high-resolution mass spectrometry data to determine the impact of sample preparation on the interpretability of results. Here, the SPE samples were prepared at 40 milligrams per liter (mg/L) based on the known DOC extraction efficiency of the samples (ranging from ~30 to ~75%) compared to the common practice of assuming the DOC extraction efficiency of freshwater samples at 60%. This data package folder consists of one main data folder with one subfolder (Data_Input). The main data folder contains (1) readme; (2) data dictionary (dd); (3) file-level metadata (flmd); (4) final data summary output from processing script; and (5) the processing script. The R-markdown processing script (SPE_Manuscript_Rmarkdown_Data_Package.rmd) contains all code needed to reproduce manuscript statistics and figures (with the exception of that stated below). The Data_Input folder has two subfolders: (1) FTICR and (2) Optics. Additionally, the Data_Input folder contains dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC) data (SPS_NPOC_Summary.csv) and relevant supporting Solid Phase Extraction Volume information (SPS_SPE_Volumes.csv). Methods information for the optical and FTICR data is embedded in the header rows of SPS_EEMs_Methods.csv and SPS_FTICR_Methods.csv, respectively. In addition, the data dictionary (SPS_SPE_dd.csv), file level metadata (SPS_SPE_flmd.csv), and methods codes (SPS_SPE_Methods_codes.csv) are provided. The FTICR subfolder contains all raw FTICR data as well as instructions for processing. In addition, post processed FTICR molecular information (Processed_FTICRMS_Mol.csv) and sample data (Processed_FTICRMS_Data.csv) is provided that can be directly read into R with the associated R-markdown file. The Optics subfolder contains all Absorbance and Fluorescence Spectra. Fluorescence spectra have been blank corrected, inner filter corrected, and undergone scatter removal. In addition, this folder contains Matlab code used to make a portion of Figure 1 within the manuscript, derive various spectral parameters used within the manuscript, and used for parallel factor analysis (PARAFAC) modeling. Spectral indices (SPS_SpectralIndices.csv) and PARAFAC outputs (SPS_PARAFAC_Model_Loadings.csv and SPS_PARAFAC_Sample_Scores.csv) are directly read into the associated R-markdown file.

README

Authors

César E. Corona-González, Claudia Rebeca De Stefano-Ramos, Juan Pablo Rosado-Aíza, Fabiola R Gómez-Velázquez, David I. Ibarra-Zarate, Luz María Alonso-Valerdi

Contact person

César E. Corona-González

https://orcid.org/0000-0002-7680-2953

a00833959@tec.mx

Project name

Psychophysiological data from Mexican children with learning difficulties who strengthen reading and math skills by assistive technology

Year that the project ran

2023

Brief overview of the tasks in the experiment

The current dataset consists of psychometric and electrophysiological data from children with reading or math learning difficulties. These data were collected to evaluate improvements in reading or math skills resulting from using an online learning method called Smartick.

The psychometric evaluations from children with reading difficulties encompassed: spelling tests, where 1) orthographic and 2) phonological errors were considered, 3) reading speed, expressed in words read per minute, and 4) reading comprehension, where multiple-choice questions were given to the children. The last 2 parameters were determined according to the standards from the Ministry of Public Education (Secretaría de Educación Pública in Spanish) in Mexico. On the other hand, group 2 assessments embraced: 1) an assessment of general mathematical knowledge, as well as 2) the hits percentage, and 3) reaction time from an arithmetical task. Additionally, selective attention and intelligence quotient (IQ) were also evaluated.

Then, individuals underwent an EEG experimental paradigm where two conditions were recorded: 1) a 3-minute eyes-open resting state and 2) performing either reading or mathematical activities. EEG recordings from the reading experiment consisted of reading a text aloud and then answering questions about the text. Alternatively, EEG recordings from the math experiment involved the solution of two blocks with 20 arithmetic operations (addition and subtraction). Subsequently, each child was randomly subcategorized as 1) the experimental group, who were asked to engage with Smartick for three months, and 2) the control group, who were not involved with the intervention. Once the 3-month period was over, every child was reassessed as described before.

Description of the contents of the dataset

The dataset contains a total of 76 subjects (sub-), where two study groups were assessed: 1) reading difficulties (R) and 2) math difficulties (M). Then, each individual was subcategorized as experimental subgroup (e), where children were compromised to engage with Smartick, or control subgroup (c), where they did not get involved with any intervention.

Every subject was followed up on for three months. During this period, each subject underwent two EEG sessions, representing the PRE-intervention (ses-1) and the POST-intervention (ses-2).

The EEG recordings from the reading difficulties group consisted of a resting state condition (run-1) and while performing active reading and reading comprehension activities (run-2). On the other hand, EEG data from the math difficulties group was collected from a resting state condition (run-1) and when solving two blocks of 20 arithmetic operations (run-2 and run-3). All EEG files were stored in .set format. The nomenclature and description from filenames are shown below:

Example: the file sub-Rc11_ses-1_task-SmartickDataset_run-2_eeg.set is related to: - The 11th subject from the reading difficulties group, control subgroup (sub-Rc11). - EEG recording from the PRE-intervention (ses-1) while performing the reading activity (run-2)

Independent variables

• Study groups:
  • Reading difficulties
    • Control: children did not follow any intervention
    • Experimental: Children used the reading program of Smartick for 3 months
  • Math difficulties
    • Control: children did not follow any intervention
    • Experimental: Children used the math program of Smartick for 3 months
• Condition:
  • PRE-intervention: first psychological and electroencephalographic evaluation
  • POST-intervention: second psychological and electroencephalographic evaluation

Dependent variables

• Psychometric data from the reading difficulties group:

  • Orthographic_ERR: number of orthographic errors.
  • Phonological_ERR: number of phonological errors.
  • Selective_Attention: score from the selective attention test.
  • Reading_Speed: reading speed in words per minute.
  • Comprehension: score on a reading comprehension task.
  • GROUP: C for the control group, E for the experimental group.
  • GENDER: M for male, F for Female.
  • AGE: age at the beginning of the study.
  • IQ: intelligence quotient.

• Psychometric data from the math difficulties group:

  • WRAT4: score from the WRAT-4 test.
  • hits: hits during the EEG acquisition [%].
  • RT: reaction time during the EEG acquisition [s].
  • Selective_Attention: score from the selective attention test.
  • GROUP: C for the control Group, E for the experimental group.
  • GENDER: M for male, F for female.
  • AGE: age at the beginning of the study.
  • IQ: intelligence quotient.

Psychometric data can be found in the 01_Psychometric_Data.xlsx file

• Engagement percentage within Smartick (only for experimental group)
  • These values represent the engagement percentage through Smartick.
  • Students were asked to get involved with the online method for learning for 3 months, 5 days a week.
  • Greater values than 100% denote participants who regularly logged in more than 5 days weekly.

Engagement percentage be found in the 05_SessionEngagement.xlsx file

Methods

Subjects

Seventy-six Mexican children between 7 and 13 years old were enrolled in this study.

Information about the recruitment procedure

The sample was recruited through non-profit foundations that support learning and foster care programs.

Apparatus

g.USBamp RESEARCH amplifier

Initial setup

1. Explain the task to the participant.
2. Sign informed consent.
3. Set up electrodes.

Task details

The stimuli nested folder contains all stimuli employed in the EEG experiments.

Level 1 - Math: Images used in the math experiment.​​​​​​​ - Reading: Images used in the reading experiment.

Level 2 - Math * POST_Operations: arithmetic operations from the POST-intervention.
* PRE_Operations: arithmetic operations from the PRE-intervention. - Reading * POST_Reading1: text 1 and text-related comprehension questions from the POST-intervention. * POST_Reading2: text 2 and text-related comprehension questions from the POST-intervention. * POST_Reading3: text 3 and text-related comprehension questions from the POST-intervention. * PRE_Reading1: text 1 and text-related comprehension questions from the PRE-intervention. * PRE_Reading2: text 2 and text-related comprehension questions from the PRE-intervention. * PRE_Reading3: text 3 and text-related comprehension questions from the PRE-intervention.

Level 3 - Math * Operation01.jpg to Operation20.jpg: arithmetical operations solved during the first block of the math

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.

!!!WARNING~~~This dataset has a large number of flaws and is unable to properly answer many questions that people generally use it to answer, such as whether national hate crimes are changing (or at least they use the data so improperly that they get the wrong answer). A large number of people using this data (academics, advocates, reporting, US Congress) do so inappropriately and get the wrong answer to their questions as a result. Indeed, many published papers using this data should be retracted. Before using this data I highly recommend that you thoroughly read my book on UCR data, particularly the chapter on hate crimes (https://ucrbook.com/hate-crimes.html) as well as the FBI's own manual on this data. The questions you could potentially answer well are relatively narrow and generally exclude any causal relationships. ~~~WARNING!!!For a comprehensive guide to this data and other UCR data, please see my book at ucrbook.comVersion 9 release notes:Adds 2021 data.Version 8 release notes:Adds 2019 and 2020 data. Please note that the FBI has retired UCR data ending in 2020 data so this will be the last UCR hate crime data they release. Changes .rda file to .rds.Version 7 release notes:Changes release notes description, does not change data.Version 6 release notes:Adds 2018 dataVersion 5 release notes:Adds data in the following formats: SPSS, SAS, and Excel.Changes project name to avoid confusing this data for the ones done by NACJD.Adds data for 1991.Fixes bug where bias motivation "anti-lesbian, gay, bisexual, or transgender, mixed group (lgbt)" was labeled "anti-homosexual (gay and lesbian)" prior to 2013 causing there to be two columns and zero values for years with the wrong label.All data is now directly from the FBI, not NACJD. The data initially comes as ASCII+SPSS Setup files and read into R using the package asciiSetupReader. All work to clean the data and save it in various file formats was also done in R. Version 4 release notes: Adds data for 2017.Adds rows that submitted a zero-report (i.e. that agency reported no hate crimes in the year). This is for all years 1992-2017. Made changes to categorical variables (e.g. bias motivation columns) to make categories consistent over time. Different years had slightly different names (e.g. 'anti-am indian' and 'anti-american indian') which I made consistent. Made the 'population' column which is the total population in that agency. Version 3 release notes: Adds data for 2016.Order rows by year (descending) and ORI.Version 2 release notes: Fix bug where Philadelphia Police Department had incorrect FIPS county code. The Hate Crime data is an FBI data set that is part of the annual Uniform Crime Reporting (UCR) Program data. This data contains information about hate crimes reported in the United States. Please note that the files are quite large and may take some time to open.Each row indicates a hate crime incident for an agency in a given year. I have made a unique ID column ("unique_id") by combining the year, agency ORI9 (the 9 character Originating Identifier code), and incident number columns together. Each column is a variable related to that incident or to the reporting agency. Some of the important columns are the incident date, what crime occurred (up to 10 crimes), the number of victims for each of these crimes, the bias motivation for each of these crimes, and the location of each crime. It also includes the total number of victims, total number of offenders, and race of offenders (as a group). Finally, it has a number of columns indicating if the victim for each offense was a certain type of victim or not (e.g. individual victim, business victim religious victim, etc.). The only changes I made to the data are the following. Minor changes to column names to make all column names 32 characters or fewer (so it can be saved in a Stata format), made all character values lower case, reordered columns. I also generated incident month, weekday, and month-day variables from the incident date variable included in the original data.

Overview

This dataset is the repository for the following paper submitted to Data in Brief:

Kempf, M. A dataset to model Levantine landcover and land-use change connected to climate change, the Arab Spring and COVID-19. Data in Brief (submitted: December 2023).

The Data in Brief article contains the supplement information and is the related data paper to:

Kempf, M. Climate change, the Arab Spring, and COVID-19 - Impacts on landcover transformations in the Levant. Journal of Arid Environments (revision submitted: December 2023).

Description/abstract

The Levant region is highly vulnerable to climate change, experiencing prolonged heat waves that have led to societal crises and population displacement. Since 2010, the area has been marked by socio-political turmoil, including the Syrian civil war and currently the escalation of the so-called Israeli-Palestinian Conflict, which strained neighbouring countries like Jordan due to the influx of Syrian refugees and increases population vulnerability to governmental decision-making. Jordan, in particular, has seen rapid population growth and significant changes in land-use and infrastructure, leading to over-exploitation of the landscape through irrigation and construction. This dataset uses climate data, satellite imagery, and land cover information to illustrate the substantial increase in construction activity and highlights the intricate relationship between climate change predictions and current socio-political developments in the Levant.

Folder structure

The main folder after download contains all data, in which the following subfolders are stored are stored as zipped files:

“code” stores the above described 9 code chunks to read, extract, process, analyse, and visualize the data.

“MODIS_merged” contains the 16-days, 250 m resolution NDVI imagery merged from three tiles (h20v05, h21v05, h21v06) and cropped to the study area, n=510, covering January 2001 to December 2022 and including January and February 2023.

“mask” contains a single shapefile, which is the merged product of administrative boundaries, including Jordan, Lebanon, Israel, Syria, and Palestine (“MERGED_LEVANT.shp”).

“yield_productivity” contains .csv files of yield information for all countries listed above.

“population” contains two files with the same name but different format. The .csv file is for processing and plotting in R. The .ods file is for enhanced visualization of population dynamics in the Levant (Socio_cultural_political_development_database_FAO2023.ods).

“GLDAS” stores the raw data of the NASA Global Land Data Assimilation System datasets that can be read, extracted (variable name), and processed using code “8_GLDAS_read_extract_trend” from the respective folder. One folder contains data from 1975-2022 and a second the additional January and February 2023 data.

“built_up” contains the landcover and built-up change data from 1975 to 2022. This folder is subdivided into two subfolder which contain the raw data and the already processed data. “raw_data” contains the unprocessed datasets and “derived_data” stores the cropped built_up datasets at 5 year intervals, e.g., “Levant_built_up_1975.tif”.

Code structure

1_MODIS_NDVI_hdf_file_extraction.R

This is the first code chunk that refers to the extraction of MODIS data from .hdf file format. The following packages must be installed and the raw data must be downloaded using a simple mass downloader, e.g., from google chrome. Packages: terra. Download MODIS data from after registration from: https://lpdaac.usgs.gov/products/mod13q1v061/ or https://search.earthdata.nasa.gov/search (MODIS/Terra Vegetation Indices 16-Day L3 Global 250m SIN Grid V061, last accessed, 09th of October 2023). The code reads a list of files, extracts the NDVI, and saves each file to a single .tif-file with the indication “NDVI”. Because the study area is quite large, we have to load three different (spatially) time series and merge them later. Note that the time series are temporally consistent.

2_MERGE_MODIS_tiles.R

In this code, we load and merge the three different stacks to produce large and consistent time series of NDVI imagery across the study area. We further use the package gtools to load the files in (1, 2, 3, 4, 5, 6, etc.). Here, we have three stacks from which we merge the first two (stack 1, stack 2) and store them. We then merge this stack with stack 3. We produce single files named NDVI_final_*consecutivenumber*.tif. Before saving the final output of single merged files, create a folder called “merged” and set the working directory to this folder, e.g., setwd("your directory_MODIS/merged").

3_CROP_MODIS_merged_tiles.R

Now we want to crop the derived MODIS tiles to our study area. We are using a mask, which is provided as .shp file in the repository, named "MERGED_LEVANT.shp". We load the merged .tif files and crop the stack with the vector. Saving to individual files, we name them “NDVI_merged_clip_*consecutivenumber*.tif. We now produced single cropped NDVI time series data from MODIS.
The repository provides the already clipped and merged NDVI datasets.

4_TREND_analysis_NDVI.R

Now, we want to perform trend analysis from the derived data. The data we load is tricky as it contains 16-days return period across a year for the period of 22 years. Growing season sums contain MAM (March-May), JJA (June-August), and SON (September-November). December is represented as a single file, which means that the period DJF (December-February) is represented by 5 images instead of 6. For the last DJF period (December 2022), the data from January and February 2023 can be added. The code selects the respective images from the stack, depending on which period is under consideration. From these stacks, individual annually resolved growing season sums are generated and the slope is calculated. We can then extract the p-values of the trend and characterize all values with high confidence level (0.05). Using the ggplot2 package and the melt function from reshape2 package, we can create a plot of the reclassified NDVI trends together with a local smoother (LOESS) of value 0.3.
To increase comparability and understand the amplitude of the trends, z-scores were calculated and plotted, which show the deviation of the values from the mean. This has been done for the NDVI values as well as the GLDAS climate variables as a normalization technique.

5_BUILT_UP_change_raster.R

Let us look at the landcover changes now. We are working with the terra package and get raster data from here: https://ghsl.jrc.ec.europa.eu/download.php?ds=bu (last accessed 03. March 2023, 100 m resolution, global coverage). Here, one can download the temporal coverage that is aimed for and reclassify it using the code after cropping to the individual study area. Here, I summed up different raster to characterize the built-up change in continuous values between 1975 and 2022.

6_POPULATION_numbers_plot.R

For this plot, one needs to load the .csv-file “Socio_cultural_political_development_database_FAO2023.csv” from the repository. The ggplot script provided produces the desired plot with all countries under consideration.

7_YIELD_plot.R

In this section, we are using the country productivity from the supplement in the repository “yield_productivity” (e.g., "Jordan_yield.csv". Each of the single country yield datasets is plotted in a ggplot and combined using the patchwork package in R.

8_GLDAS_read_extract_trend

The last code provides the basis for the trend analysis of the climate variables used in the paper. The raw data can be accessed https://disc.gsfc.nasa.gov/datasets?keywords=GLDAS%20Noah%20Land%20Surface%20Model%20L4%20monthly&page=1 (last accessed 9th of October 2023). The raw data comes in .nc file format and various variables can be extracted using the [“^a variable name”] command from the spatraster collection. Each time you run the code, this variable name must be adjusted to meet the requirements for the variables (see this link for abbreviations: https://disc.gsfc.nasa.gov/datasets/GLDAS_CLSM025_D_2.0/summary, last accessed 09th of October 2023; or the respective code chunk when reading a .nc file with the ncdf4 package in R) or run print(nc) from the code or use names(the spatraster collection).
Choosing one variable, the code uses the MERGED_LEVANT.shp mask from the repository to crop and mask the data to the outline of the study area.
From the processed data, trend analysis are conducted and z-scores were calculated following the code described above. However, annual trends require the frequency of the time series analysis to be set to value = 12. Regarding, e.g., rainfall, which is measured as annual sums and not means, the chunk r.sum=r.sum/12 has to be removed or set to r.sum=r.sum/1 to avoid calculating annual mean values (see other variables). Seasonal subset can be calculated as described in the code. Here, 3-month subsets were chosen for growing seasons, e.g. March-May (MAM), June-July (JJA), September-November (SON), and DJF (December-February, including Jan/Feb of the consecutive year).
From the data, mean values of 48 consecutive years are calculated and trend analysis are performed as describe above. In the same way, p-values are extracted and 95 % confidence level values are marked with dots on the raster plot. This analysis can be performed with a much longer time series, other variables, ad different spatial extent across the globe due to the availability of the GLDAS variables.

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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

Background The Infinium EPIC array measures the methylation status of > 850,000 CpG sites. The EPIC BeadChip uses a two-array design: Infinium Type I and Type II probes. These probe types exhibit different technical characteristics which may confound analyses. Numerous normalization and pre-processing methods have been developed to reduce probe type bias as well as other issues such as background and dye bias.
Methods This study evaluates the performance of various normalization methods using 16 replicated samples and three metrics: absolute beta-value difference, overlap of non-replicated CpGs between replicate pairs, and effect on beta-value distributions. Additionally, we carried out Pearson’s correlation and intraclass correlation coefficient (ICC) analyses using both raw and SeSAMe 2 normalized data.
Results The method we define as SeSAMe 2, which consists of the application of the regular SeSAMe pipeline with an additional round of QC, pOOBAH masking, was found to be the best-performing normalization method, while quantile-based methods were found to be the worst performing methods. Whole-array Pearson’s correlations were found to be high. However, in agreement with previous studies, a substantial proportion of the probes on the EPIC array showed poor reproducibility (ICC < 0.50). The majority of poor-performing probes have beta values close to either 0 or 1, and relatively low standard deviations. These results suggest that probe reliability is largely the result of limited biological variation rather than technical measurement variation. Importantly, normalizing the data with SeSAMe 2 dramatically improved ICC estimates, with the proportion of probes with ICC values > 0.50 increasing from 45.18% (raw data) to 61.35% (SeSAMe 2). Methods

Study Participants and Samples

The whole blood samples were obtained from the Health, Well-being and Aging (Saúde, Ben-estar e Envelhecimento, SABE) study cohort. SABE is a cohort of census-withdrawn elderly from the city of São Paulo, Brazil, followed up every five years since the year 2000, with DNA first collected in 2010. Samples from 24 elderly adults were collected at two time points for a total of 48 samples. The first time point is the 2010 collection wave, performed from 2010 to 2012, and the second time point was set in 2020 in a COVID-19 monitoring project (9±0.71 years apart). The 24 individuals were 67.41±5.52 years of age (mean ± standard deviation) at time point one; and 76.41±6.17 at time point two and comprised 13 men and 11 women.

All individuals enrolled in the SABE cohort provided written consent, and the ethic protocols were approved by local and national institutional review boards COEP/FSP/USP OF.COEP/23/10, CONEP 2044/2014, CEP HIAE 1263-10, University of Toronto RIS 39685.

Blood Collection and Processing

Genomic DNA was extracted from whole peripheral blood samples collected in EDTA tubes. DNA extraction and purification followed manufacturer’s recommended protocols, using Qiagen AutoPure LS kit with Gentra automated extraction (first time point) or manual extraction (second time point), due to discontinuation of the equipment but using the same commercial reagents. DNA was quantified using Nanodrop spectrometer and diluted to 50ng/uL. To assess the reproducibility of the EPIC array, we also obtained technical replicates for 16 out of the 48 samples, for a total of 64 samples submitted for further analyses. Whole Genome Sequencing data is also available for the samples described above.

Characterization of DNA Methylation using the EPIC array

Approximately 1,000ng of human genomic DNA was used for bisulphite conversion. Methylation status was evaluated using the MethylationEPIC array at The Centre for Applied Genomics (TCAG, Hospital for Sick Children, Toronto, Ontario, Canada), following protocols recommended by Illumina (San Diego, California, USA).

Processing and Analysis of DNA Methylation Data

The R/Bioconductor packages Meffil (version 1.1.0), RnBeads (version 2.6.0), minfi (version 1.34.0) and wateRmelon (version 1.32.0) were used to import, process and perform quality control (QC) analyses on the methylation data. Starting with the 64 samples, we first used Meffil to infer the sex of the 64 samples and compared the inferred sex to reported sex. Utilizing the 59 SNP probes that are available as part of the EPIC array, we calculated concordance between the methylation intensities of the samples and the corresponding genotype calls extracted from their WGS data. We then performed comprehensive sample-level and probe-level QC using the RnBeads QC pipeline. Specifically, we (1) removed probes if their target sequences overlap with a SNP at any base, (2) removed known cross-reactive probes (3) used the iterative Greedycut algorithm to filter out samples and probes, using a detection p-value threshold of 0.01 and (4) removed probes if more than 5% of the samples having a missing value. Since RnBeads does not have a function to perform probe filtering based on bead number, we used the wateRmelon package to extract bead numbers from the IDAT files and calculated the proportion of samples with bead number < 3. Probes with more than 5% of samples having low bead number (< 3) were removed. For the comparison of normalization methods, we also computed detection p-values using out-of-band probes empirical distribution with the pOOBAH() function in the SeSAMe (version 1.14.2) R package, with a p-value threshold of 0.05, and the combine.neg parameter set to TRUE. In the scenario where pOOBAH filtering was carried out, it was done in parallel with the previously mentioned QC steps, and the resulting probes flagged in both analyses were combined and removed from the data.

Normalization Methods Evaluated

The normalization methods compared in this study were implemented using different R/Bioconductor packages and are summarized in Figure 1. All data was read into R workspace as RG Channel Sets using minfi’s read.metharray.exp() function. One sample that was flagged during QC was removed, and further normalization steps were carried out in the remaining set of 63 samples. Prior to all normalizations with minfi, probes that did not pass QC were removed. Noob, SWAN, Quantile, Funnorm and Illumina normalizations were implemented using minfi. BMIQ normalization was implemented with ChAMP (version 2.26.0), using as input Raw data produced by minfi’s preprocessRaw() function. In the combination of Noob with BMIQ (Noob+BMIQ), BMIQ normalization was carried out using as input minfi’s Noob normalized data. Noob normalization was also implemented with SeSAMe, using a nonlinear dye bias correction. For SeSAMe normalization, two scenarios were tested. For both, the inputs were unmasked SigDF Sets converted from minfi’s RG Channel Sets. In the first, which we call “SeSAMe 1”, SeSAMe’s pOOBAH masking was not executed, and the only probes filtered out of the dataset prior to normalization were the ones that did not pass QC in the previous analyses. In the second scenario, which we call “SeSAMe 2”, pOOBAH masking was carried out in the unfiltered dataset, and masked probes were removed. This removal was followed by further removal of probes that did not pass previous QC, and that had not been removed by pOOBAH. Therefore, SeSAMe 2 has two rounds of probe removal. Noob normalization with nonlinear dye bias correction was then carried out in the filtered dataset. Methods were then compared by subsetting the 16 replicated samples and evaluating the effects that the different normalization methods had in the absolute difference of beta values (|β|) between replicated samples.