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.

Publication

This child item describes R code used to determine public supply consumptive use estimates. Consumptive use was estimated by scaling an assumed fraction of deliveries used for outdoor irrigation by spatially explicit estimates of evaporative demand using estimated domestic and commercial, industrial, and institutional deliveries from the public supply delivery machine learning model child item. This method scales public supply water service area outdoor water use by the relationship between service area gross reference evapotranspiration provided by GridMET and annual continental U.S. (CONUS) growing season maximum evapotranspiration. This relationship to climate at the CONUS scale could result in over- or under-estimation of consumptive use at public supply service areas where local variations differ from national variations in climate. This method also assumes that 50% of deliveries for total domestic and commercial, industrial, and institutional deliveries is used for outdoor purposes. This dataset is part of a larger data release using machine learning to predict public supply water use for 12-digit hydrologic units from 2000-2020. This page includes the following file: PS_ConsumptiveUse.zip - a zip file containing input datasets, scripts, and output datasets

Input dataset for R code (first sheet), and BOLD spreadsheet downloaded on April 11, 2022 (next sheets) for "Facing the Infinity".

This folder contains the input files required for the R code used to analyse data for the Patterns and prevalence of food allergy in adulthood in the UK (PAFA) project. This includes:pafa_data_dictionary_anonymised.csv: The data dictionary describing each column in the anonymised PAFA dataset. "snomed_field_name" lists all column names in the dataset; "field_name_extended" lists the original column name in the REDCap data download, which was then recoded to include SNOMED and FoodEx2 codes for future analyses; "variable_field_name" denotes the corresponding coded field name in the REDCap form; "field_type" denotes the type of REDCap field; "field_label" describes the field name in plain language; "choices_calculations_or_slider_labels" describes the choices provided to the participant for that question.foodex2_codes_with_other.csv: A CSV file with key-value pairs for identifying foods coded in the dataset.

Trends in nutrient fluxes and streamflow for selected tributaries in the Lake Erie watershed were calculated using monitoring data at 10 locations. Trends in flow-normalized nutrient fluxes were determined by applying a weighted regression approach called WRTDS (Weighted Regression on Time, Discharge, and Season). Site information and streamflow and water-quality records are contained in 3 zipped files named as follows: INFO (site information), Daily (daily streamflow records), and Sample (water-quality records). The INFO, Daily (flow), and Sample files contain the input data, by water-quality parameter and by site as .csv files, used to run trend analyses. These files were generated by the R (version 3.1.2) software package called EGRET - Exploration and Graphics for River Trends (version 2.5.1) (Hirsch and DeCicco, 2015), and can be used directly as input to run graphical procedures and WRTDS trend analyses using EGRET R software. The .csv files are identified according to water-quality parameter (TP, SRP, TN, NO23, and TKN) and site reference number (e.g. TPfiles.1.INFO.csv, SRPfiles.1.INFO.csv, TPfiles.2.INFO.csv, etc.). Water-quality parameter abbreviations and site reference numbers are defined in the file "Site-summary_table.csv" on the landing page, where there is also a site-location map ("Site_map.pdf"). Parameter information details, including abbreviation definitions, appear in the abstract on the Landing Page. SRP data records were available at only 6 of the 10 trend sites, which are identified in the file "site-summary_table.csv" (see landing page) as monitored by the organization NCWQR (National Center for Water Quality Research). The SRP sites are: RAIS, MAUW, SAND, HONE, ROCK, and CUYA. The model-input dataset is presented in 3 parts: 1. INFO.zip (site information) 2. Daily.zip (daily streamflow records) 3. Sample.zip (water-quality records) Reference: Hirsch, R.M., and De Cicco, L.A., 2015 (revised). User Guide to Exploration and Graphics for RivEr Trends (EGRET) and dataRetrieval: R Packages for Hydrologic Data, Version 2.0, U.S. Geological Survey Techniques Methods, 4-A10. U.S. Geological Survey, Reston, VA., 93 p. (at: http://dx.doi.org/10.3133/tm4A10).

Each R script replicates all of the example code from one chapter from the book. All required data for each script are also uploaded, as are all data used in the practice problems at the end of each chapter. The data are drawn from a wide array of sources, so please cite the original work if you ever use any of these data sets for research purposes.

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 `

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

This data release contains the input-data files and R scripts associated with the analysis presented in [citation of manuscript]. The spatial extent of the data is the contiguous U.S. The input-data files include one comma separated value (csv) file of county-level data, and one csv file of city-level data. The county-level csv (“county_data.csv”) contains data for 3,109 counties. This data includes two measures of water use, descriptive information about each county, three grouping variables (climate region, urban class, and economic dependency), and contains 18 explanatory variables: proportion of population growth from 2000-2010, fraction of withdrawals from surface water, average daily water yield, mean annual maximum temperature from 1970-2010, 2005-2010 maximum temperature departure from the 40-year maximum, mean annual precipitation from 1970-2010, 2005-2010 mean precipitation departure from the 40-year mean, Gini income disparity index, percent of county population with at least some college education, Cook Partisan Voting Index, housing density, median household income, average number of people per household, median age of structures, percent of renters, percent of single family homes, percent apartments, and a numeric version of urban class. The city-level csv (city_data.csv) contains data for 83 cities. This data includes descriptive information for each city, water-use measures, one grouping variable (climate region), and 6 explanatory variables: type of water bill (increasing block rate, decreasing block rate, or uniform), average price of water bill, number of requirement-oriented water conservation policies, number of rebate-oriented water conservation policies, aridity index, and regional price parity. The R scripts construct fixed-effects and Bayesian Hierarchical regression models. The primary difference between these models relates to how they handle possible clustering in the observations that define unique water-use settings. Fixed-effects models address possible clustering in one of two ways. In a "fully pooled" fixed-effects model, any clustering by group is ignored, and a single, fixed estimate of the coefficient for each covariate is developed using all of the observations. Conversely, in an unpooled fixed-effects model, separate coefficient estimates are developed only using the observations in each group. A hierarchical model provides a compromise between these two extremes. Hierarchical models extend single-level regression to data with a nested structure, whereby the model parameters vary at different levels in the model, including a lower level that describes the actual data and an upper level that influences the values taken by parameters in the lower level. The county-level models were compared using the Watanabe-Akaike information criterion (WAIC) which is derived from the log pointwise predictive density of the models and can be shown to approximate out-of-sample predictive performance. All script files are intended to be used with R statistical software (R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org) and Stan probabilistic modeling software (Stan Development Team. 2017. RStan: the R interface to Stan. R package version 2.16.2. http://mc-stan.org).

AWC to 60cm is one of 18 attributes of soils chosen to underpin the land suitability assessment of the Roper River Water Resource Assessment (ROWRA) through the digital soil mapping process (DSM). AWC (available water capacity) indicates the ability of a soil to retain and supply water for plant growth. This AWC raster data represents a modelled dataset of AWC to 60cm (mm of water to 60cm of soil depth) and is derived from analysed site data, spline calculations and environmental covariates. AWC is a parameter used in land suitability assessments for rainfed cropping and for water use efficiency in irrigated land uses. This raster data provides improved soil information used to underpin and identify opportunities and promote detailed investigation for a range of sustainable regional development options and was created within the ‘Land Suitability’ activity of the CSIRO ROWRA. A companion dataset and statistics reflecting reliability of this data are also provided and can be found described in the lineage section of this metadata record. Processing information is supplied in ranger R scripts and attributes were modelled using a Random Forest approach. The DSM process is described in the CSIRO ROWRA published report ‘Soils and land suitability for the Roper catchment, Northern Territory’. A technical report from the CSIRO Roper River Water Resource Assessment to the Government of Australia. The Roper River Water Resource Assessment provides a comprehensive overview and integrated evaluation of the feasibility of aquaculture and agriculture development in the Roper catchment NT as well as the ecological, social and cultural (indigenous water values, rights and aspirations) impacts of development. Lineage: This AWC to 60cm dataset has been generated from a range of inputs and processing steps. Following is an overview. For more information refer to the CSIRO ROWRA published reports and in particular ' Soils and land suitability for the Roper catchment, Northern Territory’. A technical report from the CSIRO Roper River Water Resource Assessment to the Government of Australia. 1. Collated existing data (relating to: soils, climate, topography, natural resources, remotely sensed, of various formats: reports, spatial vector, spatial raster etc). 2. Selection of additional soil and land attribute site data locations by a conditioned Latin hypercube statistical sampling method applied across the covariate data space. 3. Fieldwork was carried out to collect new attribute data, soil samples for analysis and build an understanding of geomorphology and landscape processes. 4. Database analysis was performed to extract the data to specific selection criteria required for the attribute to be modelled. 5. The R statistical programming environment was used for the attribute computing. Models were built from selected input data and covariate data using predictive learning from a Random Forest approach implemented in the ranger R package. 6. Create AWC to 60cm Digital Soil Mapping (DSM) attribute raster dataset. DSM data is a geo-referenced dataset, generated from field observations and laboratory data, coupled with environmental covariate data through quantitative relationships. It applies pedometrics - the use of mathematical and statistical models that combine information from soil observations with information contained in correlated environmental variables, remote sensing images and some geophysical measurements. 7. Companion predicted reliability data was produced from the 500 individual Random Forest attribute models created. 8. QA Quality assessment of this DSM attribute data was conducted by three methods. Method 1: Statistical (quantitative) method of the model and input data. Testing the quality of the DSM models was carried out using data withheld from model computations and expressed as OOB and R squared results, giving an estimate of the reliability of the model predictions. These results are supplied. Method 2: Statistical (quantitative) assessment of the spatial attribute output data presented as a raster of the attributes “reliability”. This used the 500 individual trees of the attributes RF models to generate 500 datasets of the attribute to estimate model reliability for each attribute. For continuous attributes the method for estimating reliability is the Coefficient of Variation. This data is supplied. Method 3: Collecting independent external validation site data combined with on-ground expert (qualitative) examination of outputs during validation field trips. Across each of the study areas a two week validation field trip was conducted using a new validation site set which was produced by a random sampling design based on conditioned Latin Hypercube sampling using the reliability data of the attribute. The modelled DSM attribute value was assessed against the actual on-ground value. These results are published in the report cited in this metadata record.

Pathogen diversity resulting in quasispecies can enable persistence and adaptation to host defenses and therapies. However, accurate quasispecies characterization can be impeded by errors introduced during sample handling and sequencing which can require extensive optimizations to overcome. We present complete laboratory and bioinformatics workflows to overcome many of these hurdles. The Pacific Biosciences single molecule real-time platform was used to sequence PCR amplicons derived from cDNA templates tagged with universal molecular identifiers (SMRT-UMI). Optimized laboratory protocols were developed through extensive testing of different sample preparation conditions to minimize between-template recombination during PCR and the use of UMI allowed accurate template quantitation as well as removal of point mutations introduced during PCR and sequencing to produce a highly accurate consensus sequence from each template. Handling of the large datasets produced from SMRT-UMI sequencing was facilitated by a novel bioinformatic pipeline, Probabilistic Offspring Resolver for Primer IDs (PORPIDpipeline), that automatically filters and parses reads by sample, identifies and discards reads with UMIs likely created from PCR and sequencing errors, generates consensus sequences, checks for contamination within the dataset, and removes any sequence with evidence of PCR recombination or early cycle PCR errors, resulting in highly accurate sequence datasets. The optimized SMRT-UMI sequencing method presented here represents a highly adaptable and established starting point for accurate sequencing of diverse pathogens. These methods are illustrated through characterization of human immunodeficiency virus (HIV) quasispecies. Methods This serves as an overview of the analysis performed on PacBio sequence data that is summarized in Analysis Flowchart.pdf and was used as primary data for the paper by Westfall et al. "Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations – application to HIV-1 quasispecies" Five different PacBio sequencing datasets were used for this analysis: M027, M2199, M1567, M004, and M005 For the datasets which were indexed (M027, M2199), CCS reads from PacBio sequencing files and the chunked_demux_config files were used as input for the chunked_demux pipeline. Each config file lists the different Index primers added during PCR to each sample. The pipeline produces one fastq file for each Index primer combination in the config. For example, in dataset M027 there were 3–4 samples using each Index combination. The fastq files from each demultiplexed read set were moved to the sUMI_dUMI_comparison pipeline fastq folder for further demultiplexing by sample and consensus generation with that pipeline. More information about the chunked_demux pipeline can be found in the README.md file on GitHub. The demultiplexed read collections from the chunked_demux pipeline or CCS read files from datasets which were not indexed (M1567, M004, M005) were each used as input for the sUMI_dUMI_comparison pipeline along with each dataset's config file. Each config file contains the primer sequences for each sample (including the sample ID block in the cDNA primer) and further demultiplexes the reads to prepare data tables summarizing all of the UMI sequences and counts for each family (tagged.tar.gz) as well as consensus sequences from each sUMI and rank 1 dUMI family (consensus.tar.gz). More information about the sUMI_dUMI_comparison pipeline can be found in the paper and the README.md file on GitHub. The consensus.tar.gz and tagged.tar.gz files were moved from sUMI_dUMI_comparison pipeline directory on the server to the Pipeline_Outputs folder in this analysis directory for each dataset and appended with the dataset name (e.g. consensus_M027.tar.gz). Also in this analysis directory is a Sample_Info_Table.csv containing information about how each of the samples was prepared, such as purification methods and number of PCRs. There are also three other folders: Sequence_Analysis, Indentifying_Recombinant_Reads, and Figures. Each has an .Rmd file with the same name inside which is used to collect, summarize, and analyze the data. All of these collections of code were written and executed in RStudio to track notes and summarize results. Sequence_Analysis.Rmd has instructions to decompress all of the consensus.tar.gz files, combine them, and create two fasta files, one with all sUMI and one with all dUMI sequences. Using these as input, two data tables were created, that summarize all sequences and read counts for each sample that pass various criteria. These are used to help create Table 2 and as input for Indentifying_Recombinant_Reads.Rmd and Figures.Rmd. Next, 2 fasta files containing all of the rank 1 dUMI sequences and the matching sUMI sequences were created. These were used as input for the python script compare_seqs.py which identifies any matched sequences that are different between sUMI and dUMI read collections. This information was also used to help create Table 2. Finally, to populate the table with the number of sequences and bases in each sequence subset of interest, different sequence collections were saved and viewed in the Geneious program. To investigate the cause of sequences where the sUMI and dUMI sequences do not match, tagged.tar.gz was decompressed and for each family with discordant sUMI and dUMI sequences the reads from the UMI1_keeping directory were aligned using geneious. Reads from dUMI families failing the 0.7 filter were also aligned in Genious. The uncompressed tagged folder was then removed to save space. These read collections contain all of the reads in a UMI1 family and still include the UMI2 sequence. By examining the alignment and specifically the UMI2 sequences, the site of the discordance and its case were identified for each family as described in the paper. These alignments were saved as "Sequence Alignments.geneious". The counts of how many families were the result of PCR recombination were used in the body of the paper. Using Identifying_Recombinant_Reads.Rmd, the dUMI_ranked.csv file from each sample was extracted from all of the tagged.tar.gz files, combined and used as input to create a single dataset containing all UMI information from all samples. This file dUMI_df.csv was used as input for Figures.Rmd. Figures.Rmd used dUMI_df.csv, sequence_counts.csv, and read_counts.csv as input to create draft figures and then individual datasets for eachFigure. These were copied into Prism software to create the final figures for the paper.

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.

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.

For use with UK Biobank data. v2: Change to scoring for AUDIT questionnaire. v3: Change to coding for exercise and cannabis use to accompany revised paper

This data and code archive provides all the data and code for replicating the empirical analysis that is presented in the journal article "A Ray-Based Input Distance Function to Model Zero-Valued Output Quantities: Derivation and an Empirical Application" authored by Juan José Price and Arne Henningsen and published in the Journal of Productivity Analysis (DOI: 10.1007/s11123-023-00684-1).

We conducted the empirical analysis with the "R" statistical software (version 4.3.0) using the add-on packages "combinat" (version 0.0.8), "miscTools" (version 0.6.28), "quadprog" (version 1.5.8), sfaR (version 1.0.0), stargazer (version 5.2.3), and "xtable" (version 1.8.4) that are available at CRAN. We created the R package "micEconDistRay" that provides the functions for empirical analyses with ray-based input distance functions that we developed for the above-mentioned paper. Also this R package is available at CRAN (https://cran.r-project.org/package=micEconDistRay).

This replication package contains the following files and folders:

README This file

MuseumsDk.csv The original data obtained from the Danish Ministry of Culture and from Statistics Denmark. It includes the following variables:

museum: Name of the museum.

type: Type of museum (Kulturhistorisk museum = cultural history museum; Kunstmuseer = arts museum; Naturhistorisk museum = natural history museum; Blandet museum = mixed museum).

munic: Municipality, in which the museum is located.

yr: Year of the observation.

units: Number of visit sites.

resp: Whether or not the museum has special responsibilities (0 = no special responsibilities; 1 = at least one special responsibility).

vis: Number of (physical) visitors.

aarc: Number of articles published (archeology).

ach: Number of articles published (cultural history).

aah: Number of articles published (art history).

anh: Number of articles published (natural history).

exh: Number of temporary exhibitions.

edu: Number of primary school classes on educational visits to the museum.

ev: Number of events other than exhibitions.

ftesc: Scientific labor (full-time equivalents).

ftensc: Non-scientific labor (full-time equivalents).

expProperty: Running and maintenance costs [1,000 DKK].

expCons: Conservation expenditure [1,000 DKK].

ipc: Consumer Price Index in Denmark (the value for year 2014 is set to 1).

prepare_data.R This R script imports the data set MuseumsDk.csv, prepares it for the empirical analysis (e.g., removing unsuitable observations, preparing variables), and saves the resulting data set as DataPrepared.csv.

DataPrepared.csv This data set is prepared and saved by the R script prepare_data.R. It is used for the empirical analysis.

make_table_descriptive.R This R script imports the data set DataPrepared.csv and creates the LaTeX table /tables/table_descriptive.tex, which provides summary statistics of the variables that are used in the empirical analysis.

IO_Ray.R This R script imports the data set DataPrepared.csv, estimates a ray-based Translog input distance functions with the 'optimal' ordering of outputs, imposes monotonicity on this distance function, creates the LaTeX table /tables/idfRes.tex that presents the estimated parameters of this function, and creates several figures in the folder /figures/ that illustrate the results.

IO_Ray_ordering_outputs.R This R script imports the data set DataPrepared.csv, estimates a ray-based Translog input distance functions, imposes monotonicity for each of the 720 possible orderings of the outputs, and saves all the estimation results as (a huge) R object allOrderings.rds.

allOrderings.rds (not included in the ZIP file, uploaded separately) This is a saved R object created by the R script IO_Ray_ordering_outputs.R that contains the estimated ray-based Translog input distance functions (with and without monotonicity imposed) for each of the 720 possible orderings.

IO_Ray_model_averaging.R This R script loads the R object allOrderings.rds that contains the estimated ray-based Translog input distance functions for each of the 720 possible orderings, does model averaging, and creates several figures in the folder /figures/ that illustrate the results.

/tables/ This folder contains the two LaTeX tables table_descriptive.tex and idfRes.tex (created by R scripts make_table_descriptive.R and IO_Ray.R, respectively) that provide summary statistics of the data set and the estimated parameters (without and with monotonicity imposed) for the 'optimal' ordering of outputs.

/figures/ This folder contains 48 figures (created by the R scripts IO_Ray.R and IO_Ray_model_averaging.R) that illustrate the results obtained with the 'optimal' ordering of outputs and the model-averaged results and that compare these two sets of results.

This dataset contains Australian Community Climate and Earth-System Simulator (ACCESS) Numerical Weather Prediction (NWP) model pressure data from the High Altitude Ice Crystals - High Ice Water Content (HAIC-HIWC) project that took place in Darwin, Australia. The data is from the Australian Bureau of Meteorology (BoM) and is in digital gridded binary format netCDF files. The files are grouped into .tar files by day.

A machine learning streamflow (MLFLOW) model was developed in R (model is in the Rscripts folder) for modeling monthly streamflow from 2012 to 2017 in three watersheds on the Wyoming Range in the upper Green River basin. Geospatial information for 125 site features (vector data are in the Sites.shp file) and discrete streamflow observation data and environmental predictor data were used in fitting the MLFLOW model and predicting with the fitted model. Tabular calibration and validation data are in the Model_Fitting_Site_Data.csv file, totaling 971 discrete observations and predictions of monthly streamflow. Geospatial information for 17,518 stream grid cells (raster data are in the Streams.tif file) and environmental predictor data were used for continuous streamflow predictions with the MLFLOW model. Tabular prediction data for all the study area (17,518 stream grid cells) and study period (72 months; 2012–17) are in the Model_Prediction_Stream_Data.csv file, totaling 1,261,296 p ...

Reddit: /r/technology (Submissions & Comments)

Title, Score, ID, URL, Comment Number, and Timestamp

By Reddit [source]

About this dataset

This dataset, labeled as Reddit Technology Data, provides thorough insights into the conversations and interactions around technology-related topics shared on Reddit – a well-known Internet discussion forum. This dataset contains titles of discussions, scores as contributed by users on Reddit, the unique IDs attributed to different discussions, URLs of those hidden discussions (if any), comment counts in each discussion thread and timestamps of when those conversations were initiated. As such, this data is supremely valuable for tech-savvy people wanting to stay up to date with the new developments in their field or professionals looking to keep abreast with industry trends. In short, it is a repository which helps people make sense and draw meaning out of what’s happening in the technology world at large - inspiring action on their part or simply educating them about forthcoming changes

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For more datasets, click here.

Featured Notebooks

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How to use the dataset

The dataset includes six columns containing title, score, url address link to the discussion page on Reddit itself ,comment count ,created time stamp meaning when was it posted/uploaded/communicated and body containing actual text written regarding that particular post/discussion. By separately analyzing each column it can be made out what type information user require in regard with various aspects related to technology based discussions. One can develop hypothesis about correlations between different factors associated with rating or comment count by separate analysis within those columns themselves like discuss what does people comment or react mostly upon viewing which type of post inside reddit ? Does high rating always come along with extremely long comments.? And many more .By researching this way one can discover real facts hidden behind social networking websites such as reddit which contains large amount of rich information regarding user’s interest in different topics related to tech gadgets or otherwise .We can analyze different trends using voice search technology etc in order visualize users overall reaction towards any kind of information shared through public forums like stack overflow sites ,facebook posts etc .These small instances will allow us gain heavy insights for research purpose thereby providing another layer for potential business opportunities one may benefit from over a given period if not periodcally monitored .

Research Ideas

• Companies can use this dataset to create targeted online marketing campaigns directed towards Reddit users interested in specific areas of technology.
• Academic researchers can use the data to track and analyze trends in conversations related to technology on Reddit over time.
• Technology professionals can utilize the comments and discussions on this dataset as a way of gauging public opinion and consumer sentiment towards certain technological advancements or products

Acknowledgements

If you use this dataset in your research, please credit the original authors. Data Source

License

License: CC0 1.0 Universal (CC0 1.0) - Public Domain Dedication No Copyright - You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. See Other Information.

Columns

File: technology.csv | Column name | Description | |:--------------|:--------------------------------------------------------------------------| | title | The title of the discussion. (String) | | score | The score of the discussion as measured by Reddit contributors. (Integer) | | url | The website URL associated with the discussion. (String) | | comms_num | The number of comments associated with the discussion. (Integer) | | created | The date and time the discussion was created. (DateTime) | | body | The body content of the discussion. (String) | | timestamp | The timestamp of the discussion. (Integer) |

Acknowledgements

If you use this dataset in your research, please credit the original authors. If you use this dataset in your research, please credit Reddit.