Question Paper Solutions of chapter Subsetting of Data Analysis with R, 2nd Semester , Bachelor of Computer Application 2023-2024

This dataset provides geospatial location data and scripts used to analyze the relationship between MODIS-derived NDVI and solar and sensor angles in a pinyon-juniper ecosystem in Grand Canyon National Park. The data are provided in support of the following publication: "Solar and sensor geometry, not vegetation response, drive satellite NDVI phenology in widespread ecosystems of the western United States". The data and scripts allow users to replicate, test, or further explore results. The file GrcaScpnModisCellCenters.csv contains locations (latitude-longitude) of all the 250-m MODIS (MOD09GQ) cell centers associated with the Grand Canyon pinyon-juniper ecosystem that the Southern Colorado Plateau Network (SCPN) is monitoring through its land surface phenology and integrated upland monitoring programs. The file SolarSensorAngles.csv contains MODIS angle measurements for the pixel at the phenocam location plus a random 100 point subset of pixels within the GRCA-PJ ecosystem. The script files (folder: 'Code') consist of 1) a Google Earth Engine (GEE) script used to download MODIS data through the GEE javascript interface, and 2) a script used to calculate derived variables and to test relationships between solar and sensor angles and NDVI using the statistical software package 'R'. The file Fig_8_NdviSolarSensor.JPG shows NDVI dependence on solar and sensor geometry demonstrated for both a single pixel/year and for multiple pixels over time. (Left) MODIS NDVI versus solar-to-sensor angle for the Grand Canyon phenocam location in 2018, the year for which there is corresponding phenocam data. (Right) Modeled r-squared values by year for 100 randomly selected MODIS pixels in the SCPN-monitored Grand Canyon pinyon-juniper ecosystem. The model for forward-scatter MODIS-NDVI is log(NDVI) ~ solar-to-sensor angle. The model for back-scatter MODIS-NDVI is log(NDVI) ~ solar-to-sensor angle + sensor zenith angle. Boxplots show interquartile ranges; whiskers extend to 10th and 90th percentiles. The horizontal line marking the average median value for forward-scatter r-squared (0.835) is nearly indistinguishable from the back-scatter line (0.833). The dataset folder also includes supplemental R-project and packrat files that allow the user to apply the workflow by opening a project that will use the same package versions used in this study (eg, .folders Rproj.user, and packrat, and files .RData, and PhenocamPR.Rproj). The empty folder GEE_DataAngles is included so that the user can save the data files from the Google Earth Engine scripts to this location, where they can then be incorporated into the r-processing scripts without needing to change folder names. To successfully use the packrat information to replicate the exact processing steps that were used, the user should refer to packrat documentation available at https://cran.r-project.org/web/packages/packrat/index.html and at https://www.rdocumentation.org/packages/packrat/versions/0.5.0. Alternatively, the user may also use the descriptive documentation phenopix package documentation, and description/references provided in the associated journal article to process the data to achieve the same results using newer packages or other software programs.

The Sloan Digital Sky Survey (SDSS) is a comprehensive survey of the northern sky. This dataset contains a subset of this survey, of 60247 objects classified as galaxies, it includes a CSV file with a collection of information and a set of files for each object, namely JPG image files, FITS and spectra data. This dataset is used to train and explore the astromlp-models collection of deep learning models for galaxies characterisation.

The dataset includes a CSV data file where each row is an object from the SDSS database, and with the following columns (note that some data may not be available for all objects):

• objid: unique SDSS object identifier
• mjd: MJD of observation
• plate: plate identifier
• tile: tile identifier
• fiberid: fiber identifier
• run: run number
• rerun: rerun number
• camcol: camera column
• field: field number
• ra: right ascension
• dec: declination
• class: spectroscopic class (only objetcs with GALAXY are included)
• subclass: spectroscopic subclass
• modelMag_u: better of DeV/Exp magnitude fit for band u
• modelMag_g: better of DeV/Exp magnitude fit for band g
• modelMag_r: better of DeV/Exp magnitude fit for band r
• modelMag_i: better of DeV/Exp magnitude fit for band i
• modelMag_z: better of DeV/Exp magnitude fit for band z
• redshift: final redshift from SDSS data z
• stellarmass: stellar mass extracted from the eBOSS Firefly catalog
• w1mag: WISE W1 "standard" aperture magnitude
• w2mag: WISE W2 "standard" aperture magnitude
• w3mag: WISE W3 "standard" aperture magnitude
• w4mag: WISE W4 "standard" aperture magnitude
• gz2c_f: Galaxy Zoo 2 classification from Willett et al 2013
• gz2c_s: simplified version of Galaxy Zoo 2 classification (labels set)

Besides the CSV file a set of directories are included in the dataset, in each directory you'll find a list of files named after the objid column from the CSV file, with the corresponding data, the following directories tree is available:

sdss-gs/
├── data.csv
├── fits
├── img
├── spectra
└── ssel

Where, each directory contains:

• img: RGB images from the object in JPEG format, 150x150 pixels, generated using the SkyServer DR16 API
• fits: FITS data subsets around the object across the u, g, r, i, z bands; cut is done using the ImageCutter library
• spectra: full best fit spectra data from SDSS between 4000 and 9000 wavelengths
• ssel: best fit spectra data from SDSS for specific selected intervals of wavelengths discussed by Sánchez Almeida 2010

Changelog

• v0.0.3 - Increase number of objects to ~80k.
• v0.0.2 - Increase number of objects to ~60k.
• v0.0.1 - Initial import.

This is a clean subset of the data that was created by the OpenML R Bot that executed benchmark experiments on binary classification task of the OpenML100 benchmarking suite with six R algorithms: glmnet, rpart, kknn, svm, ranger and xgboost. The hyperparameters of these algorithms were drawn randomly. In total it contains more than 2.6 million benchmark experiments and can be used by other researchers. The subset was created by taking 500000 results of each learner (except of kknn for which only 1140 results are available). The csv-file for each learner is a table that for each benchmark experiment has a row that contains: OpenML-Data ID, hyperparameter values, performance measures (AUC, accuracy, brier score), runtime, scimark (runtime reference of the machine), and some meta features of the dataset.OpenMLRandomBotResults.RData (format for R) contains all data in seperate tables for the results, the hyperparameters, the meta features, the runtime, the scimark results and reference results.

Source Code for the manuscript "Characterizing Variability and Uncertainty for Parameter Subset Selection in PBPK Models" -- This R code generates the results presented in this manuscript; the zip folder contains PBPK model files (for chloroform and DCM) and corresponding scripts to compile the models, generate human equivalent doses, and run sensitivity analysis.

Context

To make this a seamless process, I cleaned the data and delete many variables that I thought were not important to our dataset. I then uploaded all of those files to Kaggle for each of you to download. The rideshare_data has both lyft and uber but it is still a cleaned version from the dataset we downloaded from Kaggle.

Use of Data Files

You can easily subset the data into the car types that you will be modeling by first loading the csv into R, here is the code for how you do this:

This loads the file into R

df<-read.csv('uber.csv')

The next codes is to subset the data into specific car types. The example below only has Uber 'Black' car types.

df_black<-subset(uber_df, uber_df$name == 'Black')

This next portion of code will be to load it into R. First, we must write this dataframe into a csv file on our computer in order to load it into R.

write.csv(df_black, "nameofthefileyouwanttosaveas.csv")

The file will appear in you working directory. If you are not familiar with your working directory. Run this code:

getwd()

The output will be the file path to your working directory. You will find the file you just created in that folder.

Inspiration

Your data will be in front of the world's largest data science community. What questions do you want to see answered?

This code is not mine. The dataset provided here is a balanced subset derived from the original dataset, and I do not claim ownership over the original data.

The CODE dataset was collected by the Telehealth Network of Minas Gerais (TNMG) in the period between 2010 and 2016. TNMG is a public telehealth system assisting 811 out of the 853 municipalities in the state of Minas Gerais, Brazil.

The CODE 15% dataset is obtained from stratified sampling from the CODE dataset. This subset of the CODE dataset is described in and used for assessing model performance:

"Deep neural network estimated electrocardiographic-age as a mortality predictor"
Emilly M Lima, Antônio H Ribeiro, Gabriela MM Paixão, Manoel Horta Ribeiro, Marcelo M Pinto Filho, Paulo R Gomes, Derick M Oliveira, Ester C Sabino, Bruce B Duncan, Luana Giatti, Sandhi M Barreto, Wagner Meira Jr, Thomas B Schön, Antonio Luiz P Ribeiro. MedRXiv (2021) https://www.doi.org/10.1101/2021.02.19.21251232

This dataset is a subset of the CODE 15% dataset obtained by random sampling from the negative class while maintaining all the observations of the positive class to create a balanced dataset without the need to focus on class imbalance.

The code15_hdf5 folder contains the exams and labels for the entire CODE 15% dataset. The code15_wfdb folder contains the exam records file in .dat format.

An additional file (signals_features.csv) is provided, containing handcrafted features from the ECG records (lead II) related to P, Q, R, S, and T waves. Features such as P wave duration, PR interval, PR segment, QRS duration, ST segment, and ST slope were computed by first extracting all the points using the neurokit2 Python library and then aggregated for each record ID using descriptive statistics. Heart rate variability features were also included along with the P, Q, R, S, and T waves.

Link to the original dataset: https://doi.org/10.5281/zenodo.4916206

This dataset is provided in support of the following publication: "Solar and sensor geometry, not vegetation response, drive satellite NDVI phenology in widespread ecosystems of the western United States". The data and code provided allow users to replicate, test, or further explore results. The dataset includes 2 raster datasets (folder:Rasters): 1) 'cntWinterPks2003_2018DR' provides a count of years with winter peaks from 2003-2018 in an 11-state area in the western United States. 2) 'VegClassGte5_2003_2018' raster, within the zip file 'WinterPeaksVegTypes.zip' identifies the broad vegetation types for locations with common winter peaks (5 or more years out of 16). The dataset also includes Google Earth Engine and R code files used to create the datasets. Additional files/folders provided include 1) Google Earth Engine scripts used to download MODIS data the GEE - javascript interface (folder: 'Code'). 2) Scripts used to manipulate rasters and to calculate and map the occurrence winter NDVI peaks from 2003-2018 using the statistical software package 'R'. 3) Supplemental R-project and packrat files that allow the user to apply the workflow by opening a project that will use the same package versions used in this study, for example the folders 'Rproj.user', and 'packrat', and files '.RData', and 'WinterPeakExtentPR.Rproj'. 4) Empty folders ('GEE_DataAnnPeak', 'GEE_DataLoose', and 'GEE_DataStrict') that should be used to contain the output from the GEE code files as follows: 'GEE_DataAnnPeak' should contain output from the S3 and S4 scripts, 'GEE_DataLoose' should contain output from the S1 script, and 'GEE_DataStrict' should contain output from the S2 script. 5) Graphic file 'Fig_9_MapsOfExtentPortrait2.jpg' shows temporal and ecosystem distribution of winter NDVI peaks in the western continental US, 2003 to 2018, derived from MODIS MCD43A4 product. TOP: Number of years with winter peaks in areas that meet defined thresholds for biomass (median annual peak NDVI >= 0.15) and temperature (mean December minimum daily temperature <= 0°C). BOTTOM: Predominant LANDFIRE Existing Vegetation Type physiognomy (i.e., mode of each 500-m MODIS pixel) in areas with >= 5 years of winter peaks. Present in lesser proportions but not identified on the map for legibility reasons are conifer-hardwood, exotics, riparian, and sparsely vegetated physiognomic categories as well as non-natural/non-terrestrial ecosystem categories. State abbreviations are AZ (Arizona), CA (California), CO (Colorado), ID (Idaho), MT (Montana), NV (Nevada), NM (New Mexico), OR (Oregon), WA (Washington), and WY (Wyoming). The final steps of overlaying common winter peak extent data on the Landfire data were done using ArcGIS and the publicly available Landfire dataset (see source datasets section of metadata and process steps). To successfully use the packrat information to replicate the exact processing steps that were used, the user should refer to packrat documentation available at https://cran.r-project.org/web/packages/packrat/index.html and at https://www.rdocumentation.org/packages/packrat/versions/0.5.0. Alternatively, the user may also use the descriptive documentation within this metadata along with the workflow described in the associated journal article to process the data to achieve the same results using newer packages or other software programs.

Self-citation analysis data based on PubMed Central subset (2002-2005) ---------------------------------------------------------------------- Created by Shubhanshu Mishra, Brent D. Fegley, Jana Diesner, and Vetle Torvik on April 5th, 2018 ## Introduction This is a dataset created as part of the publication titled: Mishra S, Fegley BD, Diesner J, Torvik VI (2018) Self-Citation is the Hallmark of Productive Authors, of Any Gender. PLOS ONE. It contains files for running the self citation analysis on articles published in PubMed Central between 2002 and 2005, collected in 2015. The dataset is distributed in the form of the following tab separated text files: * Training_data_2002_2005_pmc_pair_First.txt (1.2G) - Data for first authors * Training_data_2002_2005_pmc_pair_Last.txt (1.2G) - Data for last authors * Training_data_2002_2005_pmc_pair_Middle_2nd.txt (964M) - Data for middle 2nd authors * Training_data_2002_2005_pmc_pair_txt.header.txt - Header for the data * COLUMNS_DESC.txt file - Descriptions of all columns * model_text_files.tar.gz - Text files containing model coefficients and scores for model selection. * results_all_model.tar.gz - Model coefficient and result files in numpy format used for plotting purposes. v4.reviewer contains models for analysis done after reviewer comments. * README.txt file ## Dataset creation Our experiments relied on data from multiple sources including properitery data from Thompson Rueter's (now Clarivate Analytics) Web of Science collection of MEDLINE citations. Author's interested in reproducing our experiments should personally request from Clarivate Analytics for this data. However, we do make a similar but open dataset based on citations from PubMed Central which can be utilized to get similar results to those reported in our analysis. Furthermore, we have also freely shared our datasets which can be used along with the citation datasets from Clarivate Analytics, to re-create the datased used in our experiments. These datasets are listed below. If you wish to use any of those datasets please make sure you cite both the dataset as well as the paper introducing the dataset. * MEDLINE 2015 baseline: https://www.nlm.nih.gov/bsd/licensee/2015_stats/baseline_doc.html * Citation data from PubMed Central (original paper includes additional citations from Web of Science) * Author-ity 2009 dataset: - Dataset citation: Torvik, Vetle I.; Smalheiser, Neil R. (2018): Author-ity 2009 - PubMed author name disambiguated dataset. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4222651_V1 - Paper citation: Torvik, V. I., & Smalheiser, N. R. (2009). Author name disambiguation in MEDLINE. ACM Transactions on Knowledge Discovery from Data, 3(3), 1–29. https://doi.org/10.1145/1552303.1552304 - Paper citation: Torvik, V. I., Weeber, M., Swanson, D. R., & Smalheiser, N. R. (2004). A probabilistic similarity metric for Medline records: A model for author name disambiguation. Journal of the American Society for Information Science and Technology, 56(2), 140–158. https://doi.org/10.1002/asi.20105 * Genni 2.0 + Ethnea for identifying author gender and ethnicity: - Dataset citation: Torvik, Vetle (2018): Genni + Ethnea for the Author-ity 2009 dataset. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9087546_V1 - Paper citation: Smith, B. N., Singh, M., & Torvik, V. I. (2013). A search engine approach to estimating temporal changes in gender orientation of first names. In Proceedings of the 13th ACM/IEEE-CS joint conference on Digital libraries - JCDL ’13. ACM Press. https://doi.org/10.1145/2467696.2467720 - Paper citation: Torvik VI, Agarwal S. Ethnea -- an instance-based ethnicity classifier based on geo-coded author names in a large-scale bibliographic database. International Symposium on Science of Science March 22-23, 2016 - Library of Congress, Washington DC, USA. http://hdl.handle.net/2142/88927 * MapAffil for identifying article country of affiliation: - Dataset citation: Torvik, Vetle I. (2018): MapAffil 2016 dataset -- PubMed author affiliations mapped to cities and their geocodes worldwide. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4354331_V1 - Paper citation: Torvik VI. MapAffil: A Bibliographic Tool for Mapping Author Affiliation Strings to Cities and Their Geocodes Worldwide. D-Lib magazine : the magazine of the Digital Library Forum. 2015;21(11-12):10.1045/november2015-torvik * IMPLICIT journal similarity: - Dataset citation: Torvik, Vetle (2018): Author-implicit journal, MeSH, title-word, and affiliation-word pairs based on Author-ity 2009. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4742014_V1 * Novelty dataset for identify article level novelty: - Dataset citation: Mishra, Shubhanshu; Torvik, Vetle I. (2018): Conceptual novelty scores for PubMed articles. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5060298_V1 - Paper citation: Mishra S, Torvik VI. Quantifying Conceptual Novelty in the Biomedical Literature. D-Lib magazine : The Magazine of the Digital Library Forum. 2016;22(9-10):10.1045/september2016-mishra - Code: https://github.com/napsternxg/Novelty * Expertise dataset for identifying author expertise on articles: * Source code provided at: https://github.com/napsternxg/PubMed_SelfCitationAnalysis Note: The dataset is based on a snapshot of PubMed (which includes Medline and PubMed-not-Medline records) taken in the first week of October, 2016. Check here for information to get PubMed/MEDLINE, and NLMs data Terms and Conditions Additional data related updates can be found at Torvik Research Group ## Acknowledgments This work was made possible in part with funding to VIT from NIH grant P01AG039347 and NSF grant 1348742. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ## License Self-citation analysis data based on PubMed Central subset (2002-2005) by Shubhanshu Mishra, Brent D. Fegley, Jana Diesner, and Vetle Torvik is licensed under a Creative Commons Attribution 4.0 International License. Permissions beyond the scope of this license may be available at https://github.com/napsternxg/PubMed_SelfCitationAnalysis.

Question Paper Solutions of chapter Loop Functions of Data Analysis with R, 2nd Semester , Bachelor of Computer Application 2023-2024

Remarks on kernels and bandwidth selection for semiparametric density product estimator method. (DOC)

Abstract: These are results from a network of 65 tree census plots in Panama. At each, every individual stem in a rectangular area of specified size is given a unique number and identified to species, then stem diameter measured in one or more censuses. Data from these numerous plots and inventories were collected following the same methods as, and species identity harmonized with, the 50-ha long-term tree census at Barro Colorado Island. Precise location of every site, elevation, and estimated rainfall (for many sites) are also included. These data were gathered over many years, starting in 1994 and continuing to the present, by principal investigators R. Condit, R. Perez, S. Lao, and S. Aguilar. Funding has been provided by many organizations.Description:marenaRecent.full.Rdata5Jan2013.zip: A zip archive holding one R Analytical Table, a version of the Marena plots' census data in R format, designed for data analysis. This and all other tables labelled 'full' have one record per individual tree found in that census. Detailed documentations of the 'full' tables is given in RoutputFull.pdf (see component 10 below); an additional column 'plot' is included because the table includes records from many different locations. Plot coordinates are given in PanamaPlot.txt (component 12 below). This one file, 'marenaRecent.full1.rdata', has data from the latest census at 60 different plots. These are the best data to use if only a single plot census is needed. marena2cns.full.Rdata5Jan2013.zip: R Analytical Tables of the style 'full' for 44 plots with two censuses: 'marena2cns.full1.rdata' for the first census and 'marena2cns.full2.rdata' for the second census. These 44 plots are a subset of the 60 found in marenaRecent.full (component 1): the 44 that have been censused two or more times. These are the best data to use if two plot censuses are needed. marena3cns.full.Rdata5Jan2013.zip. R Analytical Tables of the style 'full' for nine plots with three censuses: 'marena3cns.full1.rdata' for the first census through 'marena2cns.full3.rdata' for the third census. These nine plots are a subset of the 44 found in marena2cns.full (component 2): the nine that have been censused three or more times. These are the best data to use if three plot censuses are needed. marena4cns.full.Rdata5Jan2013.zip. R Analytical Tables of the style 'full' for six plots with four censuses: 'marena4cns.full1.rdata' for the first census through 'marena4cns.full4.rdata' for the fourth census. These six plots are a subset of the nine found in marena3cns.full (component 3): the six that have been censused four or more times. These are the best data to use if four plot censuses are needed. marenaRecent.stem.Rdata5Jan2013.zip. A zip archive holding one R Analytical Table, a version of the Marena plots' census data in R format. These are designed for data analysis. This one file, 'marenaRecent.full1.rdata', has data from the latest census at 60 different plots. The table has one record per individual stem, necessary because some individual trees have more than one stem. Detailed documentations of these tables is given in RoutputFull.pdf (see component 11 below); an additional column 'plot' is included because the table includes records from many different locations. Plot coordinates are given in PanamaPlot.txt (component 12 below). These are the best data to use if only a single plot census is needed, and individual stems are desired. marena2cns.stem.Rdata5Jan2013.zip. R Analytical Tables of the style 'stem' for 44 plots with two censuses: 'marena2cns.stem1.rdata' for the first census and 'marena3cns.stem2.rdata' for the second census. These 44 plots are a subset of the 60 found in marenaRecent.stem (component 1): the 44 that have been censused two or more times. These are the best data to use if two plot censuses are needed, and individual stems are desired. marena3cns.stem.Rdata5Jan2013.zip. R Analytical Tables of the style 'stem' for nine plots with three censuses: 'marena3cns.stem1.rdata' for the first census through 'marena3cns.stem3.rdata' for the third census. These nine plots are a subset of the 44 found in marena2cns.stem (component 6): the nine that have been censused three or more times. These are the best data to use if three plot censuses are needed, and individual stems are desired. marena4cns.stem.Rdata5Jan2013.zip. R Analytical Tables of the style 'stem' for six plots with four censuses: 'marena3cns.stem1.rdata' for the first census through 'marena3cns.stem3.rdata' for the third census. These six plots are a subset of the nine found in marena3cns.stem (component 7): the six that have been censused four or more times. These are the best data to use if four plot censuses are needed, and individual stems are desired. bci.spptable.rdata. A list of the 1414 species found across all tree plots and inventories in Panama, in R format. The column 'sp' in this table is a code identifying the species in the full census tables (marena.full and marena.stem, components 1-4 and 5-8 above). RoutputFull.pdf: Detailed documentation of the 'full' tables in Rdata format (components 1-4 above). RoutputStem.pdf: Detailed documentation of the 'stem' tables in Rdata format (component 5-8 above). PanamaPlot.txt: Locations of all tree plots and inventories in Panama.

This is a subset of the W2S dataset: Zhou, R., El Helou, M., Sage, D., Laroche, T., Seitz, A., Süsstrunk, S. (2020). W2S: Microscopy Data with Joint Denoising and Super-Resolution for Widefield to SIM Mapping. In: Bartoli, A., Fusiello, A. (eds) Computer Vision – ECCV 2020 Workshops. ECCV 2020. Lecture Notes in Computer Science(), vol 12535. Springer, Cham. https://doi.org/10.1007/978-3-030-66415-2_31

The selected subset contains 120 images with three channels, acquired using a conventional fluorescence widefield, in the form of a single multi-channel tiff file.

Code, data, and a copy of the original paper is available at https://github.com/IVRL/w2s

AI4Life has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement number 101057970. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.

Data from the IFLS, merged across waves, most outcomes taken from wave 5. Includes birth order, family structure, Big 5 Personality, intelligence tests, and risk lotteries

Table of variables

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

[truncated]

Note

This dataset was automatically described using the codebook R package (version 0.8.2).

Dataset

This dataset contains the data used for the publication:

Jia, T., de Vries, R., Kapelan, Z., van Emmerik, T. H., & Taormina, R. (2024). Detecting floating litter in freshwater bodies with semi-supervised deep learning. Water Research, 266, 122405. https://doi.org/10.1016/j.watres.2024.122405

This dataset is a subset of the large-scale "TU Delft - Green Village" (TUD-GV), which includes 9,473 RGB images. More details on the TUD-GV dataset can be found at: https://doi.org/10.5281/zenodo.7636124. This subset used in this publication consists of 1,501 images, selected from the full TUD-GV dataset. All floating litter items in this subset have been annotated with bounding boxes. This subset is specifically for detecting floating litter in object detection tasks.

The 1,501 images are stored in the images.zip file, the annotations are stored in the labels_txt.zip file, and the class of the annotation (i.e., litter) is stored in the classes.txt file.

Cite this dataset

If you use this dataset for a publication, please cite the paper. Here is a BibTeX entry:

@article{jia2024detecting,
 title={Detecting floating litter in freshwater bodies with semi-supervised deep learning},
 author={Jia, Tianlong and de Vries, Rinze and Kapelan, Zoran and van Emmerik, Tim HM and Taormina, Riccardo},
 journal={Water Research},
 volume={266},
 pages={122405},
 year={2024},
 publisher={Elsevier}
}

Computational times, in seconds (rounded unless less than 1 second), for the four methods of the R package parallelMCMCcombine, using simulation data and T = 50,000 MCMC samples. The values in parentheses are for our example data sets; d = 2, M = 5 is for the Gamma model, and d = 5, M = 10 is for the logistic model. The results are based on a computer with operating system Windows 7 and an Intel Celeron 1007U CPU 1.5 GHz Processor.Computational time (in seconds) for the four combining methods.

This dataset contains time series observations of surface-atmosphere exchanges of sensible heat (H) and latent heat (LE) and momentum (τ) measured at UKCEH eddy covariance flux observation sites during summer 2019. The dataset includes ancillary weather and soil physics observations made at each site. Eddy covariance (EC) and micrometeorological observations were collected using open-path eddy covariance systems. Flux, meteorological and soil physics observations were collected and processed using harmonised protocols across all sites. This work was supported by the Natural Environment Research Council award number NE/R016429/1 as part of the UK-SCAPE programme delivering National Capability.

This dataset provides calculated camera-NDVI data for individual regions-of-interest (ROI's) for the phenocam named 'GRCA1PJ' (part of the Phenocam Network, https://phenocam.sr.unh.edu/webcam/). The GRCA1PJ phenocam is within a pinyon-juniper woodland in Grand Canyon National Park. Camera-NDVI refers to a modified version of NDVI calculated by the phenopix package (Filippa et al., 2016). The camera-calculated NDVI data are in the folder FinalOutput. File attributes within that folder are described in detail in the entity and attribute information section of this metadata. It should be possible for the user to use only the ROI definitions, image data downloaded from the phenocam network, and the phenopix R-package to reproduce the final NDVI dataset. However, the dataset also contains scripts and intermediate files that may be helpful in reproducing or extending the processing, but are not essential to reproducing the data. The complete dataset release includes 1) A workflow spreadsheet file that describes the processing steps, associated scripts, and output filenames (filename:Workflow_With_Filenames.ods). 2) R-code script files used in processing (folder:'Code'). 3) ROI boundary files and jpg images for the ROIs presented in the linked publication. (folder:"Phenocamdata/grca1pj/ROI") 4) Ancillary files used to create the NDVI dataset; these include exposure coordinates and training files (folder:'Phenocamdata/grca1pj/Ancillary'). 5) Files listing exposures for individual photos within the initial processing time period (folder:'Exposures'). 6) Screening parameters for cloud and poor-light-condition screening of photos, as well as a list of photos that meet the cloud-screening standards (folder:'Phenocamdata/grca1pj/BlueSkyScreening'). 7) Vegetation index files produced by the phenopix package, organized by ROI and month-year group (folder:"Phenocamdata/grca1pj/VI_Tables"). 8) Supplemental R-project and packrat files that allow the user to apply the workflow by opening a project that will use the same package versions used in this study (eg, .folders Rproj.user, and packrat, and files .RData, and PhenocamPR.Rproj). 9) The graphic 'Fig_4_ROIWithLabels.jpg' shows the phenocam field of view with labelled ROIs. outline colors correspond to juniper (red), pinyon (blue), 238 and other species (yellow). Labels correspond to NDVI curves in 'Fig_7_PhenocamCurves.JPG', (also included in this data release). The composite area comprises the field of view beneath the approximate horizon line labelled ‘J’ (gray). This image corresponds to Figure 4 in the associated journal article. 10) The graphic 'Fig_7_PhenocamCurves.JPG' shows NDVI curves derived from phenocam images from September 2017 - December 2018 for individual regions of interest (ROIs). Letter designations correspond to ROI labels in Fig_4_ROIWithLabels.jpg (also included in this data release). Data were screened to remove cloudy photos during Aqua and Terra flyover hours. Black ellipses indicate times when the ROI target vegetation was shaded. Red ellipses indicate times when the background of the ROI was shaded. To improve visibility, the Y axis is restricted and excludes 37 extreme values out of a total of 6698 values. The exposure adjustment method used by the phenopix package produces NDVI values that have a strong linear correlation with spectroradiometer-derived NDVI but are negatively shifted so that vegetated areas often have NDVI values below zero. This image corresponds to Figure 7 in the associated journal article. The file types .Rdata or .rds are commonly used in this release because these are the types created by the phenopix processing package, and these files will be needed (or the user will need to recreate new versions) for further processing. The scripts enable the user to replicate processing or to extend it to different times or areas of interest; however, these scripts require as additional input phenocam imagery that the user must download. To successfully use the packrat information to replicate the exact processing steps that were used, the user should refer to packrat documentation available at https://cran.r-project.org/web/packages/packrat/index.html and at https://www.rdocumentation.org/packages/packrat/versions/0.5.0. Alternatively, the user may also use the descriptive documentation phenopix package documentation, and description/references provided in the associated journal article to process the data to achieve the same results using newer packages or other software programs. Species-specific phenological curves included in the NDVI output section this dataset: Juniperus osteosperma, Pinus edulis, Purshia stansburiana, Artemisia tridentata, and Chamaebatiaria millefolium

The Dutch CELEX data is derived from R.H. Baayen, R. Piepenbrock & L. Gulikers, The CELEX Lexical Database (CD-ROM), Release 2, Dutch Version 3.1, Linguistic Data Consortium, University of Pennsylvania, Philadelphia, PA, 1995.Apart from orthographic features, the CELEX database comprises representations of the phonological, morphological, syntactic and frequency properties of lemmata. For the Dutch data, frequencies have been disambiguated on the basis of the 42.4m Dutch Instituut voor Nederlandse Lexicologie text corpora.To make for greater compatibility with other operating systems, the databases have not been tailored to fit any particular database management program. Instead, the information is presented in a series of plain ASCII files, which can be queried with tools such as AWK and ICON. Unique identity numbers allow the linking of information from different files.This database can be divided into different subsets:· orthography: with or without diacritics, with or without word division positions, alternative spellings, number of letters/syllables;· phonology: phonetic transcriptions with syllable boundaries or primary and secondary stress markers, consonant-vowel patterns, number of phonemes/syllables, alternative pronunciations, frequency per phonetic syllable within words;· morphology: division into stems and affixes, flat or hierarchical representations, stems and their inflections;· syntax: word class, subcategorisations per word class;· frequency of the entries: disambiguated for homographic lemmata.

The zip-file contains the data and code accompanying the paper 'Effects of nutrient enrichment on freshwater macrophyte and invertebrate abundance: A meta-analysis'. Together, these files should allow for the replication of the results.

The 'raw_data' folder contains the 'MA_database.csv' file, which contains the extracted data from all primary studies that are used in the analysis. Furthermore, this folder contains the file 'MA_database_description.txt', which gives a description of each data column in the database.

The 'derived_data' folder contains the files that are produced by the R-scripts in this study and used for data analysis. The 'MA_database_processed.csv' and 'MA_database_processed.RData' files contain the converted raw database that is suitable for analysis. The 'DB_IA_subsets.RData' file contains the 'Individual Abundance' (IA) data subsets based on taxonomic group (invertebrates/macrophytes) and inclusion criteria. The 'DB_IA_VCV_matrices.RData' contains for all IA data subsets the variance-covariance (VCV) matrices. The 'DB_AM_subsets.RData' file contains the 'Total Abundance' (TA) and 'Mean Abundance' (MA) data subsets based on taxonomic group (invertebrates/macrophytes) and inclusion criteria.

The 'output_data' folder contains maps with the output data for each data subset (i.e. for each metric, taxonomic group and set of inclusion criteria). For each data subset, the map contains random effects selection results ('Results1_REsel_

The 'scripts' folder contains all R-scripts that we used for this study. The 'PrepareData.R' script takes the database as input and adjusts the file so that it can be used for data analysis. The 'PrepareDataIA.R' and 'PrepareDataAM.R' scripts make subsets of the data and prepare the data for the meta-regression analysis and mixed-effects regression analysis, respectively. The regression analyses are performed in the 'SelectModelsIA.R' and 'SelectModelsAM.R' scripts to calculate the regression model results for the IA metric and MA/TA metrics, respectively. These scripts require the 'RandomAndFixedEffects.R' script, containing the random and fixed effects parameter combinations, as well as the 'Functions.R' script. The 'CreateMap.R' script creates a global map with the location of all studies included in the analysis (figure 1 in the paper). The 'CreateForestPlots.R' script creates plots showing the IA data distribution for both taxonomic groups (figure 2 in the paper). The 'CreateHeatMaps.R' script creates heat maps for all metrics and taxonomic groups (figure 3 in the paper, figures S11.1 and S11.2 in the appendix). The 'CalculateStatistics.R' script calculates the descriptive statistics that are reported throughout the paper, and creates the figures that describe the dataset characteristics (figures S3.1 to S3.5 in the appendix). The 'CreateFunnelPlots.R' script creates the funnel plots for both taxonomic groups (figures S6.1 and S6.2 in the appendix) and performs Egger's tests. The 'CreateControlGraphs.R' script creates graphs showing the dependency of the nutrient response to control concentrations for all metrics and taxonomic groups (figures S10.1 and S10.2 in the appendix).

The 'figures' folder contains all figures that are included in this study.