GitHub topics: research-compendium

Repositories

ee-jackson/danum-gaps

:seedling: :deciduous_tree: Growth and survival of seedlings in secondary vs primary forest

Language: R - Size: 189 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0

Pakillo/template

A template for data analysis projects structured as R packages (or not)

Language: R - Size: 1.01 MB - Last synced at: about 20 hours ago - Pushed at: almost 4 years ago - Stars: 177 - Forks: 24

benmarwick/rrtools

rrtools: Tools for Writing Reproducible Research in R

Language: R - Size: 4.87 MB - Last synced at: about 12 hours ago - Pushed at: 7 months ago - Stars: 689 - Forks: 86

ee-jackson/wytham-hawthorn

:deciduous_tree: :cherry_blossom: Code from Jackson et al. (2025) Density-dependent effects on the reproductive ecology of trees in a temperate woodland.

Language: R - Size: 176 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 0

epiverse-trace/research-compendium

Language: R - Size: 15.4 MB - Last synced at: about 8 hours ago - Pushed at: 4 days ago - Stars: 1 - Forks: 0

xronos-ch/paper

Compendium of data and code accompanying our paper 'XRONOS: An Open Data Infrastructure for Archaeological Chronology'

Language: TeX - Size: 116 MB - Last synced at: 24 days ago - Pushed at: about 2 months ago - Stars: 3 - Forks: 0

nuest/sensebox-binder

A reproducible analysis of environmental data - from hardware to plot

Language: Jupyter Notebook - Size: 1.97 MB - Last synced at: about 2 months ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 1

openplantpathology/Reproducibility_in_Plant_Pathology

A systematic/quantitative review of articles, which provides a basis for identifying what has been done so far in the field of plant pathology research reproducibility and suggestions for ways to improving it.

Language: TeX - Size: 2.06 GB - Last synced at: about 22 hours ago - Pushed at: 10 months ago - Stars: 23 - Forks: 6

everhartlab/sclerotinia-366

Analysis for "Population structure and phenotypic variation of *Sclerotinia sclerotiorum* from dry bean (*Phaseolus vulgaris*) in the United States"

Language: Shell - Size: 165 MB - Last synced at: about 1 hour ago - Pushed at: about 7 years ago - Stars: 9 - Forks: 6

cboettig/noise-phenomena

:notebook: Ecology Letters review paper: Noise-driven phenomena in population biology

Language: TeX - Size: 5.52 MB - Last synced at: about 2 months ago - Pushed at: over 5 years ago - Stars: 51 - Forks: 9

annakrystalli/rrtools-repro-research

Tutorial on Reproducible Research in R with rrtools

Language: R - Size: 11.1 MB - Last synced at: 10 days ago - Pushed at: over 5 years ago - Stars: 18 - Forks: 8

annakrystalli/rrcompendium-complete

Complete example of compendium produced during rrtools: reproducible research in R workshop

Language: TeX - Size: 470 KB - Last synced at: 3 days ago - Pushed at: over 6 years ago - Stars: 5 - Forks: 0

FRBCesab/rcompendium

:package: Create a package or compendium structure

Language: R - Size: 7.01 MB - Last synced at: 4 days ago - Pushed at: 4 months ago - Stars: 39 - Forks: 9

jhollist/manuscriptPackage

Template for writing manuscripts as an R package

Language: R - Size: 324 KB - Last synced at: about 1 month ago - Pushed at: over 7 years ago - Stars: 56 - Forks: 17

SNARL1/cmr-analysis

Analysis of capture-mark-recapture data from populations of the endangered mountain yellow-legged frog.

Language: HTML - Size: 93.5 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

cboettig/nonparametric-bayes

:notebook: Non-parametric Bayesian Inference for Conservation Decisions

Language: TeX - Size: 20.6 MB - Last synced at: about 2 months ago - Pushed at: about 5 years ago - Stars: 45 - Forks: 12

mbjoseph/neuralecology

Code for the paper "Neural hierarchical models of ecological populations"

Language: Jupyter Notebook - Size: 13.3 MB - Last synced at: 27 days ago - Pushed at: over 2 years ago - Stars: 28 - Forks: 10

joeroe/WAsiaPaleoFloraENM

Compendium of data and code accompanying our paper 'Biogeography of crop progenitors and wild plant resources in the terminal Pleistocene and Early Holocene of West Asia, 14.7–8.3 ka'

Language: HTML - Size: 683 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

njahn82/hoa_ta_effects

Source code supplement for hybrid open access study

Language: TeX - Size: 33.2 MB - Last synced at: about 2 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0

joeroe/AzraqLEENFaunaMorphometry

Compendium of data and code accompanying our paper, 'Late Pleistocene-Holocene mammalian body size change in Jordan’s Azraq Basin: a case for climate driven species distribution shifts'

Language: HTML - Size: 81.8 MB - Last synced at: 3 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

benmarwick/2020-ZGD-stone-artifacts

Research compendium for 'New Evidence of Human Occupation in Southwest China Since 44,800 Years ago'

Language: HTML - Size: 34.2 MB - Last synced at: 3 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

pat-s/2019-feature-selection

Research project

Language: R - Size: 1010 MB - Last synced at: about 2 months ago - Pushed at: over 3 years ago - Stars: 27 - Forks: 11

cboettig/decisions-vs-transients

:notebook:

Language: TeX - Size: 202 MB - Last synced at: about 2 months ago - Pushed at: almost 5 years ago - Stars: 5 - Forks: 0

mbjoseph/wildfire-extremes

Spatiotemporal modeling of wildfire extremes

Language: HTML - Size: 3.46 MB - Last synced at: 3 months ago - Pushed at: over 5 years ago - Stars: 9 - Forks: 5

willvieira/ms_STM-managed

📓 Paper: Forest management could accelerate tree range shifts

Language: TeX - Size: 87.2 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0

brazil-data-cube/wlts-paper

Research compendium of the article: A plataform for land use and land cover data integration and trajectory analysis

Language: Jupyter Notebook - Size: 14.9 MB - Last synced at: 7 days ago - Pushed at: over 3 years ago - Stars: 10 - Forks: 0

SNARL1/translocation

Project describing frog translocations to reestablish populations in the presence of infectious disease

Language: R - Size: 203 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 1

joeroe/VarnaDietClustering

Data and code for a cluster analysis of dietary stable isotope measurements from burials at Varna

Language: R - Size: 497 KB - Last synced at: 2 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 0

benmarwick/teaching-replication-in-archaeology

This repository contains the data and code for our paper: "How to use replication assignments for teaching integrity in empirical archaeology"

Language: TeX - Size: 9.57 MB - Last synced at: 3 months ago - Pushed at: over 5 years ago - Stars: 7 - Forks: 3

benmarwick/1989-excavation-report-Madjedbebe

Text, data and code to accompany the analysis of the 1989 excavation data

Language: R - Size: 32.1 MB - Last synced at: about 1 month ago - Pushed at: over 7 years ago - Stars: 15 - Forks: 4

ee-jackson/spatial-premature-fruit-drop

:melon: :desert_island: Spatial patterns of premature fruit drop on BCI

Language: R - Size: 10.1 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 0

DOE-ICoM/geowq-chesapeake

Geographically aware estimates of remotely sensed water properties for Chesapeake Bay

Language: Python - Size: 45.6 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 3 - Forks: 0

benmarwick/bayesinfmatcultphylo

Research compendium for our paper "Bayesian inference of material culture phylogenies using continuous traits from the archaeological record: A birth–death model for Late Neolithic/Early Bronze Age arrowheads from Northwestern Europe"

Language: R - Size: 282 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 1

Gchism94/NestArchOrg

Research Compendium for the preprint DOI: https://doi.org/10.1101/2022.06.30.498314

Language: R - Size: 440 MB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

sbrzt/sirius

A Risk Assessment and Management tool based on the ABC methodology, which facilitates the identification and analysis of risks, risk level measurement, and the determination of risk mitigation strategies, with the goal of comprehensive documentation, understanding, and management of data related to risk applied to cultural assets.

Language: Python - Size: 96.4 MB - Last synced at: 7 months ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

VeinsOfTheEarth/pareto_lake_area

Quantifying uncertainty in Pareto estimates of global lake area

Language: TeX - Size: 104 MB - Last synced at: 12 months ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

earowang/thesis

PhD thesis

Language: HTML - Size: 97 MB - Last synced at: 2 months ago - Pushed at: over 5 years ago - Stars: 26 - Forks: 10

khodosevichlab/dataorganizer

Organization of files inside the research project

Language: R - Size: 14.6 KB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

nevrome/mobest.analysis.2022

Research compendium for ‘Estimating human mobility in Holocene Western Eurasia with large-scale ancient genomic data’; If you want to perform spatio-temporal similary search with the mobest R package as presented in the paper, then you can directly check the documentation here: https://nevrome.de/mobest

Language: R - Size: 9.72 MB - Last synced at: about 2 months ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 3

cont-limno/bathymetry

Imperfect slope measurements drive overestimation in geometric cone model of lake and reservoir depth

Language: TeX - Size: 262 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 0

jsta/peatcollapse_methods

In-situ simulation of sea-level rise impacts on coastal wetlands using a flow-through mesocosm approach

Language: TeX - Size: 19.1 MB - Last synced at: about 2 months ago - Pushed at: almost 7 years ago - Stars: 1 - Forks: 1

jsta/dataflowchl

Improved estimation of phytoplankton abundance and fine-scale water quality features via simultaneous discrete and semi-continuous surveys

Language: TeX - Size: 35.9 MB - Last synced at: about 2 months ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

jsta/nes_connectivity_p

Does Freshwater Connectivity Influence Phosphorus Retention in Lakes?

Language: R - Size: 283 MB - Last synced at: about 2 months ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

benmarwick/ktc11

Language: R - Size: 220 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 4

research-compendium/how-to-read-a-research-compendium

"How to Read a Research Compendium" - based on S. Keshav's "How to Read a Paper"

Language: TeX - Size: 305 KB - Last synced at: 12 months ago - Pushed at: over 3 years ago - Stars: 29 - Forks: 3

RPanczak/SNC_Swiss-SEP2

Development & validation of next release of the Swiss-SEP index.

Language: TeX - Size: 369 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 2

henningte/herdersmovementpatterns

herdersmovementpatterns

Language: TeX - Size: 5.58 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

cboettig/pdg_control

:notebook: Pretty Darn Good Control: applications in optimal control

Language: R - Size: 28.5 MB - Last synced at: about 2 months ago - Pushed at: over 7 years ago - Stars: 11 - Forks: 1

joeroe/dabawa23_enm

Paper presented at "Digital Archaeology Bern – Ancient West Asia", Bern, 6–7 October 2023

Language: HTML - Size: 97.8 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

MartinHinz/bayesian.demographic.reconstruction.2022

Research compendium for ‘Bayesian inference of prehistoric population dynamics from multiple proxies: a case study from the North of the Swiss Alps’

Language: HTML - Size: 111 MB - Last synced at: 2 months ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 0

ee-jackson/bci-jacc

:palm_tree: :fallen_leaf: Pre-dispersal seed predation of Jacaranda copaia on BCI

Language: R - Size: 155 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

danielpearson90/vmacfeaturesearch

Research Compendium for VMAC Feature Search Project

Language: HTML - Size: 18.3 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 1

stonerlab/PIQSD-SingleSpinBz

Sources for: Numerical Simulations of a Spin Dynamics Model Based on a Path Integral Approach

Language: Python - Size: 235 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 4 - Forks: 0

ReproducibleQM/NES

The National Eutrophication Survey: lake characteristics and historical nutrient concentrations

Language: TeX - Size: 41.6 MB - Last synced at: 10 months ago - Pushed at: over 5 years ago - Stars: 4 - Forks: 4

pcubillos/CubillosEtal2019_rate

Compendium for Cubillos et al. (2019): Towards More Reliable Analytic Thermochemical-Equilibrium Abundances

Language: Python - Size: 42 KB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

pcubillos/CubillosBlecic2021_pyratbayI

Compendium for Pyrat Bay paper

Language: Python - Size: 729 KB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

diogo-almeida/TuckerIdrissiAlmeida2021

A compendium of code and data for reproducing all tables and figures of Tucker, Idrissi, & Almeida. (2021). https://doi.org/10.3389/fpsyg.2020.586464

Language: R - Size: 175 KB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

BCMSLab/curated_perturbed_descriptor

Code for the Adipocyte paper (Curated gene expression dataset of differentiating 3T3-L1 adipocytes under pharmacological and genetic perturbations)

Language: R - Size: 9.77 KB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

BCMSLab/target_ranking

Code for the BMC Genomics paper (Integrating binding and expression data to predict transcription factors combined function)

Language: R - Size: 28.3 KB - Last synced at: almost 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

BCMSLab/rkip

Code for the Cancers paper (Functional Linkage of RKIP to the Epithelial to Mesenchymal Transition and Autophagy during the Development of Prostate Cancer)

Language: R - Size: 56.6 KB - Last synced at: almost 2 years ago - Pushed at: almost 7 years ago - Stars: 2 - Forks: 2

BCMSLab/curated_adipo_descriptor

Code for the Adipocyte paper (Modeling the gene expression and the DNA-binding in the 3T3-L1 differentiating adipocytes)

Language: R - Size: 28.3 KB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

BCMSLab/colocrart

Code for the PeerJ paper (colocr: an R package for conducting co-localization analysis on fluorescence microscopy images)

Language: R - Size: 3.26 MB - Last synced at: almost 2 years ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

BCMSLab/auto_adipo_diff

Code for the Cells paper (Transcriptional Regulation of Autophagy Genes via Stage-Specific Activation of CEBPB and PPARG during Adipogenesis)

Language: R - Size: 51.8 KB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 1

BCMSLab/cregart

Code for the PeerJ paper (cRegulome: an R package for accessing microRNA and transcription factor-gene expression correlations in cancer)

Language: R - Size: 11.7 KB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

BCMSLab/autoreg

A research compendium: Transcriptional regulation of autophagy during adipocyte differentiation

Language: R - Size: 65.4 KB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 1

BCMSLab/3T3-L1

Code for the Oncotarget paper (Systematic characterization of autophagy-related genes during the adipocyte differentiation using public-access data.)

Language: TeX - Size: 39.4 MB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 2 - Forks: 0

BCMSLab/aacna

Code for the IJMS paper (Co-Expression Network Analysis of AMPK and Autophagy Gene Products during Adipocyte Differentiation)

Language: R - Size: 56.6 KB - Last synced at: almost 2 years ago - Pushed at: almost 7 years ago - Stars: 1 - Forks: 0

AnneLew/Lewerentz-etal_2021_Macrophytes-DDG

Data and Analysis of Lewerentz et al 2021: Depth diversity gradients of macrophytes: shape, drivers and recent shifts

Language: R - Size: 16.1 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

codecheckers/OpeningPractice Fork of lexcomber/OpeningPractice

Language: R - Size: 6.42 MB - Last synced at: almost 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

FodorLab/RYGB_IntegratedAnalysis2020 Fork of FarnazFouladi/RYGB_IntegratedAnalysis2020

Language: R - Size: 419 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

FodorLab/PublicationAnalysis_Template

A template for repositories that accompany a publication and encapsulate the analysis component.

Language: R - Size: 61.5 KB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 1

bbartholdy/byoc-starch

Research compendium for 'Investigating Biases Associated with Dietary Starch Incorporation and Retention with an Oral Biofilm Model.'

Language: HTML - Size: 44.5 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 6 - Forks: 0

nuest/reproducible-research-and-giscience

Ready to use R Markdown notebook for the paper "Reproducible research and GIScience: an evaluation using AGILE conference papers"

Language: Dockerfile - Size: 1.16 MB - Last synced at: about 2 months ago - Pushed at: almost 6 years ago - Stars: 3 - Forks: 7

Mateusz-Grzelinski/program-synthesis-documentation

Many resources about program synthesis

Language: Python - Size: 45.9 KB - Last synced at: about 2 months ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 0

C-C-A-A/CologneProtocol-R

Research compedium for "Approaching Prehistoric Demography: Proxies, Scales and Scope of the Cologne Protocol in European contexts" including a manual of the Cologne Protocol

Language: R - Size: 337 KB - Last synced at: 10 months ago - Pushed at: over 4 years ago - Stars: 8 - Forks: 4

joeroe/SWAsiaNeolithicFounderCrops

Data and code for Arranz-Otaegui & Roe (2023), "Revisiting the concept of the 'Neolithic Founder Crops' in southwest Asia'

Language: PostScript - Size: 84.5 MB - Last synced at: about 1 month ago - Pushed at: about 2 years ago - Stars: 6 - Forks: 1

ee-jackson/premature-fruit-drop 📦

:peach: :bug: Code from Jackson et al. (2022) Pre-dispersal seed predation could help explain premature fruit drop in a tropical forest.

Language: R - Size: 43.9 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

zkamvar/clonal-inference-simulations

Simulation scripts for simuPop

Language: HTML - Size: 126 MB - Last synced at: about 1 hour ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

trhermes/isotopes.sheep.goat.tianshan

Research compendium for ‘Carbon and oxygen stable isotopic evidence for diverse sheep and goat husbandry strategies amid a Final Bronze Age farming milieu in the Kyrgyz Tian Shan’

Language: R - Size: 48.6 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 5 - Forks: 0