Showing 18 of total 18 results (show query)
ropensci
drake:A Pipeline Toolkit for Reproducible Computation at Scale
A general-purpose computational engine for data analysis, drake rebuilds intermediate data objects when their dependencies change, and it skips work when the results are already up to date. Not every execution starts from scratch, there is native support for parallel and distributed computing, and completed projects have tangible evidence that they are reproducible. Extensive documentation, from beginner-friendly tutorials to practical examples and more, is available at the reference website <https://docs.ropensci.org/drake/> and the online manual <https://books.ropensci.org/drake/>.
Maintained by William Michael Landau. Last updated 3 months ago.
data-sciencedrakehigh-performance-computingmakefilepeer-reviewedpipelinereproducibilityreproducible-researchropensciworkflow
105.3 match 1.3k stars 11.49 score 1.7k scripts 1 dependents
nyuglobalties
blueprintr:Automagically Document and Test Datasets Using Targets Or Drake
Documents and tests datasets in a reproducible manner so that data lineage is easier to comprehend for small to medium tabular data. Originally designed to aid data cleaning tasks for humanitarian research groups, specifically large-scale longitudinal studies.
Maintained by Patrick Anker. Last updated 8 months ago.
17.6 match 1 stars 3.40 score 7 scripts
tomdrake
String2AdjMatrix:Creates an adjacency matrix from a list of strings
Takes a list of character strings and forms an adjacency matrix for the times the specified characters appear together in the strings provided. For use in social network analysis and data wrangling. Simple package, comprised of three functions.
Maintained by Tom Drake. Last updated 7 years ago.
9.8 match 2.70 score 5 scripts
cran
emery:Accuracy Statistic Estimation for Imperfect Gold Standards
Produce maximum likelihood estimates of common accuracy statistics for multiple measurement methods when a gold standard is not available. An R implementation of the expectation maximization algorithms described in Zhou et al. (2011) <doi:10.1002/9780470906514> with additional functions for creating simulated data and visualizing results. Supports binary, ordinal, and continuous measurement methods.
Maintained by Corie Drake. Last updated 1 years ago.
9.1 match 2.70 score 1 scriptsropensci
tarchetypes:Archetypes for Targets
Function-oriented Make-like declarative pipelines for Statistics and data science are supported in the 'targets' R package. As an extension to 'targets', the 'tarchetypes' package provides convenient user-side functions to make 'targets' easier to use. By establishing reusable archetypes for common kinds of targets and pipelines, these functions help express complicated reproducible pipelines concisely and compactly. The methods in this package were influenced by the 'targets' R package. by Will Landau (2018) <doi:10.21105/joss.00550>.
Maintained by William Michael Landau. Last updated 20 days ago.
data-sciencehigh-performance-computingpeer-reviewedpipeliner-targetopiareproducibilitytargetsworkflow
1.8 match 141 stars 11.43 score 1.7k scripts 10 dependents
ewenharrison
finalfit:Quickly Create Elegant Regression Results Tables and Plots when Modelling
Generate regression results tables and plots in final format for publication. Explore models and export directly to PDF and 'Word' using 'RMarkdown'.
Maintained by Ewen Harrison. Last updated 7 months ago.
1.7 match 270 stars 11.43 score 1.0k scripts
bmaitner
S4DM:Small Sample Size Species Distribution Modeling
Implements a set of distribution modeling methods that are suited to species with small sample sizes (e.g., poorly sampled species or rare species). While these methods can also be used on well-sampled taxa, they are united by the fact that they can be utilized with relatively few data points. More details on the currently implemented methodologies can be found in Drake and Richards (2018) <doi:10.1002/ecs2.2373>, Drake (2015) <doi:10.1098/rsif.2015.0086>, and Drake (2014) <doi:10.1890/ES13-00202.1>.
Maintained by Brian S. Maitner. Last updated 1 months ago.
open-sciencerange-modellingrare-speciesspecies-distribution-modelingspecies-distribution-modelling
2.5 match 4 stars 5.97 score 33 scripts
milesmcbain
dflow:Setup a project in the dflow style for using the drake
Has a function that sets up an R workflow in the dflow style, using drake.
Maintained by Miles McBain. Last updated 5 years ago.
3.5 match 81 stars 3.61 score 6 scriptsropensci
targets:Dynamic Function-Oriented 'Make'-Like Declarative Pipelines
Pipeline tools coordinate the pieces of computationally demanding analysis projects. The 'targets' package is a 'Make'-like pipeline tool for statistics and data science in R. The package skips costly runtime for tasks that are already up to date, orchestrates the necessary computation with implicit parallel computing, and abstracts files as R objects. If all the current output matches the current upstream code and data, then the whole pipeline is up to date, and the results are more trustworthy than otherwise. The methodology in this package borrows from GNU 'Make' (2015, ISBN:978-9881443519) and 'drake' (2018, <doi:10.21105/joss.00550>).
Maintained by William Michael Landau. Last updated 2 days ago.
data-sciencehigh-performance-computingmakepeer-reviewedpipeliner-targetopiareproducibilityreproducible-researchtargetsworkflow
0.5 match 973 stars 15.20 score 4.6k scripts 22 dependents
surgicalinformatics
encryptr:Easily Encrypt and Decrypt Data Frame/Tibble Columns or Files using RSA Public/Private Keys
It is important to ensure that sensitive data is protected. This straightforward package is aimed at the end-user. Strong RSA encryption using a public/private key pair is used to encrypt data frame or tibble columns. A public key can be shared to allow others to encrypt data to be sent to you. This is particularly aimed a healthcare settings so patient data can be pseudonymised.
Maintained by Ewen Harrison. Last updated 5 years ago.
1.6 match 92 stars 4.78 score 13 scriptscran
extraterrestrial:Astrobiology Equations Estimating Extraterrestrial Life
Finding life outside the planet Earth several is the ultimate goal of an astrobiologist. Using known astronomical measurements and assumptions the probability of extraterrestrial life existence could be estimated. Equations such as the Drake equation (1961) as stated in the paper of Molina (2019) <arXiv:1912.01783>, Seager (2013) <https://www.space.com/22648-drake-equation-alien-life-seager.html> and Foucher et al, (2017) <doi:10.3390/life7040040> are included in the 'extraterrestrial' package.
Maintained by Chester C. Deocaris. Last updated 5 years ago.
6.1 match 1.00 scorecran
CytobankAPI:Cytobank API Wrapper for R
Tools to interface with Cytobank's API via R, organized by endpoints that represent various areas of Cytobank functionality. Learn more about Cytobank at <https://www.beckman.com/flow-cytometry/software>.
Maintained by Stu Blair. Last updated 2 years ago.
1.6 match 3.00 score
justinhubbard
Euclimatch:Euclidean Climatch Algorithm
An interface for performing climate matching using the Euclidean "Climatch" algorithm. Functions provide a vector of climatch scores (0-10) for each location (i.e., grid cell) within the recipient region, the percent of climatch scores >= a threshold value, and mean climatch score. Tools for parallelization and visualizations are also provided. Note that the floor function that rounds the climatch score down to the nearest integer has been removed in this implementation and the “Climatch” algorithm, also referred to as the “Climate” algorithm, is described in: Crombie, J., Brown, L., Lizzio, J., & Hood, G. (2008). “Climatch user manual”. The method for the percent score is described in: Howeth, J.G., Gantz, C.A., Angermeier, P.L., Frimpong, E.A., Hoff, M.H., Keller, R.P., Mandrak, N.E., Marchetti, M.P., Olden, J.D., Romagosa, C.M., and Lodge, D.M. (2016). <doi:10.1111/ddi.12391>.
Maintained by Justin A. G. Hubbard. Last updated 5 months ago.
1.6 match 3.00 score 3 scripts
rekyt
fddimensionality:Test Effect of Traits of FD-Environment Relationship
Companion code for paper XXX <doi:xxx> on FD-Environment relationship, which tests to what extent we can expect FD-Environment trait relationship in function of number of traits included and type of environmental filtering.
Maintained by Matthias Grenié. Last updated 2 years ago.
1.8 match 1.70 score
duncanobrien
EWSmethods:Forecasting Tipping Points at the Community Level
Rolling and expanding window approaches to assessing abundance based early warning signals, non-equilibrium resilience measures, and machine learning. See Dakos et al. (2012) <doi:10.1371/journal.pone.0041010>, Deb et al. (2022) <doi:10.1098/rsos.211475>, Drake and Griffen (2010) <doi:10.1038/nature09389>, Ushio et al. (2018) <doi:10.1038/nature25504> and Weinans et al. (2021) <doi:10.1038/s41598-021-87839-y> for methodological details. Graphical presentation of the outputs are also provided for clear and publishable figures. Visit the 'EWSmethods' website for more information, and tutorials.
Maintained by Duncan OBrien. Last updated 7 months ago.
0.5 match 8 stars 5.51 score 20 scripts
ammercier
simplifyNet:Network Sparsification
Network sparsification with a variety of novel and known network sparsification techniques. All network sparsification techniques reduce the number of edges, not the number of nodes. Network sparsification is sometimes referred to as network dimensionality reduction. This package is based on the work of Spielman, D., Srivastava, N. (2009)<arXiv:0803.0929>. Koutis I., Levin, A., Peng, R. (2013)<arXiv:1209.5821>. Toivonen, H., Mahler, S., Zhou, F. (2010)<doi:10.1007>. Foti, N., Hughes, J., Rockmore, D. (2011)<doi:10.1371>.
Maintained by Alexander Mercier. Last updated 2 years ago.
1.6 match 1 stars 1.70 scorecran
gains:Lift (Gains) Tables and Charts
Constructs gains tables and lift charts for prediction algorithms. Gains tables and lift charts are commonly used in direct marketing applications. The method is described in Drozdenko and Drake (2002), "Optimal Database Marketing", Chapter 11.
Maintained by Craig A. Rolling. Last updated 8 years ago.
0.5 match 1.26 score