Showing 47 of total 47 results (show query)
ices-tools-prod
TAF:Transparent Assessment Framework for Reproducible Research
General framework to organize data, methods, and results used in reproducible scientific analyses. A TAF analysis consists of four scripts (data.R, model.R, output.R, report.R) that are run sequentially. Each script starts by reading files from a previous step and ends with writing out files for the next step. Convenience functions are provided to version control the required data and software, run analyses, clean residues from previous runs, manage files, manipulate tables, and produce figures. With a focus on stability and reproducible analyses, the TAF package comes with no dependencies. TAF forms a base layer for the 'icesTAF' package and other scientific applications.
Maintained by Arni Magnusson. Last updated 4 months ago.
8.1 match 3 stars 6.85 score 282 scripts 2 dependents
arnaudgallou
pakret:Cite 'R' Packages on the Fly in 'R Markdown' and 'Quarto'
References and cites 'R' and 'R' packages on the fly in 'R Markdown' and 'Quarto'. 'pakret' provides a minimalistic API that generates preformatted citations of 'R' and 'R' packages, and adds their reference to a '.bib' file directly from within your document.
Maintained by Arnaud Gallou. Last updated 9 hours ago.
bibbibtexcitationcitationsgenerate
11.5 match 5 stars 4.54 score 5 scripts
mahditeimouri
bibs:Bayesian Inference for the Birnbaum-Saunders Distribution
Developed for the following tasks. 1- Simulating and computing the maximum likelihood estimator for the Birnbaum-Saunders (BS) distribution, 2- Computing the Bayesian estimator for the parameters of the BS distribution based on reference prior proposed by Xu and Tang (2010) <doi:10.1016/j.csda.2009.08.004> and conjugate prior. 3- Computing the Bayesian estimator for the BS distribution based on conjugate prior. 4- Computing the Bayesian estimator for the BS distribution based on Jeffrey prior given by Achcar (1993) <doi:10.1016/0167-9473(93)90170-X> 5- Computing the Bayesian estimator for the BS distribution under progressive type-II censoring scheme.
Maintained by Mahdi Teimouri. Last updated 3 years ago.
51.8 match 1.00 score 4 scripts
ropensci
bibtex:Bibtex Parser
Utility to parse a bibtex file.
Maintained by James Joseph Balamuta. Last updated 1 years ago.
4.5 match 37 stars 9.75 score 496 scripts 20 dependents
cran
agricolae:Statistical Procedures for Agricultural Research
Original idea was presented in the thesis "A statistical analysis tool for agricultural research" to obtain the degree of Master on science, National Engineering University (UNI), Lima-Peru. Some experimental data for the examples come from the CIP and others research. Agricolae offers extensive functionality on experimental design especially for agricultural and plant breeding experiments, which can also be useful for other purposes. It supports planning of lattice, Alpha, Cyclic, Complete Block, Latin Square, Graeco-Latin Squares, augmented block, factorial, split and strip plot designs. There are also various analysis facilities for experimental data, e.g. treatment comparison procedures and several non-parametric tests comparison, biodiversity indexes and consensus cluster.
Maintained by Felipe de Mendiburu. Last updated 1 years ago.
6.3 match 7 stars 7.01 score 15 dependents
wviechtb
metadat:Meta-Analysis Datasets
A collection of meta-analysis datasets for teaching purposes, illustrating/testing meta-analytic methods, and validating published analyses.
Maintained by Wolfgang Viechtbauer. Last updated 4 days ago.
3.3 match 30 stars 10.54 score 65 scripts 93 dependents
jmbarbone
mark:Miscellaneous, Analytic R Kernels
Miscellaneous functions and wrappers for development in other packages created, maintained by Jordan Mark Barbone.
Maintained by Jordan Mark Barbone. Last updated 1 months ago.
5.9 match 6 stars 4.95 score 9 scriptsropensci
RefManageR:Straightforward 'BibTeX' and 'BibLaTeX' Bibliography Management
Provides tools for importing and working with bibliographic references. It greatly enhances the 'bibentry' class by providing a class 'BibEntry' which stores 'BibTeX' and 'BibLaTeX' references, supports 'UTF-8' encoding, and can be easily searched by any field, by date ranges, and by various formats for name lists (author by last names, translator by full names, etc.). Entries can be updated, combined, sorted, printed in a number of styles, and exported. 'BibTeX' and 'BibLaTeX' '.bib' files can be read into 'R' and converted to 'BibEntry' objects. Interfaces to 'NCBI Entrez', 'CrossRef', and 'Zotero' are provided for importing references and references can be created from locally stored 'PDF' files using 'Poppler'. Includes functions for citing and generating a bibliography with hyperlinks for documents prepared with 'RMarkdown' or 'RHTML'.
Maintained by Mathew W. McLean. Last updated 4 months ago.
2.3 match 115 stars 12.06 score 2.3k scripts 16 dependentsropensci
medrxivr:Access and Search MedRxiv and BioRxiv Preprint Data
An increasingly important source of health-related bibliographic content are preprints - preliminary versions of research articles that have yet to undergo peer review. The two preprint repositories most relevant to health-related sciences are medRxiv <https://www.medrxiv.org/> and bioRxiv <https://www.biorxiv.org/>, both of which are operated by the Cold Spring Harbor Laboratory. 'medrxivr' provides programmatic access to the 'Cold Spring Harbour Laboratory (CSHL)' API <https://api.biorxiv.org/>, allowing users to easily download medRxiv and bioRxiv preprint metadata (e.g. title, abstract, publication date, author list, etc) into R. 'medrxivr' also provides functions to search the downloaded preprint records using regular expressions and Boolean logic, as well as helper functions that allow users to export their search results to a .BIB file for easy import to a reference manager and to download the full-text PDFs of preprints matching their search criteria.
Maintained by Yaoxiang Li. Last updated 1 months ago.
bibliographic-databasebiorxivevidence-synthesismedrxiv-datapeer-reviewedpreprint-recordssystematic-reviews
3.4 match 56 stars 7.17 score 44 scripts
zoushucai
journalabbr:Journal Abbreviations for BibTeX Documents
Since the reference management software (such as 'Zotero', 'Mendeley') exports Bib file journal abbreviation is not detailed enough, the 'journalabbr' package only abbreviates the journal field of Bib file, and then outputs a new Bib file for generating reference format with journal abbreviation on other software (such as 'texstudio'). The abbreviation table is from 'JabRef'. At the same time, 'Shiny' application is provided to generate 'thebibliography', a reference format that can be directly used for latex paper writing based on 'Rmd' files.
Maintained by ShuCai Zou. Last updated 3 months ago.
6.4 match 1 stars 3.22 score 11 scripts
crsh
papaja:Prepare American Psychological Association Journal Articles with R Markdown
Tools to create dynamic, submission-ready manuscripts, which conform to American Psychological Association manuscript guidelines. We provide R Markdown document formats for manuscripts (PDF and Word) and revision letters (PDF). Helper functions facilitate reporting statistical analyses or create publication-ready tables and plots.
Maintained by Frederik Aust. Last updated 19 days ago.
apaapa-guidelinesjournalmanuscriptpsychologyreproducible-paperreproducible-researchrmarkdown
1.8 match 662 stars 11.74 score 1.7k scripts 1 dependents
detlew
PowerTOST:Power and Sample Size for (Bio)Equivalence Studies
Contains functions to calculate power and sample size for various study designs used in bioequivalence studies. Use known.designs() to see the designs supported. Power and sample size can be obtained based on different methods, amongst them prominently the TOST procedure (two one-sided t-tests). See README and NEWS for further information.
Maintained by Detlew Labes. Last updated 1 years ago.
2.3 match 20 stars 9.10 score 112 scripts 4 dependents
giobo
TR8:A Tool for Downloading Functional Traits Data for Plant Species
Plant ecologists often need to collect "traits" data about plant species which are often scattered among various databases: TR8 contains a set of tools which take care of automatically retrieving some of those functional traits data for plant species from publicly available databases (The Ecological Flora of the British Isles, LEDA traitbase, Ellenberg values for Italian Flora, Mycorrhizal intensity databases, BROT, PLANTS, Jepson Flora Project). The TR8 name, inspired by "car plates" jokes, was chosen since it both reminds of the main object of the package and is extremely short to type.
Maintained by Gionata Bocci. Last updated 6 months ago.
3.3 match 20 stars 6.16 score 16 scripts
hughparsonage
TeXCheckR:Parses LaTeX Documents for Errors
Checks LaTeX documents and .bib files for typing errors, such as spelling errors, incorrect quotation marks. Also provides useful functions for parsing and linting bibliography files.
Maintained by Hugh Parsonage. Last updated 1 years ago.
4.4 match 8 stars 4.44 score 23 scripts
r-lib
ymlthis:Write 'YAML' for 'R Markdown', 'bookdown', 'blogdown', and More
Write 'YAML' front matter for R Markdown and related documents. Work with 'YAML' objects more naturally and write the resulting 'YAML' to your clipboard or to 'YAML' files related to your project.
Maintained by Malcolm Barrett. Last updated 3 years ago.
1.9 match 165 stars 9.91 score 196 scripts 14 dependentsropensci
bib2df:Parse a BibTeX File to a Data Frame
Parse a BibTeX file to a data.frame to make it accessible for further analysis and visualization.
Maintained by Gianluca Baio. Last updated 7 months ago.
1.8 match 101 stars 9.82 score 212 scripts 6 dependents
bbnkmp
crossdes:Construction of Crossover Designs
Contains functions for the construction of carryover balanced crossover designs. In addition contains functions to check given designs for balance.
Maintained by Bjoern Bornkamp. Last updated 3 years ago.
4.5 match 1 stars 3.67 score 48 scripts 8 dependents
tbep-tech
tbeptools:Data and Indicators for the Tampa Bay Estuary Program
Several functions are provided for working with Tampa Bay Estuary Program data and indicators, including the water quality report card, tidal creek assessments, Tampa Bay Nekton Index, Tampa Bay Benthic Index, seagrass transect data, habitat report card, and fecal indicator bacteria. Additional functions are provided for miscellaneous tasks, such as reference library curation.
Maintained by Marcus Beck. Last updated 11 days ago.
data-analysistampa-baytbepwater-quality
1.9 match 10 stars 7.86 score 133 scriptsices-tools-prod
icesTAF:Functions to Support the ICES Transparent Assessment Framework
Functions to support the ICES Transparent Assessment Framework <https://taf.ices.dk> to organize data, methods, and results used in ICES assessments. ICES is an organization facilitating international collaboration in marine science.
Maintained by Colin Millar. Last updated 2 years ago.
2.3 match 5 stars 6.37 score 1.1k scripts 1 dependents
svmiller
stevemisc:Steve's Miscellaneous Functions
These are miscellaneous functions that I find useful for my research and teaching. The contents include themes for plots, functions for simulating quantities of interest from regression models, functions for simulating various forms of fake data for instructional/research purposes, and many more. All told, the functions provided here are broadly useful for data organization, data presentation, data recoding, and data simulation.
Maintained by Steve Miller. Last updated 7 days ago.
dplyrmixed-effects-modelsmultivariate-normal-distributiontidyverse
1.8 match 10 stars 6.85 score 392 scripts 2 dependents
frbcesab
rbibtools:Toolbox to Handle BibTeX Files
Imports, cleans, and exports BibTeX references exported by references management softwares (e.g. Mendeley, Zotero).
Maintained by Nicolas Casajus. Last updated 6 months ago.
3.5 match 3 stars 3.18 score
abhi-1u
texor:Converting 'LaTeX' 'R Journal' Articles into 'RJ-web-articles'
Articles in the 'R Journal' were first authored in 'LaTeX', which performs admirably for 'PDF' files but is less than ideal for modern online interfaces. The 'texor' package does all the transitional chores and conversions necessary to move to the online versions.
Maintained by Abhishek Ulayil. Last updated 3 months ago.
1.7 match 7 stars 6.28 score 8 scripts
mjwestgate
revtools:Tools to Support Evidence Synthesis
Researchers commonly need to summarize scientific information, a process known as 'evidence synthesis'. The first stage of a synthesis process (such as a systematic review or meta-analysis) is to download a list of references from academic search engines such as 'Web of Knowledge' or 'Scopus'. The traditional approach to systematic review is then to sort these data manually, first by locating and removing duplicated entries, and then screening to remove irrelevant content by viewing titles and abstracts (in that order). 'revtools' provides interfaces for each of these tasks. An alternative approach, however, is to draw on tools from machine learning to visualise patterns in the corpus. In this case, you can use 'revtools' to render ordinations of text drawn from article titles, keywords and abstracts, and interactively select or exclude individual references, words or topics.
Maintained by Martin J. Westgate. Last updated 5 years ago.
1.7 match 52 stars 5.57 score 72 scripts
iheid-library
iheiddown:For Writing Geneva Graduate Institute Documents
A set of tools for writing documents according to Geneva Graduate Institute conventions and regulations. The most common use is for writing and compiling theses or thesis chapters, as drafts or for examination with correct preamble formatting. However, the package also offers users to create HTML presentation slides with 'xaringan', complete problem sets, format posters, and, for course instructors, prepare a syllabus. The package includes additional functions for institutional color palettes, an institutional 'ggplot' theme, a function for counting manuscript words, and a bibliographical analysis toolkit.
Maintained by James Hollway. Last updated 2 years ago.
1.5 match 11 stars 6.14 score 5 scripts
mlaib
PGM2:Nested Resolvable Designs and their Associated Uniform Designs
Construction method of nested resolvable designs from a projective geometry defined on Galois field of order 2. The obtained Resolvable designs are used to build uniform design. The presented results are based on <https://eudml.org/doc/219563> and A. Boudraa et al. (See references).
Maintained by Mohamed Laib. Last updated 7 years ago.
3.3 match 2.70 score 6 scripts
florianjansen
vegdata:Access Vegetation Databases and Treat Taxonomy
Handling of vegetation data from different sources ( Turboveg 2.0 <https://www.synbiosys.alterra.nl/turboveg/>; the German national repository <https://www.vegetweb.de> and others. Taxonomic harmonization (given appropriate taxonomic lists, e.g. the German taxonomic standard list "GermanSL", <https://germansl.infinitenature.org>).
Maintained by Florian Jansen. Last updated 1 years ago.
2.3 match 2 stars 3.84 score 38 scripts 3 dependents
markbravington
lyxport:LyX to MSWord etc
Tools for smooth Lyx export via pandoc, currently to MSWord but to potentially other formats
Maintained by Mark Bravington. Last updated 6 days ago.
1.8 match 2.54 score
igordot
babelgene:Gene Orthologs for Model Organisms in a Tidy Data Format
Genomic analysis of model organisms frequently requires the use of databases based on human data or making comparisons to patient-derived resources. This requires harmonization of gene names into the same gene space. The 'babelgene' R package converts between human and non-human gene orthologs/homologs. The package integrates orthology assertion predictions sourced from multiple databases as compiled by the HGNC Comparison of Orthology Predictions (HCOP) (Wright et al. 2005 <doi:10.1007/s00335-005-0103-2>, Eyre et al. 2007 <doi:10.1093/bib/bbl030>, Seal et al. 2011 <doi:10.1093/nar/gkq892>).
Maintained by Igor Dolgalev. Last updated 2 years ago.
0.5 match 11 stars 7.86 score 29 scripts 25 dependents
mpierrejean
jointseg:Joint Segmentation of Multivariate (Copy Number) Signals
Methods for fast segmentation of multivariate signals into piecewise constant profiles and for generating realistic copy-number profiles. A typical application is the joint segmentation of total DNA copy numbers and allelic ratios obtained from Single Nucleotide Polymorphism (SNP) microarrays in cancer studies. The methods are described in Pierre-Jean, Rigaill and Neuvial (2015) <doi:10.1093/bib/bbu026>.
Maintained by Morgane Pierre-Jean. Last updated 6 years ago.
0.5 match 6 stars 6.50 score 44 scripts 2 dependents
centerforstatistics-ugent
xnet:Two-Step Kernel Ridge Regression for Network Predictions
Fit a two-step kernel ridge regression model for predicting edges in networks, and carry out cross-validation using shortcuts for swift and accurate performance assessment (Stock et al, 2018 <doi:10.1093/bib/bby095> ).
Maintained by Joris Meys. Last updated 4 years ago.
0.5 match 11 stars 5.30 score 12 scripts
lucaskook
comets:Covariance Measure Tests for Conditional Independence
Covariance measure tests for conditional independence testing against conditional covariance and nonlinear conditional mean alternatives. The package implements versions of the generalised covariance measure test (Shah and Peters, 2020, <doi:10.1214/19-aos1857>) and projected covariance measure test (Lundborg et al., 2023, <doi:10.1214/24-AOS2447>). The tram-GCM test, for censored responses, is implemented including the Cox model and survival forests (Kook et al., 2024, <doi:10.1080/01621459.2024.2395588>). Application examples to variable significance testing and modality selection can be found in Kook and Lundborg (2024, <doi:10.1093/bib/bbae475>).
Maintained by Lucas Kook. Last updated 2 months ago.
0.5 match 9 stars 4.95 score 2 scripts
cxzdsa2332
idopNetwork:A Network Tool to Dissect Spatial Community Ecology
Most existing approaches for network reconstruction can only infer an overall network and, also, fail to capture a complete set of network properties. To address these issues, a new model has been developed, which converts static data into their 'dynamic' form. 'idopNetwork' is an 'R' interface to this model, it can inferring informative, dynamic, omnidirectional and personalized networks. For more information on functional clustering part, see Kim et al. (2008) <doi:10.1534/genetics.108.093690>, Wang et al. (2011) <doi:10.1093/bib/bbr032>. For more information on our model, see Chen et al. (2019) <doi:10.1038/s41540-019-0116-1>, and Cao et al. (2022) <doi:10.1080/19490976.2022.2106103>.
Maintained by Ang Dong. Last updated 2 years ago.
0.5 match 4 stars 4.30 score 3 scripts
weiliu123
PCLassoReg:Group Regression Models for Risk Protein Complex Identification
Two protein complex-based group regression models (PCLasso and PCLasso2) for risk protein complex identification. PCLasso is a prognostic model that identifies risk protein complexes associated with survival. PCLasso2 is a classification model that identifies risk protein complexes associated with classes. For more information, see Wang and Liu (2021) <doi:10.1093/bib/bbab212>.
Maintained by Wei Liu. Last updated 3 years ago.
0.5 match 1 stars 3.70 score 1 scripts
han-siyu
LncFinder:LncRNA Identification and Analysis Using Heterologous Features
Long non-coding RNAs identification and analysis. Default models are trained with human, mouse and wheat datasets by employing SVM. Features are based on intrinsic composition of sequence, EIIP value (electron-ion interaction pseudopotential), and secondary structure. This package can also extract other classic features and build new classifiers. Reference: Han S., et al. (2019) <doi:10.1093/bib/bby065>.
Maintained by Siyu Han. Last updated 6 months ago.
0.5 match 2 stars 3.68 score 53 scriptshan-siyu
TIGERr:Technical Variation Elimination with Ensemble Learning Architecture
The R implementation of TIGER. TIGER integrates random forest algorithm into an innovative ensemble learning architecture. Benefiting from this advanced architecture, TIGER is resilient to outliers, free from model tuning and less likely to be affected by specific hyperparameters. TIGER supports targeted and untargeted metabolomics data and is competent to perform both intra- and inter-batch technical variation removal. TIGER can also be used for cross-kit adjustment to ensure data obtained from different analytical assays can be effectively combined and compared. Reference: Han S. et al. (2022) <doi:10.1093/bib/bbab535>.
Maintained by Siyu Han. Last updated 5 months ago.
0.5 match 6 stars 3.48 score 1 scripts
yuanmingzhang
mrMLM.GUI:Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for Genome-Wide Association Study with Graphical User Interface
Conduct multi-locus genome-wide association study under the framework of multi-locus random-SNP-effect mixed linear model (mrMLM). First, each marker on the genome is scanned. Bonferroni correction is replaced by a less stringent selection criterion for significant test. Then, all the markers that are potentially associated with the trait are included in a multi-locus genetic model, their effects are estimated by empirical Bayes and all the nonzero effects were further identified by likelihood ratio test for true QTL. Wen YJ, Zhang H, Ni YL, Huang B, Zhang J, Feng JY, Wang SB, Dunwell JM, Zhang YM, Wu R (2018) <doi:10.1093/bib/bbw145>.
Maintained by Yuanming Zhang. Last updated 4 years ago.
0.5 match 2 stars 2.30 score 10 scripts
yuanmingzhang
QTL.gCIMapping:QTL Genome-Wide Composite Interval Mapping
Conduct multiple quantitative trait loci (QTL) and QTL-by-environment interaction (QEI) mapping via ordinary or compressed variance component mixed models with random- or fixed QTL/QEI effects. First, each position on the genome is detected in order to obtain a negative logarithm P-value curve against genome position. Then, all the peaks on each effect (additive or dominant) curve or on each locus curve are viewed as potential main-effect QTLs and QEIs, all their effects are included in a multi-locus model, their effects are estimated by both least angle regression and empirical Bayes (or adaptive lasso) in backcross and F2 populations, and true QTLs and QEIs are identified by likelihood radio test. See Zhou et al. (2022) <doi:10.1093/bib/bbab596> and Wen et al. (2018) <doi:10.1093/bib/bby058>.
Maintained by Yuanming Zhang. Last updated 3 years ago.
0.8 match 1 stars 1.48 score 2 scripts 1 dependents
sebdejean
WallomicsData:Datasets for Multi-Omics Integration in a Plant Abiotic Stress Context
Datasets from the WallOmics project. Contains phenomics, metabolomics, proteomics and transcriptomics data collected from two organs of five ecotypes of the model plant Arabidopsis thaliana exposed to two temperature growth conditions. Exploratory and integrative analyses of these data are presented in Durufle et al (2020) <doi:10.1093/bib/bbaa166> and Durufle et al (2020) <doi:10.3390/cells9102249>.
Maintained by Sébastien Déjean. Last updated 3 years ago.
0.5 match 1.48 score 2 scripts 1 dependentscran
SUMO:Generating Multi-Omics Datasets
Designed to generate multi-omics datasets that closely reflect biological complexity, the package allows for testing, validation, and benchmarking of multi-omics integrative methods. The simulated data includes one or multiple predefined signals (latent/unobserved factors), giving users complete control over the data-generated characteristics. Tini, Giulia, et al (2019) <doi:10.1093/bib/bbx167>.
Maintained by Bernard Isekah Osangir. Last updated 5 months ago.
0.5 match 1.00 score 8 scripts
ashutoshdalal97
HadIBDs:Incomplete Block Designs using Hadamard Matrix (HadIBDs)
Hadamard matrix based statistical designs are of immense importance as the resultant designs carry various desirable characterizing properties. Constructing Partially Balanced Incomplete Block Designs (PBIBds) using Kronecker product of incidence matrices of Balanced Incomplete Block (BIB) and Partially Balanced Incomplete Block (PBIB) designs is much evident from literature. Here, we have constructed Incomplete Block Designs (IBDs) based on Hadamard matrices and Kronecker product of Hadamard matrices.
Maintained by Ashutosh Dalal. Last updated 7 months ago.
0.5 match 1.00 score 3 scriptsyuanmingzhang
QTL.gCIMapping.GUI:QTL Genome-Wide Composite Interval Mapping with Graphical User Interface
Conduct multiple quantitative trait loci (QTL) mapping under the framework of random-QTL-effect linear mixed model. First, each position on the genome is detected in order to obtain a negative logarithm P-value curve against genome position. Then, all the peaks on each effect (additive or dominant) curve are viewed as potential QTL, all the effects of the potential QTL are included in a multi-QTL model, their effects are estimated by empirical Bayes in doubled haploid population or by adaptive lasso in F2 population, and true QTL are identified by likelihood radio test. See Wen et al. (2018) <doi:10.1093/bib/bby058>.
Maintained by Yuanming Zhang. Last updated 4 years ago.
0.5 match 1.00 score 6 scriptscran
CeRNASeek:Identification and Analysis of ceRNA Regulation
Provides several functions to identify and analyse miRNA sponge, including popular methods for identifying miRNA sponge interactions, two types of global ceRNA regulation prediction methods and four types of context-specific prediction methods( Li Y et al.(2017) <doi:10.1093/bib/bbx137>), which are based on miRNA-messenger RNA regulation alone, or by integrating heterogeneous data, respectively. In addition, For predictive ceRNA relationship pairs, this package provides several downstream analysis algorithms, including regulatory network analysis and functional annotation analysis, as well as survival prognosis analysis based on expression of ceRNA ternary pair.
Maintained by Mengying Zhang. Last updated 5 years ago.
competing endogenous rna (cerna)geneexpressiontripletfunctionsoftware
0.5 match 1.00 score
