Showing 64 of total 64 results (show query)
rsetienne
DAISIE:Dynamical Assembly of Islands by Speciation, Immigration and Extinction
Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See Valente et al. (2015) <doi:10.1111/ele.12461>.
Maintained by Rampal S. Etienne. Last updated 1 months ago.
35.1 match 9 stars 8.59 score 55 scripts 1 dependents
uclahs-cds
BoutrosLab.plotting.general:Functions to Create Publication-Quality Plots
Contains several plotting functions such as barplots, scatterplots, heatmaps, as well as functions to combine plots and assist in the creation of these plots. These functions will give users great ease of use and customization options in broad use for biomedical applications, as well as general purpose plotting. Each of the functions also provides valid default settings to make plotting data more efficient and producing high quality plots with standard colour schemes simpler. All functions within this package are capable of producing plots that are of the quality to be presented in scientific publications and journals. P'ng et al.; BPG: Seamless, automated and interactive visualization of scientific data; BMC Bioinformatics 2019 <doi:10.1186/s12859-019-2610-2>.
Maintained by Paul Boutros. Last updated 6 months ago.
13.8 match 12 stars 8.36 score 414 scripts 6 dependents
paicecode
PAICE:Phylogeographic Analysis of Island Colonization Events
Estimation of the number of colonization events between islands of the same archipelago for a species. It uses rarefaction curves to control for both field and genetic sample sizes as it was described in Coello et al. (2022) <doi:10.1111/jbi.14341>.
Maintained by Alberto J. Coello. Last updated 8 months ago.
biogeographycolonizationisland
29.1 match 1 stars 3.00 score 4 scripts
therneau
survival:Survival Analysis
Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.
Maintained by Terry M Therneau. Last updated 3 months ago.
3.5 match 400 stars 20.43 score 29k scripts 3.9k dependents
vjontiveros
island:Stochastic Island Biogeography Theory Made Easy
Develops stochastic models based on the Theory of Island Biogeography (TIB) of MacArthur and Wilson (1967) <doi:10.1023/A:1016393430551> and extensions. It implements methods to estimate colonization and extinction rates (including environmental variables) given presence-absence data, simulates community assembly, and performs model selection.
Maintained by Vicente Jimenez. Last updated 1 years ago.
15.2 match 3.10 score 42 scripts
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.
3.5 match 270 stars 11.43 score 1.0k scripts
bioc
retrofit:RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics
RETROFIT is a Bayesian non-negative matrix factorization framework to decompose cell type mixtures in ST data without using external single-cell expression references. RETROFIT outperforms existing reference-based methods in estimating cell type proportions and reconstructing gene expressions in simulations with varying spot size and sample heterogeneity, irrespective of the quality or availability of the single-cell reference. RETROFIT recapitulates known cell-type localization patterns in a Slide-seq dataset of mouse cerebellum without using any single-cell data.
Maintained by Adam Park. Last updated 5 months ago.
transcriptomicsvisualizationrnaseqbayesianspatialsoftwaregeneexpressiondimensionreductionfeatureextractionsinglecellcpp
7.8 match 3 stars 5.08 score 9 scripts
pharmaverse
ggsurvfit:Flexible Time-to-Event Figures
Ease the creation of time-to-event (i.e. survival) endpoint figures. The modular functions create figures ready for publication. Each of the functions that add to or modify the figure are written as proper 'ggplot2' geoms or stat methods, allowing the functions from this package to be combined with any function or customization from 'ggplot2' and other 'ggplot2' extension packages.
Maintained by Daniel D. Sjoberg. Last updated 2 months ago.
3.8 match 76 stars 10.50 score 640 scripts 2 dependents
mclements
biostat3:Utility Functions, Datasets and Extended Examples for Survival Analysis
Utility functions, datasets and extended examples for survival analysis. This extends a range of other packages, some simple wrappers for time-to-event analyses, datasets, and extensive examples in HTML with R scripts. The package also supports the course Biostatistics III entitled "Survival analysis for epidemiologists in R".
Maintained by Mark Clements. Last updated 2 months ago.
7.6 match 6 stars 4.73 score 153 scripts
pachadotdev
cepiigeodist:CEPII's GeoDist datasets in R
Provides data on countries and their main city or agglomeration and the different distance measures and dummy variables indicating whether two countries are contiguous, share a common language or a colonial relationship. The reference article for these datasets is Mayer and Zignago (2011).
Maintained by Mauricio Vargas. Last updated 2 years ago.
borderscolonizationgeodistancegravitylanguagestrade
10.0 match 3 stars 3.54 score 23 scripts
pbreheny
biglasso:Extending Lasso Model Fitting to Big Data
Extend lasso and elastic-net model fitting for large data sets that cannot be loaded into memory. Designed to be more memory- and computation-efficient than existing lasso-fitting packages like 'glmnet' and 'ncvreg', thus allowing the user to analyze big data with limited RAM <doi:10.32614/RJ-2021-001>.
Maintained by Patrick Breheny. Last updated 12 days ago.
bigdatalassoout-of-coreparallel-computingcppopenmp
3.5 match 113 stars 9.84 score 74 scripts 1 dependents
wjbraun
DAAG:Data Analysis and Graphics Data and Functions
Functions and data sets used in examples and exercises in the text Maindonald, J.H. and Braun, W.J. (2003, 2007, 2010) "Data Analysis and Graphics Using R", and in an upcoming Maindonald, Braun, and Andrews text that builds on this earlier text.
Maintained by W. John Braun. Last updated 11 months ago.
3.6 match 8.25 score 1.2k scripts 1 dependents
pilaboratory
sads:Maximum Likelihood Models for Species Abundance Distributions
Maximum likelihood tools to fit and compare models of species abundance distributions and of species rank-abundance distributions.
Maintained by Paulo I. Prado. Last updated 1 years ago.
3.4 match 23 stars 8.66 score 244 scripts 3 dependents
sachsmc
eventglm:Regression Models for Event History Outcomes
A user friendly, easy to understand way of doing event history regression for marginal estimands of interest, including the cumulative incidence and the restricted mean survival, using the pseudo observation framework for estimation. For a review of the methodology, see Andersen and Pohar Perme (2010) <doi:10.1177/0962280209105020> or Sachs and Gabriel (2022) <doi:10.18637/jss.v102.i09>. The interface uses the well known formulation of a generalized linear model and allows for features including plotting of residuals, the use of sampling weights, and corrected variance estimation.
Maintained by Michael C Sachs. Last updated 17 days ago.
4.6 match 5 stars 6.33 score 24 scripts 1 dependentsbioc
pathwayPCA:Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
pathwayPCA is an integrative analysis tool that implements the principal component analysis (PCA) based pathway analysis approaches described in Chen et al. (2008), Chen et al. (2010), and Chen (2011). pathwayPCA allows users to: (1) Test pathway association with binary, continuous, or survival phenotypes. (2) Extract relevant genes in the pathways using the SuperPCA and AES-PCA approaches. (3) Compute principal components (PCs) based on the selected genes. These estimated latent variables represent pathway activities for individual subjects, which can then be used to perform integrative pathway analysis, such as multi-omics analysis. (4) Extract relevant genes that drive pathway significance as well as data corresponding to these relevant genes for additional in-depth analysis. (5) Perform analyses with enhanced computational efficiency with parallel computing and enhanced data safety with S4-class data objects. (6) Analyze studies with complex experimental designs, with multiple covariates, and with interaction effects, e.g., testing whether pathway association with clinical phenotype is different between male and female subjects. Citations: Chen et al. (2008) <https://doi.org/10.1093/bioinformatics/btn458>; Chen et al. (2010) <https://doi.org/10.1002/gepi.20532>; and Chen (2011) <https://doi.org/10.2202/1544-6115.1697>.
Maintained by Gabriel Odom. Last updated 5 months ago.
copynumbervariationdnamethylationgeneexpressionsnptranscriptiongenepredictiongenesetenrichmentgenesignalinggenetargetgenomewideassociationgenomicvariationcellbiologyepigeneticsfunctionalgenomicsgeneticslipidomicsmetabolomicsproteomicssystemsbiologytranscriptomicsclassificationdimensionreductionfeatureextractionprincipalcomponentregressionsurvivalmultiplecomparisonpathways
3.8 match 11 stars 7.74 score 42 scripts
angelacar
TwoTimeScales:Analysis of Event Data with Two Time Scales
Analyse time to event data with two time scales by estimating a smooth hazard that varies over two time scales. If covariates are available, estimate a proportional hazards model with such a two-dimensional baseline hazard. Functions are provided to prepare the raw data for estimation, to estimate and to plot the two-dimensional smooth hazard. Extension to a competing risks model are implemented. For details about the method please refer to Carollo et al. (2024) <doi:10.1002/sim.10297>.
Maintained by Angela Carollo. Last updated 1 months ago.
4.6 match 9 stars 6.26 score 5 scripts
valentint
rda:Shrunken Centroids Regularized Discriminant Analysis
Provides functions implementing the shrunken centroids regularized discriminant analysis for classification purpose in high dimensional data. The method is described in Guo at al. (2013) <doi:10.1093/biostatistics/kxj035>.
Maintained by Valentin Todorov. Last updated 2 years ago.
9.0 match 3.02 score 21 scriptsbioc
methrix:Fast and efficient summarization of generic bedGraph files from Bisufite sequencing
Bedgraph files generated by Bisulfite pipelines often come in various flavors. Critical downstream step requires summarization of these files into methylation/coverage matrices. This step of data aggregation is done by Methrix, including many other useful downstream functions.
Maintained by Anand Mayakonda. Last updated 5 months ago.
dnamethylationsequencingcoveragebedgraphbioinformaticsdna-methylation
3.6 match 31 stars 7.51 score 39 scripts 1 dependents
dankelley
oce:Analysis of Oceanographic Data
Supports the analysis of Oceanographic data, including 'ADCP' measurements, measurements made with 'argo' floats, 'CTD' measurements, sectional data, sea-level time series, coastline and topographic data, etc. Provides specialized functions for calculating seawater properties such as potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state. Produces graphical displays that conform to the conventions of the Oceanographic literature. This package is discussed extensively by Kelley (2018) "Oceanographic Analysis with R" <doi:10.1007/978-1-4939-8844-0>.
Maintained by Dan Kelley. Last updated 2 days ago.
1.8 match 146 stars 15.42 score 4.2k scripts 18 dependents
jmbarbone
fuj:Functions and Utilities for Jordan
Provides core functions and utilities for packages and other code developed by Jordan Mark Barbone.
Maintained by Jordan Mark Barbone. Last updated 8 days ago.
6.0 match 2 stars 4.48 score 8 scripts 1 dependentsbioc
SpatialDecon:Deconvolution of mixed cells from spatial and/or bulk gene expression data
Using spatial or bulk gene expression data, estimates abundance of mixed cell types within each observation. Based on "Advances in mixed cell deconvolution enable quantification of cell types in spatial transcriptomic data", Danaher (2022). Designed for use with the NanoString GeoMx platform, but applicable to any gene expression data.
Maintained by Maddy Griswold. Last updated 5 months ago.
immunooncologyfeatureextractiongeneexpressiontranscriptomicsspatial
3.5 match 36 stars 7.40 score 58 scripts
longhaisk
HTLR:Bayesian Logistic Regression with Heavy-Tailed Priors
Efficient Bayesian multinomial logistic regression based on heavy-tailed (hyper-LASSO, non-convex) priors. The posterior of coefficients and hyper-parameters is sampled with restricted Gibbs sampling for leveraging the high-dimensionality and Hamiltonian Monte Carlo for handling the high-correlation among coefficients. A detailed description of the method: Li and Yao (2018), Journal of Statistical Computation and Simulation, 88:14, 2827-2851, <arXiv:1405.3319>.
Maintained by Longhai Li. Last updated 4 months ago.
bayesianclassificationhigh-dimensional-datamachine-learningmcmcopenblascppopenmp
4.5 match 10 stars 5.18 score 7 scripts
sjmack
HLAtools:Toolkit for HLA Immunogenomics
A toolkit for the analysis and management of data for genes in the so-called "Human Leukocyte Antigen" (HLA) region. Functions extract reference data from the Anthony Nolan HLA Informatics Group/ImmunoGeneTics HLA 'GitHub' repository (ANHIG/IMGTHLA) <https://github.com/ANHIG/IMGTHLA>, validate Genotype List (GL) Strings, convert between UNIFORMAT and GL String Code (GLSC) formats, translate HLA alleles and GLSCs across ImmunoPolymorphism Database (IPD) IMGT/HLA Database release versions, identify differences between pairs of alleles at a locus, generate customized, multi-position sequence alignments, trim and convert allele-names across nomenclature epochs, and extend existing data-analysis methods.
Maintained by Steven Mack. Last updated 14 days ago.
3.4 match 4 stars 6.21 score 7 scripts 1 dependents
lmaowisc
rmt:Restricted Mean Time in Favor of Treatment
Contains inferential and graphical routines for comparing two treatment arms in terms of the restricted mean time in favor of treatment.
Maintained by Lu Mao. Last updated 3 months ago.
4.8 match 4.34 score 22 scripts
hankstevens
primer:Functions and Data for the Book, a Primer of Ecology with R
Functions are primarily functions for systems of ordinary differential equations, difference equations, and eigenanalysis and projection of demographic matrices; data are for examples.
Maintained by Hank Stevens. Last updated 4 years ago.
3.5 match 14 stars 5.92 score 118 scriptsbioc
GlobalAncova:Global test for groups of variables via model comparisons
The association between a variable of interest (e.g. two groups) and the global pattern of a group of variables (e.g. a gene set) is tested via a global F-test. We give the following arguments in support of the GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values. The framework is generalized to groups of categorical variables or even mixed data by a likelihood ratio approach. Closed and hierarchical testing procedures are supported. This work was supported by the NGFN grant 01 GR 0459, BMBF, Germany and BMBF grant 01ZX1309B, Germany.
Maintained by Manuela Hummel. Last updated 5 months ago.
microarrayonechanneldifferentialexpressionpathwaysregression
3.8 match 5.32 score 9 scripts 1 dependents
anestistouloumis
ShrinkCovMat:Shrinkage Covariance Matrix Estimators
Provides nonparametric Steinian shrinkage estimators of the covariance matrix that are suitable in high dimensional settings, that is when the number of variables is larger than the sample size.
Maintained by Anestis Touloumis. Last updated 2 years ago.
covariance-matrixshrinkage-estimatorsopenblascppopenmp
4.0 match 8 stars 4.83 score 17 scripts
chjackson
survextrap:Survival Extrapolation with a Flexible Parametric Model and External Data
Survival analysis using a flexible Bayesian model for individual-level right-censored data, optionally combined with aggregate data on counts of survivors in different periods of time. An M-spline is used to describe the hazard function, with a hierarchical prior on the coefficients to control overfitting. Proportional hazards or flexible non-proportional hazards models can be used to relate survival to predictors. Mixture cure models, additive hazards (relative survival) models and waning treatment effects models are also supported. Priors can be customised and calibrated to substantive beliefs. Posterior distributions are estimated using Stan, and outputs are arranged in a tidy format. See See Jackson (2023) <doi:10.48550/arXiv.2306.03957>.
Maintained by Christopher Jackson. Last updated 19 days ago.
3.8 match 10 stars 5.00 score 11 scripts
project-gen3sis
gen3sis:General Engine for Eco-Evolutionary Simulations
Contains an engine for spatially-explicit eco-evolutionary mechanistic models with a modular implementation and several support functions. It allows exploring the consequences of ecological and macroevolutionary processes across realistic or theoretical spatio-temporal landscapes on biodiversity patterns as a general term. Reference: Oskar Hagen, Benjamin Flueck, Fabian Fopp, Juliano S. Cabral, Florian Hartig, Mikael Pontarp, Thiago F. Rangel, Loic Pellissier (2021) "gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth's biodiversity" <doi:10.1371/journal.pbio.3001340>.
Maintained by Oskar Hagen. Last updated 1 years ago.
biodiversityecologyevolutionmechanisticmodelmodelingsimulationcpp
2.5 match 29 stars 7.56 score 69 scriptsbioc
NormqPCR:Functions for normalisation of RT-qPCR data
Functions for the selection of optimal reference genes and the normalisation of real-time quantitative PCR data.
Maintained by James Perkins. Last updated 5 months ago.
microtitreplateassaygeneexpressionqpcr
3.5 match 4.72 score 26 scripts
cran
PlasmaMutationDetector:Tumor Mutation Detection in Plasma
Aims at detecting single nucleotide variation (SNV) and insertion/deletion (INDEL) in circulating tumor DNA (ctDNA), used as a surrogate marker for tumor, at each base position of an Next Generation Sequencing (NGS) analysis. Mutations are assessed by comparing the minor-allele frequency at each position to the measured PER in control samples.
Maintained by Yves Rozenholc. Last updated 7 years ago.
12.6 match 1.30 score
cardiomoon
ggiraphExtra:Make Interactive 'ggplot2'. Extension to 'ggplot2' and 'ggiraph'
Collection of functions to enhance 'ggplot2' and 'ggiraph'. Provides functions for exploratory plots. All plot can be a 'static' plot or an 'interactive' plot using 'ggiraph'.
Maintained by Keon-Woong Moon. Last updated 4 years ago.
1.8 match 48 stars 8.93 score 402 scripts 3 dependents
arturstat
TPmsm:Estimation of Transition Probabilities in Multistate Models
Estimation of transition probabilities for the illness-death model and or the three-state progressive model.
Maintained by Artur Araujo. Last updated 1 years ago.
illness-death-modelkaplan-meiermonte-carlo-simulationmulti-state-modelsopenmp-parallelizationsurvival-analysistransition-probabilitiesopenblasopenmp
3.5 match 1 stars 4.52 score 22 scripts 1 dependents
lassehjort
cuRe:Parametric Cure Model Estimation
Contains functions for estimating generalized parametric mixture and non-mixture cure models, loss of lifetime, mean residual lifetime, and crude event probabilities.
Maintained by Lasse Hjort Jakobsen. Last updated 2 years ago.
4.0 match 9 stars 3.90 score 22 scripts
jsocolar
flocker:Flexible Occupancy Estimation with Stan
Fit occupancy models in 'Stan' via 'brms'. The full variety of 'brms' formula-based effects structures are available to use in multiple classes of occupancy model, including single-season models, models with data augmentation for never-observed species, dynamic (multiseason) models with explicit colonization and extinction processes, and dynamic models with autologistic occupancy dynamics. Formulas can be specified for all relevant distributional terms, including detection and one or more of occupancy, colonization, extinction, and autologistic depending on the model type. Several important forms of model post-processing are provided. References: Bürkner (2017) <doi:10.18637/jss.v080.i01>; Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>; Socolar & Mills (2023) <doi:10.1101/2023.10.26.564080>.
Maintained by Jacob B. Socolar. Last updated 2 months ago.
2.3 match 30 stars 6.78 score 20 scriptsbioc
CINdex:Chromosome Instability Index
The CINdex package addresses important area of high-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar high throughput technologies. It calculates the chromosome instability (CIN) index that allows to quantitatively characterize genome-wide DNA copy number alterations as a measure of chromosomal instability. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses separately at the chromosome and cytoband level.
Maintained by Yuriy Gusev. Last updated 5 months ago.
softwarecopynumbervariationgenomicvariationacghmicroarraygeneticssequencing
3.8 match 4.08 score 2 scriptsjmbarbone
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.
3.0 match 6 stars 4.95 score 9 scripts
sestelo
condSURV:Estimation of the Conditional Survival Function for Ordered Multivariate Failure Time Data
Method to implement some newly developed methods for the estimation of the conditional survival function. See Meira-Machado, Sestelo and Goncalves (2016) <doi:10.1002/bimj.201500038>.
Maintained by Marta Sestelo. Last updated 2 years ago.
3.5 match 1 stars 4.21 score 107 scripts 1 dependents
lightbluetitan
OncoDataSets:A Comprehensive Collection of Cancer Types and Cancer-related DataSets
Offers a rich collection of data focused on cancer research, covering survival rates, genetic studies, biomarkers, and epidemiological insights. Designed for researchers, analysts, and bioinformatics practitioners, the package includes datasets on various cancer types such as melanoma, leukemia, breast, ovarian, and lung cancer, among others. It aims to facilitate advanced research, analysis, and understanding of cancer epidemiology, genetics, and treatment outcomes.
Maintained by Renzo Caceres Rossi. Last updated 3 months ago.
3.5 match 3 stars 4.18 score 6 scriptswjbraun
MPV:Data Sets from Montgomery, Peck and Vining
Most of this package consists of data sets from the textbook Introduction to Linear Regression Analysis, by Montgomery, Peck and Vining. All data sets from the 3rd edition are included and many from the 6th edition are also included. The package also contains some additional data sets and functions.
Maintained by W.J. Braun. Last updated 7 months ago.
4.0 match 3.36 score 193 scripts 1 dependentsbioc
MiPP:Misclassification Penalized Posterior Classification
This package finds optimal sets of genes that seperate samples into two or more classes.
Maintained by Sukwoo Kim. Last updated 5 months ago.
3.6 match 3.60 score 1 scriptsbioc
Icens:NPMLE for Censored and Truncated Data
Many functions for computing the NPMLE for censored and truncated data.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
3.4 match 3.83 score 16 scripts 7 dependentsrsetienne
DAMOCLES:Dynamic Assembly Model of Colonization, Local Extinction and Speciation
Simulates and computes (maximum) likelihood of a dynamical model of community assembly that takes into account phylogenetic history.
Maintained by Rampal S. Etienne. Last updated 3 months ago.
2.9 match 1 stars 4.34 score 11 scripts
statjs
bspcov:Bayesian Sparse Estimation of a Covariance Matrix
Provides functions which perform Bayesian estimations of a covariance matrix for multivariate normal data. Assumes that the covariance matrix is sparse or band matrix and positive-definite. This software has been developed using funding supported by Basic Science Research Program through the National Research Foundation of Korea ('NRF') funded by the Ministry of Education ('RS-2023-00211979', 'NRF-2022R1A5A7033499', 'NRF-2020R1A4A1018207' and 'NRF-2020R1C1C1A01013338').
Maintained by Kyeongwon Lee. Last updated 4 months ago.
4.5 match 1 stars 2.70 score 3 scripts
epiforesite
facilityepimath:Analyze Mathematical Models of Healthcare Facility Transmission
Calculate useful quantities for a user-defined differential equation model of infectious disease transmission among individuals in a healthcare facility. Input rates of transition between states of individuals with and without the disease-causing organism, distributions of states at facility admission, relative infectivity of transmissible states, and the facility length of stay distribution. Calculate the model equilibrium and the basic facility reproduction number, as described in Toth et al. (2025) <doi:10.1101/2025.02.21.25322698>.
Maintained by Damon Toth. Last updated 6 days ago.
2.3 match 5.18 score
ocbe-uio
matlab2r:Translation Layer from MATLAB to R
Allows users familiar with MATLAB to use MATLAB-named functions in R. Several basic MATLAB functions are written in this package to mimic the behavior of their original counterparts, with more to come as this package grows.
Maintained by Waldir Leoncio. Last updated 2 years ago.
3.3 match 2 stars 3.48 score 1 dependents
tjmahr
rprime:Functions for Working with 'Eprime' Text Files
'Eprime' is a set of programs for administering psychological experiments by computer. This package provides functions for loading, parsing, filtering and exporting data in the text files produced by 'Eprime' experiments.
Maintained by Tristan Mahr. Last updated 4 years ago.
eprimepsychologypsychology-experiments
1.7 match 23 stars 6.56 score 35 scripts 1 dependentssestelo
survidm:Inference and Prediction in an Illness-Death Model
Newly developed methods for the estimation of several probabilities in an illness-death model. The package can be used to obtain nonparametric and semiparametric estimates for: transition probabilities, occupation probabilities, cumulative incidence function and the sojourn time distributions. Additionally, it is possible to fit proportional hazards regression models in each transition of the Illness-Death Model. Several auxiliary functions are also provided which can be used for marginal estimation of the survival functions.
Maintained by Marta Sestelo. Last updated 4 years ago.
3.5 match 1 stars 2.95 score 18 scripts
cran
EcoVirtual:Simulation of Ecological Models
Computer simulations of classical ecological models as a learning resource.
Maintained by Alexandre Adalardo de Oliveira. Last updated 6 years ago.
5.3 match 1.48 score 1 dependents
gsoutinho
presmTP:Methods for Transition Probabilities
Provides a function for estimating the transition probabilities in an illness-death model. The transition probabilities can be estimated from the unsmoothed landmark estimators developed by de Una-Alvarez and Meira-Machado (2015) <doi:10.1111/biom.12288>. Presmoothed estimates can also be obtained through the use of a parametric family of binary regression curves, such as logit, probit or cauchit. The additive logistic regression model and nonparametric regression are also alternatives which have been implemented. The idea behind the presmoothed landmark estimators is to use the presmoothing techniques developed by Cao et al. (2005) <doi:10.1007/s00180-007-0076-6> in the landmark estimation of the transition probabilities.
Maintained by Gustavo Soutinho. Last updated 5 years ago.
3.5 match 1.70 score
apedrods
HiDimDA:High Dimensional Discriminant Analysis
Performs linear discriminant analysis in high dimensional problems based on reliable covariance estimators for problems with (many) more variables than observations. Includes routines for classifier training, prediction, cross-validation and variable selection.
Maintained by Antonio Pedro Duarte Silva. Last updated 5 months ago.
3.6 match 1.52 score 33 scripts
repboxr
repboxStata:Repbox analysis of stata scripts in reproduction packages
Repbox analysis of stata scripts in reproduction packages
Maintained by Sebastian Kranz. Last updated 1 months ago.
1.9 match 2.73 score 4 scripts 2 dependents
egenn
rtemisbio:rtemis Bio-informatics
Bio-informatics utilities
Maintained by E.D. Gennatas. Last updated 5 months ago.
1.8 match 1 stars 2.60 score 1 scriptscran
dirttee:Distributional Regression for Time to Event Data
Semiparametric distributional regression methods (expectile, quantile and mode regression) for time-to-event variables with right-censoring; uses inverse probability of censoring weights or accelerated failure time models with auxiliary likelihoods. Expectile regression using inverse probability of censoring weights has been introduced in Seipp et al. (2021) ``Weighted Expectile Regression for Right-Censored Data'' <doi:10.1002/sim.9137>, mode regression for time-to-event variables has been introduced in Seipp et al. (2022) ``Flexible Semiparametric Mode Regression for Time-to-Event Data'' <doi:10.1177/09622802221122406>.
Maintained by Alexander Seipp. Last updated 1 years ago.
4.0 match 1.00 scorecran
TP.idm:Estimation of Transition Probabilities for the Illness-Death Model
Estimation of transition probabilities for the illness-death model. Both the Aalen-Johansen estimator for a Markov model and a novel non-Markovian estimator by de Una-Alvarez and Meira-Machado (2015) <doi:10.1111/biom.12288>, see also Balboa and de Una-Alvarez (2018) <doi:10.18637/jss.v083.i10>, are included.
Maintained by Vanesa Balboa-Barreiro. Last updated 2 years ago.
3.5 match 1.00 score 7 scripts
stla
prettifyAddins:'RStudio' Addins to Prettify 'JavaScript', 'C++', 'Python', and More
Provides 'RStudio' addins to prettify 'HTML', 'CSS', 'SCSS', 'JavaScript', 'JSX', 'Markdown', 'C(++)', 'LaTeX', 'Python', 'Julia', 'XML', 'Java', 'JSON', 'Ruby', and to reindent 'C(++)', 'Fortran', 'Java', 'Julia', 'Python', 'SAS', 'Scala', 'Shell', 'SQL' and "TypeScript". Two kinds of addins are provided: 'Prettify' and 'Indent'. The 'Indent' addins only reindent the code, while the 'Prettify' addins also modify the code, e.g. trailing semi-colons are added to 'JavaScript' code when they are missing.
Maintained by Stéphane Laurent. Last updated 2 years ago.
0.5 match 21 stars 4.38 score 23 scripts
