Showing 79 of total 79 results (show query)
sacema
inctools:Incidence Estimation Tools
Tools for estimating incidence from biomarker data in cross- sectional surveys, and for calibrating tests for recent infection. Implements and extends the method of Kassanjee et al. (2012) <doi:10.1097/EDE.0b013e3182576c07>.
Maintained by Eduard Grebe. Last updated 4 years ago.
biomarkersbiostatisticsepidemiologyhivincidenceincidence-estimationincidence-inferenceinfectious-diseasesstatistics
15.7 match 6 stars 6.51 score 27 scripts
mrc-ide
naomi:Naomi Model for Subnational HIV Estimates
This package implements the Naomi model for subnational HIV estimates.
Maintained by Jeff Eaton. Last updated 6 days ago.
12.6 match 9 stars 7.74 score 54 scripts 2 dependents
emmanuelparadis
ape:Analyses of Phylogenetics and Evolution
Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
Maintained by Emmanuel Paradis. Last updated 11 hours ago.
5.3 match 64 stars 17.22 score 13k scripts 599 dependents
sineadmorris
ushr:Understanding Suppression of HIV
Analyzes longitudinal data of HIV decline in patients on antiretroviral therapy using the canonical biphasic exponential decay model (pioneered, for example, by work in Perelson et al. (1997) <doi:10.1038/387188a0>; and Wu and Ding (1999) <doi:10.1111/j.0006-341X.1999.00410.x>). Model fitting and parameter estimation are performed, with additional options to calculate the time to viral suppression. Plotting and summary tools are also provided for fast assessment of model results.
Maintained by Sinead E. Morris. Last updated 5 years ago.
21.2 match 2 stars 4.04 score 11 scripts
usaid-mozambique
sismar:Arrumar dados SISMA
Fornece um conjunto de funções para a criação de conjuntos de dados analíticos a partir de downloads do SISMA e DISA. Inclui funções que arrumam os ficheiros para um formato longo, removem variáveis desnecessárias, e criam colunas úteis para a análise.
Maintained by Joe Lara. Last updated 11 days ago.
16.3 match 2 stars 5.24 score 9 scripts
juanv66x
qvirus:Quantum Computing for Analyzing CD4 Lymphocytes and Antiretroviral Therapy
Resources, tutorials, and code snippets dedicated to exploring the intersection of quantum computing and artificial intelligence (AI) in the context of analyzing Cluster of Differentiation 4 (CD4) lymphocytes and optimizing antiretroviral therapy (ART) for human immunodeficiency virus (HIV). With the emergence of quantum artificial intelligence and the development of small-scale quantum computers, there's an unprecedented opportunity to revolutionize the understanding of HIV dynamics and treatment strategies. This project leverages the R package 'qsimulatR' (Ostmeyer and Urbach, 2023, <https://CRAN.R-project.org/package=qsimulatR>), a quantum computer simulator, to explore these applications in quantum computing techniques, addressing the challenges in studying CD4 lymphocytes and enhancing ART efficacy.
Maintained by Juan Pablo Acuña González. Last updated 11 days ago.
14.2 match 5.43 score 15 scripts
molevolepid
SEEPS:Sequence evolution and epidemiological process simulator
A modular, modern simulation suite and toolkit for simulating transmission networks, phylogenies, and evolutionary pairwise distance matrices under different models and assumptions for viral/sequence evolution. While intially developed for HIV, SEEPS offers modular utilities for custom workflows for extension beyond HIV.
Maintained by Michael Kupperman. Last updated 2 months ago.
biological-sequencesepidemiologyevolutionhivsimulation-framework
19.0 match 1 stars 3.95 score 6 scripts
ecomets
npde:Normalised Prediction Distribution Errors for Nonlinear Mixed-Effect Models
Provides routines to compute normalised prediction distribution errors, a metric designed to evaluate non-linear mixed effect models such as those used in pharmacokinetics and pharmacodynamics.
Maintained by Emmanuelle Comets. Last updated 1 years ago.
18.0 match 3.70 score 119 scripts 7 dependents
hputter
mstate:Data Preparation, Estimation and Prediction in Multi-State Models
Contains functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models, see Putter, Fiocco, Geskus (2007) <doi:10.1002/sim.2712>.
Maintained by Hein Putter. Last updated 28 days ago.
5.1 match 11 stars 12.13 score 322 scripts 55 dependents
ipa-tys
ROCR:Visualizing the Performance of Scoring Classifiers
ROC graphs, sensitivity/specificity curves, lift charts, and precision/recall plots are popular examples of trade-off visualizations for specific pairs of performance measures. ROCR is a flexible tool for creating cutoff-parameterized 2D performance curves by freely combining two from over 25 performance measures (new performance measures can be added using a standard interface). Curves from different cross-validation or bootstrapping runs can be averaged by different methods, and standard deviations, standard errors or box plots can be used to visualize the variability across the runs. The parameterization can be visualized by printing cutoff values at the corresponding curve positions, or by coloring the curve according to cutoff. All components of a performance plot can be quickly adjusted using a flexible parameter dispatching mechanism. Despite its flexibility, ROCR is easy to use, with only three commands and reasonable default values for all optional parameters.
Maintained by Felix G.M. Ernst. Last updated 12 months ago.
3.2 match 38 stars 14.29 score 9.2k scripts 217 dependents
drizopoulos
JMbayes2:Extended Joint Models for Longitudinal and Time-to-Event Data
Fit joint models for longitudinal and time-to-event data under the Bayesian approach. Multiple longitudinal outcomes of mixed type (continuous/categorical) and multiple event times (competing risks and multi-state processes) are accommodated. Rizopoulos (2012, ISBN:9781439872864).
Maintained by Dimitris Rizopoulos. Last updated 11 days ago.
competing-riskslongitudinal-analysismixed-modelsmulti-statepersonalized-medicineprecision-medicineprediction-modelsurvival-modelsopenblascppopenmp
5.4 match 84 stars 8.27 score 264 scripts 2 dependents
spedygiorgio
markovchain:Easy Handling Discrete Time Markov Chains
Functions and S4 methods to create and manage discrete time Markov chains more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of their structural proprieties) analysis are provided. See Spedicato (2017) <doi:10.32614/RJ-2017-036>. Some functions for continuous times Markov chains depend on the suggested ctmcd package.
Maintained by Giorgio Alfredo Spedicato. Last updated 4 months ago.
ctmcdtmcmarkov-chainmarkov-modelr-programmingrcppopenblascpp
3.4 match 104 stars 12.78 score 712 scripts 4 dependentsmrc-ide
first90:The first90 model
Implements the Shiny90 model for estimating progress towards the UNAIDS "first 90" target for HIV awareness of status in sub-Saharan Africa.
Maintained by Jeffrey Eaton. Last updated 4 months ago.
8.6 match 5 stars 4.53 score 2 scripts 3 dependents
usaid-oha-si
mindthegap:Mind the Gap
Package to tidy UNAIDS estimates (from the EDMS database) as well as plot trends in UNAIDS 95 goals and ART coverage gap by country.
Maintained by Karishma Srikanth. Last updated 2 months ago.
6.9 match 5 stars 5.51 score 13 scripts
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 2 days ago.
3.6 match 30 stars 10.54 score 65 scripts 93 dependentsdrizopoulos
JMbayes:Joint Modeling of Longitudinal and Time-to-Event Data under a Bayesian Approach
Shared parameter models for the joint modeling of longitudinal and time-to-event data using MCMC; Dimitris Rizopoulos (2016) <doi:10.18637/jss.v072.i07>.
Maintained by Dimitris Rizopoulos. Last updated 4 years ago.
joint-modelslongitudinal-responsesprediction-modelsurvival-analysisopenblascppopenmpjags
5.4 match 60 stars 6.98 score 80 scripts
tonisusin
coda4microbiome:Compositional Data Analysis for Microbiome Studies
Functions for microbiome data analysis that take into account its compositional nature. Performs variable selection through penalized regression for both, cross-sectional and longitudinal studies, and for binary and continuous outcomes.
Maintained by Toni Susin. Last updated 8 months ago.
23.1 match 2 stars 1.60 score 20 scripts
kjhealy
gssrdoc:Document General Social Survey Variable
The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.
Maintained by Kieran Healy. Last updated 11 months ago.
15.1 match 2.28 score 38 scriptsmrc-ide
eppasm:Age-structured EPP Model for HIV Epidemic Estimates
What the package does (one paragraph).
Maintained by Jeff Eaton. Last updated 3 months ago.
6.4 match 6 stars 5.04 score 34 scripts 3 dependents
alanarnholt
BSDA:Basic Statistics and Data Analysis
Data sets for book "Basic Statistics and Data Analysis" by Larry J. Kitchens.
Maintained by Alan T. Arnholt. Last updated 2 years ago.
3.3 match 7 stars 9.11 score 1.3k scripts 6 dependents
cran
boot:Bootstrap Functions (Originally by Angelo Canty for S)
Functions and datasets for bootstrapping from the book "Bootstrap Methods and Their Application" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.
Maintained by Alessandra R. Brazzale. Last updated 7 months ago.
3.6 match 2 stars 8.21 score 2.3k dependents
magosil86
bumblebee:Quantify Disease Transmission Within and Between Population Groups
A simple tool to quantify the amount of transmission of an infectious disease of interest occurring within and between population groups. 'bumblebee' uses counts of observed directed transmission pairs, identified phylogenetically from deep-sequence data or from epidemiological contacts, to quantify transmission flows within and between population groups accounting for sampling heterogeneity. Population groups might include: geographical areas (e.g. communities, regions), demographic groups (e.g. age, gender) or arms of a randomized clinical trial. See the 'bumblebee' website for statistical theory, documentation and examples <https://magosil86.github.io/bumblebee/>.
Maintained by Lerato E Magosi. Last updated 3 years ago.
epidemiologygeneticsheterogeneityphylogeneticstransmission
7.5 match 3.88 score 15 scripts
r-forge
Sleuth3:Data Sets from Ramsey and Schafer's "Statistical Sleuth (3rd Ed)"
Data sets from Ramsey, F.L. and Schafer, D.W. (2013), "The Statistical Sleuth: A Course in Methods of Data Analysis (3rd ed)", Cengage Learning.
Maintained by Berwin A Turlach. Last updated 1 years ago.
4.5 match 6.38 score 522 scripts
kogalur
randomForestSRC:Fast Unified Random Forests for Survival, Regression, and Classification (RF-SRC)
Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. New Mahalanobis splitting for correlated outcomes. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Minimal depth variable importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.
Maintained by Udaya B. Kogalur. Last updated 2 months ago.
3.6 match 10 stars 7.90 score 1.2k scripts 12 dependentsdrizopoulos
JM:Joint Modeling of Longitudinal and Survival Data
Shared parameter models for the joint modeling of longitudinal and time-to-event data.
Maintained by Dimitris Rizopoulos. Last updated 3 years ago.
5.4 match 2 stars 4.93 score 112 scripts 1 dependents
nickch-k
causaldata:Example Data Sets for Causal Inference Textbooks
Example data sets to run the example problems from causal inference textbooks. Currently, contains data sets for Huntington-Klein, Nick (2021) "The Effect" <https://theeffectbook.net>, first and second edition, Cunningham, Scott (2021, ISBN-13: 978-0-300-25168-5) "Causal Inference: The Mixtape", and Hernán, Miguel and James Robins (2020) "Causal Inference: What If" <https://www.hsph.harvard.edu/miguel-hernan/causal-inference-book/>.
Maintained by Nick Huntington-Klein. Last updated 4 months ago.
3.5 match 136 stars 7.43 score 144 scripts 1 dependentsr-forge
Sleuth2:Data Sets from Ramsey and Schafer's "Statistical Sleuth (2nd Ed)"
Data sets from Ramsey, F.L. and Schafer, D.W. (2002), "The Statistical Sleuth: A Course in Methods of Data Analysis (2nd ed)", Duxbury.
Maintained by Berwin A Turlach. Last updated 1 years ago.
4.5 match 5.70 score 191 scripts
bioc
TBSignatureProfiler:Profile RNA-Seq Data Using TB Pathway Signatures
Gene signatures of TB progression, TB disease, and other TB disease states have been validated and published previously. This package aggregates known signatures and provides computational tools to enlist their usage on other datasets. The TBSignatureProfiler makes it easy to profile RNA-Seq data using these signatures and includes common signature profiling tools including ASSIGN, GSVA, and ssGSEA. Original models for some gene signatures are also available. A shiny app provides some functionality alongside for detailed command line accessibility.
Maintained by Aubrey R. Odom. Last updated 3 months ago.
geneexpressiondifferentialexpressionbioconductor-packagebiomarkersgene-signaturestuberculosis
3.5 match 12 stars 7.25 score 23 scriptscran
ipw:Estimate Inverse Probability Weights
Functions to estimate the probability to receive the observed treatment, based on individual characteristics. The inverse of these probabilities can be used as weights when estimating causal effects from observational data via marginal structural models. Both point treatment situations and longitudinal studies can be analysed. The same functions can be used to correct for informative censoring.
Maintained by Willem M. van der Wal. Last updated 1 years ago.
10.9 match 2.28 score
ajsims1704
rdecision:Decision Analytic Modelling in Health Economics
Classes and functions for modelling health care interventions using decision trees and semi-Markov models. Mechanisms are provided for associating an uncertainty distribution with each source variable and for ensuring transparency of the mathematical relationships between variables. The package terminology follows Briggs "Decision Modelling for Health Economic Evaluation" (2006, ISBN:978-0-19-852662-9).
Maintained by Andrew Sims. Last updated 1 months ago.
3.8 match 3 stars 6.46 score 22 scriptscran
vipor:Plot Categorical Data Using Quasirandom Noise and Density Estimates
Generate a violin point plot, a combination of a violin/histogram plot and a scatter plot by offsetting points within a category based on their density using quasirandom noise.
Maintained by Scott Sherrill-Mix. Last updated 1 years ago.
3.5 match 6.86 score 95 dependents
disohda
DiscreteDatasets:Example Data Sets for Use with Discrete Statistical Tests
Provides several data sets for use with discrete statistical tests and discrete multiple testing procedures. Some of them are also available as a four-column version, so that each row represents a 2x2 table.
Maintained by Florian Junge. Last updated 2 months ago.
6.8 match 3.56 score 4 scripts 3 dependents
hrpcisd
locfdr:Computes Local False Discovery Rates
Computation of local false discovery rates.
Maintained by Balasubramanian Narasimhan. Last updated 10 years ago.
4.0 match 5.99 score 106 scripts 14 dependents
bdwilliamson
vimp:Perform Inference on Algorithm-Agnostic Variable Importance
Calculate point estimates of and valid confidence intervals for nonparametric, algorithm-agnostic variable importance measures in high and low dimensions, using flexible estimators of the underlying regression functions. For more information about the methods, please see Williamson et al. (Biometrics, 2020), Williamson et al. (JASA, 2021), and Williamson and Feng (ICML, 2020).
Maintained by Brian D. Williamson. Last updated 1 months ago.
machine-learningnonparametric-statisticsstatistical-inferencevariable-importance
3.5 match 23 stars 6.79 score 67 scriptsbioc
MSA2dist:MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis
MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. It uses scoring matrices to be used in these pairwise distance calcualtions which can be adapted to any scoring for DNA or AA characters. E.g. by using literal distances MSA2dist calculates pairwise IUPAC distances.
Maintained by Kristian K Ullrich. Last updated 4 months ago.
alignmentsequencinggeneticsgocpp
4.5 match 5.02 score 7 scripts 1 dependents
mcguirebc
KernSmoothIRT:Nonparametric Item Response Theory
Fits nonparametric item and option characteristic curves using kernel smoothing. It allows for optimal selection of the smoothing bandwidth using cross-validation and a variety of exploratory plotting tools. The kernel smoothing is based on methods described in Silverman, B.W. (1986). Density Estimation for Statistics and Data Analysis. Chapman & Hall, London.
Maintained by Brian McGuire. Last updated 5 years ago.
11.3 match 1 stars 1.98 score 24 scripts
christophergandrud
simPH:Simulate and Plot Estimates from Cox Proportional Hazards Models
Simulates and plots quantities of interest (relative hazards, first differences, and hazard ratios) for linear coefficients, multiplicative interactions, polynomials, penalised splines, and non-proportional hazards, as well as stratified survival curves from Cox Proportional Hazard models. It also simulates and plots marginal effects for multiplicative interactions. Methods described in Gandrud (2015) <doi:10.18637/jss.v065.i03>.
Maintained by Christopher Gandrud. Last updated 3 years ago.
3.5 match 14 stars 6.23 score 48 scriptsbioc
Polytect:An R package for digital data clustering
Polytect is an advanced computational tool designed for the analysis of multi-color digital PCR data. It provides automatic clustering and labeling of partitions into distinct groups based on clusters first identified by the flowPeaks algorithm. Polytect is particularly useful for researchers in molecular biology and bioinformatics, enabling them to gain deeper insights into their experimental results through precise partition classification and data visualization.
Maintained by Yao Chen. Last updated 3 months ago.
ddpcrclusteringmultichannelclassification
4.5 match 4.74 score 4 scripts
richardli
surveyPrev:Mapping the Prevalence of Binary Indicators using Survey Data in Small Areas
Provides a pipeline to perform small area estimation and prevalence mapping of binary indicators using health and demographic survey data, described in Fuglstad et al. (2022) <doi:10.48550/arXiv.2110.09576> and Wakefield et al. (2020) <doi:10.1111/insr.12400>.
Maintained by Qianyu Dong. Last updated 5 days ago.
3.4 match 1 stars 5.76 score 11 scriptsmrc-ide
hintr:R API for calling naomi district level HIV model
R API for calling naomi district level HIV model.
Maintained by Robert Ashton. Last updated 5 days ago.
3.4 match 2 stars 5.80 score 2 scripts 1 dependentsmrc-ide
specio:Read Spectrum Files
Read data from Spectrum PJNZ file into R consumable format for EPP.
Maintained by Robert Ashton. Last updated 4 years ago.
5.1 match 1 stars 3.78 score 1 scripts 2 dependents
jmcurran
Bolstad2:Bolstad Functions
A set of R functions and data sets for the book "Understanding Computational Bayesian Statistics." This book was written by Bill (WM) Bolstad and published in 2009 by John Wiley & Sons (ISBN 978-0470046098).
Maintained by James Curran. Last updated 3 years ago.
4.0 match 1 stars 4.78 score 74 scripts 9 dependents
ubclxing
MTPS:Multi-Task Prediction using Stacking Algorithms
Simultaneous multiple outcomes prediction based on revised stacking algorithms, which enables the integration of information from predictions of individual models. An implementation of methodologies proposed in our paper: Li Xing, Mary L Lesperance, Xuekui Zhang. (2019) Bioinformatics, "Simultaneous prediction of multiple outcomes using revised stacking algorithms" <doi:10.1093/bioinformatics/btz531>.
Maintained by Li Xing. Last updated 2 years ago.
5.6 match 3.18 score 8 scripts 1 dependentsdrizopoulos
cvGEE:Cross-Validated Predictions from GEE
Calculates predictions from generalized estimating equations and internally cross-validates them using the logarithmic, quadratic and spherical proper scoring rules; Kung-Yee Liang and Scott L. Zeger (1986) <doi:10.1093/biomet/73.1.13>.
Maintained by Dimitris Rizopoulos. Last updated 6 years ago.
3.6 match 3 stars 4.18 score
jmm34
bayess:Bayesian Essentials with R
Allows the reenactment of the R programs used in the book Bayesian Essentials with R without further programming. R code being available as well, they can be modified by the user to conduct one's own simulations. Marin J.-M. and Robert C. P. (2014) <doi:10.1007/978-1-4614-8687-9>.
Maintained by Jean-Michel Marin. Last updated 1 years ago.
3.8 match 3 stars 4.01 score 68 scripts
aphp
heemod:Markov Models for Health Economic Evaluations
An implementation of the modelling and reporting features described in reference textbook and guidelines (Briggs, Andrew, et al. Decision Modelling for Health Economic Evaluation. Oxford Univ. Press, 2011; Siebert, U. et al. State-Transition Modeling. Medical Decision Making 32, 690-700 (2012).): deterministic and probabilistic sensitivity analysis, heterogeneity analysis, time dependency on state-time and model-time (semi-Markov and non-homogeneous Markov models), etc.
Maintained by Kevin Zarca. Last updated 6 months ago.
1.5 match 15 stars 8.81 score 204 scriptscran
randomLCA:Random Effects Latent Class Analysis
Fits standard and random effects latent class models. The single level random effects model is described in Qu et al <doi:10.2307/2533043> and the two level random effects model in Beath and Heller <doi:10.1177/1471082X0800900302>. Examples are given for their use in diagnostic testing.
Maintained by Ken Beath. Last updated 6 months ago.
4.0 match 3.10 score 42 scriptsjuanv66x
viralx:Explainers for Regression Models in HIV Research
A dedicated viral-explainer model tool designed to empower researchers in the field of HIV research, particularly in viral load and CD4 (Cluster of Differentiation 4) lymphocytes regression modeling. Drawing inspiration from the 'tidymodels' framework for rigorous model building of Max Kuhn and Hadley Wickham (2020) <https://www.tidymodels.org>, and the 'DALEXtra' tool for explainability by Przemyslaw Biecek (2020) <doi:10.48550/arXiv.2009.13248>. It aims to facilitate interpretable and reproducible research in biostatistics and computational biology for the benefit of understanding HIV dynamics.
Maintained by Juan Pablo Acuña González. Last updated 4 months ago.
3.8 match 3.00 score 1 scriptscran
CICI:Causal Inference with Continuous (Multiple Time Point) Interventions
Estimation of counterfactual outcomes for multiple values of continuous interventions at different time points, and plotting of causal dose-response curves. Details are given in Schomaker, McIlleron, Denti, Diaz (2024) <doi:10.48550/arXiv.2305.06645>.
Maintained by Michael Schomaker. Last updated 3 months ago.
7.5 match 1 stars 1.48 score
ostirrup
covBM:Brownian Motion Processes for 'nlme'-Models
Allows Brownian motion, fractional Brownian motion, and integrated Ornstein-Uhlenbeck process components to be added to linear and non-linear mixed effects models using the structures and methods of the 'nlme' package.
Maintained by Oliver Stirrup. Last updated 9 years ago.
3.6 match 3.00 score 10 scripts
lhvanegasp
glmtoolbox:Set of Tools to Data Analysis using Generalized Linear Models
Set of tools for the statistical analysis of data using: (1) normal linear models; (2) generalized linear models; (3) negative binomial regression models as alternative to the Poisson regression models under the presence of overdispersion; (4) beta-binomial and random-clumped binomial regression models as alternative to the binomial regression models under the presence of overdispersion; (5) Zero-inflated and zero-altered regression models to deal with zero-excess in count data; (6) generalized nonlinear models; (7) generalized estimating equations for cluster correlated data.
Maintained by Luis Hernando Vanegas. Last updated 8 months ago.
3.5 match 1 stars 3.00 score 149 scriptscran
intccr:Semiparametric Competing Risks Regression under Interval Censoring
Semiparametric regression models on the cumulative incidence function for interval-censored competing risks data as described in Bakoyannis, Yu, & Yiannoutsos (2017) /doi{10.1002/sim.7350} and the models with missing event types as described in Park, Bakoyannis, Zhang, & Yiannoutsos (2021) \doi{10.1093/biostatistics/kxaa052}. The proportional subdistribution hazards model (Fine-Gray model), the proportional odds model, and other models that belong to the class of semiparametric generalized odds rate transformation models.
Maintained by Jun Park. Last updated 3 years ago.
4.0 match 1 stars 2.57 score 37 scripts
egr95
codacore:Learning Sparse Log-Ratios for Compositional Data
In the context of high-throughput genetic data, CoDaCoRe identifies a set of sparse biomarkers that are predictive of a response variable of interest (Gordon-Rodriguez et al., 2021) <doi:10.1093/bioinformatics/btab645>. More generally, CoDaCoRe can be applied to any regression problem where the independent variable is Compositional (CoDa), to derive a set of scale-invariant log-ratios (ILR or SLR) that are maximally associated to a dependent variable.
Maintained by Elliott Gordon-Rodriguez. Last updated 3 years ago.
3.6 match 2.70 score 2 scripts
williamqjw
lmreg:Data and Functions Used in Linear Models and Regression with R: An Integrated Approach
Data files and a few functions used in the book 'Linear Models and Regression with R: An Integrated Approach' by Debasis Sengupta and Sreenivas Rao Jammalamadaka (2019).
Maintained by Jinwen Qiu. Last updated 6 years ago.
4.5 match 2.06 score 116 scripts
bdhitt
binGroup2:Identification and Estimation using Group Testing
Methods for the group testing identification problem: 1) Operating characteristics (e.g., expected number of tests) for commonly used hierarchical and array-based algorithms, and 2) Optimal testing configurations for these same algorithms. Methods for the group testing estimation problem: 1) Estimation and inference procedures for an overall prevalence, and 2) Regression modeling for commonly used hierarchical and array-based algorithms.
Maintained by Brianna Hitt. Last updated 1 years ago.
3.8 match 2.48 score 3 scripts 1 dependentscran
Rcapture:Loglinear Models for Capture-Recapture Experiments
Estimation of abundance and other demographic parameters for closed populations, open populations and the robust design in capture-recapture experiments using loglinear models.
Maintained by Louis-Paul Rivest. Last updated 3 years ago.
3.6 match 1 stars 2.53 score 1 dependents
darth-git
dampack:Decision-Analytic Modeling Package
A suite of functions for analyzing and visualizing the health economic outputs of mathematical models. This package was developed with funding from the National Institutes of Allergy and Infectious Diseases of the National Institutes of Health under award no. R01AI138783. The content of this package is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The theoretical underpinnings of 'dampack''s functionality are detailed in Hunink et al. (2014) <doi:10.1017/CBO9781139506779>.
Maintained by David Garibay. Last updated 6 months ago.
1.1 match 35 stars 8.35 score 161 scripts
imranshakoor
hivdata:Six-Year Chronological Data of HIV and ART Cases in Pakistan
We provide the monthly number of HIV and antiretroviral therapy (ART) cases of male, female, children and transgender as well as for the whole of Pakistan reported at various treatment centers in Pakistan from January 2016 to December 2021. Related works include: a) Imran, M., Nasir, J. A., & Riaz, S. (2018). Regional pattern of HIV cases in Pakistan. Journal of Postgraduate Medical Institute, 32(1), 9-13. <https://jpmi.org.pk/index.php/jpmi/article/view/2108>.
Maintained by Muhammad Imran. Last updated 1 years ago.
8.7 match 1.00 score
mayamathur
EValue:Sensitivity Analyses for Unmeasured Confounding and Other Biases in Observational Studies and Meta-Analyses
Conducts sensitivity analyses for unmeasured confounding, selection bias, and measurement error (individually or in combination; VanderWeele & Ding (2017) <doi:10.7326/M16-2607>; Smith & VanderWeele (2019) <doi:10.1097/EDE.0000000000001032>; VanderWeele & Li (2019) <doi:10.1093/aje/kwz133>; Smith & VanderWeele (2021) <arXiv:2005.02908>). Also conducts sensitivity analyses for unmeasured confounding in meta-analyses (Mathur & VanderWeele (2020a) <doi:10.1080/01621459.2018.1529598>; Mathur & VanderWeele (2020b) <doi:10.1097/EDE.0000000000001180>) and for additive measures of effect modification (Mathur et al., under review).
Maintained by Maya B. Mathur. Last updated 3 years ago.
1.3 match 3 stars 6.35 score 99 scripts 1 dependentsusaid-mozambique
sonata:Interagir com MozART 2.0
Provides a set of utilities and functions for connecting, querying, and analyzing data from the Mozambique MozART 2.0 database.
Maintained by Joe Lara. Last updated 1 days ago.
1.9 match 4.08 score
kwkim89
SizeEstimation:Estimating the Sizes of Populations at Risk of HIV Infection from Multiple Data Sources Using a Bayesian Hierarchical Model
This function develops an algorithm for presenting a Bayesian hierarchical model for estimating the sizes of local and national drug injected populations in Bangladesh. The model incorporates multiple commonly used data sources including mapping data, surveys, interventions, capture-recapture data, estimates or guesstimates from organizations, and expert opinion.
Maintained by Kyongwon Kim. Last updated 6 years ago.
2.7 match 2.70 score 1 scripts
helenxu
JSM:Semiparametric Joint Modeling of Survival and Longitudinal Data
Maximum likelihood estimation for the semiparametric joint modeling of survival and longitudinal data. Refer to the Journal of Statistical Software article: <doi:10.18637/jss.v093.i02>.
Maintained by Cong Xu. Last updated 5 years ago.
3.5 match 1.99 score 14 scripts
damurka
cancerscreening:Streamline Access to Cancer Screening Data
Retrieve cancer screening data for cervical, breast and colorectal cancers from the Kenya Health Information System <https://hiskenya.org> in a consistent way.
Maintained by David Kariuki. Last updated 9 months ago.
1.7 match 1 stars 4.00 score 2 scripts
hfloechel
kaos:Encoding of Sequences Based on Frequency Matrix Chaos Game Representation
Sequences encoding by using the chaos game representation. Löchel et al. (2019) <doi:10.1093/bioinformatics/btz493>.
Maintained by Hannah Franziska Löchel. Last updated 5 years ago.
3.8 match 1 stars 1.48 score 7 scripts 1 dependents
ropensci
DataSpaceR:Interface to 'the CAVD DataSpace'
Provides a convenient API interface to access immunological data within 'the CAVD DataSpace'(<https://dataspace.cavd.org>), a data sharing and discovery tool that facilitates exploration of HIV immunological data from pre-clinical and clinical HIV vaccine studies.
Maintained by Jason Taylor. Last updated 24 days ago.
0.8 match 5 stars 6.72 score 42 scripts
nchenderson
rvalues:R-Values for Ranking in High-Dimensional Settings
A collection of functions for computing "r-values" from various kinds of user input such as MCMC output or a list of effect size estimates and associated standard errors. Given a large collection of measurement units, the r-value, r, of a particular unit is a reported percentile that may be interpreted as the smallest percentile at which the unit should be placed in the top r-fraction of units.
Maintained by Nicholas Henderson. Last updated 4 years ago.
4.0 match 1.30 score 20 scripts
chedgala
qrNLMM:Quantile Regression for Nonlinear Mixed-Effects Models
Quantile regression (QR) for Nonlinear Mixed-Effects Models via the asymmetric Laplace distribution (ALD). It uses the Stochastic Approximation of the EM (SAEM) algorithm for deriving exact maximum likelihood estimates and full inference results for the fixed-effects and variance components. It also provides prediction and graphical summaries for assessing the algorithm convergence and fitting results.
Maintained by Christian E. Galarza. Last updated 8 months ago.
3.8 match 2 stars 1.30 score 5 scripts
shihao-yang
magi:MAnifold-Constrained Gaussian Process Inference
Provides fast and accurate inference for the parameter estimation problem in Ordinary Differential Equations, including the case when there are unobserved system components. Implements the MAGI method (MAnifold-constrained Gaussian process Inference) of Yang, Wong, and Kou (2021) <doi:10.1073/pnas.2020397118>. A user guide is provided by the accompanying software paper Wong, Yang, and Kou (2024) <doi:10.18637/jss.v109.i04>.
Maintained by Shihao Yang. Last updated 9 months ago.
1.1 match 3.67 score 47 scriptscran
icensBKL:Accompanion to the Book on Interval Censoring by Bogaerts, Komarek, and Lesaffre
Contains datasets and several smaller functions suitable for analysis of interval-censored data. The package complements the book Bogaerts, Komárek and Lesaffre (2017, ISBN: 978-1-4200-7747-6) "Survival Analysis with Interval-Censored Data: A Practical Approach" <https://www.routledge.com/Survival-Analysis-with-Interval-Censored-Data-A-Practical-Approach-with/Bogaerts-Komarek-Lesaffre/p/book/9781420077476>. Full R code related to the examples presented in the book can be found at <https://ibiostat.be/online-resources/icbook/supplemental>. Packages mentioned in the "Suggests" section are used in those examples.
Maintained by Arnošt Komárek. Last updated 1 years ago.
3.8 match 1 stars 1.00 scorecran
cdlei:Cause-Deleted Life Expectancy Improvement Procedure
The concept of cause-deleted life expectancy improvement is statistic designed to quantify the increase in life expectancy if a certain cause of death is removed. See Adamic, P. (2015) (<https://papers.ssrn.com/sol3/papers.cfm?abstract_id=2689352>).
Maintained by Alicja Wolny-Dominiak. Last updated 5 years ago.
3.4 match 1.00 scoreusaid-oha-si
gisr:Geospatial Analytics Utility functions
R Spatial functions for HIV/AIDS related Geospatial Analytics.
Maintained by Baboyma Kagniniwa. Last updated 1 years ago.
0.6 match 2 stars 5.29 score 328 scriptsmrc-ide
naomi.utils:Utility Functions For Naomi Datasets
This package contains utility functions for creating and manipulating datasets for the Naomi model and related projects.
Maintained by Jeffrey Eaton. Last updated 12 months ago.
1.8 match 1 stars 1.64 score 11 scripts
youyifong
copcor:Correlates of Protection and Correlates of Risk Functions
Correlates of protection (CoP) and correlates of risk (CoR) study the immune biomarkers associated with an infectious disease outcome, e.g. COVID or HIV-1 infection. This package contains shared functions for analyzing CoP and CoR, including bootstrapping procedures, competing risk estimation, and bootstrapping marginalized risks.
Maintained by Youyi Fong. Last updated 8 months ago.
0.5 match 2.90 score 16 scripts
noahhaber
longitudinalcascade:Longitudinal Cascade
Creates a series of sets of graphics and statistics related to the longitudinal cascade, all included in a single object. The longitudinal cascade inputs longitudinal data to identify gaps in the HIV and related cascades by observing differences using time to event and survival methods. The stage definitions are set by the user, with default standard options. Outputs include graphics, datasets, and formal statistical tests.
Maintained by Noah Haber. Last updated 2 years ago.
0.5 match 2.00 score 4 scripts
