Showing 124 of total 124 results (show query)
insightsengineering
teal:Exploratory Web Apps for Analyzing Clinical Trials Data
A 'shiny' based interactive exploration framework for analyzing clinical trials data. 'teal' currently provides a dynamic filtering facility and different data viewers. 'teal' 'shiny' applications are built using standard 'shiny' modules.
Maintained by Dawid Kaledkowski. Last updated 1 months ago.
clinical-trialsnestshinywebapp
206 stars 12.65 score 176 scripts 5 dependents
danchaltiel
crosstable:Crosstables for Descriptive Analyses
Create descriptive tables for continuous and categorical variables. Apply summary statistics and counting function, with or without a grouping variable, and create beautiful reports using 'rmarkdown' or 'officer'. You can also compute effect sizes and statistical tests if needed.
Maintained by Dan Chaltiel. Last updated 2 months ago.
descriptive-statisticsflextablefrequency-tablehtml-reportmswordofficer
116 stars 10.40 score 340 scriptsinsightsengineering
teal.modules.clinical:'teal' Modules for Standard Clinical Outputs
Provides user-friendly tools for creating and customizing clinical trial reports. By leveraging the 'teal' framework, this package provides 'teal' modules to easily create an interactive panel that allows for seamless adjustments to data presentation, thereby streamlining the creation of detailed and accurate reports.
Maintained by Dawid Kaledkowski. Last updated 1 months ago.
clinical-trialsmodulesnestoutputsshiny
35 stars 10.21 score 149 scriptsinsightsengineering
teal.modules.general:General Modules for 'teal' Applications
Prebuilt 'shiny' modules containing tools for viewing data, visualizing data, understanding missing and outlier values within your data and performing simple data analysis. This extends 'teal' framework that supports reproducible research and analysis.
Maintained by Dawid Kaledkowski. Last updated 1 days ago.
general-purposemodulesnestshiny
13 stars 9.74 score 71 scriptsinsightsengineering
teal.reporter:Reporting Tools for 'shiny' Modules
Prebuilt 'shiny' modules containing tools for the generation of 'rmarkdown' reports, supporting reproducible research and analysis.
Maintained by Dawid Kaledkowski. Last updated 2 months ago.
8 stars 9.27 score 19 scripts 6 dependents
atusy
ftExtra:Extensions for 'Flextable'
Build display tables easily by extending the functionality of the 'flextable' package. Features include spanning header, grouping rows, parsing markdown and so on.
Maintained by Atsushi Yasumoto. Last updated 2 months ago.
65 stars 9.19 score 194 scripts
jinseob2kim
jsmodule:'RStudio' Addins and 'Shiny' Modules for Medical Research
'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Maintained by Jinseob Kim. Last updated 16 days ago.
medicalrstudio-addinsshinyshiny-modulesstatistics
21 stars 8.69 score 61 scripts
isubirana
compareGroups:Descriptive Analysis by Groups
Create data summaries for quality control, extensive reports for exploring data, as well as publication-ready univariate or bivariate tables in several formats (plain text, HTML,LaTeX, PDF, Word or Excel. Create figures to quickly visualise the distribution of your data (boxplots, barplots, normality-plots, etc.). Display statistics (mean, median, frequencies, incidences, etc.). Perform the appropriate tests (t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...) depending on the nature of the described variable (normal, non-normal or qualitative). Summarize genetic data (Single Nucleotide Polymorphisms) data displaying Allele Frequencies and performing Hardy-Weinberg Equilibrium tests among other typical statistics and tests for these kind of data.
Maintained by Isaac Subirana. Last updated 1 months ago.
comparegroupsdescriptive-statisticsplotreporttable
36 stars 8.46 score 396 scripts 1 dependents
john-harrold
onbrand:Templated Reporting Workflows in Word and PowerPoint
Automated reporting in Word and PowerPoint can require customization for each organizational template. This package works around this by adding standard reporting functions and an abstraction layer to facilitate automated reporting workflows that can be replicated across different organizational templates.
Maintained by John Harrold. Last updated 2 months ago.
24 stars 8.11 score 45 scripts 4 dependents
cran
epiR:Tools for the Analysis of Epidemiological Data
Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Maintained by Mark Stevenson. Last updated 2 months ago.
10 stars 8.06 score 10 dependentsjohn-harrold
formods:'Shiny' Modules for General Tasks
'Shiny' apps can often make use of the same key elements, this package provides modules for common tasks (data upload, wrangling data, figure generation and saving the app state), and also a framework for developing. These modules can react and interact as well as generate code to create reproducible analyses.
Maintained by John Harrold. Last updated 23 days ago.
8 stars 7.94 score 100 scripts 1 dependents
cardiomoon
ztable:Zebra-Striped Tables in LaTeX and HTML Formats
Makes zebra-striped tables (tables with alternating row colors) in LaTeX and HTML formats easily from a data.frame, matrix, lm, aov, anova, glm, coxph, nls, fitdistr, mytable and cbind.mytable objects.
Maintained by Keon-Woong Moon. Last updated 2 years ago.
21 stars 7.90 score 212 scripts 2 dependents
mthulin
boot.pval:Bootstrap p-Values
Computation of bootstrap p-values through inversion of confidence intervals, including convenience functions for regression models and tests of location.
Maintained by Måns Thulin. Last updated 27 days ago.
bootstrapp-valueregression-models
4 stars 7.89 score 36 scripts 3 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 5 days ago.
data-analysistampa-baytbepwater-quality
10 stars 7.86 score 133 scripts
sciviews
SciViews:'SciViews' - Data Processing and Visualization with the 'SciViews::R' Dialect
The 'SciViews::R' dialect provides a set of functions that streamlines data input, process, analysis and visualization especially, but not exclusively, for beginners or occasional users. It mixes base R and tidyverse, plus another set of CRAN packages for an easy and coherent use of R.
Maintained by Philippe Grosjean. Last updated 7 months ago.
8 stars 7.62 score 116 scripts 1 dependentsjohn-harrold
ubiquity:PKPD, PBPK, and Systems Pharmacology Modeling Tools
Complete work flow for the analysis of pharmacokinetic pharmacodynamic (PKPD), physiologically-based pharmacokinetic (PBPK) and systems pharmacology models including: creation of ordinary differential equation-based models, pooled parameter estimation, individual/population based simulations, rule-based simulations for clinical trial design and modeling assays, deployment with a customizable 'Shiny' app, and non-compartmental analysis. System-specific analysis templates can be generated and each element includes integrated reporting with 'PowerPoint' and 'Word'.
Maintained by John Harrold. Last updated 12 days ago.
13 stars 7.14 score 33 scriptscardiomoon
autoReg:Automatic Linear and Logistic Regression and Survival Analysis
Make summary tables for descriptive statistics and select explanatory variables automatically in various regression models. Support linear models, generalized linear models and cox-proportional hazard models. Generate publication-ready tables summarizing result of regression analysis and plots. The tables and plots can be exported in "HTML", "pdf('LaTex')", "docx('MS Word')" and "pptx('MS Powerpoint')" documents.
Maintained by Keon-Woong Moon. Last updated 1 years ago.
49 stars 7.13 score 69 scripts
john-harrold
ruminate:A Pharmacometrics Data Transformation and Analysis Tool
Exploration of pharmacometrics data involves both general tools (transformation and plotting) and specific techniques (non-compartmental analysis). This kind of exploration is generally accomplished by utilizing different packages. The purpose of 'ruminate' is to create a 'shiny' interface to make these tools more broadly available while creating reproducible results.
Maintained by John Harrold. Last updated 23 days ago.
2 stars 7.06 score 84 scripts
bioc
GenomicSuperSignature:Interpretation of RNA-seq experiments through robust, efficient comparison to public databases
This package provides a novel method for interpreting new transcriptomic datasets through near-instantaneous comparison to public archives without high-performance computing requirements. Through the pre-computed index, users can identify public resources associated with their dataset such as gene sets, MeSH term, and publication. Functions to identify interpretable annotations and intuitive visualization options are implemented in this package.
Maintained by Sehyun Oh. Last updated 5 months ago.
transcriptomicssystemsbiologyprincipalcomponentrnaseqsequencingpathwaysclusteringbioconductor-packageexploratory-data-analysisgseameshprincipal-component-analysisrna-sequencing-profilestransferlearningu24ca289073
16 stars 6.97 score 59 scripts
tsmodels
tsgarch:Univariate GARCH Models
Multiple flavors of the Generalized Autoregressive Conditional Heteroskedasticity (GARCH) model with a large choice of conditional distributions. Methods for specification, estimation, prediction, filtering, simulation, statistical testing and more. Represents a partial re-write and re-think of 'rugarch', making use of automatic differentiation for estimation.
Maintained by Alexios Galanos. Last updated 4 months ago.
13 stars 6.93 score 16 scripts 1 dependents
nmfs-ost
asar:Build NOAA Stock Assessment Report
Build a full or update stock assessment report for any stock assessment model. Parameterization allows the user to call a template based on their regional science center, species, area, ect.
Maintained by Samantha Schiano. Last updated 1 hours ago.
latexnoaa-nsapquartostock-assessmentstock-assessment-reports
22 stars 6.85 score 3 scriptsinsightsengineering
rtables.officer:Exporting Tools for 'rtables'
Designed to create and display complex tables with R, the 'rtables' R package allows cells in an 'rtables' object to contain any high-dimensional data structure, which can then be displayed with cell-specific formatting instructions. Additionally, the 'rtables.officer' package supports export formats related to the Microsoft Office software suite, including Microsoft Word ('docx') and Microsoft PowerPoint ('pptx').
Maintained by Joe Zhu. Last updated 13 days ago.
1 stars 6.84 score 3 scripts 7 dependentscardiomoon
webr:Data and Functions for Web-Based Analysis
Several analysis-related functions for the book entitled "Web-based Analysis without R in Your Computer"(written in Korean, ISBN 978-89-5566-185-9) by Keon-Woong Moon. The main function plot.htest() shows the distribution of statistic for the object of class 'htest'.
Maintained by Keon-Woong Moon. Last updated 5 years ago.
33 stars 6.80 score 181 scripts
harrison4192
autostats:Auto Stats
Automatically do statistical exploration. Create formulas using 'tidyselect' syntax, and then determine cross-validated model accuracy and variable contributions using 'glm' and 'xgboost'. Contains additional helper functions to create and modify formulas. Has a flagship function to quickly determine relationships between categorical and continuous variables in the data set.
Maintained by Harrison Tietze. Last updated 29 days ago.
6 stars 6.76 score 5 scripts 2 dependents
imbi-heidelberg
DescrTab2:Publication Quality Descriptive Statistics Tables
Provides functions to create descriptive statistics tables for continuous and categorical variables. By default, summary statistics such as mean, standard deviation, quantiles, minimum and maximum for continuous variables and relative and absolute frequencies for categorical variables are calculated. 'DescrTab2' features a sophisticated algorithm to choose appropriate test statistics for your data and provides p-values. On top of this, confidence intervals for group differences of appropriated summary measures are automatically produces for two-group comparison. Tables generated by 'DescrTab2' can be integrated in a variety of document formats, including .html, .tex and .docx documents. 'DescrTab2' also allows printing tables to console and saving table objects for later use.
Maintained by Jan Meis. Last updated 1 years ago.
categorical-variablescontinuous-variabledescriptive-statisticsp-valuesstatistical-testsstatistics
9 stars 6.71 score 19 scripts 1 dependentsharrison4192
presenter:Present Data with Style
Consists of custom wrapper functions using packages 'openxlsx', 'flextable', and 'officer' to create highly formatted MS office friendly output of your data frames. These viewer friendly outputs are intended to match expectations of professional looking presentations in business and consulting scenarios. The functions are opinionated in the sense that they expect the input data frame to have certain properties in order to take advantage of the automated formatting.
Maintained by Harrison Tietze. Last updated 2 years ago.
11 stars 6.69 score 15 scripts 4 dependentsinsightsengineering
teal.goshawk:Longitudinal Visualization `teal` Modules
Modules that produce web interfaces through which longitudinal visualizations can be dynamically modified and displayed. These included box plot, correlation plot, density distribution plot, line plot, scatter plot and spaghetti plot with accompanying summary. Data are expected in ADaM structure. Requires analysis subject level (ADSL) and analysis laboratory (ADLB) data sets. Beyond core variables, Limit of Quantification flag variable (LOQFL) is expected with levels 'Y', 'N' or NA.
Maintained by Nick Paszty. Last updated 1 months ago.
3 stars 6.56 score 2 scriptscardiomoon
rrtable:Reproducible Research with a Table of R Codes
Makes documents containing plots and tables from a table of R codes. Can make "HTML", "pdf('LaTex')", "docx('MS Word')" and "pptx('MS Powerpoint')" documents with or without R code. In the package, modularized 'shiny' app codes are provided. These modules are intended for reuse across applications.
Maintained by Keon-Woong Moon. Last updated 2 years ago.
3 stars 6.45 score 76 scripts 2 dependents
pierreroudier
spectacles:Storing, Manipulating and Analysis Spectroscopy and Associated Data
Stores and eases the manipulation of spectra and associated data, with dedicated classes for spatial and soil-related data.
Maintained by Pierre Roudier. Last updated 2 years ago.
11 stars 6.17 score 45 scripts 1 dependentsinsightsengineering
autoslider.core:Slide Automation for Tables, Listings and Figures
The normal process of creating clinical study slides is that a statistician manually type in the numbers from outputs and a separate statistician to double check the typed in numbers. This process is time consuming, resource intensive, and error prone. Automatic slide generation is a solution to address these issues. It reduces the amount of work and the required time when creating slides, and reduces the risk of errors from manually typing or copying numbers from the output to slides. It also helps users to avoid unnecessary stress when creating large amounts of slide decks in a short time window.
Maintained by Joe Zhu. Last updated 3 months ago.
4 stars 6.03 score 3 scriptscardiomoon
interpretCI:Estimate the Confidence Interval and Interpret Step by Step
Estimate confidence intervals for mean, proportion, mean difference for unpaired and paired samples and proportion difference. Plot the confidence intervals. Generate documents explaining the statistical result step by step.
Maintained by Keon-Woong Moon. Last updated 3 years ago.
4 stars 6.03 score 49 scripts
aravind-j
augmentedRCBD:Analysis of Augmented Randomised Complete Block Designs
Functions for analysis of data generated from experiments in augmented randomised complete block design according to Federer, W.T. (1961) <doi:10.2307/2527837>. Computes analysis of variance, adjusted means, descriptive statistics, genetic variability statistics etc. Further includes data visualization and report generation functions.
Maintained by J. Aravind. Last updated 6 months ago.
augmented-blockaugmented-designaugmented-rcbd
7 stars 5.94 score 21 scripts
tscnlab
LightLogR:Process Data from Wearable Light Loggers and Optical Radiation Dosimeters
Import, processing, validation, and visualization of personal light exposure measurement data from wearable devices. The package implements features such as the import of data and metadata files, conversion of common file formats, validation of light logging data, verification of crucial metadata, calculation of common parameters, and semi-automated analysis and visualization.
Maintained by Johannes Zauner. Last updated 1 months ago.
dosimetrylighttime-series-analysiswearable-deviceswearable-sensors
12 stars 5.88 score 28 scripts
tingtingzhan
DanielBiostatistics10th:Functions for Wayne W. Daniel's Biostatistics, Tenth Edition
Functions to accompany Wayne W. Daniel's Biostatistics: A Foundation for Analysis in the Health Sciences, Tenth Edition.
Maintained by Tingting Zhan. Last updated 3 days ago.
5.83 score 27 scriptsmthulin
ivo.table:Nicely Formatted Contingency Tables and Frequency Tables
Nicely formatted frequency tables and contingency tables (1-way, 2-way, 3-way and 4-way tables), that can easily be exported to HTML or 'Office' documents. Designed to work with pipes.
Maintained by Måns Thulin. Last updated 1 months ago.
4 stars 5.81 score 6 scriptstsmodels
tsmarch:Multivariate ARCH Models
Feasible Multivariate Generalized Autoregressive Conditional Heteroscedasticity (GARCH) models including Dynamic Conditional Correlation (DCC), Copula GARCH and Generalized Orthogonal GARCH with Generalized Hyperbolic distribution. A review of some of these models can be found in Boudt, Galanos, Payseur and Zivot (2019) <doi:10.1016/bs.host.2019.01.001>.
Maintained by Alexios Galanos. Last updated 9 days ago.
econometricsfinancegarchmultivariate-timeseriestime-seriesopenblascpp
7 stars 5.80 score 3 scripts
wa-department-of-agriculture
soils:Visualize and Report Soil Health Data
Collection of soil health data visualization and reporting tools, including a RStudio project template with everything you need to generate custom HTML and Microsoft Word reports for each participant in your soil health sampling project.
Maintained by Jadey N Ryan. Last updated 8 days ago.
10 stars 5.73 score 9 scripts
atorus-research
clinify:Clinical Table Styling Tools and Utilities
The primary motivation of this package is to take the things that are great about the R packages 'flextable' <https://davidgohel.github.io/flextable/> and 'officer' <https://davidgohel.github.io/officer/>, take the standard and complex pieces of formatting clinical tables for regulatory use, and simplify the tedious pieces.
Maintained by Mike Stackhouse. Last updated 2 days ago.
3 stars 5.65 score
insightsengineering
teal.modules.hermes:RNA-Seq Analysis Modules to Add to a Teal Application
RNA-seq analysis teal modules based on the `hermes` package.
Maintained by Daniel Sabanés Bové. Last updated 1 years ago.
7 stars 5.54 score 32 scripts
openanalytics
inTextSummaryTable:Creation of in-Text Summary Table
Creation of tables of summary statistics or counts for clinical data (for 'TLFs'). These tables can be exported as in-text table (with the 'flextable' package) for a Clinical Study Report (Word format) or a 'topline' presentation (PowerPoint format), or as interactive table (with the 'DT' package) to an html document for clinical data review.
Maintained by Laure Cougnaud. Last updated 10 months ago.
1 stars 5.52 score 47 scripts
matteo21q
dani:Design and Analysis of Non-Inferiority Trials
Provides tools to help with the design and analysis of non-inferiority trials. These include functions for doing sample size calculations and for analysing non-inferiority trials, using a variety of outcome types and population-level sumamry measures. It also features functions to make trials more resilient by using the concept of non-inferiority frontiers, as described in Quartagno et al. (2019) <arXiv:1905.00241>. Finally it includes function to design and analyse MAMS-ROCI (aka DURATIONS) trials.
Maintained by Matteo Quartagno. Last updated 7 months ago.
2 stars 5.33 score 27 scripts
massbays-tech
MassWateR:Quality Control and Analysis of Massachusetts Water Quality Data
Methods for quality control and exploratory analysis of surface water quality data collected in Massachusetts, USA. Functions are developed to facilitate data formatting for the Water Quality Exchange Network <https://www.epa.gov/waterdata/water-quality-data-upload-wqx> and reporting of data quality objectives to state agencies. Quality control methods are from Massachusetts Department of Environmental Protection (2020) <https://www.mass.gov/orgs/massachusetts-department-of-environmental-protection>.
Maintained by Marcus Beck. Last updated 12 days ago.
13 stars 5.29 score 10 scriptsharrison4192
validata:Validate Data Frames
Functions for validating the structure and properties of data frames. Answers essential questions about a data set after initial import or modification. What are the unique or missing values? What columns form a primary key? What are the properties of the numeric or categorical columns? What kind of overlap or mapping exists between 2 columns?
Maintained by Harrison Tietze. Last updated 29 days ago.
6 stars 5.26 score 4 scripts 1 dependents
pydemull
activAnalyzer:A 'Shiny' App to Analyze Accelerometer-Measured Daily Physical Behavior Data
A tool to analyse 'ActiGraph' accelerometer data and to implement the use of the PROactive Physical Activity in COPD (chronic obstructive pulmonary disease) instruments. Once analysis is completed, the app allows to export results to .csv files and to generate a report of the measurement. All the configured inputs relevant for interpreting the results are recorded in the report. In addition to the existing 'R' packages that are fully integrated with the app, the app uses some functions from the 'actigraph.sleepr' package developed by Petkova (2021) <https://github.com/dipetkov/actigraph.sleepr/>.
Maintained by Pierre-Yves de Müllenheim. Last updated 12 days ago.
accelerometeractigraphappmonitorshiny
5 stars 5.24 score 8 scripts
lydialucchesi
smallsets:Visual Documentation for Data Preprocessing
Data practitioners regularly use the 'R' and 'Python' programming languages to prepare data for analyses. Thus, they encode important data preprocessing decisions in 'R' and 'Python' code. The 'smallsets' package subsequently decodes these decisions into a Smallset Timeline, a static, compact visualisation of data preprocessing decisions (Lucchesi et al. (2022) <doi:10.1145/3531146.3533175>). The visualisation consists of small data snapshots of different preprocessing steps. The 'smallsets' package builds this visualisation from a user's dataset and preprocessing code located in an 'R', 'R Markdown', 'Python', or 'Jupyter Notebook' file. Users simply add structured comments with snapshot instructions to the preprocessing code. One optional feature in 'smallsets' requires installation of the 'Gurobi' optimisation software and 'gurobi' 'R' package, available from <https://www.gurobi.com>. More information regarding the optional feature and 'gurobi' installation can be found in the 'smallsets' vignette.
Maintained by Lydia R. Lucchesi. Last updated 2 months ago.
data-sciencedata-visualizationdocumentation-toolmachine-learningpreprocessingpythonvisualization-tools
14 stars 5.19 score 11 scripts
tsmodels
tstests:Time Series Goodness of Fit and Forecast Evaluation Tests
Goodness of Fit and Forecast Evaluation Tests for timeseries models. Includes, among others, the Generalized Method of Moments (GMM) Orthogonality Test of Hansen (1982), the Nyblom (1989) parameter constancy test, the sign-bias test of Engle and Ng (1993), and a range of tests for value at risk and expected shortfall evaluation.
Maintained by Alexios Galanos. Last updated 5 months ago.
5 stars 5.10 score 3 scriptsinsightsengineering
teal.osprey:'teal' Modules for TLG Functions in Osprey
Community efforts to collect 'teal' modules for TLGs defined in 'osprey' package. Enables 'teal' app developers to create 'shiny' applications with a use of 'osprey' analysis functions.
Maintained by Nina Qi. Last updated 1 months ago.
5 stars 5.05 score 1 scripts
tunsmart
interactionR:Full Reporting of Interaction Analyses
Produces a publication-ready table that includes all effect estimates necessary for full reporting effect modification and interaction analysis as recommended by Knol and Vanderweele (2012) [<doi:10.1093/ije/dyr218>]. It also estimates confidence interval for the trio of additive interaction measures using the delta method (see Hosmer and Lemeshow (1992), [<doi:10.1097/00001648-199209000-00012>]), variance recovery method (see Zou (2008), [<doi:10.1093/aje/kwn104>]), or percentile bootstrapping (see Assmann et al. (1996), [<doi:10.1097/00001648-199605000-00012>]).
Maintained by Babatunde Alli. Last updated 1 years ago.
21 stars 4.95 score 84 scripts
gokmenzararsiz
dtComb:Statistical Combination of Diagnostic Tests
A system for combining two diagnostic tests using various approaches that include statistical and machine-learning-based methodologies. These approaches are divided into four groups: linear combination methods, non-linear combination methods, mathematical operators, and machine learning algorithms. See the <https://biotools.erciyes.edu.tr/dtComb/> website for more information, documentation, and examples.
Maintained by Gokmen Zararsiz. Last updated 6 days ago.
4.85 score 7 scriptsharrison4192
tidybins:Make Tidy Bins
Multiple ways to bin numeric columns with a tidy output. Wraps a variety of existing binning methods into one function, and includes a new method for binning by equal value, which is useful for sales data. Provides a function to automatically summarize the properties of the binned columns.
Maintained by Harrison Tietze. Last updated 10 months ago.
4 stars 4.78 score 2 scripts 1 dependents
nlmixr2
nlmixr2rpt:Templated Word and PowerPoint Reporting of 'nlmixr2' Fitting Results
This allows you to generate reporting workflows around 'nlmixr2' analyses with outputs in Word and PowerPoint. You can specify figures, tables and report structure in a user-definable 'YAML' file. Also you can use the internal functions to access the figures and tables to allow their including in other outputs (e.g. R Markdown).
Maintained by John Harrold. Last updated 7 months ago.
2 stars 4.75 score 14 scripts
brad-cannell
codebookr:Create Codebooks from Data Frames
Quickly and easily create codebooks (i.e. data dictionaries) directly from a data frame.
Maintained by Brad Cannell. Last updated 1 years ago.
28 stars 4.74 score 39 scripts
abusjahn
wrappedtools:Useful Wrappers Around Commonly Used Functions
The main functionalities of 'wrappedtools' are: adding backticks to variable names; rounding to desired precision with special case for p-values; selecting columns based on pattern and storing their position, name, and backticked name; computing and formatting of descriptive statistics (e.g. mean±SD), comparing groups and creating publication-ready tables with descriptive statistics and p-values; creating specialized plots for correlation matrices. Functions were mainly written for my own daily work or teaching, but may be of use to others as well.
Maintained by Andreas Busjahn. Last updated 3 days ago.
descriptive-statisticstest-statistic
2 stars 4.70 score 8 scriptsbioc
GNOSIS:Genomics explorer using statistical and survival analysis in R
GNOSIS incorporates a range of R packages enabling users to efficiently explore and visualise clinical and genomic data obtained from cBioPortal. GNOSIS uses an intuitive GUI and multiple tab panels supporting a range of functionalities. These include data upload and initial exploration, data recoding and subsetting, multiple visualisations, survival analysis, statistical analysis and mutation analysis, in addition to facilitating reproducible research.
Maintained by Lydia King. Last updated 5 months ago.
5 stars 4.70 score 2 scripts
phuse-org
toxSummary:Visualize and Summarize Repeat-Dose Toxicology Study Results
A 'shiny' app that generates plots and summary tables from repeat-dose toxicology study results to facilitate holistic evaluation of the drug safety of active pharmaceutical ingredients (API) prior to initiation of clinical trials.
Maintained by Yousuf Ali. Last updated 12 months ago.
cdisc-sendr-shiny-apptoxicologyvisualization
9 stars 4.65 score 4 scriptssciviews
tabularise:Create Tabular Outputs from R
Create rich-formatted tabular outputs from R that can be incorporated into R Markdown/Quarto documents with correct output at least in HTML, LaTeX/PDF, Word and PowerPoint formats for various R objects.
Maintained by Philippe Grosjean. Last updated 10 months ago.
4.56 score 12 scripts 4 dependents
andresfloresg
BiVariAn:Bivariate Automatic Analysis
Simplify bivariate and regression analyses by automating result generation, including summary tables, statistical tests, and customizable graphs. It supports tests for continuous and dichotomous data, as well as stepwise regression for linear, logistic, and Firth penalized logistic models. While not a substitute for tailored analysis, 'BiVariAn' accelerates workflows and is expanding features like multilingual interpretations of results.The methods for selecting significant statistical tests, as well as the predictor selection in prediction functions, can be referenced in the works of Marc Kery (2003) <doi:10.1890/0012-9623(2003)84[92:NORDIG]2.0.CO;2> and Rainer Puhr (2017) <doi:10.1002/sim.7273>.
Maintained by José Andrés Flores-García. Last updated 28 days ago.
4.54 scorebioc
granulator:Rapid benchmarking of methods for *in silico* deconvolution of bulk RNA-seq data
granulator is an R package for the cell type deconvolution of heterogeneous tissues based on bulk RNA-seq data or single cell RNA-seq expression profiles. The package provides a unified testing interface to rapidly run and benchmark multiple state-of-the-art deconvolution methods. Data for the deconvolution of peripheral blood mononuclear cells (PBMCs) into individual immune cell types is provided as well.
Maintained by Sabina Pfister. Last updated 5 months ago.
rnaseqgeneexpressiondifferentialexpressiontranscriptomicssinglecellstatisticalmethodregression
3 stars 4.48 score 7 scripts
r4epi
sitrep:Report templates and helper functions for applied epidemiology
Report templates and helper functions for applied epidemiology.
Maintained by Alexander Spina. Last updated 27 days ago.
epidemiologymsfoutbreaksreport-generator
41 stars 4.46 score 9 scripts
stephen-amori
apmx:Automated Population Pharmacokinetic Dataset Assembly
Automated methods to assemble population PK (pharmacokinetic) and PKPD (pharmacodynamic) datasets for analysis in 'NONMEM' (non-linear mixed effects modeling) by Bauer (2019) <doi:10.1002/psp4.12404>. The package includes functions to build datasets from SDTM (study data tabulation module) <https://www.cdisc.org/standards/foundational/sdtm>, ADaM (analysis dataset module) <https://www.cdisc.org/standards/foundational/adam>, or other dataset formats. The package will combine population datasets, add covariates, and create documentation to support regulatory submission and internal communication.
Maintained by Stephen Amori. Last updated 1 years ago.
5 stars 4.40 score 10 scripts
jiangyouxiang
TestAnaAPP:A 'shiny' App for Test Analysis and Visualization
This application provides exploratory and confirmatory factor analysis, classical test theory, unidimensional and multidimensional item response theory, and continuous item response model analysis, through the 'shiny' interactive interface. In addition, it offers rich functionalities for visualizing and downloading results. Users can download figures, tables, and analysis reports via the interactive interface.
Maintained by Youxiang Jiang. Last updated 4 months ago.
4 stars 4.30 score 2 scriptstingtingzhan
DemographicTable:Create Demographic Table
Functions for creating demographic table of simple summary statistics and comparison(s) over one or more groups.
Maintained by Tingting Zhan. Last updated 3 days ago.
4.26 score
rsoc
soc.ca:Specific Correspondence Analysis for the Social Sciences
Specific and class specific multiple correspondence analysis on survey-like data. Soc.ca is optimized to the needs of the social scientist and presents easily interpretable results in near publication ready quality.
Maintained by Anton Grau Larsen. Last updated 1 years ago.
14 stars 4.15 score 50 scripts
sfcheung
manymome.table:Publication-Ready Tables for 'manymome' Results
Converts results from the 'manymome' package, presented in Cheung and Cheung (2023) <doi:10.3758/s13428-023-02224-z>, to publication-ready tables.
Maintained by Shu Fai Cheung. Last updated 4 months ago.
lavaanmanymomemediationmoderated-mediationmoderationregressionsemstructural-equation-modeling
4.00 score 2 scripts
guokai8
eoffice:Export or Graph and Tables to 'Microsoft' Office and Import Figures and Tables
Provides wrap functions to export and import graphics and data frames in R to 'microsoft' office. And This package also provide write out figures with lots of different formats. Since people may work on the platform without GUI support, the package also provide function to easily write out figures to lots of different type of formats. Now this package provide function to extract colors from all types of figures and pdf files.
Maintained by Kai Guo. Last updated 2 years ago.
1 stars 3.80 score 100 scripts
medianasoft
MedianaDesigner:Power and Sample Size Calculations for Clinical Trials
Efficient simulation-based power and sample size calculations are supported for a broad class of late-stage clinical trials. The following modules are included in the package: Adaptive designs with data-driven sample size or event count re-estimation, Adaptive designs with data-driven treatment selection, Adaptive designs with data-driven population selection, Optimal selection of a futility stopping rule, Event prediction in event-driven trials, Adaptive trials with response-adaptive randomization (experimental module), Traditional trials with multiple objectives (experimental module). Traditional trials with cluster-randomized designs (experimental module).
Maintained by Alex Dmitrienko. Last updated 2 years ago.
20 stars 3.79 score 31 scripts
sooyongl
GRShiny:Graded Response Model
Simulation and analysis of graded response data with different types of estimators. Also, an interactive shiny application is provided with graphics for characteristic and information curves. Samejima (2018) <doi:10.1007/978-1-4757-2691-6_5>.
Maintained by Sooyong Lee. Last updated 2 years ago.
3.70 score 3 scripts
markhogue
AeroSampleR:Estimate Aerosol Particle Collection Through Sample Lines
Estimate ideal efficiencies of aerosol sampling through sample lines. Functions were developed consistent with the approach described in Hogue, Mark; Thompson, Martha; Farfan, Eduardo; Hadlock, Dennis, (2014), "Hand Calculations for Transport of Radioactive Aerosols through Sampling Systems" Health Phys 106, 5, S78-S87, <doi:10.1097/HP.0000000000000092>.
Maintained by Mark Hogue. Last updated 2 years ago.
3.70 score 2 scripts
jo-theo
shinySbm:'shiny' Application to Use the Stochastic Block Model
A 'shiny' interface for a simpler use of the 'sbm' R package. It also contains useful functions to easily explore the 'sbm' package results. With this package you should be able to use the stochastic block model without any knowledge in R, get automatic reports and nice visuals, as well as learning the basic functions of 'sbm'.
Maintained by Theodore Vanrenterghem. Last updated 2 years ago.
3.70 score 6 scripts
harrison4192
TidyConsultant:Tidy Consultant Universe
Loads the 5 packages in the Tidy Consultant Universe. This collection of packages is useful for anyone doing data science, data analysis, or quantitative consulting. The functions in these packages range from data cleaning, data validation, data binning, statistical modeling, and file exporting.
Maintained by Harrison Tietze. Last updated 10 months ago.
8 stars 3.60 score 2 scripts
rameshram96
visvaR:Shiny-Based Statistical Solutions for Agricultural Research
Visualize Variance is an intuitive 'shiny' applications tailored for agricultural research data analysis, including one-way and two-way analysis of variance, correlation, and other essential statistical tools. Users can easily upload their datasets, perform analyses, and download the results as a well-formatted document, streamlining the process of data analysis and reporting in agricultural research.The experimental design methods are based on classical work by Fisher (1925) and Scheffe (1959). The correlation visualization approaches follow methods developed by Wei & Simko (2021) and Friendly (2002) <doi:10.1198/000313002533>.
Maintained by Ramesh Ramasamy. Last updated 5 months ago.
agricultureanova-analysiscorrelationexperexperimentalexperimental-design
3.54 score 6 scripts
knickodem
kfa:K-Fold Cross Validation for Factor Analysis
Provides functions to identify plausible and replicable factor structures for a set of variables via k-fold cross validation. The process combines the exploratory and confirmatory factor analytic approach to scale development (Flora & Flake, 2017) <doi:10.1037/cbs0000069> with a cross validation technique that maximizes the available data (Hastie, Tibshirani, & Friedman, 2009) <isbn:978-0-387-21606-5>. Also available are functions to determine k by drawing on power analytic techniques for covariance structures (MacCallum, Browne, & Sugawara, 1996) <doi:10.1037/1082-989X.1.2.130>, generate model syntax, and summarize results in a report.
Maintained by Kyle Nickodem. Last updated 1 years ago.
cross-validationfactor-analysispsychometricsscale-development
7 stars 3.54 score 7 scripts
anspiess
reverseR:Linear Regression Stability to Significance Reversal
Tests linear regressions for significance reversal through leave-one(multiple)-out.
Maintained by Andrej-Nikolai Spiess. Last updated 4 months ago.
3 stars 3.48 score
aus-doh-safety-and-quality
qiverse.qimatrix:QI Matrix
Defines functions needed to generate Quality Improvement Matrices in R.
Maintained by Healthcare Quality Intelligence Unit (Western Australia Health). Last updated 9 hours ago.
3 stars 3.48 score
certe-medical-epidemiology
certetoolbox:A Certe R Package for Miscellaneous Functions
A Certe R Package for miscellaneous functions that do not fit a dedicated package. This package also mitigates the 'vctrs' package by allowing numeric-character coercions. This package is part of the 'certedata' universe.
Maintained by Erwin E. A. Hassing. Last updated 13 days ago.
3.45 score 1 scripts 1 dependents
ices-tools-prod
icesFO:Functions to support the creation of ICES Fisheries Overviews
Functions to support the creation of ICES Fisheries Overviews.
Maintained by Adriana Villamor. Last updated 10 months ago.
2 stars 3.41 score 260 scripts
framverse
TAMMsupport:Streamline working with Terminal Area Management Modules
A convenient tool for interfacing with Terminal Area Manamagement Modules (TAMMs) in R environments.
Maintained by Collin Edwards. Last updated 3 months ago.
3 stars 3.35 score 5 scripts
sciurus365
Isinglandr:Landscape Construction and Simulation for Ising Networks
A toolbox for constructing potential landscapes for Ising networks. The parameters of the networks can be directly supplied by users or estimated by the 'IsingFit' package by van Borkulo and Epskamp (2016) <https://CRAN.R-project.org/package=IsingFit> from empirical data. The Ising model's Boltzmann distribution is preserved for the potential landscape function. The landscape functions can be used for quantifying and visualizing the stability of network states, as well as visualizing the simulation process.
Maintained by Jingmeng Cui. Last updated 6 months ago.
1 stars 3.30 score 3 scriptssciviews
modelit:Statistical Models for 'SciViews::R'
Create and use statistical models (linear, general, nonlinear...) with extensions to support rich-formatted tables, equations and plots for the 'SciViews::R' dialect.
Maintained by Philippe Grosjean. Last updated 4 months ago.
1 stars 3.30 score 8 scripts
philipdelff
tracee:Easily Save Output and Trace it Back to Code
Write output (plots and tables) ensuring traceability back to code. Includes a graphics saver with simple automation of stamping with source, destination and creation time. A list of plots can be saved at once. A user-friendly selection of output dimensions for presentations, on-screen inspections, and more available.
Maintained by Philip Delff. Last updated 9 months ago.
4 stars 3.30 score 8 scriptswa-department-of-agriculture
washi:Washington Soil Health Initiative Branding
Create plots and tables in a consistent style with WaSHI (Washington Soil Health Initiative) branding. Use 'washi' to easily style your 'ggplot2' plots and 'flextable' tables.
Maintained by Jadey Ryan. Last updated 1 years ago.
3 stars 3.18 score 2 scripts
ejikeugba
gofcat:Goodness-of-Fit Measures for Categorical Response Models
A post-estimation method for categorical response models (CRM). Inputs from objects of class serp(), clm(), polr(), multinom(), mlogit(), vglm() and glm() are currently supported. Available tests include the Hosmer-Lemeshow tests for the binary, multinomial and ordinal logistic regression; the Lipsitz and the Pulkstenis-Robinson tests for the ordinal models. The proportional odds, adjacent-category, and constrained continuation-ratio models are particularly supported at ordinal level. Tests for the proportional odds assumptions in ordinal models are also possible with the Brant and the Likelihood-Ratio tests. Moreover, several summary measures of predictive strength (Pseudo R-squared), and some useful error metrics, including, the brier score, misclassification rate and logloss are also available for the binary, multinomial and ordinal models. Ugba, E. R. and Gertheiss, J. (2018) <http://www.statmod.org/workshops_archive_proceedings_2018.html>.
Maintained by Ejike R. Ugba. Last updated 2 years ago.
brant-testbrier-scoreshosmer-lemeshow-testlikelihood-ratio-testlipsitz-testlog-loss-score-metriclogistic-regressionmisclassificationordinal-regressionproportional-odds-testpseudo-r2pulkstenis-robinson-test
2 stars 3.18 score 15 scriptsframverse
xldiff:Compare excel sheets
`xldiff` provides tools to compare excel sheets, broadly inspired by "diff"-type functions. Provided functions can read sheets of two excel files and produce a third file that highlights cells that have changed. In the case of numeric changes, the direction of change is highlighted. These tools do not account for structural changes in the sheets (e.g., the addition of a column), but are useful in tracking changed values in tables or parameter files. Utility functions developed to streamline formatting output files are also more broadly useful in programmatically formatting excel files using openxlsx.
Maintained by Collin Edwards. Last updated 19 days ago.
3.02 score 1 dependentssciviews
inferit:Hypothesis Tests and Statistical Distributions for 'SciViews::R'
Statistical distributions (including their visual representation) and hypothesis tests with rich-formatted tabular outputs for the 'SciViews::R' dialect.
Maintained by Philippe Grosjean. Last updated 10 months ago.
sciviewsstatistical-inferencestatistical-tests
3.00 score 6 scripts
amalan-constat
fitODBODRshiny:'Shiny' Application for R Package 'fitODBOD'
For binomial outcome data Alternate Binomial Distributions and Binomial Mixture Distributions are fitted when overdispersion is available.
Maintained by Amalan Mahendran. Last updated 6 months ago.
3.00 scorecerte-medical-epidemiology
certedb:A Certe R Package for Connecting to Databases
A Certe R Package for connecting to internal Certe cBases and local DuckDB databases. This package is part of the 'certedata' universe.
Maintained by Matthijs S. Berends. Last updated 27 days ago.
2.95 score 1 scripts
igrave
ladder:Get on to the Slides
Create tables from within R directly on Google Slides presentations. Currently supports matrix, data.frame and 'flextable' objects.
Maintained by Isaac Gravestock. Last updated 18 days ago.
1 stars 2.93 score 3 scripts
ctu-bern
SwissASR:Automated Completion of the SwissEthics Annual Safety Report
Completing the SwissEthics Annual Safety Report can be tiresome. This package eases the pain by providing an automated method to fill it out.
Maintained by Alan G. Haynes. Last updated 3 months ago.
1 stars 2.85 score 4 scripts
terminological
ggrrr:Addressing Annoyances and Irritations
Visualisation hacks, tabular data helpers, fonts, caching, tidy data functions. It is an swiss army knife, jack of all trades.
Maintained by Robert Challen. Last updated 10 months ago.
1 stars 2.74 score 11 scripts
sciviews
exploreit:Exploratory Data Analysis for 'SciViews::R'
Multivariate analysis and data exploration for the 'SciViews::R' dialect.
Maintained by Philippe Grosjean. Last updated 11 months ago.
multivariate-analysissciviewsstatistical-methods
2.70 score 4 scripts
a2-ai
reportifyr:Reproducible Reporting Made Simple in R
Create reproducible reports with Microsoft Word and R.
Maintained by Jacob Dumbleton. Last updated 1 months ago.
1 stars 2.70 score 10 scripts
iiasa
ODPSCP:A standard reporting protocol for conservation planning
This repository contains the environment and shiny code underlying the reporting protocol.
Maintained by Martin Jung. Last updated 1 days ago.
conservation-prioritizationprotocolr-shinystandardsystematic-conservation-planning
1 stars 2.70 score 1 scripts
aalfons
robmedExtra:Extra Functionality for (Robust) Mediation Analysis
This companion package extends the package 'robmed' (Alfons, Ates & Groenen, 2022b; <doi:10.18637/jss.v103.i13>) in various ways. Most notably, it provides a graphical user interface for the robust bootstrap test ROBMED (Alfons, Ates & Groenen, 2022a; <doi:10.1177/1094428121999096>) to make the method more accessible to less proficient 'R' users, as well as functions to export the results as a table in a 'Microsoft Word' or 'Microsoft Powerpoint' document, or as a 'LaTeX' table. Furthermore, the package contains a 'shiny' app to compare various bootstrap procedures for mediation analysis on simulated data.
Maintained by Andreas Alfons. Last updated 5 months ago.
1 stars 2.70 score
ajpelu
famexploreR:Exploration of Threathened Flora field data
A shiny app that explores data from Threathened Flora. It uses customized forms to explore the data and generate several plots, tables.
Maintained by Antonio Jesús Pérez-Luque. Last updated 4 months ago.
2 stars 2.60 score 2 scripts
david-hervas
repmod:Create Report Table from Different Objects
Tools for generating descriptives and report tables for different models, data.frames and tables and exporting them to different formats.
Maintained by David Hervas Marin. Last updated 2 months ago.
2.60 score 6 scripts
ices-tools-prod
fisheryO:Fisheries Overviews for ICES Advice
Functions that work with International Council for the Exploration of the Sea (ICES) web services and databases to collate, aggregate, and plot Fisheries Overview products.
Maintained by Scott Large. Last updated 7 years ago.
3 stars 2.45 score 19 scripts
medianasoft
MCPModPack:Simulation-Based Design and Analysis of Dose-Finding Trials
An efficient implementation of the MCPMod (Multiple Comparisons and Modeling) method to support a simulation-based design and analysis of dose-finding trials with normally distributed, binary and count endpoints (Bretz et al. (2005) <doi:10.1111/j.1541-0420.2005.00344.x>).
Maintained by Alex Dmitrienko. Last updated 2 years ago.
1 stars 2.00 score 1 scripts
tomashovorka
WordR:Rendering Word Documents with R Inline Code
Serves for rendering MS Word documents with R inline code and inserting tables and plots.
Maintained by Tomas Hovorka. Last updated 2 years ago.
1 stars 2.00 score 7 scripts
certara-jcraig
Certara.DarwinReporter:Data Visualization Utilities for 'pyDarwin' Machine Learning Pharmacometric Model Development
Utilize the 'shiny' interface for visualizing results from a 'pyDarwin' (<https://certara.github.io/pyDarwin/>) machine learning pharmacometric model search. It generates Goodness-of-Fit plots and summary tables for selected models, allowing users to customize diagnostic outputs within the interface. The underlying R code for generating plots and tables can be extracted for use outside the interactive session. Model diagnostics can also be incorporated into an R Markdown document and rendered in various output formats.
Maintained by James Craig. Last updated 26 days ago.
1.70 scoreices-tools-prod
icesdown:ICES Rmarkdown tools
A collection of rmarkdown and pandoc versions of various ICES templates can be found here.
Maintained by Iago Mosqueira. Last updated 3 years ago.
1.70 score 1 scriptscertara-jcraig
Certara.ModelResults:Generate Diagnostics for Pharmacometric Models Using 'shiny'
Utilize the 'shiny' interface to generate Goodness of Fit (GOF) plots and tables for Non-Linear Mixed Effects (NLME / NONMEM) pharmacometric models. From the interface, users can customize model diagnostics and generate the underlying R code to reproduce the diagnostic plots and tables outside of the 'shiny' session. Model diagnostics can be included in a 'rmarkdown' document and rendered to desired output format.
Maintained by James Craig. Last updated 30 days ago.
1.70 scorecran
SurveyDefense:Survey Defense Tool
This tool is designed to analyze up to 5 Fraud Detection Questions integrated into a survey, focusing on potential fraudulent participants to clean the survey dataset from potential fraud. Fraud Detection Questions and further information available at <https://surveydefense.org>.
Maintained by Philipp Brüggemann. Last updated 7 months ago.
1.30 scorecran
rsides:SIDES-Based Subgroup Search Algorithms
R implementation of SIDES-based subgroup search algorithms (Lipkovich et al. (2017) <doi:10.1002/sim.7064>).
Maintained by Alex Dmitrienko. Last updated 10 months ago.
1.00 score
danny-ldc
RcmdrPlugin.EBM:Rcmdr Evidence Based Medicine Plug-in Package
Rcmdr plug-in GUI extension for Evidence Based Medicine medical indicators calculations (Sensitivity, specificity, absolute risk reduction, relative risk, ...).
Maintained by Daniel-Corneliu Leucuta. Last updated 10 years ago.
1.00 score 1 scriptscran
sMSROC:Assessment of Diagnostic and Prognostic Markers
Provides estimations of the Receiver Operating Characteristic (ROC) curve and the Area Under the Curve (AUC) based on the two-stages mixed-subjects ROC curve estimator (Diaz-Coto et al. (2020) <doi:10.1515/ijb-2019-0097> and Diaz-Coto et al. (2020) <doi:10.1080/00949655.2020.1736071>).
Maintained by Susana Diaz-Coto. Last updated 1 years ago.
1.00 scorecran
Dtableone:Tabular Comparison of Paired Diagnostic Tests
Offers statistical methods to compare diagnostic performance between two binary diagnostic tests on the same subject in clinical studies. Includes functions for generating formatted tables to display diagnostic outcomes, facilitating a clear and comprehensive comparison directly through the R console. Inspired by and extending the functionalities of the 'DTComPair', 'tableone', and 'gtsummary' packages.
Maintained by Youngmi Park. Last updated 1 years ago.
1.00 score