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dvdscripter

ini:Read and Write '.ini' Files

Parse simple '.ini' configuration files to an structured list. Users can manipulate this resulting list with lapply() functions. This same structured list can be used to write back to file after modifications.

Maintained by David Valentim Dias. Last updated 7 years ago.

66.7 match 7 stars 10.48 score 219 scripts 417 dependents

miachol

configr:An Implementation of Parsing and Writing Configuration File (JSON/INI/YAML/TOML)

Implements the JSON, INI, YAML and TOML parser for R setting and writing of configuration file. The functionality of this package is similar to that of package 'config'.

Maintained by Jianfeng Li. Last updated 2 years ago.

configparserconfiguration-fileinijsontomlyaml

29.8 match 59 stars 8.45 score 280 scripts 5 dependents

nlmixr2

rxode2:Facilities for Simulating from ODE-Based Models

Facilities for running simulations from ordinary differential equation ('ODE') models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The 'VODE' and 'LSODA' are in the public domain. The information is available in the inst/COPYRIGHTS.

Maintained by Matthew L. Fidler. Last updated 1 months ago.

fortranopenblascppopenmp

14.7 match 40 stars 11.24 score 220 scripts 13 dependents

rte-antares-rpackage

antaresEditObject:Edit an 'Antares' Simulation

Edit an 'Antares' simulation before running it : create new areas, links, thermal clusters or binding constraints or edit existing ones. Update 'Antares' general & optimization settings. 'Antares' is an open source power system generator, more information available here : <https://antares-simulator.org/>.

Maintained by Tatiana Vargas. Last updated 29 days ago.

antares-simulationclusterenergymonte-carlo-simulationrte

8.8 match 8 stars 8.76 score 101 scripts

nlmixr2

nlmixr2:Nonlinear Mixed Effects Models in Population PK/PD

Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).

Maintained by Matthew Fidler. Last updated 26 days ago.

6.3 match 50 stars 8.45 score 120 scripts 3 dependents

the-mad-statter

wubik:Helpful R Functions for Databricks at WashU

This package provides helpful functions for using R on Databricks at WashU.

Maintained by Matthew Schuelke. Last updated 10 months ago.

30.0 match 1.70 score 1 scripts

bioc

fabia:FABIA: Factor Analysis for Bicluster Acquisition

Biclustering by "Factor Analysis for Bicluster Acquisition" (FABIA). FABIA is a model-based technique for biclustering, that is clustering rows and columns simultaneously. Biclusters are found by factor analysis where both the factors and the loading matrix are sparse. FABIA is a multiplicative model that extracts linear dependencies between samples and feature patterns. It captures realistic non-Gaussian data distributions with heavy tails as observed in gene expression measurements. FABIA utilizes well understood model selection techniques like the EM algorithm and variational approaches and is embedded into a Bayesian framework. FABIA ranks biclusters according to their information content and separates spurious biclusters from true biclusters. The code is written in C.

Maintained by Andreas Mitterecker. Last updated 5 months ago.

statisticalmethodmicroarraydifferentialexpressionmultiplecomparisonclusteringvisualization

6.3 match 5.84 score 32 scripts 6 dependents

mxjki

EfficientMaxEigenpair:Efficient Initials for Computing the Maximal Eigenpair

An implementation for using efficient initials to compute the maximal eigenpair in R. It provides three algorithms to find the efficient initials under two cases: the tridiagonal matrix case and the general matrix case. Besides, it also provides two algorithms for the next to the maximal eigenpair under these two cases.

Maintained by Xiao-Jun Mao. Last updated 7 years ago.

9.3 match 3.85 score 14 scripts

rspatial

raster:Geographic Data Analysis and Modeling

Reading, writing, manipulating, analyzing and modeling of spatial data. This package has been superseded by the "terra" package <https://CRAN.R-project.org/package=terra>.

Maintained by Robert J. Hijmans. Last updated 2 months ago.

cpp

2.0 match 164 stars 17.05 score 58k scripts 555 dependents

dyfanjones

ConfigINI:A Fast INI File Parser

Provides a simple yet efficient parser for INI configuration files, converting them into structured list formats for easy manipulation and access within R. The structured list can seamlessly be written back to an INI configuration file, ensuring smooth round-trip data handling.

Maintained by Dyfan Jones. Last updated 3 months ago.

inicpp

18.6 match 1 stars 1.70 score

dyfanjones

inih:Fast INI File Parser for R

Provide a simple 'INI' file parser to structured list format. Using the 'C' library 'inih' <https://github.com/benhoyt/inih> as backend of fast performance.

Maintained by Dyfan Jones. Last updated 3 months ago.

cppinicpp

18.1 match 1 stars 1.70 score

nlmixr2

nlmixr2est:Nonlinear Mixed Effects Models in Population PK/PD, Estimation Routines

Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).

Maintained by Matthew Fidler. Last updated 10 hours ago.

openblascppopenmp

3.3 match 9 stars 8.33 score 26 scripts 9 dependents

irsn

Renext:Renewal Method for Extreme Values Extrapolation

Peaks Over Threshold (POT) or 'methode du renouvellement'. The distribution for the excesses can be chosen, and heterogeneous data (including historical data or block data) can be used in a Maximum-Likelihood framework.

Maintained by Yann Richet. Last updated 1 years ago.

4.5 match 4.99 score 82 scripts 4 dependents

nlmixr2

nonmem2rx:Converts 'NONMEM' Models to 'rxode2'

'NONMEM' has been a tool for running nonlinear mixed effects models since the 80s and is still used today (Bauer 2019 <doi:10.1002/psp4.12404>). This tool allows you to convert 'NONMEM' models to 'rxode2' (Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>) and with simple models 'nlmixr2' syntax (Fidler et al (2019) <doi:10.1002/psp4.12445>). The 'nlmixr2' syntax requires the residual specification to be included and it is not always translated. If available, the 'rxode2' model will read in the 'NONMEM' data and compare the simulation for the population model ('PRED') individual model ('IPRED') and residual model ('IWRES') to immediately show how well the translation is performing. This saves the model development time for people who are creating an 'rxode2' model manually. Additionally, this package reads in all the information to allow simulation with uncertainty (that is the number of observations, the number of subjects, and the covariance matrix) with a 'rxode2' model. This is complementary to the 'babelmixr2' package that translates 'nlmixr2' models to 'NONMEM' and can convert the objects converted from 'nonmem2rx' to a full 'nlmixr2' fit.

Maintained by Matthew Fidler. Last updated 4 months ago.

nlmixr2nonmempharmacometricsrxode2cpp

3.3 match 11 stars 6.42 score 23 scripts 1 dependents

hhoeflin

ConfigParser:Package to Parse an INI File, Including Variable Interpolation

Enhances the 'ini' package by adding the ability to interpolate variables. The INI configuration file is read into an R6 ConfigParser object (loosely inspired by Pythons ConfigParser module) and the keys can be read, where '%(....)s' instances are interpolated by other included options or outside variables.

Maintained by Holger Hoefling. Last updated 8 years ago.

5.5 match 1 stars 3.62 score 28 scripts 1 dependents

moviedo5

fda.usc:Functional Data Analysis and Utilities for Statistical Computing

Routines for exploratory and descriptive analysis of functional data such as depth measurements, atypical curves detection, regression models, supervised classification, unsupervised classification and functional analysis of variance.

Maintained by Manuel Oviedo de la Fuente. Last updated 4 months ago.

functional-data-analysisfortran

2.0 match 12 stars 9.72 score 560 scripts 22 dependents

nlmixr2

nlmixr2extra:Nonlinear Mixed Effects Models in Population PK/PD, Extra Support Functions

Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for support functions like preconditioned fits <doi:10.1208/s12248-016-9866-5>, boostrap and stepwise covariate selection.

Maintained by Matthew Fidler. Last updated 29 days ago.

openblascpp

3.3 match 3 stars 5.80 score 11 scripts 5 dependents

r-hyperspec

hyperSpec:Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)

Comfortable ways to work with hyperspectral data sets, i.e. spatially or time-resolved spectra, or spectra with any other kind of information associated with each of the spectra. The spectra can be data as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS, etc. More generally, any data that is recorded over a discretized variable, e.g. absorbance = f(wavelength), stored as a vector of absorbance values for discrete wavelengths is suitable.

Maintained by Claudia Beleites. Last updated 10 months ago.

data-wranglinghyperspectralimaginginfrarednmrramanspectroscopyuv-visxrf

2.3 match 16 stars 8.13 score 233 scripts 2 dependents

fauvernierma

survPen:Multidimensional Penalized Splines for (Excess) Hazard Models, Relative Mortality Ratio Models and Marginal Intensity Models

Fits (excess) hazard, relative mortality ratio or marginal intensity models with multidimensional penalized splines allowing for time-dependent effects, non-linear effects and interactions between several continuous covariates. In survival and net survival analysis, in addition to modelling the effect of time (via the baseline hazard), one has often to deal with several continuous covariates and model their functional forms, their time-dependent effects, and their interactions. Model specification becomes therefore a complex problem and penalized regression splines represent an appealing solution to that problem as splines offer the required flexibility while penalization limits overfitting issues. Current implementations of penalized survival models can be slow or unstable and sometimes lack some key features like taking into account expected mortality to provide net survival and excess hazard estimates. In contrast, survPen provides an automated, fast, and stable implementation (thanks to explicit calculation of the derivatives of the likelihood) and offers a unified framework for multidimensional penalized hazard and excess hazard models. Later versions (>2.0.0) include penalized models for relative mortality ratio, and marginal intensity in recurrent event setting. survPen may be of interest to those who 1) analyse any kind of time-to-event data: mortality, disease relapse, machinery breakdown, unemployment, etc 2) wish to describe the associated hazard and to understand which predictors impact its dynamics, 3) wish to model the relative mortality ratio between a cohort and a reference population, 4) wish to describe the marginal intensity for recurrent event data. See Fauvernier et al. (2019a) <doi:10.21105/joss.01434> for an overview of the package and Fauvernier et al. (2019b) <doi:10.1111/rssc.12368> for the method.

Maintained by Mathieu Fauvernier. Last updated 4 months ago.

cpp

2.3 match 12 stars 6.82 score 85 scripts 1 dependents

snoweye

phyclust:Phylogenetic Clustering (Phyloclustering)

Phylogenetic clustering (phyloclustering) is an evolutionary Continuous Time Markov Chain model-based approach to identify population structure from molecular data without assuming linkage equilibrium. The package phyclust (Chen 2011) provides a convenient implementation of phyloclustering for DNA and SNP data, capable of clustering individuals into subpopulations and identifying molecular sequences representative of those subpopulations. It is designed in C for performance, interfaced with R for visualization, and incorporates other popular open source programs including ms (Hudson 2002) <doi:10.1093/bioinformatics/18.2.337>, seq-gen (Rambaut and Grassly 1997) <doi:10.1093/bioinformatics/13.3.235>, Hap-Clustering (Tzeng 2005) <doi:10.1002/gepi.20063> and PAML baseml (Yang 1997, 2007) <doi:10.1093/bioinformatics/13.5.555>, <doi:10.1093/molbev/msm088>, for simulating data, additional analyses, and searching the best tree. See the phyclust website for more information, documentations and examples.

Maintained by Wei-Chen Chen. Last updated 2 years ago.

1.8 match 9 stars 8.45 score 126 scripts 8 dependents

nlmixr2

monolix2rx:Converts 'Monolix' Models to 'rxode2'

'Monolix' is a tool for running mixed effects model using 'saem'. This tool allows you to convert 'Monolix' models to 'rxode2' (Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>) using the form compatible with 'nlmixr2' (Fidler et al (2019) <doi:10.1002/psp4.12445>). If available, the 'rxode2' model will read in the 'Monolix' data and compare the simulation for the population model individual model and residual model to immediately show how well the translation is performing. This saves the model development time for people who are creating an 'rxode2' model manually. Additionally, this package reads in all the information to allow simulation with uncertainty (that is the number of observations, the number of subjects, and the covariance matrix) with a 'rxode2' model. This is complementary to the 'babelmixr2' package that translates 'nlmixr2' models to 'Monolix' and can convert the objects converted from 'monolix2rx' to a full 'nlmixr2' fit. While not required, you can get/install the 'lixoftConnectors' package in the 'Monolix' installation, as described at the following url <https://monolixsuite.slp-software.com/r-functions/2024R1/installation-and-initialization>. When 'lixoftConnectors' is available, 'Monolix' can be used to load its model library instead manually setting up text files (which only works with old versions of 'Monolix').

Maintained by Matthew Fidler. Last updated 4 months ago.

monolixnlmixr2pharmacometricsrxode2cpp

3.3 match 1 stars 4.47 score 14 scripts 1 dependents

sticsrpacks

SticsRFiles:Read and Modify 'STICS' Input/Output Files

Manipulating input and output files of the 'STICS' crop model. Files are either 'JavaSTICS' XML files or text files used by the model 'fortran' executable. Most basic functionalities are reading or writing parameter names and values in both XML or text input files, and getting data from output files. Advanced functionalities include XML files generation from XML templates and/or spreadsheets, or text files generation from XML files by using 'xslt' transformation.

Maintained by Patrice Lecharpentier. Last updated 20 days ago.

1.7 match 4 stars 8.27 score 124 scripts

nlmixr2

nlmixr2lib:A Model Library for 'nlmixr2'

A model library for 'nlmixr2'. The models include (and plan to include) pharmacokinetic, pharmacodynamic, and disease models used in pharmacometrics. Where applicable, references for each model are included in the meta-data for each individual model. The package also includes model composition and modification functions to make model updates easier.

Maintained by Bill Denney. Last updated 3 months ago.

1.9 match 6 stars 6.38 score 9 scripts

rubenfcasal

npsp:Nonparametric Spatial Statistics

Multidimensional nonparametric spatial (spatio-temporal) geostatistics. S3 classes and methods for multidimensional: linear binning, local polynomial kernel regression (spatial trend estimation), density and variogram estimation. Nonparametric methods for simultaneous inference on both spatial trend and variogram functions (for spatial processes). Nonparametric residual kriging (spatial prediction). For details on these methods see, for example, Fernandez-Casal and Francisco-Fernandez (2014) <doi:10.1007/s00477-013-0817-8> or Castillo-Paez et al. (2019) <doi:10.1016/j.csda.2019.01.017>.

Maintained by Ruben Fernandez-Casal. Last updated 4 months ago.

geostatisticsspatial-data-analysisstatisticsfortranopenblas

2.0 match 4 stars 5.71 score 64 scripts

analythium

rconfig:Manage R Configuration at the Command Line

Configuration management using files (YAML, JSON, INI, TXT), JSON strings, and command line arguments. Command line arguments can be used to override configuration. Period-separated command line flags are parsed as hierarchical lists. Environment variables, R global variables, and configuration values can be substituted.

Maintained by Peter Solymos. Last updated 2 years ago.

cliconfigjsonyaml

2.5 match 26 stars 4.11 score 3 scripts

ropensci

virtuoso:Interface to 'Virtuoso' using 'ODBC'

Provides users with a simple and convenient mechanism to manage and query a 'Virtuoso' database using the 'DBI' (Data-Base Interface) compatible 'ODBC' (Open Database Connectivity) interface. 'Virtuoso' is a high-performance "universal server," which can act as both a relational database, supporting standard Structured Query Language ('SQL') queries, while also supporting data following the Resource Description Framework ('RDF') model for Linked Data. 'RDF' data can be queried using 'SPARQL' ('SPARQL' Protocol and 'RDF' Query Language) queries, a graph-based query that supports semantic reasoning. This allows users to leverage the performance of local or remote 'Virtuoso' servers using popular 'R' packages such as 'DBI' and 'dplyr', while also providing a high-performance solution for working with large 'RDF' 'triplestores' from 'R.' The package also provides helper routines to install, launch, and manage a 'Virtuoso' server locally on 'Mac', 'Windows' and 'Linux' platforms using the standard interactive installers from the 'R' command-line. By automatically handling these setup steps, the package can make using 'Virtuoso' considerably faster and easier for a most users to deploy in a local environment. Managing the bulk import of triples from common serializations with a single intuitive command is another key feature of this package. Bulk import performance can be tens to hundreds of times faster than the comparable imports using existing 'R' tools, including 'rdflib' and 'redland' packages.

Maintained by Carl Boettiger. Last updated 11 months ago.

1.8 match 9 stars 5.61 score 15 scripts

wactbprot

R4CouchDB:A R Convenience Layer for CouchDB 2.0

Provides a collection of functions for basic database and document management operations such as add (cdbAddDoc()), get (cdbGetDoc()), list access (cdbGetList()) or delete (cdbDeleteDoc()). Every cdbFunction() gets and returns a list() containing the connection setup. Such a list (named 'cdb' in the documentation) can be generated by cdb <- cdbIni(). Moreover, cdb provides some functions respectively functionality e.g cdb$baseUrl() or cdb$getDocRev().

Maintained by Thomas Bock. Last updated 8 years ago.

couchdbdatabase

2.3 match 31 stars 4.45 score 18 scripts

kwb-r

kwb.iview:Interface to IrfanView

Wrapper functions to IrfanView functionality.

Maintained by Hauke Sonnenberg. Last updated 4 years ago.

irfanview

5.4 match 1.70 score

hypertidy

ffraster:Native Raster Files

Provides a loose couplings between the facilities of `raster` and `ff`, to allow a file-backed raster grid to be modified as if it were an array in memory.

Maintained by Michael D. Sumner. Last updated 6 years ago.

2.0 match 5 stars 3.40 score 9 scripts

bruceqd

PLSiMCpp:Methods for Partial Linear Single Index Model

Estimation, hypothesis tests, and variable selection in partially linear single-index models. Please see H. (2010) at <doi:10.1214/10-AOS835> for more details.

Maintained by Shunyao Wu. Last updated 2 years ago.

openblascppopenmp

2.3 match 3 stars 2.18 score 1 scripts

hypertidy

tidyff:Create Native raster Files With ff

Couplings between raster and ff files.

Maintained by Michael D. Sumner. Last updated 8 years ago.

2.0 match 1 stars 1.70 score 6 scripts

tyler-hansen

HodgesTools:Common Use Tools for Genomic Analysis

Built by Hodges lab members for current and future Hodges lab members. Other individuals are welcome to use as well. Provides useful functions that the lab uses everyday to analyze various genomic datasets. Critically, only general use functions are provided; functions specific to a given technique are reserved for a separate package. As the lab grows, we expect to continue adding functions to the package to build on previous lab members code.

Maintained by Tyler Hansen. Last updated 2 years ago.

1.9 match 1.70 score 1 scripts

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