Showing 32 of total 32 results (show query)
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 dependentsmiachol
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 dependentsnlmixr2
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.
14.7 match 40 stars 11.24 score 220 scripts 13 dependentsrte-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 scriptsnlmixr2
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 dependentsthe-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 scriptsbioc
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 dependentsmxjki
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 scriptsrspatial
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.
2.0 match 164 stars 17.05 score 58k scripts 555 dependentsdyfanjones
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 2 months ago.
18.6 match 1 stars 1.70 scoredyfanjones
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.
18.1 match 1 stars 1.70 scorenlmixr2
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 6 hours ago.
3.3 match 9 stars 8.33 score 26 scripts 9 dependentsirsn
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 dependentsnlmixr2
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 dependentshhoeflin
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 dependentsmoviedo5
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 dependentsnlmixr2
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.
3.3 match 3 stars 5.80 score 11 scripts 5 dependentsr-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 dependentsnlmixr2
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 dependentssticsrpacks
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 scriptsnlmixr2
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 scriptsrubenfcasal
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 scriptsanalythium
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.
2.5 match 26 stars 4.11 score 3 scriptswactbprot
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.
2.3 match 31 stars 4.45 score 18 scriptskwb-r
kwb.iview:Interface to IrfanView
Wrapper functions to IrfanView functionality.
Maintained by Hauke Sonnenberg. Last updated 4 years ago.
5.4 match 1.70 scorehypertidy
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 scriptsbruceqd
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.
2.3 match 3 stars 2.18 score 1 scriptshypertidy
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 scriptstyler-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