Package: RTMBp 1.6
RTMBp: 'R' Bindings for 'TMB'
Native 'R' interface to 'TMB' (Template Model Builder) so models can be written entirely in 'R' rather than 'C++'. Automatic differentiation, to any order, is available for a rich subset of 'R' features, including linear algebra for dense and sparse matrices, complex arithmetic, Fast Fourier Transform, probability distributions and special functions. 'RTMBp' provides easy access to model fitting and validation following the principles of Kristensen, K., Nielsen, A., Berg, C. W., Skaug, H., & Bell, B. M. (2016) <doi:10.18637/jss.v070.i05> and Thygesen, U.H., Albertsen, C.M., Berg, C.W. et al. (2017) <doi:10.1007/s10651-017-0372-4>.
Authors:
RTMBp_1.6.tar.gz
RTMBp_1.6.zip(r-4.5)RTMBp_1.6.zip(r-4.4)RTMBp_1.6.zip(r-4.3)
RTMBp_1.6.tgz(r-4.4-x86_64)RTMBp_1.6.tgz(r-4.4-arm64)RTMBp_1.6.tgz(r-4.3-x86_64)RTMBp_1.6.tgz(r-4.3-arm64)
RTMBp_1.6.tar.gz(r-4.5-noble)RTMBp_1.6.tar.gz(r-4.4-noble)
RTMBp_1.6.tgz(r-4.4-emscripten)RTMBp_1.6.tgz(r-4.3-emscripten)
RTMBp.pdf |RTMBp.html✨
RTMBp/json (API)
| # Install 'RTMBp' in R: |
| install.packages('RTMBp', repos = c('https://kaskr.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/kaskr/rtmbp/issues
Last updated 6 days agofrom:db0a40188a (on RTMBp). Checks:OK: 1 ERROR: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 12 2024 |
| R-4.5-win-x86_64 | ERROR | Sep 12 2024 |
| R-4.5-linux-x86_64 | ERROR | Sep 12 2024 |
| R-4.4-win-x86_64 | ERROR | Sep 12 2024 |
| R-4.4-mac-x86_64 | ERROR | Sep 12 2024 |
| R-4.4-mac-aarch64 | ERROR | Sep 12 2024 |
| R-4.3-win-x86_64 | ERROR | Sep 12 2024 |
| R-4.3-mac-x86_64 | ERROR | Sep 12 2024 |
| R-4.3-mac-aarch64 | ERROR | Sep 12 2024 |
Exports:[.advector[.osa[.simref[[.advector[<-.advector[<-.simref%~%$.TapeADadcomplexADjointADoverloadADREPORTadvectoraperm.advectorapplyas.array.simrefas.vector.advectorbesselIbesselJbesselKbesselYc.advectorcbind.advectorcheckConsistencycolSumsComplex.advectorcov2corDataEvaldautoregdbetadbinomdbinom_robustdcompoisdcompois2dexpdfdgammadgmrfdiagdiff.advectordiff.simrefdim.simrefdim<-.simrefdlgammadlnormdlogisdmultinomdmvnormdnbinomdnbinom_robustdnbinom2dnormdpoisdseparabledSHASHodsndtdtweediedweibulleigenexpAvfftgetAllGetTapeifelseinterpol1Dfuninterpol2Dfunis.array.simrefis.matrix.simrefis.na.simrefis.numeric.advectorlength.simrefMakeADFunMakeTapeMath.advectorMath.simrefmatrixOBSoneStepPredictOps.advectorOps.simrefpbetapbinompexppgammaplogispnormppoisprint.advectorprint.Tapeprod.advectorpweibullqbetaqexpqgammaqlogisqnormqweibullrbind.advectorrep.advectorREPORTrowSumssapplysdreportsimrefsolvesplinefunsum.advectorSummary.advectorSummary.simrefsvdt.simrefTapeConfigunstructured
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| RTMB: R bindings for 'TMB' | RTMB-package RTMB |
| Distributional assignment operator | %~% |
| Convert R object to AD | AD |
| AD apply functions | ADapply apply,advector-method sapply,ANY-method |
| AD complex numbers | %*%,adcomplex,ANY-method *.adcomplex +.adcomplex -.adcomplex /.adcomplex ADcomplex adcomplex Arg.adcomplex as.matrix.adcomplex as.vector.adcomplex colSums,adcomplex-method Conj.adcomplex diag,adcomplex,ANY,ANY-method dim.adcomplex dim<-.adcomplex exp.adcomplex fft,adcomplex-method fft,advector-method Im.adcomplex is.matrix.adcomplex length.adcomplex log.adcomplex Mod.adcomplex Ops,adcomplex,advector-method Ops,advector,adcomplex-method Re.adcomplex rep.adcomplex rowSums,adcomplex-method show,adcomplex-method solve,adcomplex,ANY-method sqrt.adcomplex t.adcomplex [.adcomplex [<-.adcomplex |
| AD aware numeric constructors | ADconstruct diag,advector,ANY,ANY-method matrix,advector-method matrix,num.-method |
| AD adjoint code from R | ADjoint |
| AD matrix methods (sparse and dense) | %*%,ad,ad-method %*%,ad,anysparse-method %*%,adsparse,adsparse-method %*%,anysparse,ad-method ADmatrix cbind.advector chol.advector colSums,advector-method cov2cor,advector-method crossprod,ad,ad.-method determinant.advector diag,adsparse,missing,missing-method dim,adsparse-method eigen,adcomplex-method eigen,advector-method expm,adsparse-method expm,advector-method rbind.advector rowSums,advector-method solve,ad,ad.-method solve,anysparse,ad.-method solve,num,num.-method svd,advector-method t.adsparse tcrossprod,ad,ad.-method [.adsparse [<-.adsparse |
| Enable extra RTMB convenience methods | ADoverload |
| The AD vector and its methods | ADvector advector aperm.advector as.complex.advector as.double.advector as.vector.advector c.advector Complex.advector diff.advector ifelse,num,ad,ad-method ifelse,num,num,num-method is.finite.advector is.infinite.advector is.na.advector is.nan.advector is.numeric.advector Math.advector mean.advector Ops.advector print.advector prod.advector rep.advector sum.advector Summary.advector [.advector [<-.advector [[.advector |
| Distributions and special functions for which AD is implemented | besselI,ad,ad,missing-method besselI,num,num,missing-method besselJ,ad,ad-method besselJ,num,num-method besselK,ad,ad,missing-method besselK,num,num,missing-method besselY,ad,ad-method besselY,num,num-method dbeta,ad,ad,ad,missing,logical.-method dbeta,num,num,num,missing,logical.-method dbeta,osa,ANY,ANY,ANY,ANY-method dbeta,simref,ANY,ANY,ANY,ANY-method dbinom,ad,ad,ad,logical.-method dbinom,num,num,num,logical.-method dbinom,osa,ANY,ANY,ANY-method dbinom,simref,ANY,ANY,ANY-method dbinom_robust dcompois dcompois2 dexp,ad,ad.,logical.-method dexp,num,num.,logical.-method dexp,osa,ANY,ANY-method dexp,simref,ANY,ANY-method df,ad,ad,ad,missing,logical.-method df,num,num,num,missing,logical.-method df,osa,ANY,ANY,ANY,ANY-method df,simref,ANY,ANY,ANY,ANY-method dgamma,ad,ad,missing,ad.,logical.-method dgamma,num,num,missing,num.,logical.-method dgamma,osa,ANY,ANY,ANY,ANY-method dgamma,simref,ANY,ANY,ANY,ANY-method Distributions dlgamma dlnorm,ANY,ANY,ANY,ANY-method dlnorm,num,num.,num.,logical.-method dlnorm,osa,ANY,ANY,ANY-method dlogis,ad,ad.,ad.,logical.-method dlogis,num,num.,num.,logical.-method dlogis,osa,ANY,ANY,ANY-method dlogis,simref,ANY,ANY,ANY-method dmultinom,ad,ad.,ad,logical.-method dmultinom,ANY,ANY,ANY,ANY-method dmultinom,num,num.,num,logical.-method dmultinom,osa,ANY,ANY,ANY-method dmultinom,simref,ANY,ANY,ANY-method dnbinom,ad,ad,ad,missing,logical.-method dnbinom,num,num,num,missing,logical.-method dnbinom,osa,ANY,ANY,ANY,ANY-method dnbinom,simref,ANY,ANY,ANY,ANY-method dnbinom2 dnbinom_robust dnorm,ad,ad.,ad.,logical.-method dnorm,num,num.,num.,logical.-method dnorm,osa,ANY,ANY,ANY-method dnorm,simref,ANY,ANY,ANY-method dpois,ad,ad,logical.-method dpois,num,num,logical.-method dpois,osa,ANY,ANY-method dpois,simref,ANY,ANY-method dSHASHo dsn dt,ad,ad,missing,logical.-method dt,num,num,missing,logical.-method dt,osa,ANY,ANY,ANY-method dt,simref,ANY,ANY,ANY-method dtweedie dweibull,ad,ad,ad.,logical.-method dweibull,num,num,num.,logical.-method dweibull,osa,ANY,ANY,ANY-method dweibull,simref,ANY,ANY,ANY-method pbeta,ad,ad,ad,missing,missing,missing-method pbeta,num,num,num,missing,missing,missing-method pbinom,ad,ad,ad,missing,missing-method pbinom,num,num,num,missing,missing-method pexp,ad,ad.,missing,missing-method pexp,num,num.,missing,missing-method pgamma,ad,ad,missing,ad.,missing,missing-method pgamma,num,num,missing,num.,missing,missing-method plogis,advector,missing,missing,missing,missing-method pnorm,ad,ad.,ad.,missing,missing-method pnorm,num,num.,num.,missing,missing-method ppois,ad,ad,missing,missing-method ppois,num,num,missing,missing-method pweibull,ad,ad,ad.,missing,missing-method pweibull,num,num,num.,missing,missing-method qbeta,ad,ad,ad,missing,missing,missing-method qbeta,num,num,num,missing,missing,missing-method qexp,ad,ad.,missing,missing-method qexp,num,num.,missing,missing-method qgamma,ad,ad,missing,ad.,missing,missing-method qgamma,num,num,missing,num.,missing,missing-method qlogis,advector,missing,missing,missing,missing-method qnorm,ad,ad.,ad.,missing,missing-method qnorm,num,num.,num.,missing,missing-method qweibull,ad,ad,ad.,missing,missing-method qweibull,num,num,num.,missing,missing-method |
| Matrix exponential of sparse matrix multiplied by a vector. | expAv |
| Interpolation | interpol1Dfun interpol2Dfun Interpolation splinefun,advector,missing,ANY,missing-method splinefun,ANY,advector,ANY,missing-method |
| Multivariate Gaussian densities | dautoreg dgmrf dmvnorm dseparable MVgauss unstructured |
| Recursive quantile residuals | dim.osa is.array.osa is.matrix.osa length.osa oneStepPredict OSA-residuals [.osa |
| Simulation | as.array.simref diff.simref dim.simref dim<-.simref is.array.simref is.matrix.simref is.na.simref length.simref Math.simref Ops.simref simref Simulation Summary.simref t.simref [.simref [<-.simref |
| The AD tape | $.Tape DataEval GetTape MakeTape print.Tape Tape TapeConfig |
| Interface to TMB | ADREPORT checkConsistency getAll MakeADFun OBS REPORT sdreport TMB-interface |
