From f7681fdf031b7bd602ccf904b14e5a013f529334 Mon Sep 17 00:00:00 2001 From: Jeff Date: Thu, 26 Sep 2024 14:28:18 -0400 Subject: [PATCH] prep for CRAN --- DESCRIPTION | 2 +- NEWS.md | 1 + README.Rmd | 10 +- README.html | 28 ++-- README.md | 6 +- src/sfMsNMixNNGP.cpp | 42 ++--- src/spAbundance.h | 363 +++++++++++++++++++++++-------------------- src/spDSNNGP.cpp | 38 ++--- 8 files changed, 257 insertions(+), 233 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 44a6485..ee5157d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -9,7 +9,7 @@ Encoding: UTF-8 LazyData: true URL: https://www.doserlab.com/files/spabundance-web https://groups.google.com/g/spocc-spabund-users -BugReports: https://github.com/doserjef/spAbundance/issues +BugReports: https://github.com/biodiverse/spAbundance/issues Depends: R (>= 3.5.0) Imports: stats, coda, abind, RANN, lme4, foreach, doParallel, methods diff --git a/NEWS.md b/NEWS.md index 401fcc4..209df2e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -6,6 +6,7 @@ + Fixed some typos in the documentation. + Updated C++ code to adhere to the new lack of re-mapping of functions in Rinternals.h and R_ext/Error.h when building packages on CRAN. + Fixed a typo in the generation of initial values for latent unstructured random effects in all model functions. The typo had no major ramifications, if anything it just led to slower convergence, as it resulted in very large (or very small) initial values for the latent random effects that are not really viable on the log scale. ++ Moved GitHub development page to the "biodiverse" group. The GitHub link for the development repository is now [https://github.com/biodiverse/spAbundance](https://github.com/biodiverse/spAbundance). # spAbundance 0.1.3 diff --git a/README.Rmd b/README.Rmd index 29375e3..2f4ce0a 100644 --- a/README.Rmd +++ b/README.Rmd @@ -11,13 +11,13 @@ knitr::opts_chunk$set( out.width = "100%") ``` -# spAbundance +# spAbundance [![](http://cranlogs.r-pkg.org/badges/grand-total/spAbundance?color=blue)](https://CRAN.R-project.org/package=spAbundance) [![CRAN](https://www.r-pkg.org/badges/version/spAbundance)](https://CRAN.R-project.org/package=spAbundance) -[![Codecov test coverage](https://codecov.io/gh/doserjef/spAbundance/branch/main/graph/badge.svg)](https://codecov.io/gh/doserjef/spAbundance?branch=main) +[![Codecov test coverage](https://codecov.io/gh/biodiverse/spAbundance/branch/main/graph/badge.svg)](https://app.codecov.io/gh/biodiverse/spAbundance?branch=main) -`spAbundance` fits univariate (i.e., single-species) and multivariate (i.e., multi-species) spatial N-mixture models, hierarchical distance sampling models, and generalized linear mixed models using Markov chain Monte Carlo (MCMC). Spatial models are fit using Nearest Neighbor Gaussian Processes (NNGPs) to facilitate model fitting to large spatial datasets. `spAbundance` uses analogous syntax to its "sister package" [spOccupancy](https://www.doserlab.com/files/spoccupancy-web/) (Doser et al. 2022). Below we provide a very brief introduction to some of the package's functionality, and illustrate just one of the model fitting functions. For more information, see the resources referenced at the bottom of this page and the "Articles" tab at the top of the page. Please also consider joining the [`spAbundance` and `spOccupancy` users google group](https://groups.google.com/g/spocc-spabund-users). +`spAbundance` fits univariate (i.e., single-species) and multivariate (i.e., multi-species) spatial N-mixture models, hierarchical distance sampling models, and generalized linear mixed models using Markov chain Monte Carlo (MCMC). Spatial models are fit using Nearest Neighbor Gaussian Processes (NNGPs) to facilitate model fitting to large spatial datasets. `spAbundance` uses analogous syntax to its "sister package" [spOccupancy](https://doserlab.com/files/spoccupancy-web/) (Doser et al. 2022). Below we provide a very brief introduction to some of the package's functionality, and illustrate just one of the model fitting functions. For more information, see the resources referenced at the bottom of this page and the "Articles" tab at the top of the page. Please also consider joining the [`spAbundance` and `spOccupancy` users google group](https://groups.google.com/g/spocc-spabund-users). ## Installation @@ -30,7 +30,7 @@ install.packages("spAbundance") To download the development version of the package, you can use `devtools` as follows: ```{r, eval = FALSE} -devtools::install_github("doserjef/spAbundance") +devtools::install_github("biodiverse/spAbundance") ``` Note that because we implement the MCMC in C++, you will need a C++ compiler on your computer to install the package from GitHub. To compile C++ on Windows, you can install [`RTools`](https://cran.r-project.org/bin/windows/Rtools/). To compile C++ on a Mac, you can install `XCode` from the Mac app store. @@ -147,7 +147,7 @@ out.pred <- predict(out, X.0, coords.0, verbose = FALSE) ## Learn more -The `vignette("distanceSampling")`, `vignette("nMixtureModels")`, and `vignette("glmm")` provide detailed descriptions and tutorials of all hierarchical distance sampling models, N-mixture models, and generalized linear mixed models in `spAbundance`, respectively. Given the similarity in syntax to fitting occupancy models in the `spOccupancy` package, much of the documentation on the [`spOccupancy` website](https://www.doserlab.com/files/spoccupancy-web/) will also be helpful for fitting models in `spAbundance`. Please also consider joining the [`spAbundance` and `spOccupancy` users google group](https://groups.google.com/g/spocc-spabund-users) to learn from others who use the two packages. +The `vignette("distanceSampling")`, `vignette("nMixtureModels")`, and `vignette("glmm")` provide detailed descriptions and tutorials of all hierarchical distance sampling models, N-mixture models, and generalized linear mixed models in `spAbundance`, respectively. Given the similarity in syntax to fitting occupancy models in the `spOccupancy` package, much of the documentation on the [`spOccupancy` website](https://doserlab.com/files/spoccupancy-web/) will also be helpful for fitting models in `spAbundance`. Please also consider joining the [`spAbundance` and `spOccupancy` users google group](https://groups.google.com/g/spocc-spabund-users) to learn from others who use the two packages. ## Citing `spAbundance` diff --git a/README.html b/README.html index 799c856..ad94e14 100644 --- a/README.html +++ b/README.html @@ -605,28 +605,28 @@

spAbundance

-

+

CRAN - - + + - - + + - - - - + + + + codecov codecov - 78% - 78% + unknown + unknown - +

spAbundance fits univariate (i.e., single-species) and @@ -648,7 +648,7 @@

Installation

install.packages("spAbundance")

To download the development version of the package, you can use devtools as follows:

-
devtools::install_github("doserjef/spAbundance")
+
devtools::install_github("biodiverse/spAbundance")

Note that because we implement the MCMC in C++, you will need a C++ compiler on your computer to install the package from GitHub. To compile C++ on Windows, you can install RTools. @@ -839,7 +839,7 @@

Fit a #> Thinning Rate: 5 #> Number of Chains: 3 #> Total Posterior Samples: 6000 -#> Run Time (min): 0.9219 +#> Run Time (min): 0.7582 #> #> Abundance (log scale): #> Mean SD 2.5% 50% 97.5% Rhat ESS diff --git a/README.md b/README.md index 40b5ca4..8e2219c 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ [![](http://cranlogs.r-pkg.org/badges/grand-total/spAbundance?color=blue)](https://CRAN.R-project.org/package=spAbundance) [![CRAN](https://www.r-pkg.org/badges/version/spAbundance)](https://CRAN.R-project.org/package=spAbundance) [![Codecov test -coverage](https://codecov.io/gh/doserjef/spAbundance/branch/main/graph/badge.svg)](https://codecov.io/gh/doserjef/spAbundance?branch=main) +coverage](https://codecov.io/gh/biodiverse/spAbundance/branch/main/graph/badge.svg)](https://codecov.io/gh/biodiverse/spAbundance?branch=main) `spAbundance` fits univariate (i.e., single-species) and multivariate (i.e., multi-species) spatial N-mixture models, hierarchical distance @@ -35,7 +35,7 @@ To download the development version of the package, you can use `devtools` as follows: ``` r -devtools::install_github("doserjef/spAbundance") +devtools::install_github("biodiverse/spAbundance") ``` Note that because we implement the MCMC in C++, you will need a C++ @@ -160,7 +160,7 @@ summary(out) #> Thinning Rate: 5 #> Number of Chains: 3 #> Total Posterior Samples: 6000 -#> Run Time (min): 0.9219 +#> Run Time (min): 0.7582 #> #> Abundance (log scale): #> Mean SD 2.5% 50% 97.5% Rhat ESS diff --git a/src/sfMsNMixNNGP.cpp b/src/sfMsNMixNNGP.cpp index 79c3669..9527a54 100644 --- a/src/sfMsNMixNNGP.cpp +++ b/src/sfMsNMixNNGP.cpp @@ -64,27 +64,27 @@ void updateBFSFNMix(double *B, double *F, double *c, double *C, double *coords, extern "C" { SEXP sfMsNMixNNGP(SEXP y_r, SEXP X_r, SEXP Xp_r, SEXP coords_r, SEXP XRE_r, SEXP XpRE_r, SEXP XRandom_r, SEXP XpRandom_r, SEXP yMax_r, - SEXP consts_r, SEXP nAbundRELong_r, SEXP nDetRELong_r, - SEXP m_r, SEXP nnIndx_r, - SEXP nnIndxLU_r, SEXP uIndx_r, SEXP uIndxLU_r, SEXP uiIndx_r, - SEXP betaStarting_r, SEXP alphaStarting_r, SEXP kappaStarting_r, SEXP NStarting_r, - SEXP betaCommStarting_r, SEXP alphaCommStarting_r, - SEXP phiStarting_r, SEXP lambdaStarting_r, SEXP nuStarting_r, SEXP wStarting_r, - SEXP tauSqBetaStarting_r, SEXP tauSqAlphaStarting_r, - SEXP sigmaSqMuStarting_r, SEXP sigmaSqPStarting_r, - SEXP betaStarStarting_r, SEXP alphaStarStarting_r, - SEXP NLongIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, - SEXP alphaStarIndx_r, SEXP alphaLevelIndx_r, - SEXP muBetaComm_r, SEXP muAlphaComm_r, - SEXP SigmaBetaComm_r, SEXP SigmaAlphaComm_r, SEXP kappaA_r, - SEXP kappaB_r, SEXP tauSqBetaA_r, - SEXP tauSqBetaB_r, SEXP tauSqAlphaA_r, SEXP tauSqAlphaB_r, - SEXP spatialPriors_r, SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, - SEXP sigmaSqPA_r, SEXP sigmaSqPB_r, - SEXP tuning_r, SEXP covModel_r, - SEXP batchInfo_r, SEXP acceptRate_r, - SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, - SEXP samplesInfo_r, SEXP chainInfo_r, SEXP family_r, SEXP offset_r){ + SEXP consts_r, SEXP nAbundRELong_r, SEXP nDetRELong_r, + SEXP m_r, SEXP nnIndx_r, + SEXP nnIndxLU_r, SEXP uIndx_r, SEXP uIndxLU_r, SEXP uiIndx_r, + SEXP betaStarting_r, SEXP alphaStarting_r, SEXP kappaStarting_r, SEXP NStarting_r, + SEXP betaCommStarting_r, SEXP alphaCommStarting_r, + SEXP phiStarting_r, SEXP lambdaStarting_r, SEXP nuStarting_r, SEXP wStarting_r, + SEXP tauSqBetaStarting_r, SEXP tauSqAlphaStarting_r, + SEXP sigmaSqMuStarting_r, SEXP sigmaSqPStarting_r, + SEXP betaStarStarting_r, SEXP alphaStarStarting_r, + SEXP NLongIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, + SEXP alphaStarIndx_r, SEXP alphaLevelIndx_r, + SEXP muBetaComm_r, SEXP muAlphaComm_r, + SEXP SigmaBetaComm_r, SEXP SigmaAlphaComm_r, SEXP kappaA_r, + SEXP kappaB_r, SEXP tauSqBetaA_r, + SEXP tauSqBetaB_r, SEXP tauSqAlphaA_r, SEXP tauSqAlphaB_r, + SEXP spatialPriors_r, SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, + SEXP sigmaSqPA_r, SEXP sigmaSqPB_r, + SEXP tuning_r, SEXP covModel_r, + SEXP batchInfo_r, SEXP acceptRate_r, + SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, + SEXP samplesInfo_r, SEXP chainInfo_r, SEXP family_r, SEXP offset_r){ /********************************************************************** * Initial constants diff --git a/src/spAbundance.h b/src/spAbundance.h index 73aec97..3b89116 100644 --- a/src/spAbundance.h +++ b/src/spAbundance.h @@ -6,14 +6,14 @@ extern "C" { SEXP abund(SEXP y_r, SEXP X_r, SEXP XRE_r, SEXP XRandom_r, SEXP consts_r,SEXP nAbundRELong_r, SEXP betaStarting_r, SEXP kappaStarting_r, - SEXP sigmaSqMuStarting_r, SEXP betaStarStarting_r, + SEXP sigmaSqMuStarting_r, SEXP betaStarStarting_r, SEXP siteIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, - SEXP muBeta_r, SEXP SigmaBeta_r, - SEXP kappaA_r, SEXP kappaB_r, SEXP sigmaSqMuA_r, - SEXP sigmaSqMuB_r, SEXP tuning_r, - SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, SEXP nThreads_r, + SEXP muBeta_r, SEXP SigmaBeta_r, + SEXP kappaA_r, SEXP kappaB_r, SEXP sigmaSqMuA_r, + SEXP sigmaSqMuB_r, SEXP tuning_r, + SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, SEXP samplesInfo_r, - SEXP chainInfo_r, SEXP family_r, SEXP offset_r); + SEXP chainInfo_r, SEXP family_r, SEXP offset_r); SEXP abundGaussian(SEXP y_r, SEXP X_r, SEXP XRE_r, SEXP XRandom_r, SEXP consts_r, SEXP nRELong_r, @@ -21,7 +21,7 @@ extern "C" { SEXP betaStarStarting_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, SEXP muBeta_r, SEXP SigmaBeta_r, - SEXP tauSqA_r, SEXP tauSqB_r, + SEXP tauSqA_r, SEXP tauSqB_r, SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, SEXP samplesInfo_r, SEXP chainInfo_r); @@ -36,8 +36,8 @@ extern "C" { SEXP nuStarting_r, SEXP siteIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, SEXP muBeta_r, SEXP SigmaBeta_r, - SEXP kappaA_r, SEXP kappaB_r, - SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, + SEXP kappaA_r, SEXP kappaB_r, + SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, SEXP phiA_r, SEXP phiB_r, SEXP sigmaSqA_r, SEXP sigmaSqB_r, SEXP nuA_r, SEXP nuB_r, SEXP tuning_r, SEXP covModel_r, @@ -54,14 +54,14 @@ extern "C" { SEXP sigmaSqStarting_r, SEXP nuStarting_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, SEXP muBeta_r, SEXP SigmaBeta_r, - SEXP tauSqA_r, SEXP tauSqB_r, SEXP phiA_r, SEXP phiB_r, + SEXP tauSqA_r, SEXP tauSqB_r, SEXP phiA_r, SEXP phiB_r, SEXP sigmaSqA_r, SEXP sigmaSqB_r, SEXP nuA_r, SEXP nuB_r, SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, SEXP tuning_r, SEXP covModel_r, SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, - SEXP nThreads_r, SEXP verbose_r, + SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, SEXP samplesInfo_r, SEXP chainInfo_r, - SEXP sigmaSqIG_r); + SEXP sigmaSqIG_r); SEXP svcAbundNNGPPredict(SEXP coords_r, SEXP J_r, SEXP nObs_r, SEXP pAbund_r, SEXP pTilde_r, SEXP m_r, SEXP X0_r, SEXP Xw0_r, @@ -91,10 +91,10 @@ extern "C" { SEXP betaStarting_r, SEXP betaCommStarting_r, SEXP tauSqBetaStarting_r, SEXP tauSqStarting_r, SEXP sigmaSqMuStarting_r, SEXP betaStarStarting_r, - SEXP betaStarIndx_r, SEXP betaLevelIndx_r, + SEXP betaStarIndx_r, SEXP betaLevelIndx_r, SEXP muBetaComm_r, SEXP SigmaBetaComm_r, SEXP tauSqBetaA_r, SEXP tauSqBetaB_r, SEXP tauSqA_r, SEXP tauSqB_r, - SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, + SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, SEXP tuning_r, SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, @@ -104,13 +104,13 @@ extern "C" { SEXP lfMsAbund(SEXP y_r, SEXP X_r, SEXP XRE_r, SEXP XRandom_r, SEXP consts_r, SEXP nAbundRELong_r, SEXP betaStarting_r, SEXP kappaStarting_r, SEXP betaCommStarting_r, - SEXP tauSqBetaStarting_r, SEXP lambdaStarting_r, SEXP wStarting_r, + SEXP tauSqBetaStarting_r, SEXP lambdaStarting_r, SEXP wStarting_r, SEXP sigmaSqMuStarting_r, SEXP betaStarStarting_r, SEXP siteIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, SEXP muBetaComm_r, SEXP SigmaBetaComm_r, SEXP kappaA_r, SEXP kappaB_r, SEXP tauSqBetaA_r, SEXP tauSqBetaB_r, SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, SEXP tuning_r, - SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, + SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, SEXP samplesInfo_r, SEXP chainInfo_r, SEXP family_r, SEXP offset_r); @@ -118,12 +118,12 @@ extern "C" { SEXP XRandom_r, SEXP consts_r, SEXP nRELong_r, SEXP betaStarting_r, SEXP betaCommStarting_r, SEXP tauSqBetaStarting_r, SEXP tauSqStarting_r, - SEXP lambdaStarting_r, SEXP wStarting_r, + SEXP lambdaStarting_r, SEXP wStarting_r, SEXP sigmaSqMuStarting_r, SEXP betaStarStarting_r, - SEXP betaStarIndx_r, SEXP betaLevelIndx_r, + SEXP betaStarIndx_r, SEXP betaLevelIndx_r, SEXP muBetaComm_r, SEXP SigmaBetaComm_r, SEXP tauSqBetaA_r, SEXP tauSqBetaB_r, SEXP tauSqA_r, SEXP tauSqB_r, - SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, + SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, SEXP tuning_r, SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, @@ -131,51 +131,51 @@ extern "C" { SEXP z_r, SEXP family_r); SEXP sfMsAbundNNGP(SEXP y_r, SEXP X_r, SEXP coords_r, SEXP XRE_r, SEXP XRandom_r, - SEXP consts_r, SEXP nAbundRELong_r, SEXP m_r, SEXP nnIndx_r, - SEXP nnIndxLU_r, SEXP uIndx_r, SEXP uIndxLU_r, SEXP uiIndx_r, - SEXP betaStarting_r, SEXP kappaStarting_r, SEXP betaCommStarting_r, - SEXP tauSqBetaStarting_r, SEXP phiStarting_r, - SEXP lambdaStarting_r, SEXP nuStarting_r, SEXP wStarting_r, - SEXP sigmaSqMuStarting_r, SEXP betaStarStarting_r, - SEXP siteIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, - SEXP muBetaComm_r, SEXP SigmaBetaComm_r, SEXP kappaA_r, - SEXP kappaB_r, SEXP tauSqBetaA_r, SEXP tauSqBetaB_r, - SEXP phiA_r, SEXP phiB_r, SEXP nuA_r, SEXP nuB_r, - SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, - SEXP tuning_r, SEXP covModel_r, - SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, - SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, - SEXP samplesInfo_r, SEXP chainInfo_r, SEXP family_r, SEXP offset_r); + SEXP consts_r, SEXP nAbundRELong_r, SEXP m_r, SEXP nnIndx_r, + SEXP nnIndxLU_r, SEXP uIndx_r, SEXP uIndxLU_r, SEXP uiIndx_r, + SEXP betaStarting_r, SEXP kappaStarting_r, SEXP betaCommStarting_r, + SEXP tauSqBetaStarting_r, SEXP phiStarting_r, + SEXP lambdaStarting_r, SEXP nuStarting_r, SEXP wStarting_r, + SEXP sigmaSqMuStarting_r, SEXP betaStarStarting_r, + SEXP siteIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, + SEXP muBetaComm_r, SEXP SigmaBetaComm_r, SEXP kappaA_r, + SEXP kappaB_r, SEXP tauSqBetaA_r, SEXP tauSqBetaB_r, + SEXP phiA_r, SEXP phiB_r, SEXP nuA_r, SEXP nuB_r, + SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, + SEXP tuning_r, SEXP covModel_r, + SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, + SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, + SEXP samplesInfo_r, SEXP chainInfo_r, SEXP family_r, SEXP offset_r); SEXP sfMsAbundGaussianNNGP(SEXP y_r, SEXP X_r, SEXP coords_r, SEXP XRE_r, SEXP XRandom_r, SEXP consts_r, SEXP nRELong_r, - SEXP m_r, SEXP nnIndx_r, + SEXP m_r, SEXP nnIndx_r, SEXP nnIndxLU_r, SEXP uIndx_r, SEXP uIndxLU_r, SEXP uiIndx_r, SEXP betaStarting_r, SEXP betaCommStarting_r, SEXP tauSqBetaStarting_r, SEXP tauSqStarting_r, SEXP phiStarting_r, SEXP lambdaStarting_r, SEXP nuStarting_r, SEXP wStarting_r, SEXP sigmaSqMuStarting_r, SEXP betaStarStarting_r, SEXP betaStarIndx_r, - SEXP betaLevelIndx_r, + SEXP betaLevelIndx_r, SEXP muBetaComm_r, SEXP SigmaBetaComm_r, SEXP tauSqBetaA_r, SEXP tauSqBetaB_r, SEXP tauSqA_r, SEXP tauSqB_r, SEXP phiA_r, SEXP phiB_r, SEXP nuA_r, SEXP nuB_r, SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, SEXP tuning_r, SEXP covModel_r, - SEXP nBatch_r, SEXP batchLength_r, + SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, SEXP nThreads_r, - SEXP verbose_r, SEXP nReport_r, + SEXP verbose_r, SEXP nReport_r, SEXP samplesInfo_r, SEXP chainInfo_r, - SEXP z_r, SEXP family_r); + SEXP z_r, SEXP family_r); SEXP sfMsAbundNNGPPredict(SEXP coords_r, SEXP J_r, SEXP nObs_r, SEXP family_r, SEXP nSp_r, - SEXP q_r, SEXP pAbund_r, SEXP m_r, SEXP X0_r, SEXP coords0_r, - SEXP J0_r, SEXP nObs0_r, SEXP sitesLink_r, SEXP sites0Sampled_r, - SEXP sites0_r, SEXP nnIndx0_r, SEXP betaSamples_r, - SEXP thetaSamples_r, SEXP kappaSamples_r, SEXP lambdaSamples_r, - SEXP wSamples_r, SEXP betaStarSiteSamples_r, - SEXP nSamples_r, SEXP covModel_r, SEXP nThreads_r, SEXP verbose_r, - SEXP nReport_r); + SEXP q_r, SEXP pAbund_r, SEXP m_r, SEXP X0_r, SEXP coords0_r, + SEXP J0_r, SEXP nObs0_r, SEXP sitesLink_r, SEXP sites0Sampled_r, + SEXP sites0_r, SEXP nnIndx0_r, SEXP betaSamples_r, + SEXP thetaSamples_r, SEXP kappaSamples_r, SEXP lambdaSamples_r, + SEXP wSamples_r, SEXP betaStarSiteSamples_r, + SEXP nSamples_r, SEXP covModel_r, SEXP nThreads_r, SEXP verbose_r, + SEXP nReport_r); SEXP NMix(SEXP y_r, SEXP X_r, SEXP Xp_r, SEXP XRE_r, SEXP XpRE_r, SEXP XRandom_r, SEXP XpRandom_r, SEXP yMax_r, @@ -184,119 +184,141 @@ extern "C" { SEXP sigmaSqMuStarting_r, SEXP sigmaSqPStarting_r, SEXP betaStarStarting_r, SEXP alphaStarStarting_r, SEXP NStarting_r, SEXP NLongIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, - SEXP alphaStarIndx_r, SEXP alphaLevelIndx_r, - SEXP muBeta_r, SEXP SigmaBeta_r, - SEXP muAlpha_r, SEXP SigmaAlpha_r, + SEXP alphaStarIndx_r, SEXP alphaLevelIndx_r, + SEXP muBeta_r, SEXP SigmaBeta_r, + SEXP muAlpha_r, SEXP SigmaAlpha_r, SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, SEXP sigmaSqPA_r, SEXP sigmaSqPB_r, - SEXP kappaA_r, SEXP kappaB_r, SEXP tuning_r, - SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, SEXP nThreads_r, + SEXP kappaA_r, SEXP kappaB_r, SEXP tuning_r, + SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, SEXP samplesInfo_r, - SEXP chainInfo_r, SEXP family_r, SEXP offset_r); + SEXP chainInfo_r, SEXP family_r, SEXP offset_r); SEXP spNMixNNGP(SEXP y_r, SEXP X_r, SEXP Xp_r, SEXP coords_r, SEXP XRE_r, SEXP XpRE_r, - SEXP XRandom_r, SEXP XpRandom_r, SEXP yMax_r, + SEXP XRandom_r, SEXP XpRandom_r, SEXP yMax_r, SEXP consts_r, SEXP nAbundRELong_r, SEXP nDetRELong_r, SEXP m_r, SEXP nnIndx_r, SEXP nnIndxLU_r, SEXP uIndx_r, SEXP uIndxLU_r, SEXP uiIndx_r, SEXP betaStarting_r, SEXP alphaStarting_r, SEXP kappaStarting_r, SEXP sigmaSqMuStarting_r, SEXP sigmaSqPStarting_r, SEXP betaStarStarting_r, SEXP alphaStarStarting_r, SEXP NStarting_r, - SEXP wStarting_r, SEXP phiStarting_r, SEXP sigmaSqStarting_r, SEXP nuStarting_r, + SEXP wStarting_r, SEXP phiStarting_r, SEXP sigmaSqStarting_r, SEXP nuStarting_r, SEXP NLongIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, - SEXP alphaStarIndx_r, SEXP alphaLevelIndx_r, - SEXP muBeta_r, SEXP SigmaBeta_r, - SEXP muAlpha_r, SEXP SigmaAlpha_r, - SEXP phiA_r, SEXP phiB_r, SEXP sigmaSqA_r, SEXP sigmaSqB_r, - SEXP nuA_r, SEXP nuB_r, SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, + SEXP alphaStarIndx_r, SEXP alphaLevelIndx_r, + SEXP muBeta_r, SEXP SigmaBeta_r, + SEXP muAlpha_r, SEXP SigmaAlpha_r, + SEXP phiA_r, SEXP phiB_r, SEXP sigmaSqA_r, SEXP sigmaSqB_r, + SEXP nuA_r, SEXP nuB_r, SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, SEXP sigmaSqPA_r, SEXP sigmaSqPB_r, - SEXP kappaA_r, SEXP kappaB_r, SEXP tuning_r, SEXP covModel_r, - SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, SEXP nThreads_r, + SEXP kappaA_r, SEXP kappaB_r, SEXP tuning_r, SEXP covModel_r, + SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, SEXP samplesInfo_r, - SEXP chainInfo_r, SEXP sigmaSqIG_r, SEXP family_r, SEXP offset_r); + SEXP chainInfo_r, SEXP sigmaSqIG_r, SEXP family_r, SEXP offset_r); SEXP spNMixNNGPPredict(SEXP coords_r, SEXP J_r, SEXP family_r, - SEXP pAbund_r, SEXP m_r, SEXP X0_r, SEXP coords0_r, - SEXP J0_r, SEXP nnIndx0_r, SEXP betaSamples_r, - SEXP thetaSamples_r, SEXP kappaSamples_r, SEXP wSamples_r, - SEXP betaStarSiteSamples_r, + SEXP pAbund_r, SEXP m_r, SEXP X0_r, SEXP coords0_r, + SEXP J0_r, SEXP nnIndx0_r, SEXP betaSamples_r, + SEXP thetaSamples_r, SEXP kappaSamples_r, SEXP wSamples_r, + SEXP betaStarSiteSamples_r, SEXP sitesLink_r, SEXP sites0Sampled_r, SEXP sites0_r, - SEXP nSamples_r, SEXP covModel_r, SEXP nThreads_r, SEXP verbose_r, - SEXP nReport_r); + SEXP nSamples_r, SEXP covModel_r, SEXP nThreads_r, SEXP verbose_r, + SEXP nReport_r); SEXP msNMix(SEXP y_r, SEXP X_r, SEXP Xp_r, SEXP XRE_r, SEXP XpRE_r, SEXP XRandom_r, SEXP XpRandom_r, SEXP yMax_r, - SEXP consts_r, SEXP nAbundRELong_r, SEXP nDetRELong_r, - SEXP betaStarting_r, SEXP alphaStarting_r, SEXP kappaStarting_r, SEXP NStarting_r, - SEXP betaCommStarting_r, SEXP alphaCommStarting_r, - SEXP tauSqBetaStarting_r, SEXP tauSqAlphaStarting_r, - SEXP sigmaSqMuStarting_r, SEXP sigmaSqPStarting_r, - SEXP betaStarStarting_r, SEXP alphaStarStarting_r, - SEXP NLongIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, - SEXP alphaStarIndx_r, SEXP alphaLevelIndx_r, - SEXP muBetaComm_r, SEXP muAlphaComm_r, - SEXP SigmaBetaComm_r, SEXP SigmaAlphaComm_r, SEXP kappaA_r, - SEXP kappaB_r, SEXP tauSqBetaA_r, - SEXP tauSqBetaB_r, SEXP tauSqAlphaA_r, SEXP tauSqAlphaB_r, - SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, - SEXP sigmaSqPA_r, SEXP sigmaSqPB_r, - SEXP tuning_r, SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, - SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, - SEXP samplesInfo_r, SEXP chainInfo_r, SEXP family_r, SEXP offset_r); + SEXP consts_r, SEXP nAbundRELong_r, SEXP nDetRELong_r, + SEXP betaStarting_r, SEXP alphaStarting_r, SEXP kappaStarting_r, SEXP NStarting_r, + SEXP betaCommStarting_r, SEXP alphaCommStarting_r, + SEXP tauSqBetaStarting_r, SEXP tauSqAlphaStarting_r, + SEXP sigmaSqMuStarting_r, SEXP sigmaSqPStarting_r, + SEXP betaStarStarting_r, SEXP alphaStarStarting_r, + SEXP NLongIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, + SEXP alphaStarIndx_r, SEXP alphaLevelIndx_r, + SEXP muBetaComm_r, SEXP muAlphaComm_r, + SEXP SigmaBetaComm_r, SEXP SigmaAlphaComm_r, SEXP kappaA_r, + SEXP kappaB_r, SEXP tauSqBetaA_r, + SEXP tauSqBetaB_r, SEXP tauSqAlphaA_r, SEXP tauSqAlphaB_r, + SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, + SEXP sigmaSqPA_r, SEXP sigmaSqPB_r, + SEXP tuning_r, SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, + SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, + SEXP samplesInfo_r, SEXP chainInfo_r, SEXP family_r, SEXP offset_r); SEXP lfMsNMix(SEXP y_r, SEXP X_r, SEXP Xp_r, SEXP XRE_r, SEXP XpRE_r, SEXP XRandom_r, SEXP XpRandom_r, SEXP yMax_r, - SEXP consts_r, SEXP nAbundRELong_r, SEXP nDetRELong_r, - SEXP betaStarting_r, SEXP alphaStarting_r, - SEXP kappaStarting_r, SEXP NStarting_r, - SEXP betaCommStarting_r, SEXP alphaCommStarting_r, - SEXP lambdaStarting_r, SEXP wStarting_r, - SEXP tauSqBetaStarting_r, SEXP tauSqAlphaStarting_r, - SEXP sigmaSqMuStarting_r, SEXP sigmaSqPStarting_r, - SEXP betaStarStarting_r, SEXP alphaStarStarting_r, - SEXP NLongIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, - SEXP alphaStarIndx_r, SEXP alphaLevelIndx_r, - SEXP muBetaComm_r, SEXP muAlphaComm_r, - SEXP SigmaBetaComm_r, SEXP SigmaAlphaComm_r, SEXP kappaA_r, - SEXP kappaB_r, SEXP tauSqBetaA_r, - SEXP tauSqBetaB_r, SEXP tauSqAlphaA_r, SEXP tauSqAlphaB_r, - SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, - SEXP sigmaSqPA_r, SEXP sigmaSqPB_r, SEXP tuning_r, - SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, - SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, - SEXP samplesInfo_r, SEXP chainInfo_r, SEXP family_r, SEXP offset_r); + SEXP consts_r, SEXP nAbundRELong_r, SEXP nDetRELong_r, + SEXP betaStarting_r, SEXP alphaStarting_r, + SEXP kappaStarting_r, SEXP NStarting_r, + SEXP betaCommStarting_r, SEXP alphaCommStarting_r, + SEXP lambdaStarting_r, SEXP wStarting_r, + SEXP tauSqBetaStarting_r, SEXP tauSqAlphaStarting_r, + SEXP sigmaSqMuStarting_r, SEXP sigmaSqPStarting_r, + SEXP betaStarStarting_r, SEXP alphaStarStarting_r, + SEXP NLongIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, + SEXP alphaStarIndx_r, SEXP alphaLevelIndx_r, + SEXP muBetaComm_r, SEXP muAlphaComm_r, + SEXP SigmaBetaComm_r, SEXP SigmaAlphaComm_r, SEXP kappaA_r, + SEXP kappaB_r, SEXP tauSqBetaA_r, + SEXP tauSqBetaB_r, SEXP tauSqAlphaA_r, SEXP tauSqAlphaB_r, + SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, + SEXP sigmaSqPA_r, SEXP sigmaSqPB_r, SEXP tuning_r, + SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, + SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, + SEXP samplesInfo_r, SEXP chainInfo_r, SEXP family_r, SEXP offset_r); + + SEXP lfMsNMix(SEXP y_r, SEXP X_r, SEXP Xp_r, SEXP XRE_r, SEXP XpRE_r, + SEXP XRandom_r, SEXP XpRandom_r, SEXP yMax_r, + SEXP consts_r, SEXP nAbundRELong_r, SEXP nDetRELong_r, + SEXP betaStarting_r, SEXP alphaStarting_r, + SEXP kappaStarting_r, SEXP NStarting_r, + SEXP betaCommStarting_r, SEXP alphaCommStarting_r, + SEXP lambdaStarting_r, SEXP wStarting_r, + SEXP tauSqBetaStarting_r, SEXP tauSqAlphaStarting_r, + SEXP sigmaSqMuStarting_r, SEXP sigmaSqPStarting_r, + SEXP betaStarStarting_r, SEXP alphaStarStarting_r, + SEXP NLongIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, + SEXP alphaStarIndx_r, SEXP alphaLevelIndx_r, + SEXP muBetaComm_r, SEXP muAlphaComm_r, + SEXP SigmaBetaComm_r, SEXP SigmaAlphaComm_r, SEXP kappaA_r, + SEXP kappaB_r, SEXP tauSqBetaA_r, + SEXP tauSqBetaB_r, SEXP tauSqAlphaA_r, SEXP tauSqAlphaB_r, + SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, + SEXP sigmaSqPA_r, SEXP sigmaSqPB_r, SEXP tuning_r, + SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, + SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, + SEXP samplesInfo_r, SEXP chainInfo_r, SEXP family_r, SEXP offset_r); SEXP sfMsNMixNNGP(SEXP y_r, SEXP X_r, SEXP Xp_r, SEXP coords_r, SEXP XRE_r, SEXP XpRE_r, SEXP XRandom_r, SEXP XpRandom_r, SEXP yMax_r, - SEXP consts_r, SEXP nAbundRELong_r, SEXP nDetRELong_r, - SEXP m_r, SEXP nnIndx_r, - SEXP nnIndxLU_r, SEXP uIndx_r, SEXP uIndxLU_r, SEXP uiIndx_r, - SEXP betaStarting_r, SEXP alphaStarting_r, SEXP kappaStarting_r, SEXP NStarting_r, - SEXP betaCommStarting_r, SEXP alphaCommStarting_r, - SEXP phiStarting_r, SEXP lambdaStarting_r, SEXP nuStarting_r, SEXP wStarting_r, - SEXP tauSqBetaStarting_r, SEXP tauSqAlphaStarting_r, - SEXP sigmaSqMuStarting_r, SEXP sigmaSqPStarting_r, - SEXP betaStarStarting_r, SEXP alphaStarStarting_r, - SEXP NLongIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, - SEXP alphaStarIndx_r, SEXP alphaLevelIndx_r, - SEXP muBetaComm_r, SEXP muAlphaComm_r, - SEXP SigmaBetaComm_r, SEXP SigmaAlphaComm_r, SEXP kappaA_r, - SEXP kappaB_r, SEXP tauSqBetaA_r, - SEXP tauSqBetaB_r, SEXP tauSqAlphaA_r, SEXP tauSqAlphaB_r, - SEXP spatialPriors_r, SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, - SEXP sigmaSqPA_r, SEXP sigmaSqPB_r, - SEXP tuning_r, SEXP covModel_r, - SEXP batchInfo_r, SEXP acceptRate_r, - SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, - SEXP samplesInfo_r, SEXP chainInfo_r, SEXP family_r, SEXP offset_r); + SEXP consts_r, SEXP nAbundRELong_r, SEXP nDetRELong_r, + SEXP m_r, SEXP nnIndx_r, + SEXP nnIndxLU_r, SEXP uIndx_r, SEXP uIndxLU_r, SEXP uiIndx_r, + SEXP betaStarting_r, SEXP alphaStarting_r, SEXP kappaStarting_r, SEXP NStarting_r, + SEXP betaCommStarting_r, SEXP alphaCommStarting_r, + SEXP phiStarting_r, SEXP lambdaStarting_r, SEXP nuStarting_r, SEXP wStarting_r, + SEXP tauSqBetaStarting_r, SEXP tauSqAlphaStarting_r, + SEXP sigmaSqMuStarting_r, SEXP sigmaSqPStarting_r, + SEXP betaStarStarting_r, SEXP alphaStarStarting_r, + SEXP NLongIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, + SEXP alphaStarIndx_r, SEXP alphaLevelIndx_r, + SEXP muBetaComm_r, SEXP muAlphaComm_r, + SEXP SigmaBetaComm_r, SEXP SigmaAlphaComm_r, SEXP kappaA_r, + SEXP kappaB_r, SEXP tauSqBetaA_r, + SEXP tauSqBetaB_r, SEXP tauSqAlphaA_r, SEXP tauSqAlphaB_r, + SEXP spatialPriors_r, SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, + SEXP sigmaSqPA_r, SEXP sigmaSqPB_r, + SEXP tuning_r, SEXP covModel_r, + SEXP batchInfo_r, SEXP acceptRate_r, + SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, + SEXP samplesInfo_r, SEXP chainInfo_r, SEXP family_r, SEXP offset_r); SEXP sfMsNMixNNGPPredict(SEXP coords_r, SEXP J_r, SEXP family_r, SEXP nSp_r, SEXP q_r, - SEXP pAbund_r, SEXP m_r, SEXP X0_r, SEXP coords0_r, - SEXP JStr_r, SEXP nnIndx0_r, SEXP betaSamples_r, - SEXP thetaSamples_r, SEXP kappaSamples_r, SEXP lambdaSamples_r, - SEXP wSamples_r, SEXP betaStarSiteSamples_r, - SEXP nSamples_r, SEXP covModel_r, SEXP nThreads_r, SEXP verbose_r, - SEXP nReport_r, SEXP sitesLink_r, SEXP sites0Sampled_r); + SEXP pAbund_r, SEXP m_r, SEXP X0_r, SEXP coords0_r, + SEXP JStr_r, SEXP nnIndx0_r, SEXP betaSamples_r, + SEXP thetaSamples_r, SEXP kappaSamples_r, SEXP lambdaSamples_r, + SEXP wSamples_r, SEXP betaStarSiteSamples_r, + SEXP nSamples_r, SEXP covModel_r, SEXP nThreads_r, SEXP verbose_r, + SEXP nReport_r, SEXP sitesLink_r, SEXP sites0Sampled_r); SEXP DS(SEXP y_r, SEXP X_r, SEXP Xp_r, SEXP XRE_r, SEXP XpRE_r, SEXP XRandom_r, SEXP XpRandom_r, SEXP yMax_r, SEXP offset_r, @@ -311,38 +333,38 @@ extern "C" { SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, SEXP sigmaSqPA_r, SEXP sigmaSqPB_r, SEXP kappaA_r, SEXP kappaB_r, SEXP detModel_r, - SEXP transect_r, SEXP distBreaks_r, SEXP tuning_r, + SEXP transect_r, SEXP distBreaks_r, SEXP tuning_r, SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, SEXP samplesInfo_r, SEXP chainInfo_r, SEXP family_r); SEXP spDSNNGP(SEXP y_r, SEXP X_r, SEXP Xp_r, SEXP coords_r, SEXP XRE_r, SEXP XpRE_r, - SEXP XRandom_r, SEXP XpRandom_r, SEXP yMax_r, SEXP offset_r, - SEXP consts_r, SEXP K_r, SEXP nAbundRELong_r, SEXP nDetRELong_r, - SEXP m_r, SEXP nnIndx_r, - SEXP nnIndxLU_r, SEXP uIndx_r, SEXP uIndxLU_r, SEXP uiIndx_r, - SEXP betaStarting_r, SEXP alphaStarting_r, SEXP kappaStarting_r, - SEXP sigmaSqMuStarting_r, SEXP sigmaSqPStarting_r, - SEXP betaStarStarting_r, SEXP alphaStarStarting_r, SEXP NStarting_r, - SEXP wStarting_r, SEXP phiStarting_r, SEXP sigmaSqStarting_r, SEXP nuStarting_r, - SEXP NLongIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, - SEXP alphaStarIndx_r, SEXP alphaLevelIndx_r, - SEXP muBeta_r, SEXP SigmaBeta_r, - SEXP muAlpha_r, SEXP SigmaAlpha_r, SEXP spatialPriors_r, - SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, - SEXP sigmaSqPA_r, SEXP sigmaSqPB_r, - SEXP kappaA_r, SEXP kappaB_r, SEXP detModel_r, - SEXP transect_r, SEXP distBreaks_r, SEXP tuning_r, SEXP covModel_r, - SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, SEXP nThreads_r, - SEXP verbose_r, SEXP nReport_r, SEXP samplesInfo_r, - SEXP chainInfo_r, SEXP sigmaSqIG_r, SEXP family_r); + SEXP XRandom_r, SEXP XpRandom_r, SEXP yMax_r, SEXP offset_r, + SEXP consts_r, SEXP K_r, SEXP nAbundRELong_r, SEXP nDetRELong_r, + SEXP m_r, SEXP nnIndx_r, + SEXP nnIndxLU_r, SEXP uIndx_r, SEXP uIndxLU_r, SEXP uiIndx_r, + SEXP betaStarting_r, SEXP alphaStarting_r, SEXP kappaStarting_r, + SEXP sigmaSqMuStarting_r, SEXP sigmaSqPStarting_r, + SEXP betaStarStarting_r, SEXP alphaStarStarting_r, SEXP NStarting_r, + SEXP wStarting_r, SEXP phiStarting_r, SEXP sigmaSqStarting_r, SEXP nuStarting_r, + SEXP NLongIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, + SEXP alphaStarIndx_r, SEXP alphaLevelIndx_r, + SEXP muBeta_r, SEXP SigmaBeta_r, + SEXP muAlpha_r, SEXP SigmaAlpha_r, SEXP spatialPriors_r, + SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, + SEXP sigmaSqPA_r, SEXP sigmaSqPB_r, + SEXP kappaA_r, SEXP kappaB_r, SEXP detModel_r, + SEXP transect_r, SEXP distBreaks_r, SEXP tuning_r, SEXP covModel_r, + SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, SEXP nThreads_r, + SEXP verbose_r, SEXP nReport_r, SEXP samplesInfo_r, + SEXP chainInfo_r, SEXP sigmaSqIG_r, SEXP family_r); SEXP msDS(SEXP y_r, SEXP X_r, SEXP Xp_r, SEXP XRE_r, SEXP XpRE_r, SEXP XRandom_r, SEXP XpRandom_r, SEXP yMax_r, SEXP offset_r, SEXP consts_r, SEXP K_r, SEXP nAbundRELong_r, SEXP nDetRELong_r, SEXP betaStarting_r, SEXP alphaStarting_r, SEXP kappaStarting_r, SEXP NStarting_r, SEXP betaCommStarting_r, SEXP alphaCommStarting_r, - SEXP tauSqBetaStarting_r, SEXP tauSqAlphaStarting_r, + SEXP tauSqBetaStarting_r, SEXP tauSqAlphaStarting_r, SEXP sigmaSqMuStarting_r, SEXP sigmaSqPStarting_r, SEXP betaStarStarting_r, SEXP alphaStarStarting_r, SEXP NLongIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, @@ -352,9 +374,9 @@ extern "C" { SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, SEXP sigmaSqPA_r, SEXP sigmaSqPB_r, SEXP kappaA_r, SEXP kappaB_r, - SEXP tauSqBetaA_r, SEXP tauSqBetaB_r, - SEXP tauSqAlphaA_r, SEXP tauSqAlphaB_r, SEXP detModel_r, - SEXP transect_r, SEXP distBreaks_r, SEXP tuning_r, + SEXP tauSqBetaA_r, SEXP tauSqBetaB_r, + SEXP tauSqAlphaA_r, SEXP tauSqAlphaB_r, SEXP detModel_r, + SEXP transect_r, SEXP distBreaks_r, SEXP tuning_r, SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, SEXP samplesInfo_r, SEXP chainInfo_r, SEXP family_r); @@ -364,8 +386,8 @@ extern "C" { SEXP consts_r, SEXP K_r, SEXP nAbundRELong_r, SEXP nDetRELong_r, SEXP betaStarting_r, SEXP alphaStarting_r, SEXP kappaStarting_r, SEXP NStarting_r, SEXP betaCommStarting_r, SEXP alphaCommStarting_r, - SEXP lambdaStarting_r, SEXP wStarting_r, - SEXP tauSqBetaStarting_r, SEXP tauSqAlphaStarting_r, + SEXP lambdaStarting_r, SEXP wStarting_r, + SEXP tauSqBetaStarting_r, SEXP tauSqAlphaStarting_r, SEXP sigmaSqMuStarting_r, SEXP sigmaSqPStarting_r, SEXP betaStarStarting_r, SEXP alphaStarStarting_r, SEXP NLongIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, @@ -375,9 +397,9 @@ extern "C" { SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, SEXP sigmaSqPA_r, SEXP sigmaSqPB_r, SEXP kappaA_r, SEXP kappaB_r, - SEXP tauSqBetaA_r, SEXP tauSqBetaB_r, - SEXP tauSqAlphaA_r, SEXP tauSqAlphaB_r, SEXP detModel_r, - SEXP transect_r, SEXP distBreaks_r, SEXP tuning_r, + SEXP tauSqBetaA_r, SEXP tauSqBetaB_r, + SEXP tauSqAlphaA_r, SEXP tauSqAlphaB_r, SEXP detModel_r, + SEXP transect_r, SEXP distBreaks_r, SEXP tuning_r, SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, SEXP samplesInfo_r, SEXP chainInfo_r, SEXP family_r); @@ -388,8 +410,8 @@ extern "C" { SEXP nnIndx_r, SEXP nnIndxLU_r, SEXP uIndx_r, SEXP uIndxLU_r, SEXP uiIndx_r, SEXP betaStarting_r, SEXP alphaStarting_r, SEXP kappaStarting_r, SEXP NStarting_r, SEXP betaCommStarting_r, SEXP alphaCommStarting_r, - SEXP phiStarting_r, SEXP lambdaStarting_r, SEXP nuStarting_r, SEXP wStarting_r, - SEXP tauSqBetaStarting_r, SEXP tauSqAlphaStarting_r, + SEXP phiStarting_r, SEXP lambdaStarting_r, SEXP nuStarting_r, SEXP wStarting_r, + SEXP tauSqBetaStarting_r, SEXP tauSqAlphaStarting_r, SEXP sigmaSqMuStarting_r, SEXP sigmaSqPStarting_r, SEXP betaStarStarting_r, SEXP alphaStarStarting_r, SEXP NLongIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, @@ -399,9 +421,9 @@ extern "C" { SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, SEXP sigmaSqPA_r, SEXP sigmaSqPB_r, SEXP kappaA_r, SEXP kappaB_r, - SEXP tauSqBetaA_r, SEXP tauSqBetaB_r, - SEXP tauSqAlphaA_r, SEXP tauSqAlphaB_r, SEXP spatialPriors_r, - SEXP transect_r, SEXP distBreaks_r, SEXP tuning_r, + SEXP tauSqBetaA_r, SEXP tauSqBetaB_r, + SEXP tauSqAlphaA_r, SEXP tauSqAlphaB_r, SEXP spatialPriors_r, + SEXP transect_r, SEXP distBreaks_r, SEXP tuning_r, SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, SEXP samplesInfo_r, SEXP chainInfo_r); @@ -409,7 +431,7 @@ extern "C" { SEXP waicAbund(SEXP J_r, SEXP yNA_r, SEXP dist_r, SEXP modelType_r, SEXP y_r, SEXP nSamples_r, SEXP NSamples_r, SEXP kappaSamples_r, SEXP muSamples_r, SEXP pSamples_r, SEXP NMax_r, SEXP KMax_r, - SEXP yMax_r); + SEXP yMax_r); SEXP checkAlphaDS(SEXP y_r, SEXP Xp_r, SEXP XpRE_r, SEXP XpRandom_r, SEXP yMax_r, @@ -421,20 +443,20 @@ extern "C" { SEXP alphaStarIndx_r, SEXP alphaLevelIndx_r, SEXP muAlpha_r, SEXP SigmaAlpha_r, SEXP detModel_r, - SEXP transect_r, SEXP distBreaks_r); + SEXP transect_r, SEXP distBreaks_r); SEXP checkMSAlphaDS(SEXP y_r, SEXP Xp_r, SEXP XpRE_r, SEXP XpRandom_r, SEXP yMax_r, SEXP consts_r, SEXP K_r, SEXP alphaStarting_r, SEXP alphaCommStarting_r, - SEXP tauSqAlphaStarting_r, + SEXP tauSqAlphaStarting_r, SEXP sigmaSqPStarting_r, SEXP alphaStarStarting_r, SEXP NStarting_r, SEXP alphaStarIndx_r, SEXP alphaLevelIndx_r, SEXP muAlphaComm_r, SEXP SigmaAlphaComm_r, - SEXP detModel_r, - SEXP transect_r, SEXP distBreaks_r); + SEXP detModel_r, + SEXP transect_r, SEXP distBreaks_r); SEXP svcAbundNNGP(SEXP y_r, SEXP X_r, SEXP Xw_r, SEXP coords_r, SEXP XRE_r, SEXP XRandom_r, SEXP consts_r, SEXP nAbundRELong_r, @@ -515,4 +537,5 @@ extern "C" { SEXP nSamples_r, SEXP covModel_r, SEXP nThreads_r, SEXP verbose_r, SEXP nReport_r, SEXP z0Samples_r); + } diff --git a/src/spDSNNGP.cpp b/src/spDSNNGP.cpp index 98242b8..4cb1df7 100755 --- a/src/spDSNNGP.cpp +++ b/src/spDSNNGP.cpp @@ -63,25 +63,25 @@ void updateBFDS(double *B, double *F, double *c, double *C, double *coords, int extern "C" { SEXP spDSNNGP(SEXP y_r, SEXP X_r, SEXP Xp_r, SEXP coords_r, SEXP XRE_r, SEXP XpRE_r, - SEXP XRandom_r, SEXP XpRandom_r, SEXP yMax_r, SEXP offset_r, - SEXP consts_r, SEXP K_r, SEXP nAbundRELong_r, SEXP nDetRELong_r, - SEXP m_r, SEXP nnIndx_r, - SEXP nnIndxLU_r, SEXP uIndx_r, SEXP uIndxLU_r, SEXP uiIndx_r, - SEXP betaStarting_r, SEXP alphaStarting_r, SEXP kappaStarting_r, - SEXP sigmaSqMuStarting_r, SEXP sigmaSqPStarting_r, - SEXP betaStarStarting_r, SEXP alphaStarStarting_r, SEXP NStarting_r, - SEXP wStarting_r, SEXP phiStarting_r, SEXP sigmaSqStarting_r, SEXP nuStarting_r, - SEXP NLongIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, - SEXP alphaStarIndx_r, SEXP alphaLevelIndx_r, - SEXP muBeta_r, SEXP SigmaBeta_r, - SEXP muAlpha_r, SEXP SigmaAlpha_r, SEXP spatialPriors_r, - SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, - SEXP sigmaSqPA_r, SEXP sigmaSqPB_r, - SEXP kappaA_r, SEXP kappaB_r, SEXP detModel_r, - SEXP transect_r, SEXP distBreaks_r, SEXP tuning_r, SEXP covModel_r, - SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, SEXP nThreads_r, - SEXP verbose_r, SEXP nReport_r, SEXP samplesInfo_r, - SEXP chainInfo_r, SEXP sigmaSqIG_r, SEXP family_r){ + SEXP XRandom_r, SEXP XpRandom_r, SEXP yMax_r, SEXP offset_r, + SEXP consts_r, SEXP K_r, SEXP nAbundRELong_r, SEXP nDetRELong_r, + SEXP m_r, SEXP nnIndx_r, + SEXP nnIndxLU_r, SEXP uIndx_r, SEXP uIndxLU_r, SEXP uiIndx_r, + SEXP betaStarting_r, SEXP alphaStarting_r, SEXP kappaStarting_r, + SEXP sigmaSqMuStarting_r, SEXP sigmaSqPStarting_r, + SEXP betaStarStarting_r, SEXP alphaStarStarting_r, SEXP NStarting_r, + SEXP wStarting_r, SEXP phiStarting_r, SEXP sigmaSqStarting_r, SEXP nuStarting_r, + SEXP NLongIndx_r, SEXP betaStarIndx_r, SEXP betaLevelIndx_r, + SEXP alphaStarIndx_r, SEXP alphaLevelIndx_r, + SEXP muBeta_r, SEXP SigmaBeta_r, + SEXP muAlpha_r, SEXP SigmaAlpha_r, SEXP spatialPriors_r, + SEXP sigmaSqMuA_r, SEXP sigmaSqMuB_r, + SEXP sigmaSqPA_r, SEXP sigmaSqPB_r, + SEXP kappaA_r, SEXP kappaB_r, SEXP detModel_r, + SEXP transect_r, SEXP distBreaks_r, SEXP tuning_r, SEXP covModel_r, + SEXP nBatch_r, SEXP batchLength_r, SEXP acceptRate_r, SEXP nThreads_r, + SEXP verbose_r, SEXP nReport_r, SEXP samplesInfo_r, + SEXP chainInfo_r, SEXP sigmaSqIG_r, SEXP family_r){ /********************************************************************** * Initial constants