Last updated on 2024-06-14 00:53:46 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.6 | 1177.64 | 346.79 | 1524.43 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 0.2.6 | 773.59 | 95.74 | 869.33 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2.6 | 2132.70 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2.6 | 2277.07 | NOTE | |||
| r-devel-windows-x86_64 | 0.2.6 | 858.00 | 399.00 | 1257.00 | NOTE | |
| r-patched-linux-x86_64 | 0.2.6 | 969.99 | 334.50 | 1304.49 | NOTE | |
| r-release-linux-x86_64 | 0.2.6 | 973.91 | 339.01 | 1312.92 | NOTE | |
| r-release-macos-arm64 | 0.2.6 | 377.00 | NOTE | |||
| r-release-macos-x86_64 | 0.2.6 | 417.00 | NOTE | |||
| r-release-windows-x86_64 | 0.2.6 | 861.00 | 401.00 | 1262.00 | NOTE | |
| r-oldrel-macos-arm64 | 0.2.6 | 372.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 0.2.6 | 480.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 0.2.6 | 1037.00 | 460.00 | 1497.00 | NOTE |
Version: 0.2.6
Check: Rd files
Result: NOTE
checkRd: (-1) jSDM_binomial_probit_long_format.Rd:45: Lost braces
45 | \code{species} \tab numeric or character eqn{n_{obs}}{n_obs}-length vector indicating the species observed, \cr
| ^
checkRd: (-1) jSDM_binomial_probit_long_format.Rd:45: Lost braces; missing escapes or markup?
45 | \code{species} \tab numeric or character eqn{n_{obs}}{n_obs}-length vector indicating the species observed, \cr
| ^
checkRd: (-1) jSDM_binomial_probit_long_format.Rd:45: Lost braces
45 | \code{species} \tab numeric or character eqn{n_{obs}}{n_obs}-length vector indicating the species observed, \cr
| ^
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64
Version: 0.2.6
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'kableExtra', 'dplyr', 'testthat', 'boral', 'Hmsc', 'ggplot2'
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.6
Check: examples
Result: ERROR
Running examples in ‘jSDM-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: jSDM_binomial_probit_sp_constrained
> ### Title: Binomial probit regression with selected constrained species
> ### Aliases: jSDM_binomial_probit_sp_constrained
> ### Keywords: Bayesian Binomial Carlo Chains Gibbs JSDM MCMC Markov Monte
> ### Sampling biodiversity hierarchical models probit regression
>
> ### ** Examples
>
> #======================================
> # jSDM_binomial_probit_sp_constrained()
> # Example with simulated data
> #====================================
>
> #=================
> #== Load libraries
> library(jSDM)
>
> #==================
> #== Data simulation
>
> #= Number of sites
> nsite <- 30
>
> #= Set seed for repeatability
> seed <- 1234
> set.seed(seed)
>
> #= Number of species
> nsp <- 10
>
> #= Number of latent variables
> n_latent <- 2
>
> #= Ecological process (suitability)
> x1 <- rnorm(nsite,0,1)
> x2 <- rnorm(nsite,0,1)
> X <- cbind(rep(1,nsite),x1,x2)
> np <- ncol(X)
> #= Latent variables W
> W <- matrix(rnorm(nsite*n_latent,0,1), nsite, n_latent)
> #= Fixed species effect beta
> beta.target <- t(matrix(runif(nsp*np,-2,2),
+ byrow=TRUE, nrow=nsp))
> #= Factor loading lambda
> lambda.target <- matrix(0, n_latent, nsp)
> mat <- t(matrix(runif(nsp*n_latent, -2, 2), byrow=TRUE, nrow=nsp))
> lambda.target[upper.tri(mat, diag=TRUE)] <- mat[upper.tri(mat, diag=TRUE)]
> diag(lambda.target) <- runif(n_latent, 0, 2)
> #= Variance of random site effect
> V_alpha.target <- 0.5
> #= Random site effect alpha
> alpha.target <- rnorm(nsite,0 , sqrt(V_alpha.target))
> # Simulation of response data with probit link
> probit_theta <- X%*%beta.target + W%*%lambda.target + alpha.target
> theta <- pnorm(probit_theta)
> e <- matrix(rnorm(nsp*nsite,0,1),nsite,nsp)
> # Latent variable Z
> Z_true <- probit_theta + e
> # Presence-absence matrix Y
> Y <- matrix (NA, nsite,nsp)
> for (i in 1:nsite){
+ for (j in 1:nsp){
+ if ( Z_true[i,j] > 0) {Y[i,j] <- 1}
+ else {Y[i,j] <- 0}
+ }
+ }
>
> #==================================
> #== Site-occupancy model
>
> # Increase number of iterations (burnin and mcmc) to get convergence
> mod <- jSDM_binomial_probit_sp_constrained(# Iteration
+ burnin=100,
+ mcmc=100,
+ thin=1,
+ # parallel MCMCs
+ nchains=2, ncores=2,
+ # Response variable
+ presence_data=Y,
+ # Explanatory variables
+ site_formula=~x1+x2,
+ site_data = X,
+ n_latent=2,
+ site_effect="random",
+ # Starting values
+ alpha_start=0,
+ beta_start=0,
+ lambda_start=0,
+ W_start=0,
+ V_alpha=1,
+ # Priors
+ shape_Valpha=0.5,
+ rate_Valpha=0.0005,
+ mu_beta=0, V_beta=1,
+ mu_lambda=0, V_lambda=1,
+ seed=c(123,1234), verbose=1)
>
> # ===================================================
> # Result analysis
> # ===================================================
>
> #==========
> #== Outputs
> oldpar <- par(no.readonly = TRUE)
> burnin <- mod[[1]]$model_spec$burnin
> ngibbs <- burnin + mod[[1]]$model_spec$mcmc
> thin <- mod[[1]]$model_spec$thin
> require(coda)
Loading required package: coda
> arr2mcmc <- function(x) {
+ return(mcmc(as.data.frame(x),
+ start=burnin+1 , end=ngibbs, thin=thin))
+ }
> mcmc_list_Deviance <- mcmc.list(lapply(lapply(mod,"[[","mcmc.Deviance"), arr2mcmc))
> mcmc_list_alpha <- mcmc.list(lapply(lapply(mod,"[[","mcmc.alpha"), arr2mcmc))
> mcmc_list_V_alpha <- mcmc.list(lapply(lapply(mod,"[[","mcmc.V_alpha"), arr2mcmc))
> mcmc_list_param <- mcmc.list(lapply(lapply(mod,"[[","mcmc.sp"), arr2mcmc))
> mcmc_list_lv <- mcmc.list(lapply(lapply(mod,"[[","mcmc.latent"), arr2mcmc))
> mcmc_list_beta <- mcmc_list_param[,grep("beta",colnames(mcmc_list_param[[1]]))]
> mcmc_list_beta0 <- mcmc_list_beta[,grep("Intercept", colnames(mcmc_list_beta[[1]]))]
> mcmc_list_lambda <- mcmc.list(
+ lapply(mcmc_list_param[, grep("lambda", colnames(mcmc_list_param[[1]]))],
+ arr2mcmc))
> # Compute Rhat
> psrf_alpha <- mean(gelman.diag(mcmc_list_alpha, multivariate=FALSE)$psrf[,2])
> psrf_V_alpha <- gelman.diag(mcmc_list_V_alpha)$psrf[,2]
> psrf_beta0 <- mean(gelman.diag(mcmc_list_beta0)$psrf[,2])
> psrf_beta <- mean(gelman.diag(mcmc_list_beta[,grep("Intercept",
+ colnames(mcmc_list_beta[[1]]),
+ invert=TRUE)])$psrf[,2])
> psrf_lambda <- mean(gelman.diag(mcmc_list_lambda,
+ multivariate=FALSE)$psrf[,2],
+ na.rm=TRUE)
> psrf_lv <- mean(gelman.diag(mcmc_list_lv, multivariate=FALSE)$psrf[,2])
> Rhat <- data.frame(Rhat=c(psrf_alpha, psrf_V_alpha, psrf_beta0, psrf_beta,
+ psrf_lambda, psrf_lv),
+ Variable=c("alpha", "Valpha", "beta0", "beta",
+ "lambda", "W"))
> # Barplot
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
jSDM_binomial_probit_long_format 5.233 0.08 7.055
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
Error in library(testthat) : there is no package called 'testthat'
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.6
Check: installed package size
Result: NOTE
installed size is 5.0Mb
sub-directories of 1Mb or more:
libs 3.6Mb
Flavors: r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64