Merge pull request #103 from emstruong/options

Options

Author: ecmerkle

DESCRIPTION

@@ -34,7 +34,7 @@ Description: Fit a variety of Bayesian latent variable models, including confirm
    factor analysis, structural equation models, and latent growth curve models. References: Merkle & Rosseel (2018) <doi:10.18637/jss.v085.i04>; Merkle et al. (2021) <doi:10.18637/jss.v100.i06>.
 License: GPL (>= 3)
 ByteCompile: true
-Depends: R(>= 3.5.0), methods, Rcpp(>= 0.12.15)
+Depends: R(>= 4.1.0), methods, Rcpp(>= 0.12.15)
 Imports: stats, utils, graphics, lavaan(>= 0.6-18), coda, mnormt, nonnest2(>= 0.5-7), loo(>= 2.0), rstan(>= 2.26.0), rstantools(>= 1.5.0), RcppParallel (>= 5.0.1), bayesplot, Matrix, future.apply, tmvnsim, igraph
 LinkingTo: StanHeaders (>= 2.26.0), rstan (>= 2.26.0), BH (>= 1.69.0), Rcpp (>= 0.12.15), RcppEigen (>= 0.3.3.4.0), RcppParallel (>= 5.0.1)
 Suggests: runjags(>= 2.0.4-3), modeest(>= 2.3.3), rjags, cmdstanr, semTools, blavsam, tinytest

R/blavaan.R

@@ -11,7 +11,7 @@ blavaan <- function(...,  # default lavaan arguments
                     mcmcextra          = list(),
                     inits              = "simple",
                     convergence        = "manual",
-                    target             = "stan",
+                    target             = getOption("blavaan.target", "stan"),
                     save.lvs           = FALSE,
                     wiggle             = NULL,
                     wiggle.sd          = 0.1,
@@ -1196,7 +1196,7 @@ blavaan <- function(...,  # default lavaan arguments
 bcfa <- bsem <- function(..., cp = "srs", dp = NULL,
     n.chains = 3, burnin, sample, adapt,
     mcmcfile = FALSE, mcmcextra = list(), inits = "simple",
-    convergence = "manual", target = "stan", save.lvs = FALSE, wiggle = NULL,
+    convergence = "manual", target = getOption("blavaan.target", "stan"), save.lvs = FALSE, wiggle = NULL,
     wiggle.sd = 0.1, prisamp = FALSE, jags.ic = FALSE, seed = NULL,
     bcontrol = list()) {
 
@@ -1237,7 +1237,7 @@ bcfa <- bsem <- function(..., cp = "srs", dp = NULL,
 bgrowth <- function(..., cp = "srs", dp = NULL,
     n.chains = 3, burnin, sample, adapt,
     mcmcfile = FALSE, mcmcextra = list(), inits = "simple",
-    convergence = "manual", target = "stan", save.lvs = FALSE, wiggle = NULL,
+    convergence = "manual", target = getOption("blavaan.target", "stan"), save.lvs = FALSE, wiggle = NULL,
     wiggle.sd = 0.1, prisamp = FALSE, jags.ic = FALSE, seed = NULL,
     bcontrol = list()) {
 

R/zzz.R

@@ -3,5 +3,6 @@
                       fields="Version")
     packageStartupMessage("This is ",paste(pkgname, version))
     packageStartupMessage('On multicore systems, we suggest use of future::plan("multicore") or\n', '  future::plan("multisession") for faster post-MCMC computations.')
+    packageStartupMessage('If cmdstanr is installed, consider setting options(blavaan.target = "cmdstan") for speed.')
 }
 

man/bcfa.Rd

@@ -7,9 +7,9 @@ Fit a Confirmatory Factor Analysis (CFA) model.}
 bcfa(..., cp = "srs",
      dp = NULL, n.chains = 3, burnin, sample,
      adapt, mcmcfile = FALSE, mcmcextra = list(), inits = "simple",
-     convergence = "manual", target = "stan", save.lvs = FALSE,
-     wiggle = NULL, wiggle.sd = 0.1, prisamp = FALSE, jags.ic = FALSE,
-     seed = NULL, bcontrol = list())
+     convergence = "manual", target = getOption("blavaan.target", "stan"),
+     save.lvs = FALSE, wiggle = NULL, wiggle.sd = 0.1, prisamp = FALSE,
+     jags.ic = FALSE, seed = NULL, bcontrol = list())
 }
 \arguments{
 \item{...}{Default lavaan arguments.  See \code{\link[lavaan]{lavaan}}.}

man/bgrowth.Rd

@@ -6,7 +6,7 @@ Fit a Growth Curve model.}
 \usage{
 bgrowth(..., cp = "srs", dp = NULL, n.chains = 3,
 burnin, sample, adapt, mcmcfile = FALSE, mcmcextra = list(), 
-inits = "simple", convergence = "manual", target = "stan",
+inits = "simple", convergence = "manual", target = getOption("blavaan.target", "stan"),
 save.lvs = FALSE, wiggle = NULL, wiggle.sd = 0.1, prisamp = FALSE,
 jags.ic = FALSE, seed = NULL, bcontrol = list())
 }

man/blavaan.Rd

@@ -7,8 +7,8 @@ Fit a Bayesian latent variable model.}
 blavaan(..., cp = "srs",
     dp = NULL, n.chains = 3, burnin, sample,
     adapt, mcmcfile = FALSE, mcmcextra = list(), inits = "simple",
-    convergence = "manual", target = "stan", save.lvs = FALSE,
-    wiggle = NULL, wiggle.sd = 0.1, prisamp = FALSE, jags.ic = FALSE,
+    convergence = "manual", target = getOption("blavaan.target", "stan"),
+    save.lvs = FALSE, wiggle = NULL, wiggle.sd = 0.1, prisamp = FALSE, jags.ic = FALSE,
     seed = NULL, bcontrol = list())
 }
 \arguments{

man/bsem.Rd

@@ -7,9 +7,9 @@ Fit a Structural Equation Model (SEM).}
 bsem(..., cp = "srs",
      dp = NULL, n.chains = 3, burnin, sample,
      adapt, mcmcfile = FALSE, mcmcextra = list(), inits = "simple",
-     convergence = "manual", target = "stan", save.lvs = FALSE,
-     wiggle = NULL, wiggle.sd = 0.1, prisamp = FALSE, jags.ic = FALSE,
-     seed = NULL, bcontrol = list())
+     convergence = "manual", target = getOption("blavaan.target", "stan"),
+     save.lvs = FALSE, wiggle = NULL, wiggle.sd = 0.1, prisamp = FALSE,
+     jags.ic = FALSE, seed = NULL, bcontrol = list())
 }
 \arguments{
 \item{...}{Default lavaan arguments.  See \code{\link[lavaan]{lavaan}}.}