v1.59 - patch for rstan 2.10.1

- Brings map2stan up to date with syntax changes in rstan 2.10.1. Now
requires rstan 2.10.0 or greater. See changes to R/map2stan-templates.r
if curious about internal syntax changes. Older Stan code will still
function, but will throw deprecation warnings.
- A book errata file is now included: ERRATA.md
- A few documentation fixes
- Adjusted namespace and added manually constructed generics
(R/aa_generics.r) to hopefully fix the odd issues with plot methods
that some people have had. I still can’t repeat the issue myself, so
flying blind. Sorry.
- fixed an unusual variable name bug with glimmer()
- fixed an issue with negative bounds in uniform densities and map2stan.

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: rethinking
 Type: Package
 Title: Statistical Rethinking book package
-Version: 1.58
-Date: 2015-12-24
+Version: 1.59
+Date: 2016-6-24
 Author: Richard McElreath
 Maintainer: Richard McElreath <mcelreath@ucdavis.edu>
 Imports: coda, MASS, mvtnorm, loo
-Depends: rstan, parallel, methods
+Depends: rstan (>= 2.10.0), parallel, methods, stats, graphics
 Description: Utilities for fitting and comparing models
 License: GPL (>= 3)

ERRATA.md

@@ -0,0 +1,34 @@
+Statistical Rethinking book Errata
+==========
+
+page 42: Just below R code box 2.6, the text says that map requires a list of start values. It does not, as long as priors are provided for each parameter. And indeed the example in box 2.6 does not contain a list of start values.
+
+page 87: The marginal description of the model reads "mu ~ dnorm(156, 10)" but the model is Normal(178, 20). Same error on p 95 and in code 4.38. It is corrected in code 4.39.
+
+page 95-96: dnorm(156,100) should be dnorm(178,100) in both model presentation and then R code on top of page 96.
+
+page 103, R code 4.50: The ``post`` object implied here is the one from R code 4.46: ``post <- extract.samples(m4.3)``.
+
+page 125: Below R code 5.4, "The posterior mean for age at marriage, ba, ..." 'ba' should be 'bA'.
+
+page 156, near top: "In fact, if you try to include a dummy variable for apes, you'll up with..." Should be "you'll end up with".
+
+page 196-200: The data.frame d has 17 cases. However in the discussion of the four models (on e.g. page 200), the text repeatedly refers to 12 cases.
+
+page 212, the next-to-last sentence on the page refers to "the Rethinking box at the end of this section." That box is not in the text.
+
+page 237 Exercise H1: "...index variable, as explained in Chapter 6.",
+should be chapter 5 (at least that's their first appearance)
+
+page 253 ("...the functions postcheck, link and sim work on map2stan
+just as they do on map models...") postcheck appears somewhat out of thin air. Need a better introduction to it.
+
+page 314: "Islands that are better network acquire or sustain more tool types.": network should be networked.
+
+page 331, line 1: "a women" -> "a woman"
+
+page 435: "FIGURE 14.4 display ... imputed neocortex values in blue ...
+shown by the blue line segments". The imputed values are actually the
+open black dots (and corresponding black line segments) as the caption
+of the figure correctly states.
+

NAMESPACE

@@ -1,4 +1,12 @@
 exportPattern("^[^x]")
+importFrom(graphics, "plot")
+importFrom(stats, "coef")
+importFrom(stats, "vcov")
+importFrom(stats, "nobs")
+importFrom(stats, "logLik")
+importFrom(stats, "deviance")
+importFrom(stats, "AIC")
+importFrom(graphics, "pairs")
 importFrom(coda, HPDinterval)
 importFrom(coda, as.mcmc)
 importFrom(MASS, mvrnorm)

R/aa_generics.r

@@ -0,0 +1,23 @@
+if (!isGeneric("plot"))
+      setGeneric("plot", function(x, y, ...) standardGeneric("plot"))
+
+if (!isGeneric("coef"))
+      setGeneric("coef", function(object, ...) standardGeneric("coef"))
+
+if (!isGeneric("vcov"))
+      setGeneric("vcov", function(object, ...) standardGeneric("vcov"))
+
+if (!isGeneric("nobs"))
+      setGeneric("nobs", function(object, ...) standardGeneric("nobs"))
+
+if (!isGeneric("logLik"))
+      setGeneric("logLik", function(object, ...) standardGeneric("logLik"))
+
+if (!isGeneric("deviance"))
+      setGeneric("deviance", function(object, ...) standardGeneric("deviance"))
+
+if (!isGeneric("AIC"))
+      setGeneric("AIC", function(object, ..., k=2) standardGeneric("AIC"))
+
+if (!isGeneric("pairs"))
+      setGeneric("pairs", function(x, ...) standardGeneric("pairs"))

R/glimmer.R

@@ -53,6 +53,7 @@ xparse_glimmer_formula <- function( formula , data ) {
     if ( class(f_nobars)=="name" & length(f_nobars)==1 ) {
         f_nobars <- nobars( as.formula( paste( deparse(formula) , "+ 1" ) ) )
     }
+    #fixef <- make.names( colnames( model.matrix( f_nobars , data ) ) )
     fixef <- colnames( model.matrix( f_nobars , data ) )
 
     # convert to all fixed effects and build needed model matrix

R/map.r

@@ -67,7 +67,7 @@ map <- function( flist , data , start , method="BFGS" , hessian=TRUE , debug=FAL
         laplace = 'dlaplace'
     )
 
-    idx_marker_string <- "_._"
+    idx_marker_string <- "___"
 
     # function to sample from prior specified with density function
     sample_from_prior <- function( f ) {

R/map2stan-class.r

@@ -295,20 +295,22 @@ setMethod("pairs" , "map2stan" , function(x, n=500 , alpha=0.7 , cex=0.7 , pch=1
 rethink_palette <- c("#8080FF","#F98400","#F2AD00","#00A08A","#FF0000")
 rethink_cmyk <- c(col.alpha("black",0.25),"cyan")
 tracerplot <- function( object , pars , col=rethink_palette , alpha=1 , bg=col.alpha("black",0.15) , ask=TRUE , window , n_cols=3 , max_rows=5 , ... ) {
-    chain.cols <- col
 
-    if ( class(object)!="map2stan" ) stop( "requires map2stan fit" )
+    if ( !(class(object) %in% c("map2stan","stanfit")) ) stop( "requires map2stan or stanfit fit object" )
 
+    if ( class(object)=="map2stan" ) object <- object@stanfit
+
     # get all chains, not mixed, from stanfit
     if ( missing(pars) )
-        post <- extract(object@stanfit,permuted=FALSE,inc_warmup=TRUE)
+        post <- extract(object,permuted=FALSE,inc_warmup=TRUE)
     else
-        post <- extract(object@stanfit,pars=pars,permuted=FALSE,inc_warmup=TRUE)
+        post <- extract(object,pars=pars,permuted=FALSE,inc_warmup=TRUE)
 
     # names
     dimnames <- attr(post,"dimnames")
     chains <- dimnames$chains
     pars <- dimnames$parameters
+    chain.cols <- rep_len(col,length(chains))
     # cut out "dev" and "lp__"
     wdev <- which(pars=="dev")
     if ( length(wdev)>0 ) pars <- pars[-wdev]
@@ -326,8 +328,8 @@ tracerplot <- function( object , pars , col=rethink_palette , alpha=1 , bg=col.a
         n_pages <- ceiling(n_pars/(n_cols*n_rows_per_page))
         paging <- TRUE
     }
-    n_iter <- object@stanfit@sim$iter
-    n_warm <- object@stanfit@sim$warmup
+    n_iter <- object@sim$iter
+    n_warm <- object@sim$warmup
     wstart <- 1
     wend <- n_iter
     if ( !missing(window) ) {
@@ -351,7 +353,7 @@ tracerplot <- function( object , pars , col=rethink_palette , alpha=1 , bg=col.a
     }
 
     # fetch n_eff
-    n_eff <- summary(object@stanfit)$summary[,'n_eff']
+    n_eff <- summary(object)$summary[,'n_eff']
 
     # make window
     #set_nice_margins()