merged v. 1.0.1 onto master

README.md

@@ -100,8 +100,9 @@ and depends on additional third-party libraries with compatible licenses.
 The development of NIMBLE has been funded by:
 
 * an NSF Advances in Biological Informatics grant (DBI-1147230) to P. de Valpine, C. Paciorek, and D. Temple Lang;
-* an NSF SI2-SSI grant  (ACI-1550488) to P. de Valpine, C. Paciorek, and D. Temple Lang; and
-* an NSF Collaborative Research grant (DMS-1622444) to P. de Valpine, A. Rodriguez, and C. Paciorek.
+* an NSF SI2-SSI grant  (ACI-1550488) to P. de Valpine, C. Paciorek, and D. Temple Lang;
+* an NSF Collaborative Research grant (DMS-1622444) to P. de Valpine, A. Rodriguez, and C. Paciorek; and
+* an NSF Collaborative Research grant (DMS-2152860) to P. de Valpine, C. Paciorek, and D. Turek.
 
 with additional support provided by postdoctoral funding for D. Turek from the Berkeley Institute for Data Science and Google Summer of Code fellowships for N. Michaud (2015) and C. Lewis-Beck (2017).
 

UserManual/cha-RCfunctions.html

@@ -159,7 +159,7 @@
 <ul class="summary">
 <img src="./nimble-icon.png"
      width=100>
-<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.0</a></li>
+<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.1</a></li>
 <li><a href="https://github.com/nimble-dev/nimble">NIMBLE Development Team</a></li>
 <li><a href="https://R-nimble.org">https://R-nimble.org</a></li>
 
@@ -1574,14 +1574,14 @@ <h4><span class="header-section-number">11.3.2.7</span> Understanding dimensions
 <h4><span class="header-section-number">11.3.2.8</span> Size warnings and the potential for crashes<a href="cha-RCfunctions.html#sec:size-warn-potent" class="anchor-section" aria-label="Anchor link to header"></a></h4>
 <p>For matrix algebra, NIMBLE cannot ensure perfect behavior because
 sizes are not known until run time. Therefore, it is possible for you
-to write code that will crash your R session. In Version 1.0.0, NIMBLE
+to write code that will crash your R session. In Version 1.0.1, NIMBLE
 attempts to issue a warning if sizes are not compatible, but it does not
 halt execution. Therefore, if you execute <code>A &lt;- M1 %*% M2</code>, and <code>M1</code> and <code>M2</code> are not compatible for matrix multiplication,
 NIMBLE will output a warning that the number of rows of <code>M1</code> does not
 match the number of columns of <code>M2</code>. After that warning the statement
 will be executed and may result in a crash. Another easy way to write
 code that will crash is to do things like <code>Y[5:10, 20:30] &lt;- x</code> without ensuring Y is at least 10x30. In the future we hope to
-prevent crashes, but in Version 1.0.0 we limit ourselves to trying to provide
+prevent crashes, but in Version 1.0.1 we limit ourselves to trying to provide
 useful information.</p>
 </div>
 </div>

UserManual/cha-algos-provided.html

@@ -159,7 +159,7 @@
 <ul class="summary">
 <img src="./nimble-icon.png"
      width=100>
-<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.0</a></li>
+<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.1</a></li>
 <li><a href="https://github.com/nimble-dev/nimble">NIMBLE Development Team</a></li>
 <li><a href="https://R-nimble.org">https://R-nimble.org</a></li>
 

UserManual/cha-bnp.html

@@ -159,7 +159,7 @@
 <ul class="summary">
 <img src="./nimble-icon.png"
      width=100>
-<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.0</a></li>
+<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.1</a></li>
 <li><a href="https://github.com/nimble-dev/nimble">NIMBLE Development Team</a></li>
 <li><a href="https://R-nimble.org">https://R-nimble.org</a></li>
 

UserManual/cha-building-models.html

@@ -159,7 +159,7 @@
 <ul class="summary">
 <img src="./nimble-icon.png"
      width=100>
-<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.0</a></li>
+<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.1</a></li>
 <li><a href="https://github.com/nimble-dev/nimble">NIMBLE Development Team</a></li>
 <li><a href="https://R-nimble.org">https://R-nimble.org</a></li>
 
@@ -555,7 +555,7 @@ <h4><span class="header-section-number">6.1.1.1</span> Data and constants<a href
 which case NIMBLE handles values for stochastic nodes as data and
 everything else as constants.</p>
 <p>Values for nodes that appear only on the right-hand side of BUGS
-declarations (e.g., covariates/predictors) can be provided as constants or as data or initial values. There is no real difference between providing as data or initial values and the values can be added after building a model via <code>setInits</code> or <code>setData</code>.</p>
+declarations (e.g., covariates/predictors) can be provided as constants or as data or initial values. There is no real difference between providing as data or initial values and the values can be added after building a model via <code>setInits</code> or <code>setData</code>. However if provided as data, calls to <code>setInits</code> will not overwrite those values (though direct assignment of values will overwrite those values).</p>
 </div>
 <div id="providing-or-changing-data-and-initial-values-for-an-existing-model" class="section level4 hasAnchor" number="6.1.1.2">
 <h4><span class="header-section-number">6.1.1.2</span> Providing (or changing) data and initial values for an existing model<a href="cha-building-models.html#providing-or-changing-data-and-initial-values-for-an-existing-model" class="anchor-section" aria-label="Anchor link to header"></a></h4>
@@ -575,7 +575,10 @@ <h4><span class="header-section-number">6.1.1.2</span> Providing (or changing) d
 by using the <code>resetData</code> method, e.g. <code>pump$resetData()</code>.</p>
 <p>Data nodes cannot be deterministic, and using <code>setData</code> on
 deterministic nodes (or passing values for deterministic nodes
-via the <code>data</code> argument to <code>nimbleModel</code>) will produce an error.</p>
+via the <code>data</code> argument to <code>nimbleModel</code>) will not flag those
+nodes as containing data. It will set the values of those nodes,
+but that will presumably be overwritten as soon as the nodes
+are deterministically calculated.</p>
 <p>To change data values without any modification of which nodes are
 flagged as containing data, simply use R’s usual assignment syntax
 to assign values in a compiled (or, more rarely, an uncompiled) model, e.g.,</p>

UserManual/cha-data-structures.html

@@ -159,7 +159,7 @@
 <ul class="summary">
 <img src="./nimble-icon.png"
      width=100>
-<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.0</a></li>
+<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.1</a></li>
 <li><a href="https://github.com/nimble-dev/nimble">NIMBLE Development Team</a></li>
 <li><a href="https://R-nimble.org">https://R-nimble.org</a></li>
 

UserManual/cha-installing-nimble.html

@@ -159,7 +159,7 @@
 <ul class="summary">
 <img src="./nimble-icon.png"
      width=100>
-<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.0</a></li>
+<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.1</a></li>
 <li><a href="https://github.com/nimble-dev/nimble">NIMBLE Development Team</a></li>
 <li><a href="https://R-nimble.org">https://R-nimble.org</a></li>
 

UserManual/cha-lightning-intro.html

@@ -159,7 +159,7 @@
 <ul class="summary">
 <img src="./nimble-icon.png"
      width=100>
-<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.0</a></li>
+<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.1</a></li>
 <li><a href="https://github.com/nimble-dev/nimble">NIMBLE Development Team</a></li>
 <li><a href="https://R-nimble.org">https://R-nimble.org</a></li>
 

UserManual/cha-mcmc.html

@@ -159,7 +159,7 @@
 <ul class="summary">
 <img src="./nimble-icon.png"
      width=100>
-<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.0</a></li>
+<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.1</a></li>
 <li><a href="https://github.com/nimble-dev/nimble">NIMBLE Development Team</a></li>
 <li><a href="https://R-nimble.org">https://R-nimble.org</a></li>
 
@@ -1394,7 +1394,7 @@ <h4><span class="header-section-number">7.11.2.1</span> HMC example<a href="cha-
 <span id="cb192-2"><a href="cha-mcmc.html#cb192-2" aria-hidden="true" tabindex="-1"></a><span class="co"># The compiled HMC will use the compiled model.</span></span>
 <span id="cb192-3"><a href="cha-mcmc.html#cb192-3" aria-hidden="true" tabindex="-1"></a>samples <span class="ot">&lt;-</span> <span class="fu">runMCMC</span>(CHMC, <span class="at">niter =</span> <span class="dv">1000</span>, <span class="at">nburnin =</span> <span class="dv">500</span>) <span class="co"># short run for illustration</span></span></code></pre></div>
 <pre><code>##   [Note] HMC sampler (nodes: intercept, beta, sigma, ran_eff[1], ran_eff[2], ran_eff[3], ran_eff[4], ran_eff[5], ran_eff[6], r...) is using 500 warmup iterations.
-##   [Note] HMC sampler (nodes: intercept, beta, sigma, ran_eff[1], ran_eff[2], ran_eff[3], ran_eff[4], ran_eff[5], ran_eff[6], r...) encountered 7 divergent paths.</code></pre>
+##   [Note] HMC sampler (nodes: intercept, beta, sigma, ran_eff[1], ran_eff[2], ran_eff[3], ran_eff[4], ran_eff[5], ran_eff[6], r...) encountered 8 divergent paths.</code></pre>
 <p>We will not investigate results in detail, but here is a summary to see that reasonable results were generated.</p>
 <div class="sourceCode" id="cb194"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb194-1"><a href="cha-mcmc.html#cb194-1" aria-hidden="true" tabindex="-1"></a><span class="fu">summary</span>(coda<span class="sc">::</span><span class="fu">as.mcmc</span>(samples))</span></code></pre></div>
 <pre><code>## 
@@ -1407,16 +1407,16 @@ <h4><span class="header-section-number">7.11.2.1</span> HMC example<a href="cha-
 ##    plus standard error of the mean:
 ## 
 ##              Mean     SD Naive SE Time-series SE
-## beta       0.1822 0.1424 0.006367       0.007605
-## intercept -0.1752 0.3022 0.013513       0.026437
-## sigma      0.7336 0.2792 0.012484       0.022891
+## beta       0.1901 0.1422 0.006358       0.006358
+## intercept -0.1865 0.2983 0.013341       0.026606
+## sigma      0.7460 0.2691 0.012036       0.020029
 ## 
 ## 2. Quantiles for each variable:
 ## 
-##              2.5%      25%     50%      75%  97.5%
-## beta      -0.1068  0.08895  0.1836 0.281308 0.4543
-## intercept -0.8498 -0.34765 -0.1668 0.003649 0.4021
-## sigma      0.3107  0.50522  0.6993 0.909613 1.4183</code></pre>
+##               2.5%      25%     50%     75%  97.5%
+## beta      -0.08399  0.08895  0.1893 0.30176 0.4595
+## intercept -0.79899 -0.38862 -0.1843 0.01333 0.3963
+## sigma      0.31865  0.55724  0.7078 0.88552 1.3849</code></pre>
 </div>
 <div id="automatic-parameter-transformation" class="section level4 hasAnchor" number="7.11.2.2">
 <h4><span class="header-section-number">7.11.2.2</span> Automatic parameter transformation<a href="cha-mcmc.html#automatic-parameter-transformation" class="anchor-section" aria-label="Anchor link to header"></a></h4>

UserManual/cha-more-introduction.html

@@ -159,7 +159,7 @@
 <ul class="summary">
 <img src="./nimble-icon.png"
      width=100>
-<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.0</a></li>
+<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.1</a></li>
 <li><a href="https://github.com/nimble-dev/nimble">NIMBLE Development Team</a></li>
 <li><a href="https://R-nimble.org">https://R-nimble.org</a></li>
 
@@ -606,7 +606,7 @@ <h2><span class="header-section-number">3.2</span> nimbleFunctions for writing a
 </div>
 <div id="sec:nimble-algor-libr" class="section level2 hasAnchor" number="3.3">
 <h2><span class="header-section-number">3.3</span> The NIMBLE algorithm library<a href="cha-more-introduction.html#sec:nimble-algor-libr" class="anchor-section" aria-label="Anchor link to header"></a></h2>
-<p>In Version 1.0.0, the NIMBLE algorithm library includes:</p>
+<p>In Version 1.0.1, the NIMBLE algorithm library includes:</p>
 <ol style="list-style-type: decimal">
 <li><p>MCMC with samplers including conjugate (Gibbs), slice, adaptive
 random walk (with options for reflection or sampling on a log

UserManual/cha-progr-with-models.html

@@ -159,7 +159,7 @@
 <ul class="summary">
 <img src="./nimble-icon.png"
      width=100>
-<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.0</a></li>
+<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.1</a></li>
 <li><a href="https://github.com/nimble-dev/nimble">NIMBLE Development Team</a></li>
 <li><a href="https://R-nimble.org">https://R-nimble.org</a></li>
 
@@ -1084,7 +1084,7 @@ <h3><span class="header-section-number">15.4.8</span> Virtual nimbleFunctions an
 <code>nimbleFunctionVirtual</code>. Other nimbleFunctions can inherit from
 virtual nimbleFunctions, which in R is called ‘containing’ them.
 Readers familiar with object oriented programming will recognize this
-as a simple class inheritance system. In Version 1.0.0 it is limited to
+as a simple class inheritance system. In Version 1.0.1 it is limited to
 simple, single-level inheritance.</p>
 <p>Here is how it works:</p>
 <div class="sourceCode" id="cb452"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb452-1"><a href="cha-progr-with-models.html#cb452-1" aria-hidden="true" tabindex="-1"></a>baseClass <span class="ot">&lt;-</span> <span class="fu">nimbleFunctionVirtual</span>(</span>

UserManual/cha-spatial.html

@@ -159,7 +159,7 @@
 <ul class="summary">
 <img src="./nimble-icon.png"
      width=100>
-<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.0</a></li>
+<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.1</a></li>
 <li><a href="https://github.com/nimble-dev/nimble">NIMBLE Development Team</a></li>
 <li><a href="https://R-nimble.org">https://R-nimble.org</a></li>
 

UserManual/cha-user-defined.html

@@ -159,7 +159,7 @@
 <ul class="summary">
 <img src="./nimble-icon.png"
      width=100>
-<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.0</a></li>
+<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.1</a></li>
 <li><a href="https://github.com/nimble-dev/nimble">NIMBLE Development Team</a></li>
 <li><a href="https://R-nimble.org">https://R-nimble.org</a></li>
 

UserManual/cha-using-models.html

@@ -159,7 +159,7 @@
 <ul class="summary">
 <img src="./nimble-icon.png"
      width=100>
-<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.0</a></li>
+<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.1</a></li>
 <li><a href="https://github.com/nimble-dev/nimble">NIMBLE Development Team</a></li>
 <li><a href="https://R-nimble.org">https://R-nimble.org</a></li>
 

UserManual/cha-welcome-nimble.html

@@ -159,7 +159,7 @@
 <ul class="summary">
 <img src="./nimble-icon.png"
      width=100>
-<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.0</a></li>
+<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.1</a></li>
 <li><a href="https://github.com/nimble-dev/nimble">NIMBLE Development Team</a></li>
 <li><a href="https://R-nimble.org">https://R-nimble.org</a></li>
 
@@ -492,7 +492,7 @@ <h1><span class="header-section-number">Chapter 1</span> Welcome to NIMBLE<a hre
 computationally-intensive methods. While NIMBLE is embedded in R, it
 goes beyond R by supporting separate programming of models and
 algorithms along with compilation for fast execution.</p>
-<p>As of version 1.0.0, NIMBLE has been around for a while and is reasonably
+<p>As of version 1.0.1, NIMBLE has been around for a while and is reasonably
 stable, but we have a lot of plans to expand and improve it. The
 algorithm library provides MCMC with a lot of user control and ability
 to write new samplers easily. Other algorithms include particle

UserManual/cha-writing-models.html

@@ -159,7 +159,7 @@
 <ul class="summary">
 <img src="./nimble-icon.png"
      width=100>
-<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.0</a></li>
+<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.1</a></li>
 <li><a href="https://github.com/nimble-dev/nimble">NIMBLE Development Team</a></li>
 <li><a href="https://R-nimble.org">https://R-nimble.org</a></li>
 

UserManual/overview.html

@@ -159,7 +159,7 @@
 <ul class="summary">
 <img src="./nimble-icon.png"
      width=100>
-<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.0</a></li>
+<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.1</a></li>
 <li><a href="https://github.com/nimble-dev/nimble">NIMBLE Development Team</a></li>
 <li><a href="https://R-nimble.org">https://R-nimble.org</a></li>
 

UserManual/references.html

@@ -159,7 +159,7 @@
 <ul class="summary">
 <img src="./nimble-icon.png"
      width=100>
-<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.0</a></li>
+<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.1</a></li>
 <li><a href="https://github.com/nimble-dev/nimble">NIMBLE Development Team</a></li>
 <li><a href="https://R-nimble.org">https://R-nimble.org</a></li>
 

UserManual/src/_output.yml

@@ -5,7 +5,7 @@ bookdown::gitbook:
       before: |
         <img src="./nimble-icon.png"
              width=100>
-        <li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.0</a></li>
+        <li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.0.1</a></li>
         <li><a href="https://github.com/nimble-dev/nimble">NIMBLE Development Team</a></li>
         <li><a href="https://R-nimble.org">https://R-nimble.org</a></li>
       after: |

UserManual/src/chapter_BuildingModels.Rmd

@@ -74,7 +74,7 @@ which case NIMBLE handles values for stochastic nodes as data and
 everything else as constants.
 
 Values for nodes that appear only on the right-hand side of BUGS
-declarations (e.g., covariates/predictors) can be provided as constants or as data or initial values. There is no real difference between providing as data or initial values and the values can be added after building a model via `setInits` or `setData`. 
+declarations (e.g., covariates/predictors) can be provided as constants or as data or initial values. There is no real difference between providing as data or initial values and the values can be added after building a model via `setInits` or `setData`. However if provided as data, calls to `setInits` will not overwrite those values (though direct assignment of values will overwrite those values). 
 
 #### Providing (or changing) data and initial values for an existing model
 
@@ -96,7 +96,10 @@ by using the `resetData` method, e.g. `pump$resetData()`.
 
 Data nodes cannot be deterministic, and using `setData` on
 deterministic nodes (or passing values for deterministic nodes
-via the `data` argument to `nimbleModel`) will produce an error.
+via the `data` argument to `nimbleModel`) will not flag those
+nodes as containing data. It will set the values of those nodes,
+but that will presumably be overwritten as soon as the nodes
+are deterministically calculated.
 
 To change data values without any modification of which nodes are
 flagged as containing data, simply use R's usual assignment syntax

UserManual/src/title.tex

@@ -4,7 +4,7 @@
 \vspace{0.2in}
 {\large NIMBLE Development Team}\\
 \vspace{0.2in}
-{\large Version 1.0.0}\\
+{\large Version 1.0.1}\\
 \vspace{3in}
 \includegraphics[width=1.5in]{../nimble-icon.png}\\
 {\large

install_revDeps.R

@@ -8,7 +8,7 @@ revDeps <- c(
 ## Note that if don't specify repos, the RStudio repo seems to install from
 ## Linux binary (that is what the .tar.gz is?) and doesn't install tests.
 for (package in revDeps) {
-        install.packages(package, type = 'source', INSTALL_opts = '--install-tests', repos = 'https://cran.us.r-project.org')
+        install.packages(package, type = 'source', INSTALL_opts = '--install-tests', repos = 'https://cran.r-project.org')
     }
 print(list.files(system.file('tests','testthat', package='nimbleSMC')))
 print(list.files(system.file('', package='nimbleSMC')))