diff --git a/docs/as_data.html b/docs/as_data.html index 1e896702..cc11d2c3 100644 --- a/docs/as_data.html +++ b/docs/as_data.html @@ -23,8 +23,8 @@ - - + + @@ -34,10 +34,12 @@ } @@ -367,6 +369,7 @@

Examples 

+
 # numeric/integer/logical vectors, matrices and arrays can all be coerced to
 # data greta arrays
 
diff --git a/docs/build_website.R b/docs/build_website.R
index 6d385b42..842791a8 100644
--- a/docs/build_website.R
+++ b/docs/build_website.R
@@ -115,9 +115,9 @@ sections <- list(list(title = "creating greta arrays",
                  list(title = "modelling",
                       desc = "Define and visualise models and fit them to data",
                       members = c("model.html", "inference.html")),
-                 list(title = "modules",
-                      desc = "Collections of methods for doing more specialist analyses",
-                      members = c("dynamics-module.html")))
+                 list(title = "extending greta",
+                      desc = "Write R packages that extend or use greta",
+                      members = c("internals.html")))
 
 # loop through these, splitting the existing index into these sections
 sections_combined <- lapply(sections, make_section, data_index)
diff --git a/docs/contribute.html b/docs/contribute.html
index 029c9ea8..91ed9aae 100644
--- a/docs/contribute.html
+++ b/docs/contribute.html
@@ -20,8 +20,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -31,10 +31,12 @@
   }
 
 
 
diff --git a/docs/distribution.html b/docs/distribution.html
index 30f0661d..c009085f 100644
--- a/docs/distribution.html
+++ b/docs/distribution.html
@@ -23,8 +23,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -34,10 +34,12 @@
   }
 
 
 
@@ -373,6 +375,7 @@ 

 Examples
 

 
+
 # define a model likelihood
 
 # observed data and mean parameter to be estimated
diff --git a/docs/distributions.html b/docs/distributions.html
index 4e14f37d..a05c63bc 100644
--- a/docs/distributions.html
+++ b/docs/distributions.html
@@ -23,8 +23,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -34,10 +34,12 @@
   }
 
 
 
@@ -467,6 +469,8 @@ 

 
 greta
 
+
+
 
 reference
 
@@ -475,6 +479,8 @@ 

 
 uniform
 
+
+
 
 stats::dunif
 
@@ -483,6 +489,8 @@ 

 
 normal
 
+
+
 
 stats::dnorm
 
@@ -491,6 +499,8 @@ 

 
 lognormal
 
+
+
 
 stats::dlnorm
 
@@ -499,6 +509,8 @@ 

 
 bernoulli
 
+
+
 
 extraDistr::dbern
 
@@ -507,6 +519,8 @@ 

 
 binomial
 
+
+
 
 stats::dbinom
 
@@ -515,6 +529,8 @@ 

 
 beta_binomial
 
+
+
 
 extraDistr::dbbinom
 
@@ -523,6 +539,8 @@ 

 
 negative_binomial
 
+
+
 
 stats::dnbinom
 
@@ -531,6 +549,8 @@ 

 
 hypergeometric
 
+
+
 
 stats::dhyper
 
@@ -539,6 +559,8 @@ 

 
 poisson
 
+
+
 
 stats::dpois
 
@@ -547,6 +569,8 @@ 

 
 gamma
 
+
+
 
 stats::dgamma
 
@@ -555,6 +579,8 @@ 

 
 inverse_gamma
 
+
+
 
 extraDistr::dinvgamma
 
@@ -563,6 +589,8 @@ 

 
 weibull
 
+
+
 
 stats::dweibull
 
@@ -571,6 +599,8 @@ 

 
 exponential
 
+
+
 
 stats::dexp
 
@@ -579,6 +609,8 @@ 

 
 pareto
 
+
+
 
 extraDistr::dpareto
 
@@ -587,14 +619,18 @@ 

 
 student
 
+
+
 
-extraDistr::dnst
+extraDistr::dlst
 
 
 
 
 laplace
 
+
+
 
 extraDistr::dlaplace
 
@@ -603,6 +639,8 @@ 

 
 beta
 
+
+
 
 stats::dbeta
 
@@ -611,6 +649,8 @@ 

 
 cauchy
 
+
+
 
 stats::dcauchy
 
@@ -619,6 +659,8 @@ 

 
 chi_squared
 
+
+
 
 stats::dchisq
 
@@ -627,6 +669,8 @@ 

 
 logistic
 
+
+
 
 stats::dlogis
 
@@ -635,6 +679,8 @@ 

 
 f
 
+
+
 
 stats::df
 
@@ -643,6 +689,8 @@ 

 
 multivariate_normal
 
+
+
 
 mvtnorm::dmvnorm
 
@@ -651,6 +699,8 @@ 

 
 multinomial
 
+
+
 
 stats::dmultinom
 
@@ -659,6 +709,8 @@ 

 
 categorical
 
+
+
 
 stats::dmultinom (size = 1)
 
@@ -667,6 +719,8 @@ 

 
 dirichlet
 
+
+
 
 extraDistr::ddirichlet
 
@@ -675,6 +729,8 @@ 

 
 dirichlet_multinomial
 
+
+
 
 extraDistr::ddirmnom
 
@@ -683,6 +739,8 @@ 

 
 wishart
 
+
+
 
 stats::rWishart
 
@@ -691,6 +749,8 @@ 

 
 lkj_correlation
 
+
+
 
 rethinking::dlkjcorr
 
@@ -699,7 +759,9 @@ 

 

 Examples
 

-
# a uniform parameter constrained to be between 0 and 1
+
+
+# a uniform parameter constrained to be between 0 and 1
 phi = uniform(min = 0, max = 1)
 
 # a length-three variable, with each element following a standard normal
diff --git a/docs/dynamics-module.html b/docs/dynamics-module.html
index 9fc68454..a81504f8 100644
--- a/docs/dynamics-module.html
+++ b/docs/dynamics-module.html
@@ -23,8 +23,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -34,10 +34,12 @@
   }
 
 
 
diff --git a/docs/example_models.html b/docs/example_models.html
index f086cc01..3003140f 100644
--- a/docs/example_models.html
+++ b/docs/example_models.html
@@ -23,8 +23,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -34,10 +34,12 @@
   }
 
 
 
diff --git a/docs/extract-replace-combine.html b/docs/extract-replace-combine.html
index c474d65a..c7464798 100644
--- a/docs/extract-replace-combine.html
+++ b/docs/extract-replace-combine.html
@@ -23,8 +23,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -34,10 +34,12 @@
   }
 
 
 
@@ -352,17 +354,25 @@ 

 

  Arguments
 

+x
+

+a greta array
+

 i, j
 

 indices specifying elements to extract or replace
 

+n
+

+a single integer, as in utils::head() and utils::tail()
+

 value
 

-a greta array to replace elements
+for [&lt;- a greta array to replace elements, for dim&lt;- either NULL or a numeric vector of dimensions
 

 ...
 

-either further indices specifying elements to extract or replace ([), or multiple greta arrays to combine (cbind(), rbind() & c()), or additional arguments (rep())
+either further indices specifying elements to extract or replace ([), or multiple greta arrays to combine (cbind(), rbind() & c()), or additional arguments (rep(), head(), tail())
 

 drop, recursive
 

@@ -377,6 +387,8 @@ 

 # extract
 x[i]
 x[i, j, ..., drop = FALSE]
+head(x, n = 6L, ...)
+tail(x, n = 6L, ...)
 # replace
 x[i] <- value
 x[i, j, ...] <- value
@@ -385,11 +397,16 @@ 

 rbind(...)
 c(..., recursive = FALSE)
 rep(x, times, ..., recursive = FALSE)
+# get and set dimensions
+length(x)
+dim(x)
+dim(x) <- value
 

 

 Examples
 

 
+
  x = as_data(matrix(1:12, 3, 4))
 
  # extract/replace
diff --git a/docs/functions.html b/docs/functions.html
index ca8d2efa..a6ad8b9e 100644
--- a/docs/functions.html
+++ b/docs/functions.html
@@ -23,8 +23,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -34,10 +34,12 @@
   }
 
 
 
@@ -407,13 +409,23 @@ 

  prod(..., na.rm = TRUE)
  min(..., na.rm = TRUE)
  max(..., na.rm = TRUE)
+# cumulative operations
+ cumsum(x)
+ cumprod(x)
 # miscellaneous operations
  sweep(x, MARGIN, STATS, FUN = c('-', '+', '/', '*'))
+# solve an upper or lower triangular system
+ backsolve(r, x, k = ncol(r), upper.tri = TRUE,
+           transpose = FALSE)
+ forwardsolve(l, x, k = ncol(l), upper.tri = FALSE,
+              transpose = FALSE)
 

 

 Examples
 

-
x = as_data(matrix(1:9, nrow = 3, ncol = 3))
+
+
+x = as_data(matrix(1:9, nrow = 3, ncol = 3))
 a = log(exp(x))
 b = log1p(expm1(x))
 c = sign(x - 5)
diff --git a/docs/get_started.html b/docs/get_started.html
index e26f7109..808e6930 100644
--- a/docs/get_started.html
+++ b/docs/get_started.html
@@ -23,8 +23,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -34,10 +34,12 @@
   }
 
 
 
diff --git a/docs/greta.html b/docs/greta.html
index dd692078..a2979fe6 100644
--- a/docs/greta.html
+++ b/docs/greta.html
@@ -23,8 +23,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -34,10 +34,12 @@
   }
 
 
 
diff --git a/docs/index.html b/docs/index.html
index 8cfcf249..5d7f8cc0 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -20,8 +20,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -31,10 +31,12 @@
   }
 
 
 
diff --git a/docs/index_files/figure-html/vis-1.png b/docs/index_files/figure-html/vis-1.png
index 13c681a1..4954319d 100644
Binary files a/docs/index_files/figure-html/vis-1.png and b/docs/index_files/figure-html/vis-1.png differ
diff --git a/docs/inference.html b/docs/inference.html
index aed9e7c3..7beb12ad 100644
--- a/docs/inference.html
+++ b/docs/inference.html
@@ -23,8 +23,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -34,10 +34,12 @@
   }
 
 
 
diff --git a/docs/internals.html b/docs/internals.html
new file mode 100644
index 00000000..6275aba2
--- /dev/null
+++ b/docs/internals.html
@@ -0,0 +1,418 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+internal greta methods
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
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+
+
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+
+
+
+
+
+
+

+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

+

+

+

+

+
+

+
+
+
+
+
+
+
+
+
+
+

+ Description
+

+

+A list of functions and R6 class objects that can be used to develop extensions to greta. Most users will not need to access these methods, and it is not recommended to use them directly in model code.
+

+

+ Usage
+

+

+Details
+

+

+This help file lists the available internals, but they are not fully documented and are subject to change and deprecation without warning (though care will be taken not to break dependent packages on CRAN). For an overview of how greta works internally, see the technical details vignette. See https://github.com/greta-dev for examples of R packages extending and building on greta.
+

+

+Please get in contact via GitHub if you want to develop an extension to greta and need more details of how to use these internal functions.
+

+

+You can use attach() to put a sublist in the search path. E.g. attach(.internals\(nodes\)constructors) will enable you to call op(), vble() and distrib() directly.
+

+

+Usage
+

+

+

+
+ .internals$greta_arrays$unknowns        # greta array print methods
+ .internals$inference$progress_bar       # progress bar tools
+                      samplers           # MCMC samplers
+                      stash              # stashing MCMC samples
+ .internals$nodes$constructors           # node creation wrappers
+                  distribution_classes   # R6 distribution classes
+                  node_classes           # R6 node classes
+ .internals$tensors                      # functions on tensors
+ .internals$utils$checks                 # checking function inputs
+                  colours                # greta colour scheme
+                  dummy_arrays           # mocking up extract/replace
+                  misc                   # code simplification etc.
+                  samplers               # mcmc helpers
+

+
+
+
+

+

+
+

+
+
+
+
+
+
+
+
diff --git a/docs/model.html b/docs/model.html
index a6b6f1cd..8b963f24 100644
--- a/docs/model.html
+++ b/docs/model.html
@@ -23,8 +23,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -34,10 +34,12 @@
   }
 
 
 
@@ -352,9 +354,6 @@ 

 
model(..., precision = c("single", "double"), n_cores = NULL,
   compile = TRUE)
 
-define_model(..., precision = c("single", "double"), n_cores = NULL,
-  compile = TRUE)
-
 # S3 method for greta_model
 print(x, ...)
 
@@ -398,7 +397,7 @@ 

 Details
 

 

-model() takes greta arrays as arguments, and defines a statistical model by finding all of the other greta arrays on which they depend, or which depend on them. Further arguments to model can be used to configure the tensorflow graph representing the model, to tweak performance. define_model is an alias for model. It is deprecated, and will be removed in version 0.2.
+model() takes greta arrays as arguments, and defines a statistical model by finding all of the other greta arrays on which they depend, or which depend on them. Further arguments to model can be used to configure the tensorflow graph representing the model, to tweak performance.
 

 

 The plot method produces a visual representation of the defined model. It uses the DiagrammeR package, which must be installed first. Here’s a key to the plots: 
diff --git a/docs/operators.html b/docs/operators.html
index 320d2b2f..cc4db3c3 100644
--- a/docs/operators.html
+++ b/docs/operators.html
@@ -23,8 +23,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -34,10 +34,12 @@
   }
 
 
 
@@ -387,23 +389,24 @@ 

 Examples
 

 
- x = as_data(-1:12)
-
- # arithmetic
- a = x + 1
- b = 2 * x + 3
- c = x %% 2
- d = x %/% 5
-
- # logical
- e = (x > 1) | (x < 1)
- f = e & (x < 2)
- g = !f
-
- # relational
- h = x < 1
- i = (-x) >= x
- j = h == x

+
+x = as_data(-1:12)
+
+# arithmetic
+a = x + 1
+b = 2 * x + 3
+c = x %% 2
+d = x %/% 5
+
+# logical
+e = (x > 1) | (x < 1)
+f = e & (x < 2)
+g = !f
+
+# relational
+h = x < 1
+i = (-x) >= x
+j = h == x

 
 
 
diff --git a/docs/overloaded.html b/docs/overloaded.html
index b29d174e..773c99af 100644
--- a/docs/overloaded.html
+++ b/docs/overloaded.html
@@ -23,8 +23,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -34,10 +34,12 @@
   }
 
 
 
@@ -353,11 +355,23 @@ 

 
 diag(x = 1, nrow, ncol)
 
-sweep(x, MARGIN, STATS, FUN = "-", check.margin = TRUE, ...) 

+colMeans(x, na.rm = FALSE, dims = 1L)
+
+rowMeans(x, na.rm = FALSE, dims = 1L)
+
+colSums(x, na.rm = FALSE, dims = 1L)
+
+rowSums(x, na.rm = FALSE, dims = 1L)
+
+sweep(x, MARGIN, STATS, FUN = "-", check.margin = TRUE, ...)
+
+backsolve(r, x, k = ncol(r), upper.tri = TRUE, transpose = FALSE)
+
+forwardsolve(l, x, k = ncol(l), upper.tri = FALSE, transpose = FALSE) 

 

  Arguments
 

-x, y, nrow, ncol, MARGIN, STATS, FUN, check.margin, ...
+x, y, nrow, ncol, MARGIN, STATS, FUN, check.margin, ..., r, k, upper.tri, transpose, l, na.rm, dims
 

 arguments as in original documentation
 

diff --git a/docs/reexports.html b/docs/reexports.html
index daf59ee1..4afb21c2 100644
--- a/docs/reexports.html
+++ b/docs/reexports.html
@@ -23,8 +23,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -34,10 +34,12 @@
   }
 
 
 
diff --git a/docs/reference-index.html b/docs/reference-index.html
index eda59f3d..38ad1804 100644
--- a/docs/reference-index.html
+++ b/docs/reference-index.html
@@ -23,8 +23,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -34,10 +34,12 @@
   }
 
 
 
@@ -411,7 +413,7 @@ 
modelling

 

 

 
greta model objects

-
model define_model print plot

+
model print plot

 

 

 
 
-

-
modules

-
Collections of methods for doing more specialist analyses

+

+
extending greta

+
Write R packages that extend or use greta

 

-

-
methods for modelling structured dynamical systems

-
dynamics-module

+
diff --git a/docs/site_libs/highlightjs-9.12.0/default.css b/docs/site_libs/highlightjs-9.12.0/default.css
new file mode 100644
index 00000000..6e7234a1
--- /dev/null
+++ b/docs/site_libs/highlightjs-9.12.0/default.css
@@ -0,0 +1,21 @@
+.hljs-literal {
+  color: #990073;
+}
+
+.hljs-number {
+  color: #099;
+}
+
+.hljs-comment {
+  color: #998;
+  font-style: italic;
+}
+
+.hljs-keyword {
+  color: #900;
+  font-weight: bold;
+}
+
+.hljs-string {
+  color: #d14;
+}
diff --git a/docs/site_libs/highlightjs-9.12.0/highlight.js b/docs/site_libs/highlightjs-9.12.0/highlight.js
new file mode 100644
index 00000000..c1a8f62b
--- /dev/null
+++ b/docs/site_libs/highlightjs-9.12.0/highlight.js
@@ -0,0 +1,2 @@
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new file mode 100644
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+++ b/docs/site_libs/highlightjs-9.12.0/textmate.css
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deleted file mode 100644
index 6268ec99..00000000
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diff --git a/docs/site_libs/navigation-1.1/sourceembed.js b/docs/site_libs/navigation-1.1/sourceembed.js
index e1b2cf85..8464b0c8 100644
--- a/docs/site_libs/navigation-1.1/sourceembed.js
+++ b/docs/site_libs/navigation-1.1/sourceembed.js
@@ -1,9 +1,12 @@
 
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diff --git a/docs/software.html b/docs/software.html
index 142e4aaf..2b35f590 100644
--- a/docs/software.html
+++ b/docs/software.html
@@ -20,8 +20,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -31,10 +31,12 @@
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diff --git a/docs/structures.html b/docs/structures.html
index 61ed53ee..0852a57f 100644
--- a/docs/structures.html
+++ b/docs/structures.html
@@ -23,8 +23,8 @@
 
 
 
-
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+
 
 
 
@@ -34,10 +34,12 @@
   }
 
 
 
@@ -384,7 +386,9 @@ 

 

 Examples
 

-
# a 3 row, 4 column greta array of 0s
+
+
+# a 3 row, 4 column greta array of 0s
 z <- zeros(3, 4)
 
 # a 3x3x3 greta array of 1s
diff --git a/docs/technical_details.html b/docs/technical_details.html
index ff9a207d..016e91b7 100644
--- a/docs/technical_details.html
+++ b/docs/technical_details.html
@@ -23,8 +23,8 @@
 
 
 
-
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@@ -34,10 +34,12 @@
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diff --git a/docs/transforms.html b/docs/transforms.html
index fa1a87ac..12541514 100644
--- a/docs/transforms.html
+++ b/docs/transforms.html
@@ -23,8 +23,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -34,10 +34,12 @@
   }
 
 
 
@@ -377,7 +379,9 @@ 

 

 Examples
 

-
 x = normal(1, 3, dim = 10)
+
+
+ x = normal(1, 3, dim = 10)
 
  # transformation to the unit interval
  p1 <- iprobit(x)
diff --git a/docs/variable.html b/docs/variable.html
index eca8abf4..6768fa4d 100644
--- a/docs/variable.html
+++ b/docs/variable.html
@@ -23,8 +23,8 @@
 
 
 
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+
+
 
 
 
@@ -34,10 +34,12 @@
   }
 
 
 
@@ -370,7 +372,9 @@ 

 

 Examples
 

-
# a scalar variable
+
+
+# a scalar variable
 a <- variable()
 
 # a positive length-three variable
diff --git a/docs/why_greta.html b/docs/why_greta.html
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--- a/docs/why_greta.html
+++ b/docs/why_greta.html
@@ -20,8 +20,8 @@
 
 
 
-
-
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