| Title: | Simple Automatic Differentiation |
|---|---|
| Description: | Handles both vector and matrices, using a flexible S4 class for automatic differentiation. The method used is forward automatic differentiation. Many functions and methods have been defined, so that in most cases, functions written without automatic differentiation in mind can be used without change. |
| Authors: | Hervé Perdry [aut, cre] |
| Maintainer: | Hervé Perdry <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 1.1 |
| Built: | 2024-11-05 06:54:06 UTC |
| Source: | CRAN |
This method generalizes 'base::apply' to dual objects.
## S4 method for signature 'dual' apply(X, MARGIN, FUN, ..., simplify = TRUE)## S4 method for signature 'dual' apply(X, MARGIN, FUN, ..., simplify = TRUE)
X |
a dual object (with array or matrix shape) |
MARGIN |
a vector giving the subscript which the function will be applied over |
FUN |
the function to be applied |
... |
extra arguments for 'FUN' |
simplify |
a logical indicating whether the results should be simplified |
The returned value depends on the values returned by 'FUN', similarly to 'base::apply'
A <- matrix( c(1,2,3,4), 2, 2) x <- dual(A) cs <- apply(x, 2, sum) cs d(cs) # prefered method for summing over the columns colSums(x)A <- matrix( c(1,2,3,4), 2, 2) x <- dual(A) cs <- apply(x, 2, sum) cs d(cs) # prefered method for summing over the columns colSums(x)
Arithmetic operators for objects of class 'dual'
## S4 method for signature 'dual,dual' e1 + e2 ## S4 method for signature 'dual,numericOrArray' e1 + e2 ## S4 method for signature 'numericOrArray,dual' e1 + e2 ## S4 method for signature 'dual,missing' e1 + e2 ## S4 method for signature 'dual,dual' e1 - e2 ## S4 method for signature 'dual,missing' e1 - e2 ## S4 method for signature 'dual,numericOrArray' e1 - e2 ## S4 method for signature 'numericOrArray,dual' e1 - e2 ## S4 method for signature 'dual,dual' e1 * e2 ## S4 method for signature 'dual,numeric' e1 * e2 ## S4 method for signature 'numeric,dual' e1 * e2 ## S4 method for signature 'dual,numeric' e1 / e2 ## S4 method for signature 'numeric,dual' e1 / e2 ## S4 method for signature 'dual,dual' e1 / e2 ## S4 method for signature 'dual,numeric' e1 ^ e2 ## S4 method for signature 'numeric,dual' e1 ^ e2 ## S4 method for signature 'dual,dual' e1 ^ e2## S4 method for signature 'dual,dual' e1 + e2 ## S4 method for signature 'dual,numericOrArray' e1 + e2 ## S4 method for signature 'numericOrArray,dual' e1 + e2 ## S4 method for signature 'dual,missing' e1 + e2 ## S4 method for signature 'dual,dual' e1 - e2 ## S4 method for signature 'dual,missing' e1 - e2 ## S4 method for signature 'dual,numericOrArray' e1 - e2 ## S4 method for signature 'numericOrArray,dual' e1 - e2 ## S4 method for signature 'dual,dual' e1 * e2 ## S4 method for signature 'dual,numeric' e1 * e2 ## S4 method for signature 'numeric,dual' e1 * e2 ## S4 method for signature 'dual,numeric' e1 / e2 ## S4 method for signature 'numeric,dual' e1 / e2 ## S4 method for signature 'dual,dual' e1 / e2 ## S4 method for signature 'dual,numeric' e1 ^ e2 ## S4 method for signature 'numeric,dual' e1 ^ e2 ## S4 method for signature 'dual,dual' e1 ^ e2
e1 |
object of class 'dual' or 'numeric' |
e2 |
object of class 'dual' or 'numeric' |
The usual operations are performed, with appropriate propagation of the derivatives
An object of class 'dual'.
x <- dual( c(1,2) ) a <- 2 * x + 3 a d(a) b <- x[1] + 3*x[2] b d(b)x <- dual( c(1,2) ) a <- 2 * x + 3 a d(a) b <- x[1] + 3*x[2] b d(b)
Methods allowing to use 'cbind' and 'rbind' with dual objects.
## S4 method for signature 'dual,dual' rbind2(x,y,...) ## S4 method for signature 'dual,numericOrArray' rbind2(x,y,...) ## S4 method for signature 'numericOrArray,dual' rbind2(x,y,...) ## S4 method for signature 'dual,missing' rbind2(x,y,...) ## S4 method for signature 'dual,dual' cbind2(x,y,...) ## S4 method for signature 'dual,numericOrArray' cbind2(x,y,...) ## S4 method for signature 'numericOrArray,dual' cbind2(x,y,...) ## S4 method for signature 'dual,missing' cbind2(x,y,...)## S4 method for signature 'dual,dual' rbind2(x,y,...) ## S4 method for signature 'dual,numericOrArray' rbind2(x,y,...) ## S4 method for signature 'numericOrArray,dual' rbind2(x,y,...) ## S4 method for signature 'dual,missing' rbind2(x,y,...) ## S4 method for signature 'dual,dual' cbind2(x,y,...) ## S4 method for signature 'dual,numericOrArray' cbind2(x,y,...) ## S4 method for signature 'numericOrArray,dual' cbind2(x,y,...) ## S4 method for signature 'dual,missing' cbind2(x,y,...)
x, y
|
dual or numeric objects |
... |
extra parameters (ignored) |
A dual matrix combining the arguments.
x <- dual( c(1, 3) ) y <- cbind(x, 2*x+1, 3*x+2, c(0,1)) y d(y, "x1")x <- dual( c(1, 3) ) y <- cbind(x, 2*x+1, 3*x+2, c(0,1)) y d(y, "x1")
Methods have been defined in order to allow the concatenation of 'dual' objects together and with constant objects.
## S4 method for signature 'numericOrArray' c(x, ...)## S4 method for signature 'numericOrArray' c(x, ...)
x |
first object to concatenate |
... |
other objects |
an object of class dual.
x <- dual( 1 ) # concatenation with a constant x <- c(x, 2) x d(x) # concatenation of dual objects x1 <- sum(x) x2 <- sum(x**2) y <- c(a = x1, b = x2) # you can use named arguments y d(y)x <- dual( 1 ) # concatenation with a constant x <- c(x, 2) x d(x) # concatenation of dual objects x1 <- sum(x) x2 <- sum(x**2) y <- c(a = x1, b = x2) # you can use named arguments y d(y)
Method extending to dual matrices the corresponding methods for dual matrices.
rowSums.dual(x, na.rm = FALSE, dims = 1, ...) ## S4 method for signature 'dual' rowSums(x, na.rm = FALSE, dims = 1, ...) colSums.dual(x, na.rm = FALSE, dims = 1, ...) ## S4 method for signature 'dual' colSums(x, na.rm = FALSE, dims = 1, ...) rowMeans.dual(x, na.rm = FALSE, dims = 1, ...) ## S4 method for signature 'dual' rowMeans(x, na.rm = FALSE, dims = 1, ...) colMeans.dual(x, na.rm = FALSE, dims = 1, ...) ## S4 method for signature 'dual' colMeans(x, na.rm = FALSE, dims = 1, ...)rowSums.dual(x, na.rm = FALSE, dims = 1, ...) ## S4 method for signature 'dual' rowSums(x, na.rm = FALSE, dims = 1, ...) colSums.dual(x, na.rm = FALSE, dims = 1, ...) ## S4 method for signature 'dual' colSums(x, na.rm = FALSE, dims = 1, ...) rowMeans.dual(x, na.rm = FALSE, dims = 1, ...) ## S4 method for signature 'dual' rowMeans(x, na.rm = FALSE, dims = 1, ...) colMeans.dual(x, na.rm = FALSE, dims = 1, ...) ## S4 method for signature 'dual' colMeans(x, na.rm = FALSE, dims = 1, ...)
x |
a dual matrix or array |
na.rm |
if 'TRUE', missing values are removed |
dims |
which dimensions are regarded as rows and cols |
... |
extra parameters (ignored) |
a dual object (usually a dual vector).
x <- dual( c(1,2) ) x <- cbind(x, 2*x+1) rowSums(x) d(rowSums(x), "x1")x <- dual( c(1,2) ) x <- cbind(x, 2*x+1) rowSums(x) d(rowSums(x), "x1")
Comparison operators for objects of class 'dual'
## S4 method for signature 'dual,ANY' Compare(e1, e2)## S4 method for signature 'dual,ANY' Compare(e1, e2)
e1 |
object of class 'dual' or 'numeric' |
e2 |
object of class 'dual' or 'numeric' |
usual comparison operators, ignoring derivatives valuesa
a logical vector
Get value, differential of a dual object, and the names of associated variables.
d(x, varnames) value(x) ## S3 method for class 'dual' value(x) ## S3 method for class 'numeric' value(x) varnames(x) ## S3 method for class 'dual' varnames(x) ## S3 method for class 'numeric' varnames(x)d(x, varnames) value(x) ## S3 method for class 'dual' value(x) ## S3 method for class 'numeric' value(x) varnames(x) ## S3 method for class 'dual' varnames(x) ## S3 method for class 'numeric' varnames(x)
x |
a dual (or numeric) oject |
varnames |
(optional) a vector or varnames to take derivatives along |
If 'varnames' is provided to the function 'd', a list of derivatives along the given variables will be sent back. In general, it sends back the derivatives along all associated variables.
The 'varnames' function sends back the names of all variables for which a derivative is defined.
A named list of derivatives.
x <- dual(c(3,2)) varnames(x^2) x**2 value(x**2) d(x**2) d(x**2, "x1") # you can use these methods with a numerical constant value(1) varnames(1) d(1, "x1")x <- dual(c(3,2)) varnames(x^2) x**2 value(x**2) d(x**2) d(x**2, "x1") # you can use these methods with a numerical constant value(1) varnames(1) d(1, "x1")
Methods extending to dual objects the corresponding methods for numeric objects.
diag.dual(x, nrow, ncol, names = TRUE) ## S4 method for signature 'dual' diag(x = 1, nrow, ncol, names = TRUE) ## S4 replacement method for signature 'dual,dual' diag(x) <- value ## S4 replacement method for signature 'dual,numericOrArray' diag(x) <- valuediag.dual(x, nrow, ncol, names = TRUE) ## S4 method for signature 'dual' diag(x = 1, nrow, ncol, names = TRUE) ## S4 replacement method for signature 'dual,dual' diag(x) <- value ## S4 replacement method for signature 'dual,numericOrArray' diag(x) <- value
x |
a dual object |
nrow, ncol
|
(optional) dimensions of result |
names |
if 'TRUE', pass names along |
value |
replacement value |
A dual object, similarly to 'base::diag'
x <- dual( c(1,2) ) diag(x) d(diag(x), "x1") y <- matrix(x, 2, 2) diag(y) <- 2*diag(y) y d(y) diag(y)x <- dual( c(1,2) ) diag(x) d(diag(x), "x1") y <- matrix(x, 2, 2) diag(y) <- 2*diag(y) y d(y) diag(y)
Density for the normal distribution, accepting objects of class 'dual'
dnorm(x, mean = 0, sd = 1, log = FALSE) dnorm.dual(x, mean = 0, sd = 1, log = FALSE)dnorm(x, mean = 0, sd = 1, log = FALSE) dnorm.dual(x, mean = 0, sd = 1, log = FALSE)
x |
vector of values |
mean |
vector of means |
sd |
vector of standard deviations |
log |
logical. If TRUE, log of densities are returned |
'dnorm.dual' will make straightfoward a computation (in R), that works both with numeric or dual objects. 'dnorm' will call 'dnorm.dual' if any of the objects is of class dual, or 'stats::dnorm' is all objects are of class numeric. As 'stats::dnorm' is in written in C it is factor.
If you care for performance, use 'stats::dnorm' directly for non dual numbers, and 'dnorm.dual' for dual numbers.
a dual object.
x <- dual(0) dnx <- dnorm(x) dnx d(dnx)x <- dual(0) dnx <- dnorm(x) dnx d(dnx)
Create a dual object
dual(x, varnames, dx, constant = FALSE)dual(x, varnames, dx, constant = FALSE)
x |
a numeric object (vector, matrix, or array) |
varnames |
(optional) the name of the variables in x |
dx |
(optional) a list of derivatives for the elements of x |
constant |
if 'TRUE', then a constant is returned. |
The basic usage is dual(x) which will create an object of
class 'dual' with unit derivatives in each of its components. The variable
names will be derived from the names of x, or generated in the form
x1, x2, etc.
Another possible usage is dual(x, varnames = c('x1', 'x2'), constant = TRUE)
which returns an object with null derivatives in x1 and x2.
Finally, a list of derivatives can be defined using option dx.
an object of class 'dual'
# simple usage x <- dual( c(1,2) ) x d(x) x <- dual(matrix(c(1,2,3,4), 2, 2)) x d(x, "x1.1") # using an object with names x <- dual( c(a = 1, b = 2) ) x d(x) # generate a constant x <- dual(1, varnames = c("x1", "x2"), constant = TRUE) # specify dx x <- dual(c(1,2), dx = list(x1 = c(1,1))) x d(x) # this is equivalent to : x <- dual(1) x <- c(x, x + 1) x d(x)# simple usage x <- dual( c(1,2) ) x d(x) x <- dual(matrix(c(1,2,3,4), 2, 2)) x d(x, "x1.1") # using an object with names x <- dual( c(a = 1, b = 2) ) x d(x) # generate a constant x <- dual(1, varnames = c("x1", "x2"), constant = TRUE) # specify dx x <- dual(c(1,2), dx = list(x1 = c(1,1))) x d(x) # this is equivalent to : x <- dual(1) x <- c(x, x + 1) x d(x)
An S4 class for forward differentiation of vector and matrix computations.
A dual object can be either a vector or a matrix. It can contain derivatives with respect to several variables. The derivatives will have the same shape as the value.
The shape of an object can be changed using 'dim<-'. Note that by default 'as.matrix' and 'as.vector' will send back a regular vector/matrix object, dropping the derivatives. See 'salad' to change this behaviour if needed (this is not the recommended solution).
Many methods and functions have been redefined in the package, in order to allow to apply existing code to 'dual' objects, with no or little change.
xthe value of the object. Use the function 'value' to access this slot.
da (named) list of derivatives. Use the function 'd' to access this slot.
# creating a vector of length 4 x <- dual( c(1,2,1,0) ) x d(x) # turning x into a matrix dim(x) <- c(2,2) x d(x) # and back into a vector dim(x) <- NULL x # weighted sum of the elements of x S <- sum(1:4 * x) S d(S)# creating a vector of length 4 x <- dual( c(1,2,1,0) ) x d(x) # turning x into a matrix dim(x) <- c(2,2) x d(x) # and back into a vector dim(x) <- NULL x # weighted sum of the elements of x S <- sum(1:4 * x) S d(S)
Defining the differential of a univariate function
dualFun1(f, df)dualFun1(f, df)
f |
a function with a unique argument |
df |
the differential of f |
This function returns a new function that can be applied to a dual object. This allows to extend the package by defining functions it is currenlty unable to derive. It can also gain some time for intensively used functions (see examples below).
Returns a function.
# using salad do compute the differential of a quadratic function f <- function(x) x**2 + x + 1 x <- dual(4) f(x) d(f(x)) # using `dualFun1` to define the differential of f saves time f1 <- dualFun1(f, \(x) 2*x + 1) f1(x) d(f1(x)) system.time( for(i in 1:500) f(x) ) system.time( for(i in 1:500) f1(x) )# using salad do compute the differential of a quadratic function f <- function(x) x**2 + x + 1 x <- dual(4) f(x) d(f(x)) # using `dualFun1` to define the differential of f saves time f1 <- dualFun1(f, \(x) 2*x + 1) f1(x) d(f1(x)) system.time( for(i in 1:500) f(x) ) system.time( for(i in 1:500) f1(x) )
Methods for extraction or replacements of parts of dual objects.
## S4 replacement method for signature 'dual,index,index,dual' x[i, j, ...] <- value ## S4 replacement method for signature 'dual,missing,index,dual' x[i, j, ...] <- value ## S4 replacement method for signature 'dual,index,missing,dual' x[i, j, ...] <- value ## S4 replacement method for signature 'dual,missing,missing,dual' x[i, j, ...] <- value ## S4 replacement method for signature 'dual,index,index,logicalOrNumericOrArray' x[i, j, ...] <- value ## S4 replacement method for signature 'dual,missing,index,logicalOrNumericOrArray' x[i, j, ...] <- value ## S4 replacement method for signature 'dual,index,missing,logicalOrNumericOrArray' x[i, j, ...] <- value ## S4 replacement method for signature 'dual,missing,missing,logicalOrNumericOrArray' x[i, j, ...] <- value ## S4 method for signature 'dual,index,index' x[i, j, ..., drop = TRUE] ## S4 method for signature 'dual,missing,index' x[i, j, ..., drop = TRUE] ## S4 method for signature 'dual,index,missing' x[i, j, ..., drop = TRUE] ## S4 method for signature 'dual,missing,missing' x[i, j, ..., drop = TRUE]## S4 replacement method for signature 'dual,index,index,dual' x[i, j, ...] <- value ## S4 replacement method for signature 'dual,missing,index,dual' x[i, j, ...] <- value ## S4 replacement method for signature 'dual,index,missing,dual' x[i, j, ...] <- value ## S4 replacement method for signature 'dual,missing,missing,dual' x[i, j, ...] <- value ## S4 replacement method for signature 'dual,index,index,logicalOrNumericOrArray' x[i, j, ...] <- value ## S4 replacement method for signature 'dual,missing,index,logicalOrNumericOrArray' x[i, j, ...] <- value ## S4 replacement method for signature 'dual,index,missing,logicalOrNumericOrArray' x[i, j, ...] <- value ## S4 replacement method for signature 'dual,missing,missing,logicalOrNumericOrArray' x[i, j, ...] <- value ## S4 method for signature 'dual,index,index' x[i, j, ..., drop = TRUE] ## S4 method for signature 'dual,missing,index' x[i, j, ..., drop = TRUE] ## S4 method for signature 'dual,index,missing' x[i, j, ..., drop = TRUE] ## S4 method for signature 'dual,missing,missing' x[i, j, ..., drop = TRUE]
x |
dual object |
i, j
|
indices of elements to extract or replace |
... |
supplementary indices (for arrays) |
value |
replacement value |
drop |
for dual matrices or array. |
returns a dual object (the semantic is the same as base extraction and replacement methods).
x <- c(1, 2, 3) x[2] <- dual(4) x d(x)x <- c(1, 2, 3) x[2] <- dual(4) x d(x)
A simple implementation of the gradient descent algorithm
gradient.descent( par, fn, ..., step = 0.1, maxit = 100, reltol = sqrt(.Machine$double.eps), trace = FALSE )gradient.descent( par, fn, ..., step = 0.1, maxit = 100, reltol = sqrt(.Machine$double.eps), trace = FALSE )
par |
Initial value |
fn |
A function to be minimized (or maximized if 'step' < 0) |
... |
Further arguments to be passed to 'fn' |
step |
Step size. Use a negative value to perform a gradient ascent. |
maxit |
Maximum number of iterations |
reltol |
Relative convergence tolerance |
trace |
If 'TRUE', keep trace of the visited points |
First note that this is not an efficient optimisation method. It is included in the package as a demonstration only.
The function iterates
until convergence. The gradient is computed using automatic differentiation.
The convergence criterion is as in optim
.
a list with components: 'par' is the final value of the parameter,
'value' is the value of 'f' at 'par', 'counts' is the number of iterations performed,
'convergence' is '0' is the convergence criterion was met. If 'trace' is 'TRUE', an
extra component 'trace' is included, which is a matrix giving the successive values of
.
f <- function(x) (x[1] - x[2])**4 + (x[1] + 2*x[2])**2 + x[1] + x[2] X <- seq(-1, .5, by = 0.01) Y <- seq(-0.5, 0.5, by = 0.01) Z <- matrix(NA_real_, nrow = length(X), ncol = length(Y)) for(i in seq_along(X)) for(j in seq_along(Y)) Z[i,j] <- f(c(X[i],Y[j])) par(mfrow = c(2,2), mai = c(1,1,1,1)/3) contour(X,Y,Z, levels = c(-0.2, 0, 0.3, 2**(0:6)), main = "step = 0.01") gd1 <- gradient.descent(c(0,0), f, step = 0.01, trace = TRUE) lines(t(gd1$trace), type = "o", col = "red") contour(X,Y,Z, levels = c(-0.2, 0, 0.3, 2**(0:6))) gd2 <- gradient.descent(c(0,0), f, step = 0.1, trace = TRUE) lines(t(gd2$trace), type = "o", col = "red") contour(X,Y,Z, levels = c(-0.2, 0, 0.3, 2**(0:6))) gd3 <- gradient.descent(c(0,0), f, step = 0.18, trace = TRUE) lines(t(gd3$trace), type = "o", col = "red") contour(X,Y,Z, levels = c(-0.2, 0, 0.3, 2**(0:6))) gd4 <- gradient.descent(c(0,0), f, step = 0.2, trace = TRUE) lines(t(gd4$trace), type = "o", col = "red")f <- function(x) (x[1] - x[2])**4 + (x[1] + 2*x[2])**2 + x[1] + x[2] X <- seq(-1, .5, by = 0.01) Y <- seq(-0.5, 0.5, by = 0.01) Z <- matrix(NA_real_, nrow = length(X), ncol = length(Y)) for(i in seq_along(X)) for(j in seq_along(Y)) Z[i,j] <- f(c(X[i],Y[j])) par(mfrow = c(2,2), mai = c(1,1,1,1)/3) contour(X,Y,Z, levels = c(-0.2, 0, 0.3, 2**(0:6)), main = "step = 0.01") gd1 <- gradient.descent(c(0,0), f, step = 0.01, trace = TRUE) lines(t(gd1$trace), type = "o", col = "red") contour(X,Y,Z, levels = c(-0.2, 0, 0.3, 2**(0:6))) gd2 <- gradient.descent(c(0,0), f, step = 0.1, trace = TRUE) lines(t(gd2$trace), type = "o", col = "red") contour(X,Y,Z, levels = c(-0.2, 0, 0.3, 2**(0:6))) gd3 <- gradient.descent(c(0,0), f, step = 0.18, trace = TRUE) lines(t(gd3$trace), type = "o", col = "red") contour(X,Y,Z, levels = c(-0.2, 0, 0.3, 2**(0:6))) gd4 <- gradient.descent(c(0,0), f, step = 0.2, trace = TRUE) lines(t(gd4$trace), type = "o", col = "red")
‘ifelse' methods extend 'base::ifelse' to allow using dual objects for ’yes' or 'no' arguments.
ifelse(test, yes, no)ifelse(test, yes, no)
test |
an object which can be coerced to logical mode. |
yes |
return values for true elements of 'test'. |
no |
return values for false elements of 'test'. |
A dual object (dual vector).
x <- dual(c(1,2,4,6)) y <- ifelse(x > 2, x, x/2) y d(y)x <- dual(c(1,2,4,6)) y <- ifelse(x > 2, x, x/2) y d(y)
Methods extending to dual matrices the corresponding methods for numeric matrices.
det.dual(x, ...) ## S4 method for signature 'dual' det(x, ...) ## S3 method for class 'dual' determinant(x, logarithm = TRUE, ...) ## S4 method for signature 'dual,dual' solve(a, b, ...) ## S4 method for signature 'dual,missing' solve(a, b, ...) ## S4 method for signature 'numericOrArray,dual' solve(a, b, ...) ## S4 method for signature 'dual,numericOrArray' solve(a, b, ...)det.dual(x, ...) ## S4 method for signature 'dual' det(x, ...) ## S3 method for class 'dual' determinant(x, logarithm = TRUE, ...) ## S4 method for signature 'dual,dual' solve(a, b, ...) ## S4 method for signature 'dual,missing' solve(a, b, ...) ## S4 method for signature 'numericOrArray,dual' solve(a, b, ...) ## S4 method for signature 'dual,numericOrArray' solve(a, b, ...)
x |
a dual matrix |
... |
extra parameters (ignored) |
logarithm |
if 'TRUE', get logarithm of modulus of determinant |
a, b
|
dual or numerical arguments for 'solve' |
'det' returns a dual scalar, 'determinant' a list with components 'modulus' (which is a dual object) and 'sign', and 'solve' returns a dual object (vector or matrix).
x <- dual( matrix(c(1,2,1,3), 2, 2) ) det(x) d(det(x), "x1.1") solve(x) d(solve(x), "x1.1")x <- dual( matrix(c(1,2,1,3), 2, 2) ) det(x) d(det(x), "x1.1") solve(x) d(solve(x), "x1.1")
various mathematical functions and methods
## S3 method for class 'dual' exp(x) ## S3 method for class 'dual' expm1(x) logNeper(x) ## S3 method for class 'dual' log(x, base = exp(1)) ## S3 method for class 'dual' log10(x) ## S3 method for class 'dual' log2(x) ## S3 method for class 'dual' log1p(x) ## S3 method for class 'dual' sqrt(x) ## S3 method for class 'dual' cos(x) ## S3 method for class 'dual' sin(x) ## S3 method for class 'dual' tan(x) ## S3 method for class 'dual' cospi(x) ## S3 method for class 'dual' sinpi(x) ## S3 method for class 'dual' tanpi(x) ## S3 method for class 'dual' acos(x) ## S3 method for class 'dual' asin(x) ## S3 method for class 'dual' atan(x) ## S4 method for signature 'dual,dual' atan2(y, x) ## S4 method for signature 'dual,numericOrArray' atan2(y, x) ## S4 method for signature 'numericOrArray,dual' atan2(y, x) ## S3 method for class 'dual' cosh(x) ## S3 method for class 'dual' sinh(x) ## S3 method for class 'dual' tanh(x) ## S3 method for class 'dual' acosh(x) ## S3 method for class 'dual' asinh(x) ## S3 method for class 'dual' atanh(x) ## S3 method for class 'dual' abs(x) ## S3 method for class 'dual' sign(x) ## S3 method for class 'dual' ceiling(x) ## S3 method for class 'dual' floor(x) ## S3 method for class 'dual' trunc(x, ...) ## S3 method for class 'dual' gamma(x) ## S3 method for class 'dual' lgamma(x) ## S3 method for class 'dual' digamma(x) ## S3 method for class 'dual' trigamma(x) psigamma.dual(x, deriv = 0) ## S4 method for signature 'dual' psigamma(x, deriv = 0) ## S4 method for signature 'dual,dual' beta(a, b) ## S4 method for signature 'dual,numericOrArray' beta(a, b) ## S4 method for signature 'numericOrArray,dual' beta(a, b) ## S4 method for signature 'dual,dual' lbeta(a, b) ## S4 method for signature 'dual,numericOrArray' lbeta(a, b) ## S4 method for signature 'numericOrArray,dual' lbeta(a, b) factorial.dual(x) lfactorial.dual(x) ## S4 method for signature 'dual,numeric' choose(n, k) ## S4 method for signature 'dual,numeric' lchoose(n, k)## S3 method for class 'dual' exp(x) ## S3 method for class 'dual' expm1(x) logNeper(x) ## S3 method for class 'dual' log(x, base = exp(1)) ## S3 method for class 'dual' log10(x) ## S3 method for class 'dual' log2(x) ## S3 method for class 'dual' log1p(x) ## S3 method for class 'dual' sqrt(x) ## S3 method for class 'dual' cos(x) ## S3 method for class 'dual' sin(x) ## S3 method for class 'dual' tan(x) ## S3 method for class 'dual' cospi(x) ## S3 method for class 'dual' sinpi(x) ## S3 method for class 'dual' tanpi(x) ## S3 method for class 'dual' acos(x) ## S3 method for class 'dual' asin(x) ## S3 method for class 'dual' atan(x) ## S4 method for signature 'dual,dual' atan2(y, x) ## S4 method for signature 'dual,numericOrArray' atan2(y, x) ## S4 method for signature 'numericOrArray,dual' atan2(y, x) ## S3 method for class 'dual' cosh(x) ## S3 method for class 'dual' sinh(x) ## S3 method for class 'dual' tanh(x) ## S3 method for class 'dual' acosh(x) ## S3 method for class 'dual' asinh(x) ## S3 method for class 'dual' atanh(x) ## S3 method for class 'dual' abs(x) ## S3 method for class 'dual' sign(x) ## S3 method for class 'dual' ceiling(x) ## S3 method for class 'dual' floor(x) ## S3 method for class 'dual' trunc(x, ...) ## S3 method for class 'dual' gamma(x) ## S3 method for class 'dual' lgamma(x) ## S3 method for class 'dual' digamma(x) ## S3 method for class 'dual' trigamma(x) psigamma.dual(x, deriv = 0) ## S4 method for signature 'dual' psigamma(x, deriv = 0) ## S4 method for signature 'dual,dual' beta(a, b) ## S4 method for signature 'dual,numericOrArray' beta(a, b) ## S4 method for signature 'numericOrArray,dual' beta(a, b) ## S4 method for signature 'dual,dual' lbeta(a, b) ## S4 method for signature 'dual,numericOrArray' lbeta(a, b) ## S4 method for signature 'numericOrArray,dual' lbeta(a, b) factorial.dual(x) lfactorial.dual(x) ## S4 method for signature 'dual,numeric' choose(n, k) ## S4 method for signature 'dual,numeric' lchoose(n, k)
x |
function argument (dual or numeric object) |
base |
base to which log is computed |
y |
first argument of atan2 function (dual or numeric) |
... |
extra arguments to trunc (unused) |
deriv |
integer argument to psigamma |
a, b
|
arguments of beta and lbeta (dual or nueumeric) |
n |
first argument of choose and lchoose (dual) |
k |
second argument of choose and lchoose (numeric) |
The derivative of 'abs' is set to be the function 'sign', so its derivative in 0 is considered as null. You may want to redefine 'abs' using 'dualFun1' to get an undefined derivative.
All functions return dual objects.
x <- dual(1) y <- log(x) y d(y)x <- dual(1) y <- log(x) y d(y)
Methods and functions for dual matrix arithmetic
matrixprod_dn(x, y) matrixprod_nd(x, y) matrixprod_dd(x, y) ## S4 method for signature 'dual,numericOrArray' x %*% y ## S4 method for signature 'numericOrArray,dual' x %*% y ## S4 method for signature 'dual,dual' x %*% y ## S4 method for signature 'dual,dual' crossprod(x, y) ## S4 method for signature 'dual,numericOrArray' crossprod(x, y) ## S4 method for signature 'numericOrArray,dual' crossprod(x, y) ## S4 method for signature 'dual,missing' crossprod(x, y) ## S4 method for signature 'dual,dual' tcrossprod(x, y) ## S4 method for signature 'dual,numericOrArray' tcrossprod(x, y) ## S4 method for signature 'numericOrArray,dual' tcrossprod(x, y) ## S4 method for signature 'dual,missing' tcrossprod(x, y)matrixprod_dn(x, y) matrixprod_nd(x, y) matrixprod_dd(x, y) ## S4 method for signature 'dual,numericOrArray' x %*% y ## S4 method for signature 'numericOrArray,dual' x %*% y ## S4 method for signature 'dual,dual' x %*% y ## S4 method for signature 'dual,dual' crossprod(x, y) ## S4 method for signature 'dual,numericOrArray' crossprod(x, y) ## S4 method for signature 'numericOrArray,dual' crossprod(x, y) ## S4 method for signature 'dual,missing' crossprod(x, y) ## S4 method for signature 'dual,dual' tcrossprod(x, y) ## S4 method for signature 'dual,numericOrArray' tcrossprod(x, y) ## S4 method for signature 'numericOrArray,dual' tcrossprod(x, y) ## S4 method for signature 'dual,missing' tcrossprod(x, y)
x, y
|
Dual or numeric matrices or vectors |
All methods are the analog of the corresponding methods for matrices. The functions 'matrixprod_dd', 'matrixprod_nd' and 'matrixprod_dn' are for multiplication of two dual objects, of a numeric and a dual object, or of a dual and a numeric object, respectively. You may use these functions to save the method dispatching time.
A dual object.
x <- dual( matrix(c(0,1,3,1), 2, 2) ) y <- x %*% c(2,-2) d(y, "x1.1")x <- dual( matrix(c(0,1,3,1), 2, 2) ) y <- x %*% c(2,-2) d(y, "x1.1")
Methods for 'matrix', 'array', 'as.matrix' and 'as.vector'
## S4 method for signature 'dual' matrix(data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL) ## S4 method for signature 'dual' array(data = NA, dim = length(data), dimnames = NULL) ## S3 method for class 'dual' as.matrix(x, ...) ## S4 method for signature 'dual' as.matrix(x, ...) ## S3 method for class 'dual' as.vector(x, mode = "any") ## S4 method for signature 'dual' as.vector(x, mode = "any")## S4 method for signature 'dual' matrix(data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL) ## S4 method for signature 'dual' array(data = NA, dim = length(data), dimnames = NULL) ## S3 method for class 'dual' as.matrix(x, ...) ## S4 method for signature 'dual' as.matrix(x, ...) ## S3 method for class 'dual' as.vector(x, mode = "any") ## S4 method for signature 'dual' as.vector(x, mode = "any")
data, x
|
A dual object |
nrow |
the desired number of rows |
ncol |
the desired number of cols |
byrow |
if 'TRUE' the matrix is filled by rows |
dimnames |
A 'dimnames' attributes for a matrix or an array |
dim |
A 'dim' attributes for an array |
... |
additional arguments (ignored) |
mode |
The mode of the vector to create |
The default behaviour for 'as.matrix' dans 'as.vector' is to drop the derivatives. This can be modified using 'salad' (to use with care). The prefered method to change the shape is to use 'dim<-'.
A dual object for 'matrix' and 'array', a base object for 'as.matrix' and 'as.vector'.
x <- dual(c(1,2,0,4)) y <- matrix(x, 2, 2) y as.matrix(y) dim(x) <- c(2,2) xx <- dual(c(1,2,0,4)) y <- matrix(x, 2, 2) y as.matrix(y) dim(x) <- c(2,2) x
Wrapper for calling stats::optim with a gradient
computed by automatic differentiation
optiWrap( par, fn, ..., method = c("BFGS", "L-BFGS-B", "CG"), lower = -Inf, upper = Inf, control = list(), hessian = FALSE, trace = FALSE )optiWrap( par, fn, ..., method = c("BFGS", "L-BFGS-B", "CG"), lower = -Inf, upper = Inf, control = list(), hessian = FALSE, trace = FALSE )
par |
Initial value |
fn |
Function to be minimized |
... |
Further argument to be passed to 'fn' |
method |
Optimization method |
lower, upper
|
Bounds on the variables for 'L-BFGS-B' |
control |
A list of control parameters passed to 'optim' |
hessian |
If 'TRUE' a *numerically* differentiated matrix is returned. |
trace |
If 'TRUE', keep trace of the visited points |
The gradient of fn is computed using unlist(d(fn(x))). It is
computed at the same time as fn(x)' and stored for when optim calls
the gradient. In most cases this should be more efficient than defining
gr = \(x) unlist(d(f(dual(x)))).
Parameters 'method' 'lower' 'upper' 'control' and 'hessian' are passed directly to
optim.
f <- function(x) (x[1] - x[2])**4 + (x[1] + 2*x[2])**2 + x[1] + x[2] X <- seq(-1, 0.5, by = 0.01) Y <- seq(-1, 0.5, by = 0.01) Z <- matrix(NA_real_, nrow = length(X), ncol = length(Y)) for(i in seq_along(X)) for(j in seq_along(Y)) Z[i,j] <- f(c(X[i],Y[j])) contour(X,Y,Z, levels = c(-0.2, 0, 0.3, 2**(0:6)), main = "BFGS") opt <- optiWrap(c(0,0), f, method = "BFGS", trace = TRUE) lines(t(opt$trace), type = "o", col = "red")f <- function(x) (x[1] - x[2])**4 + (x[1] + 2*x[2])**2 + x[1] + x[2] X <- seq(-1, 0.5, by = 0.01) Y <- seq(-1, 0.5, by = 0.01) Z <- matrix(NA_real_, nrow = length(X), ncol = length(Y)) for(i in seq_along(X)) for(j in seq_along(Y)) Z[i,j] <- f(c(X[i],Y[j])) contour(X,Y,Z, levels = c(-0.2, 0, 0.3, 2**(0:6)), main = "BFGS") opt <- optiWrap(c(0,0), f, method = "BFGS", trace = TRUE) lines(t(opt$trace), type = "o", col = "red")
Method extending to dual object the usual method method
outer.dual(X, Y, FUN = "*", ...) ## S4 method for signature 'dual,dual' outer(X, Y, FUN = "*", ...) ## S4 method for signature 'numericOrArray,dual' outer(X, Y, FUN = "*", ...) ## S4 method for signature 'dual,numericOrArray' outer(X, Y, FUN = "*", ...) ## S4 method for signature 'dual,dual' X %o% Y ## S4 method for signature 'numericOrArray,dual' X %o% Y ## S4 method for signature 'dual,numericOrArray' X %o% Youter.dual(X, Y, FUN = "*", ...) ## S4 method for signature 'dual,dual' outer(X, Y, FUN = "*", ...) ## S4 method for signature 'numericOrArray,dual' outer(X, Y, FUN = "*", ...) ## S4 method for signature 'dual,numericOrArray' outer(X, Y, FUN = "*", ...) ## S4 method for signature 'dual,dual' X %o% Y ## S4 method for signature 'numericOrArray,dual' X %o% Y ## S4 method for signature 'dual,numericOrArray' X %o% Y
X, Y
|
arguments of 'FUN' |
FUN |
function to use in the outer product |
... |
extra arguments passed to 'FUN' |
Methods extending 'outer' and '
A dual matrix.
x <- dual(1:3) outer(x, x) d(outer(x,x), "x2")x <- dual(1:3) outer(x, x) d(outer(x,x), "x2")
A method extending 'rep' to dual objects
## S3 method for class 'dual' rep(x, ...)## S3 method for class 'dual' rep(x, ...)
x |
a dual vector |
... |
extra parameters (typically, 'times', 'length.out' or 'each') |
A dual object.
x <- rep( dual(1:2), each = 4 ) x d(x)x <- rep( dual(1:2), each = 4 ) x d(x)
Set or get options values for package 'salad'
salad(...)salad(...)
... |
options to be defined, using 'name = value', or name(s) of option(s) to get. |
Currently, only one option can be defined, drop.derivatives,
which modifies the bevahiour of S3 methods as.vector and as.matrix
and corresponding S4 methods.
The default value is set to 'TRUE', which means that
as.vector and as.matrix will return a 'base' objects, without
derivatives. Setting drop.derivatives = FALSE will make these functions
return an object of class dual. This might be useful to re-use exiting code,
but may cause some functions to break, and should be use with care.
Use salad() to get the current value of all options, or
salad(name) to get the current value of a given option.
A list with the defined options, or a single element when salad(name)
is used.
salad("drop.derivatives") x <- dual(matrix(c(1,2,3,4), 2, 2)) salad(drop.derivatives = FALSE) as.vector(x) salad(drop.derivatives = TRUE) as.vector(x)salad("drop.derivatives") x <- dual(matrix(c(1,2,3,4), 2, 2)) salad(drop.derivatives = FALSE) as.vector(x) salad(drop.derivatives = TRUE) as.vector(x)
S3 methods for length, dim, names and dimnames
## S3 method for class 'dual' length(x) ## S3 method for class 'dual' dim(x) ## S3 replacement method for class 'dual' dim(x) <- value ## S3 method for class 'dual' dimnames(x) ## S3 replacement method for class 'dual' dimnames(x) <- value ## S3 method for class 'dual' names(x) ## S3 replacement method for class 'dual' names(x) <- value## S3 method for class 'dual' length(x) ## S3 method for class 'dual' dim(x) ## S3 replacement method for class 'dual' dim(x) <- value ## S3 method for class 'dual' dimnames(x) ## S3 replacement method for class 'dual' dimnames(x) <- value ## S3 method for class 'dual' names(x) ## S3 replacement method for class 'dual' names(x) <- value
x |
a dual object |
value |
for replacement methods, the new value |
As the methods 'dimnames' and 'dimnanes<-.dual' have been defined, you can use 'rownames' and 'colnames' as with numeric matrices (see examples).
Return values are similar to the base methods.
x <- dual( matrix(c(1,0,2,3,2,4), 2, 3) ) dim(x) length(x) rownames(x) <- c("L1", "L2") x d(x, "x1.1") # modifying dim is the recommended way to change dual object shape dim(x) <- NULL x # back to matrix shape dim(x) <- c(2, 3) xx <- dual( matrix(c(1,0,2,3,2,4), 2, 3) ) dim(x) length(x) rownames(x) <- c("L1", "L2") x d(x, "x1.1") # modifying dim is the recommended way to change dual object shape dim(x) <- NULL x # back to matrix shape dim(x) <- c(2, 3) x
Methods extending to dual objects the corresponding methods for numeric objects.
## S3 method for class 'dual' sum(x, ..., na.rm = FALSE) ## S4 method for signature 'numericOrArray' sum(x, ..., na.rm = FALSE) ## S3 method for class 'dual' prod(x, ..., na.rm = FALSE) ## S4 method for signature 'numericOrArray' prod(x, ..., na.rm = FALSE) ## S3 method for class 'dual' max(x, ..., na.rm = TRUE) ## S4 method for signature 'numericOrArray' max(x, ..., na.rm = TRUE) ## S3 method for class 'dual' min(x, ..., na.rm = TRUE) ## S4 method for signature 'numericOrArray' min(x, ..., na.rm = TRUE) ## S3 method for class 'dual' range(x, ..., na.rm = TRUE) ## S4 method for signature 'numericOrArray' range(x, ..., na.rm = TRUE) ## S4 method for signature 'dual' which.min(x) ## S4 method for signature 'dual' which.max(x)## S3 method for class 'dual' sum(x, ..., na.rm = FALSE) ## S4 method for signature 'numericOrArray' sum(x, ..., na.rm = FALSE) ## S3 method for class 'dual' prod(x, ..., na.rm = FALSE) ## S4 method for signature 'numericOrArray' prod(x, ..., na.rm = FALSE) ## S3 method for class 'dual' max(x, ..., na.rm = TRUE) ## S4 method for signature 'numericOrArray' max(x, ..., na.rm = TRUE) ## S3 method for class 'dual' min(x, ..., na.rm = TRUE) ## S4 method for signature 'numericOrArray' min(x, ..., na.rm = TRUE) ## S3 method for class 'dual' range(x, ..., na.rm = TRUE) ## S4 method for signature 'numericOrArray' range(x, ..., na.rm = TRUE) ## S4 method for signature 'dual' which.min(x) ## S4 method for signature 'dual' which.max(x)
x |
a dual object |
... |
extra arguments |
na.rm |
if 'TRUE', NA values are removed |
For 'max' and 'min', the derivative is equal to the derivative of maximum element as identified by 'which.max' and 'which.min'. This is unfortunately problematic in presence of ties. If this is an issue, you may redefine this function (at the expense of speed).
'which.min' and 'which.max' return an integer, the other methods return a dual object.
x <- dual( c(1,2,4) ) sum(x) d(sum(x), "x1")x <- dual( c(1,2,4) ) sum(x) d(sum(x), "x1")
Transposition of matrices and arrays
## S3 method for class 'dual' t(x) ## S3 method for class 'dual' aperm(a, perm = NULL, resize = TRUE, ...)## S3 method for class 'dual' t(x) ## S3 method for class 'dual' aperm(a, perm = NULL, resize = TRUE, ...)
x, a
|
a dual matrix or array |
perm |
subscript permutation vector |
resize |
if 'TRUE' (default) the array is reshaped |
... |
extra arguments (ignored) |
A dual matrix or array.
x <- dual( matrix(c(1,2,0,3), 2, 2) ) t(x) # creation of an array using dim<- y <- dual( c(1,-1) ) + 1:12 dim(y) <- c(2,3,2) z <- aperm(y, c(2,3,1)) z d(z, "x1")x <- dual( matrix(c(1,2,0,3), 2, 2) ) t(x) # creation of an array using dim<- y <- dual( c(1,-1) ) + 1:12 dim(y) <- c(2,3,2) z <- aperm(y, c(2,3,1)) z d(z, "x1")