Symbolic Partial Derivatives of Expressions

Takes the partial derivative of an expression with respect to given variables. The deriv3 methods are similar to the deriv methods, except that deriv3 returns the "hessian" attribute by default.

Usage

deriv(expr, ...) ## Default S3 method: deriv(expr, namevec, function.arg = NULL, tag = ".expr", hessian = FALSE, ...) ## S3 method for class 'formula': deriv(expr, namevec, function.arg = NULL, tag = ".expr", hessian = FALSE, ...)

deriv3(expr, ...) ## Default S3 method: deriv3(expr, namevec, function.arg = NULL, tag = ".expr", hessian = TRUE, ...) ## S3 method for class 'formula': deriv3(expr, namevec, function.arg = NULL, tag = ".expr", hessian = TRUE, ...)

Arguments

expr	the expression to be differentiated. Typically a formula, in which case the expression returned computes the right side of the ~ and its derivatives.
namevec	a character vector of the names of parameters. (Derivatives are computed for these variables only.)
function.arg	a character vector, a function prototype, or the logical value TRUE. Optional. If this argument is present, then the return value is in the form of a function instead of a multiple-statement expression. See Details for more information.
tag	the base of the names to give to intermediate results. The default is ".expr".
hessian	a logical value. If TRUE, then the second derivatives are calculated and included in the return value. The default is FALSE.
...	other arguments to pass to or from the function.

Details

If function.arg is a character vector, the result is a function with the arguments named in function.arg.
If function.arg is a function, the result is a function with the same arguments and default values.
If function.arg is TRUE, the argument names of namevec are used as returned function arguments.

While generating this sequence of expressions, the function attempts to eliminate repeated calculation of common subexpressions. Sometimes user assistance is needed, as in the example below.

Expressions that are used only once are folded back into the expression where they are used. This design improves readability; however, because parentheses are always added when such expressions are folded in, redundant parentheses can appear in the final expressions.

returns a multiple-statement expression. When evaluated, these statements return the value of the original expression, along with an attribute called "gradient", which is the gradient matrix of the expression value with respect to the named parameters.

If hessian is TRUE, then the evaluation also returns a "hessian" attribute containing the Hessian array.
If function.arg is specified, then deriv returns a function with those arguments rather than an expression.

# Value and gradient of the Michaelis-Menten model deriv(~ Vm*conc/(K+conc), c("Vm","K")) ## expression({ ## .expr1 <- Vm * conc ## .expr2 <- K + conc ## .value <- .expr1/.expr2 ## .grad <- array(0, c(length(.value), 2), ## list(NULL, c("Vm", "K"))) ## .grad[, "Vm"] <- conc/.expr2 ## .grad[, "K"] <- - (.expr1/(.expr2^2)) ## attr(.value, "gradient") <- .grad ## .value ## } ## )

# Return a function as the result deriv(~ Vm*conc/(K+conc), c("Vm","K"), function(Vm, K, conc = 1:10) NULL) ## function(Vm, K, conc = 1:10) ## { ## .expr1 <- Vm * conc ## .expr2 <- K + conc ## .value <- .expr1/.expr2 ## .grad <- array(0, c(length(.value), 2), ## list(NULL, c("Vm", "K"))) ## .grad[, "Vm"] <- conc/.expr2 ## .grad[, "K"] <- - (.expr1/(.expr2^2)) ## attr(.value, "gradient") <- .grad ## .value ## }

# Return a function when "function.arg" is specified as "TRUE" deriv(~ Vm*conc/(K+conc), c("Vm","K"), TRUE) ## function (Vm, K) ## { ## .expr1 <- Vm * conc ## .expr2 <- K + conc ## .value <- .expr1/.expr2 ## .grad <- array(0, c(length(.value), 2L), list(NULL, c("Vm", ## "K"))) ## .grad[, "Vm"] <- conc/.expr2 ## .grad[, "K"] <- -(.expr1/.expr2^2) ## attr(.value, "gradient") <- .grad ## .value ## }

# Investigate the effect of the argument "hessian": deriv vs. deriv3 x <- 1:3; y <- 2:4 f <- deriv(~a^2, "a", TRUE) f(x) ## [1] 1 4 9 ## attr(,"gradient") ## a ## [1,] 2 ## [2,] 4 ## [3,] 6 f3 <- deriv3(~a^2, "a", TRUE) f3(x) ## [1] 1 4 9 ## attr(,"gradient") ## a ## [1,] 2 ## [2,] 4 ## [3,] 6 ## attr(,"hessian") ## , , a ## ## a ## [1,] 2 ## [2,] 2 ## [3,] 2

# Investigate "hessian" with two variables: x <- 1:3; y <- 2:4 g <- deriv(~a*b^2, c("a","b"), TRUE) g3 <- deriv3(~a*b^2, c("a","b"), TRUE) g3(x, y) ## attr(,"gradient") ## a b ## [1,] 4 4 ## [2,] 9 12 ## [3,] 16 24 ## attr(,"hessian") ## , , a ## ## a b ## [1,] 0 4 ## [2,] 0 6 ## [3,] 0 8 ## ## , , b ## ## a b ## [1,] 4 2 ## [2,] 6 4 ## [3,] 8 6

Description

Usage

Arguments

Details