Package 'rxode2parse'

This converts NONMEM-style EVIDs to classic RxODE events

Description

This converts NONMEM-style EVIDs to classic RxODE events

Usage

.toClassicEvid(cmt = 1L, amt = 0, rate = 0, dur = 0, ii = 0, evid = 0L, ss = 0)

Arguments

cmt	compartment flag
amt	dose amount
rate	dose rate
dur	dose duration
ii	inter-dose interval
evid	event id
ss	steady state

Value

classic evids, excluding evids that are added (you need to add them manually) or simply use etTran. This is mostly for testing and really shouldn't be used directly.

Author(s)

Matthew L. Fidler

Examples

.toClassicEvid(cmt=10, amt=3, evid=1)
.toClassicEvid(cmt=10, amt=3, rate=2, evid=1)
.toClassicEvid(cmt=10, amt=3, rate=-1, evid=1)
.toClassicEvid(cmt=10, amt=3, rate=-2, evid=1)
.toClassicEvid(cmt=10, amt=3, dur=2, evid=1)
.toClassicEvid(cmt=304, amt=3, dur=2, evid=1)
.toClassicEvid(cmt=7, amt=0, rate=2, evid=1, ss=1)
.toClassicEvid(cmt=-10, amt=3, evid=1)
.toClassicEvid(cmt=10, amt=3, evid=5)
.toClassicEvid(cmt=6, amt=3, evid=6)
.toClassicEvid(cmt=6, amt=3, evid=7)
.toClassicEvid(evid=2)
.toClassicEvid(evid=4)

---

Print Values

Description

print prints its argument and returns it invisibly (via invisible(x)). It is a generic function which means that new printing methods can be easily added for new classes.

Usage

## S3 method for class 'rxModelVars'
print(x, ...)

Arguments

x	an object used to select a method.
...	further arguments passed to or from other methods.

Details

The default method, print.default has its own help page. Use methods("print") to get all the methods for the print generic.

print.factor allows some customization and is used for printing ordered factors as well.

print.table for printing tables allows other customization. As of R 3.0.0, it only prints a description in case of a table with 0-extents (this can happen if a classifier has no valid data).

See noquote as an example of a class whose main purpose is a specific print method.

Value

This returns invisibly the model variables object

References

Chambers, J. M. and Hastie, T. J. (1992) Statistical Models in S. Wadsworth & Brooks/Cole.

See Also

The default method print.default, and help for the methods above; further options, noquote.

For more customizable (but cumbersome) printing, see cat, format or also write. For a simple prototypical print method, see .print.via.format in package tools.

Examples

require(stats)

ts(1:20)  #-- print is the "Default function" --> print.ts(.) is called
for(i in 1:3) print(1:i)

## Printing of factors
attenu$station ## 117 levels -> 'max.levels' depending on width

## ordered factors: levels  "l1 < l2 < .."
esoph$agegp[1:12]
esoph$alcgp[1:12]

## Printing of sparse (contingency) tables
set.seed(521)
t1 <- round(abs(rt(200, df = 1.8)))
t2 <- round(abs(rt(200, df = 1.4)))
table(t1, t2) # simple
print(table(t1, t2), zero.print = ".") # nicer to read

## same for non-integer "table":
T <- table(t2,t1)
T <- T * (1+round(rlnorm(length(T)))/4)
print(T, zero.print = ".") # quite nicer,
print.table(T[,2:8] * 1e9, digits=3, zero.print = ".")
## still slightly inferior to  Matrix::Matrix(T)  for larger T

## Corner cases with empty extents:
table(1, NA) # < table of extent 1 x 0 >

---

Calculate derived parameters for the 1-, 2-, and 3- compartment linear models.

Description

This calculates the derived parameters based on what is provided in a data frame or arguments

Usage

rxDerived(..., verbose = FALSE, digits = 0)

Arguments

...	The input can be: A data frame with PK parameters in it; This should ideally be a data frame with one pk parameter per row since it will output a data frame with one PK parameter per row. PK parameters as either a vector or a scalar
verbose	boolean that when TRUE provides a message about the detected pk parameters and the detected compartmental model. By default this is FALSE.
digits	represents the number of significant digits for the output; If the number is zero or below (default), do not round.

Value

Return a data.frame of derived PK parameters for a 1-, 2-, or 3-compartment linear model given provided clearances and volumes based on the inferred model type.

The model parameters that will be provided in the data frame are:

• vc: Central Volume (for 1-, 2- and 3- compartment models)

• kel: First-order elimination rate (for 1-, 2-, and 3-compartment models)

• k12: First-order rate of transfer from central to first peripheral compartment; (for 2- and 3-compartment models)

• k21: First-order rate of transfer from first peripheral to central compartment, (for 2- and 3-compartment models)

• k13: First-order rate of transfer from central to second peripheral compartment; (3-compartment model)

• k31: First-order rate of transfer from second peripheral to central compartment (3-compartment model)

• vp: Peripheral Volume (for 2- and 3- compartment models)

• vp2: Peripheral Volume for 3rd compartment (3- compartment model)

• vss: Volume of distribution at steady state; (1-, 2-, and 3-compartment models)

• t12alpha: $t_{1/2,\alpha}$; (1-, 2-, and 3-compartment models)

• t12beta: $t_{1/2,\beta}$; (2- and 3-compartment models)

• t12gamma: $t_{1/2,\gamma}$; (3-compartment model)

• alpha: $\alpha$; (1-, 2-, and 3-compartment models)

• beta: $\beta$; (2- and 3-compartment models)

• gamma: $\beta$; (3-compartment model)

• A: true A; (1-, 2-, and 3-compartment models)

• B: true B; (2- and 3-compartment models)

• C: true C; (3-compartment model)

• fracA: fractional A; (1-, 2-, and 3-compartment models)

• fracB: fractional B; (2- and 3-compartment models)

• fracC: fractional C; (3-compartment model)

Author(s)

Matthew Fidler and documentation from Justin Wilkins, [email protected]

References

Shafer S. L. CONVERT.XLS

Rowland M, Tozer TN. Clinical Pharmacokinetics and Pharmacodynamics: Concepts and Applications (4th). Clipping Williams & Wilkins, Philadelphia, 2010.

Examples

## Note that rxode2 parses the names to figure out the best PK parameter

params <- rxDerived(cl = 29.4, v = 23.4, Vp = 114, vp2 = 4614, q = 270, q2 = 73)

## That is why this gives the same results as the value before

params <- rxDerived(CL = 29.4, V1 = 23.4, V2 = 114, V3 = 4614, Q2 = 270, Q3 = 73)

## You may also use micro-constants alpha/beta etc.

params <- rxDerived(k12 = 0.1, k21 = 0.2, k13 = 0.3, k31 = 0.4, kel = 10, v = 10)

## or you can mix vectors and scalars

params <- rxDerived(CL = 29.4, V = 1:3)

## If you want, you can round to a number of significant digits
## with the `digits` argument:

params <- rxDerived(CL = 29.4, V = 1:3, digits = 2)

---

Internal translation to get model variables list

Description

Internal translation to get model variables list

Usage

rxode2parse(
  model,
  linear = FALSE,
  linCmtSens = c("linCmtA", "linCmtB", "linCmtC"),
  verbose = FALSE,
  code = NULL,
  envir = parent.frame()
)

Arguments

model	Model (either file name or string)
linear	boolean indicating if linear compartment model should be generated from linCmt() (default FALSE)
linCmtSens	Linear compartment model sensitivity type
verbose	is a boolean indicating the type of model detected with linCmt() parsing
code	is a file name where the c code is written to (for testing purposes mostly, it needs rxode2 to do anything fancy)
envir	is the environment to look for R user functions (defaults to parent environment)

Value

A rxModelVars object that has the model variables of a rxode2 syntax expression

Examples

rxode2parse("a=3")

---

This assigns the c level linkages for a roxde2 model

Description

This assigns the c level linkages for a roxde2 model

Usage

rxode2parseAssignTranslation(df)

Arguments

df	data frame containing the character column names rxFun, fun, type, package, packageFun and the integer column names argMin and argMax

Value

Nothing called for side effects

Author(s)

Matthew L. Fidler

Examples

rxode2parseAssignTranslation(rxode2parseGetTranslation())

---

This gives the derivative table for rxode2

Description

This will help allow registration of functions in rxode2

Usage

rxode2parseD()

Details

This environment is a derivative table;

For example:

Derivative(f(a,b,c), a) = fa() Derivative(f(a,b,c), b) = fb() Derivative(f(a,b,c), c) = fc()

Then the derivative table for f would be:

assign("f", list(fa(a,b,c), fb(a,b,c), fc(a,b,c)), rxode2parseD())

fa translates the arguments to the derivative with respect to a fb translates the arguments to the derivative with respect to b

If any of the list is NULL then rxode2 won't know how to take a derivative with respect to the argument.

If the list is shorter than the length of the arguments then the argument then the derivative of arguments that are not specified cannot be taken.

Value

Derivative table environment for rxode2

Author(s)

Matthew L. Fidler

---

Control the packages that are loaded when a rxode2 model dll is loaded

Description

Control the packages that are loaded when a rxode2 model dll is loaded

Usage

rxode2parseGetPackagesToLoad()

rxode2parseAssignPackagesToLoad(pkgs = rxode2parseGetPackagesToLoad())

Arguments

pkgs	The packages to make sure are loaded every time you load an rxode2 model.

Value

List of packages to load

Author(s)

Matthew Fidler

Examples

rxode2parseGetPackagesToLoad()

rxode2parseAssignPackagesToLoad(rxode2parseGetPackagesToLoad())

---

This function gets the currently assigned function pointer assignments

Description

This function gets the currently assigned function pointer assignments

Usage

rxode2parseGetPointerAssignment()

Value

The currently assigned pointer assignments

Author(s)

Matthew L. Fidler

Examples

rxode2parseGetTranslation()

---

This function gets the currently assigned translations

Description

This function gets the currently assigned translations

Usage

rxode2parseGetTranslation()

Value

The currently assigned translations

Author(s)

Matthew L. Fidler

Examples

rxode2parseGetTranslation()

---

Get the MD5 hash of the current language revision

Description

Get the MD5 hash of the current language revision

Usage

rxode2parseMd5()

Value

md5 hash of language revision

Author(s)

Matthew L. Fidler

Examples

rxode2parseMd5()

---

Respect suppress messages

Description

This turns on the silent REprintf in C when suppressMessages() is turned on. This makes the REprintf act like messages in R, they can be suppressed with suppressMessages()

Usage

rxParseSuppressMsg()

Value

Nothing

Author(s)

Matthew Fidler

Examples

# rxParseSuppressMsg() is called with rxode2()

# Note the errors are output to the console

try(rxode2parse("d/dt(matt)=/3"), silent = TRUE)

# When using suppressMessages, the output is suppressed

suppressMessages(try(rxode2parse("d/dt(matt)=/3"), silent = TRUE))

# In rxode2, we use REprintf so that interrupted threads do not crash R
# if there is a user interrupt. This isn't captured by R's messages, but
# This interface allows the `suppressMessages()` to suppress the C printing
# as well

# If you  want to suppress messages from rxode2 in other packages, you can use
# this function

---

Set Initial conditions to time zero instead of the first observed/dosed time

Description

Set Initial conditions to time zero instead of the first observed/dosed time

Usage

rxSetIni0(ini0 = TRUE)

Arguments

ini0	When TRUE (default), set initial conditions to time zero. Otherwise the initial conditions are the first observed time.

Value

the boolean ini0, though this is called for its side effects

---