Description Usage Arguments Value Examples
Define parameter transformations by define()
, branch()
and insert()
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trafo |
named character vector of parametric expressions or object
of class |
expr |
character of the form |
... |
used to pass values for symbols as named arguments |
conditionMatch |
optional character, Use as regular expression to apply the reparameterization only to conditions containing conditionMatch |
table |
table of covariates as data frame. Rownames are used as unique identifier, usually called "conditions", and columns represent covariates associated with these conditions. |
conditions |
character vector with condition names. Overwrites the rownames of table. |
object of the same class as trafo or list thereof, if branch()
has been
used.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 | # Define some parameter names
parameters <- c("A", "B", "k1", "k2")
# Define a covariate table
covtable <- data.frame(dose = c(1, 1, 10),
inhibitor = c("no", "inh", "no"),
row.names = c("Low_noInh", "Low_Inh", "High_noInh"))
# Start with an empty transformation
trans <- NULL
# Generate the identity transformation for parameters
trans <- define(trans, "x ~ x", x = parameters); print(trans)
# Insert exp(x) wherever you find x
trans <- insert(trans, "x ~ exp(x)", x = parameters); print(trans)
# Some new expressions instead of k1 and k2
trans <- insert(trans, "x ~ y", x = c("k1", "k2"), y = c("q1 + q2", "q1 - q2")); print(trans)
# Define some parameters as 0
trans <- define(trans, "x ~ 0", x = "B"); print(trans)
# The parameter name can also be directly used in the formula
trans <- insert(trans, "q1 ~ Q"); print(trans)
# Replicate the transformation 3 times with the rownames of covtable as list names
trans <- branch(trans, table = covtable); print(trans)
# Insert the rhs wherever the lhs is found in the transformation
# column names of covtable can be used to perform specific replacements
# for each transformation
trans <- insert(trans, "x ~ x_inh", x = c("Q", "q2"), inh = inhibitor); print(trans)
# Also numbers can be inserted
trans <- define(trans, "A ~ dose", dose = dose); print(trans)
# Turn that into a parameter transformation function
p <- P(trans)
parnames <- getParameters(p)
pars <- rnorm(length(parnames))
names(pars) <- parnames
p(pars)
# Advanced tricks exploiting the quoting-mechanism when capturing "..."
mydataframe <- data.frame(
name = rep(letters[1:2], each = 3),
value = 1:6,
time = rep(1:3, 2),
sigma = 0.1,
par1 = rep(0:1, each = 3),
par2 = rep(9:10, each = 3),
par3 = rep(1:3, each = 2),
stringsAsFactors = FALSE
)
parameters <- c("a", "b", "par1", "par2", "par3")
pars_to_insert <- c("par1", "par2")
# this would be the usual way when setting up a model
# pars_to_insert <- intersect(getParameters(g*x), names(data))
trafo <- define(NULL, "x~x", x = parameters)
trafo <- branch(trafo, covariates(as.datalist(mydataframe)))
# Trick 1: Access values from covariates()-Table with get/mget.
# The names of the parameters which are supplied in the covariates()-table
# have to be supplied manually.
trafo <- insert(trafo, "name ~ value", value = unlist(mget(pars_to_insert)), name = pars_to_insert)
# Trick 2: Access symbols from current condition-specific trafo with .currentSymbols, access
# current condition-specific trafo by .currentTrafo
# The input passed by the dots is "quoted" (substituted) and eval()'ed in the environment
# of the lapply(1:length(conditions), function(i) {})
trafo <- insert(trafo, "x~exp(X)", x = .currentSymbols, X = toupper(.currentSymbols))
# Trick 3: Condition specificity. There are two ways to do this
# 1. Apply reparametrization only for specific conditions using Regular Expressions for the
# conditionMatch argument. This matches the condition name agains a regex
trafo <- define(NULL, "x~x", x = parameters)
trafo <- branch(trafo, covariates(as.datalist(mydataframe)))
# Conditions starting with 0_9
insert(trafo, "x~x_par3", x = "a", conditionMatch = "^0_9", par3 = par3)
# Conditions NOT starting with 0_9
insert(trafo, "x~0", x = "a", conditionMatch = "^(?!0_9)")
# 2. Specify conditions by boolean arguments
# Conditions which satisfy par1 == 0
insert(trafo, "x~x_par2", par1 == 0, x = parameters, par2 = par2)
# Special case: Pass two arguments with the same name. This is only possible if one of them
# is logical and the other is not.
# Conditions which satisfy par2 == 9
insert(trafo, "x~x_par2", par2 == 9, x = .currentSymbols, par2 = par2)
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