Usage
id_trafo(x)
rank_trafo(x, ties.method = c("mid-ranks", "random"))
normal_trafo(x, ties.method = c("mid-ranks", "average-scores"))
median_trafo(x, mid.score = c("0", "0.5", "1"))
savage_trafo(x, ties.method = c("mid-ranks", "average-scores"))
consal_trafo(x, ties.method = c("mid-ranks", "average-scores"), a = 5)
koziol_trafo(x, ties.method = c("mid-ranks", "average-scores"), j = 1)
klotz_trafo(x, ties.method = c("mid-ranks", "average-scores"))
mood_trafo(x, ties.method = c("mid-ranks", "average-scores"))
ansari_trafo(x, ties.method = c("mid-ranks", "average-scores"))
fligner_trafo(x, ties.method = c("mid-ranks", "average-scores"))
logrank_trafo(x, ties.method = c("mid-ranks", "Hothorn-Lausen", "average-scores"), weight = logrank_weight, ...)
logrank_weight(time, n.risk, n.event, type = c("logrank", "Gehan-Breslow", "Tarone-Ware", "Prentice", "Prentice-Marek", "Andersen-Borgan-Gill-Keiding", "Fleming-Harrington", "Self"), rho = NULL, gamma = NULL)
f_trafo(x)
of_trafo(x, scores = NULL)
maxstat_trafo(x, minprob = 0.1, maxprob = 1 - minprob)
fmaxstat_trafo(x, minprob = 0.1, maxprob = 1 - minprob)
ofmaxstat_trafo(x, minprob = 0.1, maxprob = 1 - minprob)
trafo(data, numeric_trafo = id_trafo, factor_trafo = f_trafo, ordered_trafo = of_trafo, surv_trafo = logrank_trafo, var_trafo = NULL, block = NULL)
mcp_trafo(...)
Arguments
x
an object of class "numeric", "factor", "ordered" or
"Surv".
ties.method
a character, the method used to handle ties. The score generating function
either uses the mid-ranks ("mid-ranks", default) or, in the case of
rank_trafo, randomly broken ties ("random"). Alternatively,
the average of the scores resulting from applying the score generating
function to randomly broken ties are used ("average-scores"). See
logrank_test for a detailed description of the methods used in
logrank_trafo.
mid.score
a character, the score assigned to observations exactly equal to the median:
either 0 ("0", default), 0.5 ("0.5") or 1 ("1"); see
median_test.
a
a numeric vector, the values taken as the constant $a$ in the
Conover-Salsburg scores. Defaults to 5.
j
a numeric, the value taken as the constant $j$ in the Koziol-Nemec
scores. Defaults to 1.
weight
a function where the first three arguments must correspond to time,
n.risk, and n.event given below. Defaults to
logrank_weight.
time
a numeric vector, the ordered distinct time points.
n.risk
a numeric vector, the number of subjects at risk at each time point
specified in time.
n.event
a numeric vector, the number of events at each time point specified in
time.
type
a character, one of "logrank" (default), "Gehan-Breslow",
"Tarone-Ware", "Prentice", "Prentice-Marek",
"Andersen-Borgan-Gill-Keiding", "Fleming-Harrington" or
"Self"; see logrank_test.
rho
a numeric vector, the $\rho$ constant when type is
"Tarone-Ware", "Fleming-Harrington" or "Self"; see
logrank_test. Defaults to NULL, implying 0.5
for type = "Tarone-Ware" and 0 otherwise.
gamma
a numeric vector, the $\gamma$ constant when type is
"Fleming-Harrington" or "Self"; see
logrank_test. Defaults to NULL, implying 0.
scores
a numeric vector or list, the scores corresponding to each level of an
ordered factor. Defaults to NULL, implying 1:nlevels(x).
minprob
a numeric, a fraction between 0 and 0.5; see maxstat_test.
Defaults to 0.1.
maxprob
a numeric, a fraction between 0.5 and 1; see maxstat_test.
Defaults to 1 - minprob.
data
an object of class "data.frame".
numeric_trafo
a function to be applied to elements of class "numeric" in
data, returning a matrix with nrow(data) rows and an arbitrary
number of columns. Defaults to id_trafo.
factor_trafo
a function to be applied to elements of class "factor" in
data, returning a matrix with nrow(data) rows and an arbitrary
number of columns. Defaults to f_trafo.
ordered_trafo
a function to be applied to elements of class "ordered" in
data, returning a matrix with nrow(data) rows and an arbitrary
number of columns. Defaults to of_trafo.
surv_trafo
a function to be applied to elements of class "Surv" in data,
returning a matrix with nrow(data) rows and an arbitrary number of
columns. Defaults to logrank_trafo.
var_trafo
an optional named list of functions to be applied to the corresponding
variables in data. Defaults to NULL.
block
an optional factor whose levels are interpreted as blocks. trafo is
applied to each level of block separately. Defaults to NULL.
...
logrank_trafo: further arguments to be passed to weight.
mcp_trafo: factor name and contrast matrix (as matrix or character)
in a tag = value format for multiple comparisons based on a single
unordered factor; see mcp in package
multcomp.