yuend_ci

0th

Percentile

Paired samples robust t-tests with confidence interval for effect size.

Custom function to get confidence intervals for effect size measure for paired samples robust t-tests.

Keywords
internal
Usage
yuend_ci(data, x, y, tr = 0.1, nboot = 100, conf.level = 0.95,
  conf.type = "norm", ...)
Arguments
data

A dataframe (or a tibble) from which variables specified are to be taken. A matrix or tables will not be accepted.

x

The grouping variable from the dataframe data.

y

The response (a.k.a. outcome or dependent) variable from the dataframe data.

tr

Trim level for the mean when carrying out robust tests. If you get error stating "Standard error cannot be computed because of Winsorized variance of 0 (e.g., due to ties). Try to decrease the trimming level.", try to play around with the value of tr, which is by default set to 0.1. Lowering the value might help.

nboot

Number of bootstrap samples for computing confidence interval for the effect size (Default: 100).

conf.level

Scalar between 0 and 1. If unspecified, the defaults return 95% lower and upper confidence intervals (0.95).

conf.type

A vector of character strings representing the type of intervals required. The value should be any subset of the values "norm", "basic", "perc", "bca". For more, see ?boot::boot.ci.

...

Arguments passed on to boot::boot

data

The data as a vector, matrix or data frame. If it is a matrix or data frame then each row is considered as one multivariate observation.

statistic

A function which when applied to data returns a vector containing the statistic(s) of interest. When sim = "parametric", the first argument to statistic must be the data. For each replicate a simulated dataset returned by ran.gen will be passed. In all other cases statistic must take at least two arguments. The first argument passed will always be the original data. The second will be a vector of indices, frequencies or weights which define the bootstrap sample. Further, if predictions are required, then a third argument is required which would be a vector of the random indices used to generate the bootstrap predictions. Any further arguments can be passed to statistic through the argument.

R

The number of bootstrap replicates. Usually this will be a single positive integer. For importance resampling, some resamples may use one set of weights and others use a different set of weights. In this case R would be a vector of integers where each component gives the number of resamples from each of the rows of weights.

sim

A character string indicating the type of simulation required. Possible values are "ordinary" (the default), "parametric", "balanced", "permutation", or "antithetic". Importance resampling is specified by including importance weights; the type of importance resampling must still be specified but may only be "ordinary" or "balanced" in this case.

stype

A character string indicating what the second argument of statistic represents. Possible values of stype are "i" (indices - the default), "f" (frequencies), or "w" (weights). Not used for sim = "parametric".

strata

An integer vector or factor specifying the strata for multi-sample problems. This may be specified for any simulation, but is ignored when sim = "parametric". When strata is supplied for a nonparametric bootstrap, the simulations are done within the specified strata.

L

Vector of influence values evaluated at the observations. This is used only when sim is "antithetic". If not supplied, they are calculated through a call to empinf. This will use the infinitesimal jackknife provided that stype is "w", otherwise the usual jackknife is used.

m

The number of predictions which are to be made at each bootstrap replicate. This is most useful for (generalized) linear models. This can only be used when sim is "ordinary". m will usually be a single integer but, if there are strata, it may be a vector with length equal to the number of strata, specifying how many of the errors for prediction should come from each strata. The actual predictions should be returned as the final part of the output of statistic, which should also take an argument giving the vector of indices of the errors to be used for the predictions.

weights

Vector or matrix of importance weights. If a vector then it should have as many elements as there are observations in data. When simulation from more than one set of weights is required, weights should be a matrix where each row of the matrix is one set of importance weights. If weights is a matrix then R must be a vector of length nrow(weights). This parameter is ignored if sim is not "ordinary" or "balanced".

ran.gen

This function is used only when sim = "parametric" when it describes how random values are to be generated. It should be a function of two arguments. The first argument should be the observed data and the second argument consists of any other information needed (e.g. parameter estimates). The second argument may be a list, allowing any number of items to be passed to ran.gen. The returned value should be a simulated data set of the same form as the observed data which will be passed to statistic to get a bootstrap replicate. It is important that the returned value be of the same shape and type as the original dataset. If ran.gen is not specified, the default is a function which returns the original data in which case all simulation should be included as part of statistic. Use of sim = "parametric" with a suitable ran.gen allows the user to implement any types of nonparametric resampling which are not supported directly.

mle

The second argument to be passed to ran.gen. Typically these will be maximum likelihood estimates of the parameters. For efficiency mle is often a list containing all of the objects needed by ran.gen which can be calculated using the original data set only.

simple

logical, only allowed to be TRUE for sim = "ordinary", stype = "i", n = 0 (otherwise ignored with a warning). By default a n by R index array is created: this can be large and if simple = TRUE this is avoided by sampling separately for each replication, which is slower but uses less memory.

parallel

The type of parallel operation to be used (if any). If missing, the default is taken from the option "boot.parallel" (and if that is not set, "no").

ncpus

integer: number of processes to be used in parallel operation: typically one would chose this to the number of available CPUs.

cl

An optional parallel or snow cluster for use if parallel = "snow". If not supplied, a cluster on the local machine is created for the duration of the boot call.

Aliases
  • yuend_ci
Examples
# NOT RUN {
# }
# NOT RUN {
ggstatsplot:::yuend_ci(
  data = dplyr::filter(
    .data = ggstatsplot::iris_long,
    condition %in% c("Sepal.Length", "Petal.Length")
  ),
  x = condition,
  y = value,
  nboot = 50,
  tr = 0.2
)
# }
# NOT RUN {
# }
Documentation reproduced from package ggstatsplot, version 0.0.11, License: GPL-3 | file LICENSE

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