Type:	Package
Title:	Grouped Hyper Data Frame
Version:	0.3.5
Description:	An S3 class 'groupedHyperframe' that inherits from the hyper data frame class from the 'spatstat' packages. Batch process and aggregation of the hyper column(s) over a nested grouping structure.
RoxygenNote:	7.3.3
LazyData:	true
LazyDataCompression:	xz
Encoding:	UTF-8
License:	GPL-2
Language:	en-US
URL:	https://github.com/tingtingzhan/groupedHyperframe, https://tingtingzhan.quarto.pub/groupedhyperframe, https://tingtingzhan-groupedhyperframe.netlify.app
Depends:	R (≥ 4.5)
Imports:	cli, methods, parallel, doParallel, foreach, matrixStats, pracma, GET, SpatialPack, ggplot2, geomtextpath, scales, survival, patchwork, knitr, spatstat.explore, spatstat.geom, spatstat.random, splines
Suggests:	spatstat.data
NeedsCompilation:	no
Packaged:	2026-03-01 20:55:59 UTC; tingtingzhan
Author:	Tingting Zhan [aut, cre]
Maintainer:	Tingting Zhan <tingtingzhan@gmail.com>
Repository:	CRAN
Date/Publication:	2026-03-02 06:10:32 UTC

groupedHyperframe: Grouped Hyper Data Frame

Description

An S3 class 'groupedHyperframe' that inherits from the hyper data frame class from the 'spatstat' packages. Batch process and aggregation of the hyper column(s) over a nested grouping structure.

Author(s)

Maintainer: Tingting Zhan tingtingzhan@gmail.com (ORCID)

See Also

Useful links:

• https://github.com/tingtingzhan/groupedHyperframe

• https://tingtingzhan.quarto.pub/groupedhyperframe

• https://tingtingzhan-groupedhyperframe.netlify.app

Syntactic Sugar for groupedHyperframe Object

Description

Syntactic Sugar for groupedHyperframe Object

Usage

## S3 replacement method for class 'groupedHyperframe'
x$name <- value

Arguments

Value

Syntactic sugar $<-.groupedHyperframe() returns a groupedHyperframe.

Note

The function $<-.hyperframe drops attributes.

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Alternative Interface of nncross.ppp

Description

An alternative interface of the function nncross.ppp.

Usage

.nncross(X, i, j, ...)

Arguments

Details

The function .nncross() creates an interface similar to The functions Gcross, etc., which takes an is.multitype ppp.object and two mark values i and j, then calls the workhorse function nncross.ppp with parameter what = 'dist'. If mark values i and j does not exist in the ppp.object, a NULL value will be returned.

Value

The function .nncross() returns a numeric vector if i and j are valid mark values of ppp.object X; otherwise returns a NULL value.

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Generic Function with Namespace

Description

Generic Function with Namespace

Usage

.ns_generic(x, backtick = TRUE, ver = FALSE)

Arguments

Examples

.ns_generic('names<-')
.ns_generic('Math', ver = TRUE)
.ns_generic('update')

Ki67 Data

Description

Ki67 cell data containing 622 patients.

Usage

Ki67

Format

patientID

factor, unique patient identifier

tissueID

factor, TMA core identifier

recurrence

integer, recurrence indicator, 1 = Recurred, 0 = not Recurred

recfreesurv_mon

integer, recurrence-free survival time in months

logKi67

double, log-transformed cell signal intensity of the protein immunofloerscence signal

age

integer, age at diagnosis

Tstage

integer, tumor stage

node

factor, node stage

HR

logical, hormone positive status

histology

integer, histology grade

Her2

logical, Her2 status

race

character, race, White, Black, Asian, Native Hawaiian or Other Pacific Islander, American Indian or Alaska Native, Unknown

adj_chemo

logical, whether completed adjuvant chemo treatment

adj_rad

integer, adjuvant radiation treatment, 0 = unknown, 1 = done, 2 = NOT done

Details

The groupedHyperframe Ki67 is the complete data, to be used in examples of downstream packages maxEff and hyper.gam.

Extract Parts of 'cumv' Object

Description

Extract Parts of 'cumv' Object

Usage

## S3 method for class 'cumv'
x[i]

Arguments

Extract Subset of groupedHyperframe

Description

Extract Subset of groupedHyperframe

Usage

## S3 method for class 'groupedHyperframe'
x[...]

Arguments

Value

The function [.groupedHyperframe returns a groupedHyperframe or a hyperframe.

⁠[.ppp_tzh⁠

Description

⁠[.ppp_tzh⁠

Usage

## S3 method for class 'ppp_tzh'
x[i, j, drop = FALSE, ..., clip = FALSE]

Arguments

Value

The function `[.ppp_tzh` returns a ppp.object, not an object of class 'ppp_tzh'.

Aggregate Hyper Data Frame

Description

Aggregate Hyper Data Frame

Usage

## S3 method for class 'hyperframe'
aggregate(x, by, ...)

Arguments

Value

The function aggregate.hyperframe() returns a hyperframe.

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Aggregate vectorlist

Description

Aggregate vectorlist

Usage

## S3 method for class 'vectorlist'
aggregate(x, by, fun = pmean, ...)

Arguments

aggregate the marks of ppp-Related Object

Description

To aggregate the marks of a ppp-related object, e.g.,

• ppp.object

• a ppplist

• the ppp-hypercolumn of a hyperframe

Usage

aggregate_marks(x, by, FUN, expr, ..., vectorize = FALSE)

## S3 method for class 'ppp'
aggregate_marks(x, by, FUN, expr, ..., vectorize = FALSE)

## S3 method for class 'ppplist'
aggregate_marks(x, ...)

## S3 method for class 'hyperframe'
aggregate_marks(x, ...)

Arguments

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Append to Existing marks

Description

Append an additional mark to existing marks.

Usage

append_marks(x) <- value

## S3 replacement method for class 'ppp'
append_marks(x) <- value

## S3 replacement method for class 'tess'
append_marks(x) <- value

## S3 replacement method for class 'psp'
append_marks(x) <- value

Arguments

Value

The S3 method dispatch append_marks<-.ppp returns a ppp.object.

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Convert a listof fv.objects into 'fvlist'

Description

Convert a listof fv.objects into 'fvlist'

Usage

as.fvlist(X, data.name)

Arguments

Value

The function as.fvlist() returns an invisible list.

Creation of groupedHyperframe

Description

To create a groupedHyperframe object

Usage

as.groupedHyperframe(x, group, ...)

## S3 method for class 'hyperframe'
as.groupedHyperframe(x, group, ...)

## S3 method for class 'data.frame'
as.groupedHyperframe(x, group, ...)

## S3 method for class 'groupedData'
as.groupedHyperframe(x, group, ...)

Arguments

Value

The function as.groupedHyperframe() returns a groupedHyperframe.

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

as.list.fvlist()

Description

Converts an fvlist to a simple list

Usage

## S3 method for class 'fvlist'
as.list(x, ...)

Arguments

Convert pairwise_cor_spatial to matrix

Description

Convert pairwise_cor_spatial to matrix

Usage

## S3 method for class 'pairwise_cor_spatial'
as.matrix(x, ...)

Arguments

Value

The function as.matrix.pairwise_cor_spatial() returns a matrix.

as.vectorlist

Description

as.vectorlist

Usage

as.vectorlist(x, ...)

Arguments

A Batch Process of attr

Description

A Batch Process of attr

Usage

attr_(x, which, exact = TRUE)

## S3 method for class 'anylist'
attr_(x, which, exact = TRUE)

## S3 method for class 'hyperframe'
attr_(x, which, exact = TRUE)

Arguments

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Batch Process

Description

See workhorse function op_hyperframe().

Usage

Emark_(X, ...)

## S3 method for class 'hyperframe'
Emark_(X, correction = "none", ...)

## S3 method for class 'ppplist'
Emark_(X, correction = "none", ...)

## S3 method for class 'ppp'
Emark_(X, ...)

Vmark_(X, ...)

## S3 method for class 'hyperframe'
Vmark_(X, correction = "none", ...)

## S3 method for class 'ppplist'
Vmark_(X, correction = "none", ...)

## S3 method for class 'ppp'
Vmark_(X, ...)

Kmark_(X, ...)

## S3 method for class 'hyperframe'
Kmark_(X, correction = "none", ...)

## S3 method for class 'ppplist'
Kmark_(X, correction = "none", ...)

## S3 method for class 'ppp'
Kmark_(X, ...)

markcorr_(X, ...)

## S3 method for class 'hyperframe'
markcorr_(X, correction = "none", ...)

## S3 method for class 'ppplist'
markcorr_(X, correction = "none", ...)

## S3 method for class 'ppp'
markcorr_(X, ...)

markvario_(X, ...)

## S3 method for class 'hyperframe'
markvario_(X, correction = "none", ...)

## S3 method for class 'ppplist'
markvario_(X, correction = "none", ...)

## S3 method for class 'ppp'
markvario_(X, ...)

Gcross_(X, ...)

## S3 method for class 'hyperframe'
Gcross_(X, correction = "none", ...)

## S3 method for class 'ppplist'
Gcross_(X, correction = "none", ...)

## S3 method for class 'ppp'
Gcross_(X, ...)

Jcross_(X, ...)

## S3 method for class 'hyperframe'
Jcross_(X, correction = "none", ...)

## S3 method for class 'ppplist'
Jcross_(X, correction = "none", ...)

## S3 method for class 'ppp'
Jcross_(X, ...)

Kcross_(X, ...)

## S3 method for class 'hyperframe'
Kcross_(X, correction = "none", ...)

## S3 method for class 'ppplist'
Kcross_(X, correction = "none", ...)

## S3 method for class 'ppp'
Kcross_(X, ...)

Lcross_(X, ...)

## S3 method for class 'hyperframe'
Lcross_(X, correction = "none", ...)

## S3 method for class 'ppplist'
Lcross_(X, correction = "none", ...)

## S3 method for class 'ppp'
Lcross_(X, ...)

markconnect_(X, ...)

## S3 method for class 'hyperframe'
markconnect_(X, correction = "none", ...)

## S3 method for class 'ppplist'
markconnect_(X, correction = "none", ...)

## S3 method for class 'ppp'
markconnect_(X, ...)

nncross_(X, ...)

## S3 method for class 'hyperframe'
nncross_(X, ...)

## S3 method for class 'ppplist'
nncross_(X, ...)

## S3 method for class 'ppp'
nncross_(X, ...)

Arguments

Details

User Interface of Operations on hyperframe with One-and-Only-One ppp-hypercolumn

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Examples

# in \CRANpkg{spatstat.data}
# no good example for [Emark_]
# no hyperframe with ppp-hypercolumn with numeric marks

fluM = spatstat.data::flu |>
 spatstat.geom::subset.hyperframe(subset = (stain == 'M2-M1') & (virustype == 'wt'))
fluM
r = seq.int(from = 0, to = 100, by = 5)
fluM |>
 nncross_(i = 'M1', j = 'M2')
 
 

bibentry for Quarto Book

Description

bibentry for Quarto Book

Usage

bioinformatics_btaf430

Format

An object of class bibentry of length 1.

cbind.groupedHyperframe()

Description

cbind.groupedHyperframe()

Usage

## S3 method for class 'groupedHyperframe'
cbind(...)

Arguments

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

.Defunct Messages using Package cli

Description

Internal helper functions, to display beautiful .Defunct messages using package cli.

Usage

cli_doi_(doi)

cli_book_(fmt, author = "tingtingzhan", pub, chapter, print_chapter = TRUE)

cli_QuartoPub_(...)

cli_Netlify_(...)

cli_RPubs_(...)

Arguments

Examples

cli_RPubs_(pub = 'groupedHyperframe')
cli_QuartoPub_(pub = 'groupedhyperframe')
cli_QuartoPub_(pub = 'groupedhyperframe', chapter = 'bioinformatics_btaf430')
cli_Netlify_(pub = 'groupedhyperframe')
cli_Netlify_(pub = 'groupedhyperframe', chapter = 'bioinformatics_btaf430')
cli_doi_('10.1002/bimj.4710230408')

Cumulative Average Vertical Height of Trapezoidal Integration

Description

Cumulative trapezoidal integration divided by x-domain.

Usage

cumvtrapz(x, ...)

## S3 method for class 'numeric'
cumvtrapz(x, y, ..., rm1 = TRUE)

## S3 method for class 'fv'
cumvtrapz(x, key = fvnames(x, a = ".y"), .x = fvnames(x, a = ".x"), ...)

## S3 method for class 'fvlist'
cumvtrapz(x, mc.cores = getOption("cores"), ...)

## S3 method for class 'hyperframe'
cumvtrapz(x, ...)

Arguments

Value

The function ⁠vtrapz.*()⁠ return a numeric scalar.

Note

This is a tentative thought: the prefix v stands for 'vertical'.

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Defunct Functions

Description

The functions mentioned in hard-copy journals, but later .Defunct.

Usage

aggregate_quantile(...)

Arguments

Kernel density of marks

Description

Kernel density of marks.

Usage

density_marks(x, ...)

## S3 method for class 'ppp'
density_marks(x, ...)

## S3 method for class 'ppplist'
density_marks(x, ...)

Arguments

Details

The function density_marks() finds the kernel density of the marks.

Value

The function density_marks() returns a numeric vector.

Note

The function spatstat.explore::density.ppp() is for x- and y-coords only!

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Tentative Fix for Illegal Function Value in fv.object

Description

Tentative Fix for Illegal Function Value in fv.object

Usage

.illegal2theo(X, ...)

.disrecommend2theo(X, ...)

## S3 method for class 'fv'
.illegal2theo(X, key = fvnames(X, a = ".y"), .x = fvnames(X, a = ".x"), ...)

## S3 method for class 'fv'
.disrecommend2theo(
  X,
  key = fvnames(X, a = ".y"),
  .x = fvnames(X, a = ".x"),
  ...
)

## S3 method for class 'fvlist'
.illegal2theo(X, ...)

## S3 method for class 'fvlist'
.disrecommend2theo(X, ...)

## S3 method for class 'hyperframe'
.illegal2theo(X, ...)

## S3 method for class 'hyperframe'
.disrecommend2theo(X, ...)

Arguments

Get Nested Levels

Description

Get Nested Levels

Usage

get_nested(group)

get_nested_factors(group, data)

Arguments

Global Envelope Test in Bath Process

Description

Global Envelope Test in Bath Process

Usage

global_envelope_test_(x, ...)

## S3 method for class 'anylist'
global_envelope_test_(x, ...)

## S3 method for class 'hyperframe'
global_envelope_test_(x, ...)

Arguments

groupGeneric of 'fvlist'

Description

...

Usage

## S3 method for class 'fvlist'
Math(x, ...)

## S3 method for class 'fvlist'
Summary(..., na.rm = FALSE)

Arguments

Value

The function Math.fvlist() returns an 'fvlist'.

The function Summary.fvlist() ..

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

groupGeneric of ppp.object

Description

...

Usage

## S3 method for class 'ppp'
Math(x, ...)

## S3 method for class 'ppp'
Summary(..., na.rm = FALSE)

Arguments

Details

The function Math.ppp() performs Math operations on the numeric marks of a ppp.object.

The function Summary.ppp() ..

Value

The function Math.ppp() returns a ppp.object.

The function Summary.ppp() ..

groupGeneric of 'ppplist'

Description

...

Usage

## S3 method for class 'ppplist'
Math(x, ...)

## S3 method for class 'ppplist'
Summary(..., na.rm = FALSE)

Arguments

Value

The function Math.ppplist() returns a 'ppplist'.

The function Summary.ppplist() ...

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

groupGeneric of psp.object

Description

...

Usage

## S3 method for class 'psp'
Math(x, ...)

## S3 method for class 'psp'
Summary(..., na.rm = FALSE)

Arguments

Details

The function Math.psp() performs Math operations on the numeric marks of a psp.object.

The function Summary.psp() ..

Value

The function Math.psp() returns a psp.object.

The function Summary.psp() ..

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

groupGeneric of tessellation

Description

...

Usage

## S3 method for class 'tess'
Math(x, ...)

## S3 method for class 'tess'
Summary(..., na.rm = FALSE)

Arguments

Details

The function Math.tess() performs Math operations on the numeric marks of a tessellation.

The function Summary.tess() ..

Value

The function Math.tess() returns a ppp.object.

The function Summary.tess() ..

groupedHyperframe with One-and-Only-One ppp-hypercolumn

Description

..

Usage

grouped_ppp(
  formula,
  data,
  coords = ~x + y,
  window = owin(xrange = range(.x), yrange = range(.y)),
  ...
)

Arguments

Value

The function grouped_ppp() returns a groupedHyperframe with one-and-only-one ppp-hypercolumn.

References

https://tingtingzhan.quarto.pub/groupedhyperframe/nonS3/grouped_ppp_appx.html

Interpolation of fv.object

Description

Interpolation of fv.object

Usage

approxfun.fv(x, key = fvnames(fv, a = ".y"), .x = fvnames(fv, a = ".x"), ...)

splinefun.fv(x, key = fvnames(fv, a = ".y"), .x = fvnames(fv, a = ".x"), ...)

interpSpline_.fv(
  x,
  key = fvnames(fv, a = ".y"),
  .x = fvnames(fv, a = ".x"),
  ...
)

Arguments

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Inspect a listof fv.objects

Description

A helper function to check the validity of a listof fv.objects.

Usage

is.fvlist(X)

Arguments

Value

The function is.fvlist() returns a logical scalar with attributes

attr(,'r')

x-axis, or the r-values

attr(,'fname')

see explanation of this attributes in function fv

attr(,'.x')

spatstat.explore::fvnames(x, a = '.x') returns

attr(,'.y')

spatstat.explore::fvnames(x, a = '.y') returns

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Is marks of ppp.object numeric ?

Description

Is marks of ppp.object numeric ?

Usage

## S3 method for class 'ppp'
is.numeric(x)

Arguments

is.vectorlist

Description

is.vectorlist

Usage

is.vectorlist(
  x,
  mode = c("any", "logical", "integer", "numeric", "double", "character")
)

Arguments

Kernel Density via density.default

Description

Kernel density estimates only.

Usage

kerndens(x, ...)

## S3 method for class 'numeric'
kerndens(x, ...)

## S3 method for class 'ppp'
kerndens(x, ...)

## S3 method for class 'ppplist'
kerndens(x, ...)

## S3 method for class 'anylist'
kerndens(x, ...)

## S3 method for class 'hyperframe'
kerndens(x, ...)

Arguments

Details

The function kerndens() finds the estimated density values, i.e., element ⁠$y⁠ of the function density.default return.

Value

The function kerndens() returns a numeric vector.

Note

Do not overwrite function spatstat.explore::density.ppp() !!

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Black-Solid-Curve in plot.fv

Description

Name and value of the black solid curve as shown in plot.fv, i.e., the primary outcome of an fv.object.

Usage

keyval(x, ...)

## S3 method for class 'fv'
keyval(x, key = fvnames(x, a = ".y"), .x = fvnames(x, a = ".x"), ...)

## S3 method for class 'fvlist'
keyval(x, key = attr(x., which = ".y", exact = TRUE), ...)

## S3 method for class 'hyperframe'
keyval(x, ...)

Arguments

Details

The function keyval.fv() finds the value of the (primary) outcome of an fv.object.

Value

The function keyval.fv() returns a numeric vector.

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Pseudo S3 Methods based on kmeans

Description

Pseudo S3 Methods based on kmeans

Usage

kmeans.ppp(
  x,
  formula,
  centers = as.integer(ceiling((x[["n"]]/clusterSize))),
  clusterSize,
  ...
)

kmeans.ppplist(x, ...)

kmeans.hyperframe(x, ...)

Arguments

Value

The function kmeans.ppp() returns an object of class 'pppkm', which inherits from ppp.object.

The function kmeans.ppplist() returns an object of class 'pppkmlist', which inherits from 'ppplist'.

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

ksmooth of fv.object

Description

ksmooth of fv.object

Usage

ksmooth.fv(x, key = fvnames(fv, a = ".y"), .x = fvnames(fv, a = ".x"), ...)

Arguments

Last Legal Index

Description

Last Legal Index

Usage

lastLegal(v)

Arguments

Details

Legal, meaning not 0, not NaN and not Inf.

References

https://tingtingzhan.quarto.pub/groupedhyperframe/nonS3/lastLegal.html

S3 method dispatch of length on hyperframe

Description

S3 method dispatch of length on hyperframe

Usage

## S3 method for class 'hyperframe'
length(x)

Arguments

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

See Also

dim.hyperframe

loess of fv.object

Description

loess of fv.object

Usage

loess.fv(x, key = fvnames(fv, a = ".y"), .x = fvnames(fv, a = ".x"), ...)

Arguments

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Check if Data Column is Identical by Grouping

Description

Check if Data Column is Identical by Grouping

Usage

mc_identical_by(data, f, mc.cores = getOption("cores"), ...)

Arguments

Note

The function aggregate.data.frame does not do parallel computing.

The function collapse::collap does not support Surv column.

Look more into nlme:::collapse.groupedData

S3 methods table in vignette

Description

S3 methods table in vignette

Usage

methods2kable(
  generic.function,
  class,
  package,
  package_pattern,
  backtick = TRUE,
  ...
)

Arguments

Value

The function methods2kable() returns a data.frame.

Handle Missing marks in ppp.object.

Description

Handle Missing marks in ppp.object.

Usage

## S3 method for class 'ppp'
na.omit(object, ...)

## S3 method for class 'ppp'
na.exclude(object, ...)

Arguments

Details

The function na.omit.ppp() omits missing marks in a ppp.object.

Value

The function na.omit.ppp() returns a ppp.object.

Note

tzh suppose missing ⁠$x⁠ and ⁠$y⁠ are forbidden in ppp.object anyway.

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Operations on hyperframe with One-and-Only-One ppp-hypercolumn

Description

Create hypercolumn(s) of fv.objects or distances from the one-and-only-one ppp-hypercolumn inside a hyperframe.

Usage

op_hyperframe(X, ...)

Arguments

Value

The function op_hyperframe() returns a hyperframe.

Batch Operations of 'ppplist' Object

Description

Batch operations for a 'ppplist' input.

Usage

op_ppplist(x, op, mc.cores = getOption("cores"), ...)

Arguments

Details

The function op_ppplist() is a parallel batch process of the workhorse function ppp_numeric2fv(), ppp_multitype2fv() or ppp2dist().

Value

The function op_ppplist() returns a listof

• function ppp_numeric2fv() returns, if op = ppp_numeric2fv.

• function ppp_multitype2fv() returns, if op = ppp_multitype2fv.

• function ppp2dist() returns, if op = ppp2dist.

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Pairwise Tjostheim's Coefficient

Description

Pairwise Tjostheim's Coefficient

Usage

pairwise_cor_spatial(x, ...)

## S3 method for class 'ppp'
pairwise_cor_spatial(x, ...)

## S3 method for class 'ppplist'
pairwise_cor_spatial(x, ...)

Arguments

Details

Workhorse function cor.spatial.

Value

The function pairwise_cor_spatial() returns a dist object.

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Plot 'pppkm' object

Description

Plot 'pppkm' object

Usage

## S3 method for class 'pppkm'
plot(
  x,
  main = "k-Means Clustering",
  ...,
  cols = pal_hue()(n = length(levels(f)))
)

Arguments

Parallel mean and median

Description

Parallel mean and median

Usage

pmean(..., na.rm = TRUE)

pmedian(..., na.rm = TRUE)

Arguments

Value

The functions pmean() and pmedian() return a numeric vector.

Note

The functions pmean() and pmedian() mimic functions pmax.int and pmin.int. They are written in a very naive way. The pipeline cbind() |> rowMeans() is extremely slow.

References

https://tingtingzhan.quarto.pub/groupedhyperframe/nonS3/pmean.html

Examples

pmean(1:3, c(11, 12, 14), c(21, 22, 25))

Operations on ppp.object

Description

Create fv.objects or distances from a ppp.object.

Usage

ppp2dist(x, fun, ...)

ppp_numeric2fv(x, fun, ...)

ppp_multitype2fv(x, fun, ...)

Arguments

Value

The functions ppp_numeric2fv() and ppp_multitype2fv() return a listof fv.objects.

The function ppp2dist() returns a listof double vectors.

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Print 'cumv' Object

Description

Print 'cumv' Object

Usage

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

Arguments

Print 'fvlist'

Description

Print 'fvlist'

Usage

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

Arguments

Print groupedHyperframe

Description

Print groupedHyperframe

Usage

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

Arguments

Value

The function print.groupedHyperframe() does not have a returned value.

See Also

?nlme:::print.groupedData

Print 'pppkm' object

Description

Print 'pppkm' object

Usage

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

Arguments

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Print Summary Information of groupedHyperframe

Description

Print Summary Information of groupedHyperframe

Usage

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

Arguments

Value

The function print.summary.groupedHyperframe() does not have a returned value.

Print a 'vectorlist'

Description

Print a 'vectorlist'

Usage

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

Arguments

Quantiles of numeric marks in anylist

Description

Quantiles of numeric marks in anylist

Usage

## S3 method for class 'anylist'
quantile(x, ...)

Arguments

Quantiles of numeric elements in hyperframe

Description

Quantiles of numeric elements in hyperframe

Usage

## S3 method for class 'hyperframe'
quantile(x, ...)

Arguments

Quantiles of numeric marks in ppp.object

Description

Quantiles of numeric marks in ppp.object

Usage

## S3 method for class 'ppp'
quantile(x, ...)

Arguments

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Quantiles of numeric marks in 'ppplist'

Description

Quantiles of numeric marks in 'ppplist'

Usage

## S3 method for class 'ppplist'
quantile(x, ...)

Arguments

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

rds2versiondate

Description

rds2versiondate

Usage

rds2versiondate(x, pkg, format = "%a %b %d, %Y", ...)

Arguments

Random Re-Labelling Envelope Residual

Description

Random Re-Labelling Envelope Residual

Usage

rlabelRes(x, ...)

## S3 method for class 'ppp'
rlabelRes(x, ...)

## S3 method for class 'ppplist'
rlabelRes(x, ...)

## S3 method for class 'hyperframe'
rlabelRes(x, ...)

Arguments

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Examples

set.seed(52); res1_anemones = spatstat.data::anemones |>
  rlabelRes(fun = spatstat.explore::Kmark)
set.seed(52); res1_anemones_times = spatstat.data::anemones |>
  rlabelRes(fun = spatstat.explore::Kmark, f = `*`)
stopifnot(!identical(res1_anemones, res1_anemones_times))
  

set.seed(52); spatstat.data::anemones |>
  rlabelRes(fun = spatstat.explore::Kmark, f = \(m1, m2) { m1*m2 }) |>
  identical(y = res1_anemones_times) |>
  stopifnot()


set.seed(12); res_ants = spatstat.data::ants |>
  rlabelRes(fun = spatstat.explore::Gcross)

Default r_\text{max} of Various Functions in Package spatstat.explore

Description

Default r_\text{max} of Various Functions in Package spatstat.explore

Usage

.rmax(X, ...)

## S3 method for class 'ppp'
.rmax(X, fun, i, j, ...)

## S3 method for class 'fv'
.rmax(X, ...)

## S3 method for class 'ppplist'
.rmax(X, ...)

## S3 method for class 'hyperframe'
.rmax(X, ...)

Arguments

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

smooth.spline of fv.object

Description

smooth.spline of fv.object

Usage

smooth.spline.fv(
  x,
  key = fvnames(fv, a = ".y"),
  .x = fvnames(fv, a = ".x"),
  ...
)

Arguments

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

split.hyperframekm()

Description

split.hyperframekm()

Usage

## S3 method for class 'hyperframekm'
split(x, ...)

Arguments

Value

The function split.hyperframekm() returns a 'groupedHyperframe'.

Split 'pppkm' object

Description

Split 'pppkm' object

Usage

## S3 method for class 'pppkm'
split(x, f = attr(x, which = "f", exact = TRUE), ...)

Arguments

Value

The function split.pppkm() returns a 'splitppp' object from the workhorse function split.ppp.

split.pppkmlist

Description

split.pppkmlist

Usage

## S3 method for class 'pppkmlist'
split(x, ...)

Arguments

Value

The function split.pppkmlist() returns a 'splitppp' object from the workhorse function split.ppp.

Summary Information of Surv Object

Description

The missing S3 method of the generic function summary for Surv object.

Usage

## S3 method for class 'Surv'
summary(object, ...)

Arguments

Value

The function summary.Surv() returns a character vector.

Note

Without function summary.Surv(), the S3 generic function summary dispatches to function summary.default if the input is a Surv object.

See Also

summary.factor

Examples

aml2 = survival::aml |>
 within.data.frame(expr = {
  os = survival::Surv(time = time, event = status)
  time = status = NULL
 })
summary(aml2$os)
summary(aml2)

heart2 = survival::heart |>
 within.data.frame(expr = {
  os = survival::Surv(time = start, time2 = stop, event = event)
  start = stop = event = NULL
 })
summary(heart2$os)
summary(heart2)

Summary Information of groupedHyperframe

Description

Summary Information of groupedHyperframe

Usage

## S3 method for class 'groupedHyperframe'
summary(object, ...)

Arguments

Value

The function summary.groupedHyperframe() returns an R object of class 'summary.groupedHyperframe'.

superimpose.hyperframe

Description

superimpose.hyperframe

Usage

## S3 method for class 'hyperframe'
superimpose(...)

Arguments

Value

The function superimpose.hyperframe() returns a hyperframe or groupedHyperframe.

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Transpose a 'vectorlist'

Description

Transpose a 'vectorlist'

Usage

## S3 method for class 'vectorlist'
t(x)

Arguments

Details

tzh defines a derived class 'vectorlist', i.e., a listof vectors, which inherits from anylist. The implementation of 'vectorlist' is inspired by class solist.

The S3 method dispatch t.vectorlist(), of the generic function t, transposes a 'vectorlist' of equi-length. We illustrate this concept using data set Kovesi in Examples.

Value

The S3 method dispatch t.vectorlist() returns a 'vectorlist' of equi-length.

Note

The motivation of the derived class 'vectorlist' and the method dispatch t.vectorlist() is that The function with.hyperframe could be slow in a batch process.

References

https://tingtingzhan.quarto.pub/groupedhyperframe/topics.html

Visualize vtrapz() and cumvtrapz()

Description

Visualize (cumulative) average vertical height of trapezoidal integration.

Usage

visualize_vtrapz(
  x,
  y,
  x_smooth,
  y_smooth,
  xlabs,
  ylabs,
  yname,
  draw.rect,
  draw.v,
  label.v,
  draw.cumv,
  label.cumv,
  ...
)

## S3 method for class 'numeric'
visualize_vtrapz(
  x,
  y,
  x_smooth = x,
  y_smooth = y,
  xlabs,
  ylabs,
  yname,
  draw.rect = TRUE,
  draw.v = draw.rect,
  label.v = "Average Vertical Height",
  draw.cumv = TRUE,
  label.cumv = "Cumulative Average Vertical Height",
  ...
)

## S3 method for class 'fv'
visualize_vtrapz(x, ...)

## S3 method for class 'listof'
visualize_vtrapz(x, ...)

## S3 method for class 'density'
visualize_vtrapz(x, ...)

## S3 method for class 'stepfun'
visualize_vtrapz(x, ...)

## S3 method for class ''function''
visualize_vtrapz(x, ..., n = 513L)

## S3 method for class 'loess'
visualize_vtrapz(x, ..., n = 513L)

## S3 method for class 'smooth.spline'
visualize_vtrapz(x, ..., n = 513L)

## S3 method for class 'ksmooth'
visualize_vtrapz(x, ...)

## S3 method for class 'spline'
visualize_vtrapz(x, ..., n = 513L)

## S3 method for class 'xyVector'
visualize_vtrapz(x, ...)

Arguments

Value

The S3 generic function visualize_vtrapz() returns a ggplot object.

Average Vertical Height of Trapezoidal Integration

Description

Trapezoidal integration divided by x-domain.

Usage

vtrapz(x, ...)

Arguments

Value

The function vtrapz() return a numeric scalar.

Note

This is a tentative thought: the prefix v stands for 'vertical'.

wrobel_lung

Description

From Dr. Julia Wrobel's data https://sph.emory.edu/profile/faculty/julia-wrobel.

Usage

wrobel_lung

Format

A data.frame