Help for package groupedHyperframe

Type:

Package

Title:

Grouped Hyper Data Frame: An Extension of Hyper Data Frame

Version:

0.3.0

Description:

An S3 class 'groupedHyperframe' that inherits from hyper data frame. Batch processes on point-pattern hyper column. Aggregation of function-value-table hyper column(s) and numeric hyper column(s) over a nested grouping structure.

RoxygenNote:

7.3.3

LazyData:

true

LazyDataCompression:

Encoding:

UTF-8

License:

GPL-2

Language:

en-US

URL:

https://github.com/tingtingzhan/groupedHyperframe

Depends:

R (≥ 4.5)

Imports:

cli, parallel, doParallel, foreach, matrixStats, pracma, GET, SpatialPack, ggplot2, geomtextpath, scales, patchwork, spatstat.explore, spatstat.geom, spatstat.random

Suggests:

knitr, quarto, rmarkdown, rpart, survival, spatstat.data

VignetteBuilder:

quarto

NeedsCompilation:

Packaged:

2025-10-12 22:26:58 UTC; tingtingzhan

Author:

Tingting Zhan

[aut, cre], Inna Chervoneva

[aut]

Maintainer:

Tingting Zhan <tingtingzhan@gmail.com>

Repository:

CRAN

Date/Publication:

2025-10-14 10:40:12 UTC

groupedHyperframe: Grouped Hyper Data Frame: An Extension of Hyper Data Frame

Description

Note

Help files of individual functions are intentionally suppressed in the pdf manual. Users are encouraged to get started with the vignettes.

https://rpubs.com/tingtingzhan/groupedHyperframe

Author(s)

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

Authors:

Inna Chervoneva Inna.Chervoneva@jefferson.edu (ORCID)

Syntactic Sugar for groupedHyperframe Object

Description

Syntactic Sugar for groupedHyperframe Object

Usage

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

Arguments

x

a groupedHyperframe

name, value

see function $<-.hyperframe

Value

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

Note

Function $<-.hyperframe drops attributes.

Alternative Interface of nncross.ppp

Description

An alternative interface of function nncross.ppp.

Usage

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

Arguments

X

see Details

i, j

character or integer scalars. See functions Gcross, etc. for more details

...

additional parameters of nncross.ppp

Details

Function .nncross() creates an interface similar to 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

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

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 Subset of groupedHyperframe

Description

Extract Subset of groupedHyperframe

Usage

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

Arguments

x

a groupedHyperframe

...

additional parameters of [.hyperframe

Value

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

x

an object of internal class 'ppp_tzh', a derived class from ppp.object

i, j

see function [.ppp

drop

...

clip

Value

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

Aggregate groupedHyperframe

Description

Aggregate groupedHyperframe

Usage

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

Arguments

x

a groupedHyperframe

by

a one-sided formula

...

additional parameters of function aggregate.vectorlist(), most importantly parameter fun

Value

Function aggregate.groupedHyperframe() returns a hyperframe.

Aggregate `vectorlist`

Description

Aggregate vectorlist

Usage

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

Arguments

x

a vectorlist

by

factor, of same length as x

fun

function, aggregation method, currently supports functions pmean(), pmedian(), pmax, and pmin.

...

additional parameters, currently of no use

aggregate_marks

Description

aggregate_marks

Usage

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

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

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

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

Arguments

x

see Usage

by, FUN, ...

additional parameters of function aggregate.data.frame

vectorize

logical scalar, whether to convert the return from function aggregate.data.frame into a vector. Default FALSE.

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

Arguments

x

currently only ppp.object is supported

value

a factor or numeric vector

Value

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

Convert a listof fv.objects into `'fvlist'`

Description

Convert a listof fv.objects into 'fvlist'

Usage

as.fvlist(X, data.name)

Arguments

X

a listof fv.objects

data.name

character scalar, name of X, for console message output

Value

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, ...)

Arguments

x

see Usage

group

formula

...

additional parameters

Value

Function as.groupedHyperframe() returns a groupedHyperframe.

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

x

a pairwise_cor_spatial

...

additional parameters, currently not in use

Value

Function as.matrix.pairwise_cor_spatial() returns a matrix.

as.vectorlist

Description

as.vectorlist

Usage

as.vectorlist(x, ...)

Arguments

x

an anylist

...

additional parameters of function is.vectorlist()

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

X

a hyperframe

...

additional parameters of user operation

correction

character scalar, see functions markcorr, Gcross, etc. Default 'none' to save computing time.

Details

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

Examples

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

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

`cbind.groupedHyperframe()`

Description

cbind.groupedHyperframe()

Usage

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

Arguments

...

see function cbind.hyperframe, the first element must be 'groupedHyperframe'

Defunct Messages using Package cli

Description

Defunct Messages using Package cli

Usage

cli_RPubs_(x)

cli_doi_(x)

Arguments

x

character scalar

Defunct Functions

Description

Functions mentioned in hard-copy journals, but later .Defunct.

Usage

aggregate_quantile(new = "<groupedHyperframe> |> quantile() |> aggregate()")

aggregate_fv(new = "<groupedHyperframe> |> summary_fv() |> aggregate()")

Arguments

new

character scalar, see function .Defunct.

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

x

a ppp.object, or 'ppplist'

...

additional parameters of function density.default

Details

Function density_marks() finds the kernel density of the marks.

Value

Function density_marks() returns a numeric vector.

Note

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

Random Re-Labelling Test

Description

Random Re-Labelling Test

Usage

foobar(
  Y,
  fun = Kmark,
  f = function(m1, m2) {
     m1 * m2
 },
  ...
)

Arguments

Y

a ppp.object, see function envelope.ppp

fun, f, ...

arguments of function envelope.ppp

Examples

set.seed(52); spatstat.data::anemones |>
  foobar() |>
  attr(which = 'p', exact = TRUE)

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, ...)

## S3 method for class 'fv'
.disrecommend2theo(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

X

an fv.object

Get Nested Levels

Description

Get Nested Levels

Usage

get_nested(group)

get_nested_factors(group, data)

Arguments

group

a language object, (nested) grouping structure

data

data.frame or hyperframe

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

formula

formula in the format of m1+m2 ~ y+x1+x2 | g1/g2, where m_i's are one or more marks, y and x_j's are the endpoint and predictor(s) for downstream analysis, and g_k are one or more nested grouping structure

data

data.frame

coords

formula, variable names of x- and y-coordinates in data. Default ~x+y.

window

an observation window owin, default is the x- and y-span of coords in data.

...

additional parameters, currently not in use

Value

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

approxfun of fv.object

Description

approxfun of fv.object

Usage

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

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

Arguments

x

an fv.object

key

character scalar, see function keyval.fv()

...

additional parameters of functions approxfun and splinefun.

Inspect a listof fv.objects

Description

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

Usage

is.fvlist(X)

Arguments

X

a listof fv.objects

Value

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

Is marks of ppp.object numeric ?

Description

Is marks of ppp.object numeric ?

Usage

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

Arguments

x

a ppp.object

is.vectorlist

Description

is.vectorlist

Usage

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

Arguments

x

an anylist

mode

character scalar other than 'any', 'complex' and 'raw', see function is.vector

Kernel Density via density.default

Description

Kernel density estimates only.

Usage

kerndens(x, ...)

## Default S3 method:
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

x

see Usage

...

additional parameters of function density.default

Details

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

Value

Function kerndens() returns a numeric vector.

Note

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

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

Arguments

x

an fv.object

key

character scalar, default value is spatstat.explore::fvnames(x, a = '.y'), to speed up batch processes.

Details

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

Value

Function keyval.fv() returns a numeric vector.

Extension of kmeans

Description

Extension of kmeans

Usage

.kmeans(x, formula, ...)

## S3 method for class 'ppp'
.kmeans(
  x,
  formula,
  centers = as.integer(ceiling((x[["n"]]/clusterSize))),
  clusterSize,
  ...
)

Arguments

x

see Usage

formula

formula

...

additional parameters of function kmeans

centers

integer scalar, number of clusters k, see function kmeans

clusterSize

integer scalar, number of points per cluster

Value

Function .kmeans() returns a kmeans object.

Last Legal Index

Description

Last Legal Index

Usage

lastLegal(v)

Arguments

v

double vector

Details

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

`S3` method dispatch of length on hyperframe

Description

S3 method dispatch of length on hyperframe

Usage

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

Arguments

x

a hyperframe

log of ppp.object

Description

...

Usage

## S3 method for class 'ppp'
log(x, base = exp(1))

## S3 method for class 'ppp'
log1p(x)

## S3 method for class 'ppp'
log10(x)

## S3 method for class 'ppp'
log2(x)

Arguments

x

a ppp.object

base

numeric scalar

Details

Function log.ppp() takes a log of continuous marks of a ppp.object.

Functions log1p.ppp(), log10.ppp() and log2.ppp() are similar.

Value

Functions log.ppp(), log1p.ppp(), log10.ppp() and log2.ppp() all return a ppp.object.

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

data

data.frame

f

factor

mc.cores

integer scalar, see function mclapply. Default is the return of function detectCores.

...

additional parameters, currently not in use

Note

Function aggregate.data.frame does not do parallel computing.

Function collapse::collap does not support Surv column.

Look more into nlme:::collapse.groupedData

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

object

a ppp.object

...

additional parameters, currently not in use

Details

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

Value

Function na.omit.ppp() returns a ppp.object.

Note

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

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

X

a hyperframe, containing one-and-only-one ppp-hypercolumn

...

additional parameters of function op_ppplist()

Value

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

x

a 'ppplist' object

op

workhorse function, either ppp_numeric2fv(), ppp_multitype2fv() or ppp2dist()

mc.cores

integer scalar, see function mclapply. Default is the return of function detectCores.

...

additional parameters of workhorse functions ppp_numeric2fv(), ppp_multitype2fv() or ppp2dist()

Details

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

Value

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.

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

x

see Usage

...

additional parameters, currently not in use

Details

Workhorse function cor.spatial.

Value

Function pairwise_cor_spatial() returns a dist object.

Parallel mean and median

Description

Parallel mean and median

Usage

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

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

Arguments

...

numeric vectors

na.rm

logical scalar, default TRUE

Value

Functions pmean() and pmedian() return a numeric vector.

Note

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.

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

x

a ppp.object

fun

a distance function, or a function that returns an fv.object, see Details

...

additional parameters of function fun

Value

Functions ppp_numeric2fv() and ppp_multitype2fv() return a listof fv.objects.

Function ppp2dist() returns a listof double vectors.

Print `'fvlist'`

Description

Print 'fvlist'

Usage

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

Arguments

x

an 'fvlist'

...

additional parameters, currently of no use

Print groupedHyperframe

Description

Print groupedHyperframe

Usage

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

Arguments

x

a groupedHyperframe

...

additional parameters, currently not in use

Value

Function print.groupedHyperframe() does not have a returned value.

Quantiles of numeric marks in anylist

Description

Quantiles of numeric marks in anylist

Usage

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

Arguments

x

an anylist

...

additional parameters of function stats:::quantile.default()

Quantiles of numeric elements in hyperframe

Description

Quantiles of numeric elements in hyperframe

Usage

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

Arguments

x

a hyperframe

...

additional parameters of function stats:::quantile.default()

Quantiles of numeric marks in ppp.object

Description

Quantiles of numeric marks in ppp.object

Usage

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

Arguments

x

a ppp.object

...

additional parameters of function stats:::quantile.default()

Quantiles of numeric marks in `'ppplist'`

Description

Quantiles of numeric marks in 'ppplist'

Usage

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

Arguments

x

a 'ppplist'

...

additional parameters of function stats:::quantile.default()

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

X

a ppp.object with one numeric or multi-type marks

...

additional parameters, currently of no use

fun

character scalar, see (the un-documented) function rmax.rule

i, j

character scalars, see functions Gcross, Kcross, Jcross, etc.

split by kmeans Clustering

Description

split by kmeans clustering

Usage

split_kmeans(x, ...)

## Default S3 method:
split_kmeans(x, ...)

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

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

Arguments

x

see Usage

...

additional parameters of function kmeans

Note

Function split_kmeans.default() is supposed to work with ppp.object.

Truncated Summary of `'fvlist'`

Description

Truncated Summary of 'fvlist'

Usage

## S3 method for class 'fvlist'
summary(
  object,
  data.name = deparse1(substitute(object)),
  rmax,
  mc.cores = getOption("cores"),
  ...
)

Arguments

object

an 'fvlist'

data.name

character scalar

rmax

(optional) numeric scalar, user r_\text{max}

mc.cores

integer scalar, see function mclapply. Default is the return of function detectCores.

...

additional parameters, currently of no use

Summarize fv-`hypercolumns`

Description

Summarize fv-hypercolumns

Usage

summary_fv(X, rmax, ...)

Arguments

X

a hyperframe or groupedHyperframe, containing one or more fv.object column(s)

rmax

numeric scalar, user-specified truncation point r_\text{max}

...

additional parameters of function summary.fvlist(), most importantly mc.cores.

Value

Function summary_fv() returns a hyperframe or groupedHyperframe.

superimpose.groupedHyperframe

Description

superimpose.groupedHyperframe

Usage

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

Arguments

...

one or more groupedHyperframes

Value

Function superimpose.groupedHyperframe() returns a groupedHyperframe.

superimpose.hyperframe

Description

superimpose.hyperframe

Usage

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

Arguments

...

one or more hyperframes

Value

Function superimpose.hyperframe() returns a hyperframe.

Transpose a `'vectorlist'`

Description

Transpose a 'vectorlist'

Usage

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

Arguments

x

a 'vectorlist' of equi-length

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 function with.hyperframe could be slow in a batch process.

Trapzoidal Integration of fv.object

Description

Trapzoidal Integration of fv.object

Usage

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

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

Arguments

x

an fv.object

key

character scalar, see function keyval.fv()

Details

Functions trapz.fv() and cumtrapz.fv() obtain the (cumulative) trapzoidal integration of the area under the primary outcome of a function value fv.object.

Value

Functions trapz.fv() and vtrapz.fv() return a numeric scalar.

Functions cumtrapz.fv() and cumvtrapz.fv() return a numeric vector.

`S3` methods table in vignette

Description

S3 methods table in vignette

Usage

vignette_methods(class, package, ...)

Arguments

class

character scalar

package

character scalar

...

additional parameters of function methods

Value

Function vignette_methods() returns a data.frame.

Visualize `vtrapz()` and `cumvtrapz()`

Description

Visualize (cumulative) average vertical height of trapezoidal integration.

Usage

visualize_vtrapz(
  x,
  y,
  x_smooth,
  y_smooth,
  x_labels,
  y_labels,
  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,
  x_labels,
  y_labels,
  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 'fvlist'
visualize_vtrapz(x, ...)

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

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

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

Arguments

x

see Usage

y

numeric vector

x_smooth, y_smooth

numeric vectors, smoothed x and y values, to beautify the geom_textpath of a stepfun

x_labels, y_labels

yname

(optional) character scalar, name of function

draw.rect

logical scalar, whether to plot the rectangle, default TRUE

draw.v

logical scalar, whether to plot the average vertical height vtrapz(), default is determined by parameter draw.rect.

label.v, label.cumv

character scalars

draw.cumv

logical scalar, whether to plot the cumulative average vertical height cumvtrapz(), default TRUE

...

additional parameters, currently of no use

n

integer, number of x-values at which to evaluate, only applicable when the input is the return of function splinefun.

Value

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

(Cumulative) Average Vertical Height of Trapezoidal Integration

Description

(Cumulative) trapezoidal integration divided by x-domain.

Usage

vtrapz(x, ...)

cumvtrapz(x, ...)

## Default S3 method:
vtrapz(x, ...)

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

## Default S3 method:
cumvtrapz(x, ...)

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

Arguments

x

numeric vector

...

additional parameters of function trapz and cumtrapz

key

character scalar, see function keyval.fv()

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

groupedHyperframe: Grouped Hyper Data Frame: An Extension of Hyper Data Frame

Description

Note

Author(s)

See Also

Syntactic Sugar for groupedHyperframe Object

Description

Usage

Arguments

Value

Note

Alternative Interface of nncross.ppp

Description

Usage

Arguments

Details

Value

Ki67 Data

Description

Usage

Format

Details

Extract Subset of groupedHyperframe

Description

Usage

Arguments

Value

⁠[.ppp_tzh⁠

Description

Usage

Arguments

Value

Aggregate groupedHyperframe

Description

Usage

Arguments

Value

Aggregate vectorlist

Description

Usage

Arguments

aggregate_marks

Description

Usage

Arguments

Append to Existing marks

Description

Usage

Arguments

Value

Convert a listof fv.objects into 'fvlist'

Description

Usage

Arguments

Value

Creation of groupedHyperframe

Description

Usage

Arguments

Value

Convert pairwise_cor_spatial to matrix

Description

Usage

Arguments

Value

as.vectorlist

Description

Usage

Arguments

Batch Process

Description

Usage

Arguments

Details

Examples

cbind.groupedHyperframe()

Description

Usage

Arguments

Defunct Messages using Package cli

`⁠[.ppp_tzh⁠`

Aggregate `vectorlist`

Convert a listof fv.objects into `'fvlist'`

Creation of `groupedHyperframe`

`cbind.groupedHyperframe()`

Tentative Fix for Illegal Function Value in `fv.object`