Title: Longitudinal Dataframes into Arrays for Machine Learning Training
Version: 0.2.0
Maintainer: Luis Garcez <luisgarcez1@gmail.com>
Description: An easy tool to transform 2D longitudinal data into 3D arrays suitable for Long short-term memory neural networks training. The array output can be used by the 'keras' package. Long short-term memory neural networks are described in: Hochreiter, S., & Schmidhuber, J. (1997) <doi:10.1162/neco.1997.9.8.1735>.
Imports: abind, dplyr
License: GPL (≥ 3)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
URL: https://github.com/luisgarcez11/long2lstmarray
BugReports: https://github.com/luisgarcez11/long2lstmarray/issues
Suggests: knitr, rmarkdown, testthat
Depends: R (≥ 2.10)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-11-28 13:30:29 UTC; jjferreira-admin
Author: Luis Garcez ORCID iD [aut, cre, cph]
Repository: CRAN
Date/Publication: 2022-11-28 14:40:05 UTC

Clinical scale example data

Description

An example dataset containing Amyotrophic Lateral Sclerosis Functional Rating Scale - Revised.

Usage

alsfrs_data

Format

A data frame with 100 rows and 15 variables:

subjid

Subject ID

visdy

Visit day

p1

Scale items

p2

Scale items

p3

Scale items

p4

Scale items

p5

Scale items

p6

Scale items

p7

Scale items

p8

Scale items

p9

Scale items

p10

Scale items

x1r

Scale items

x2r

Scale items

x3r

Scale items

Source

https://pubmed.ncbi.nlm.nih.gov/10540002/

Generate a matrix with various lags from a variable in the dataframe

Description

Generate a matrix with various lags from a variable in the dataframe

Usage

get_var_array(
  data,
  subj_var,
  var,
  time_var,
  lags,
  label_length = 1,
  label_output = FALSE
)

Arguments

data

A data frame, data frame extension (e.g. a tibble).

subj_var

A character string referring to the variable that specifies the "subject" variable.

var

A character string referring to the variable that contains the variable values.

time_var

A character string referring to the variable that contains the time variable values (e.g. visit day, minutes, years).

lags

The length of each sliced sequence.

label_length

How many values after are considered to be the label? Default to 1. If label_length = 1, the label value´ is always the value following the sliced sequence.

label_output

logical. if TRUE a list including the matrix with the sliced sequences and a vector with the label is returned.

Value

If label_output is FALSE, a matrix with the sliced sequences is returned. If label_output is TRUE, a list with the matrix and vector with the labels from the same variable is returned.

Examples

get_var_array(alsfrs_data, "subjid", 
"p2", "visdy", lags = 3, 
label_output = FALSE)

Get variable values from subject/variable name pair

Description

Get variable values from subject/variable name pair

Usage

get_var_sequence(data, subj_var, subj, var)

Arguments

data

A data frame, data frame extension (e.g. a tibble).

subj_var

A character string referring to the variable that specifies the "subject" variable.

subj

Any value that the "subject" variable can take.

var

A character string referring to the variable that contains the variable values.

Value

A vector of values from variable var which subj_var equal to subj.

Examples

get_var_sequence(sleep, subj_var = "ID", 1, "extra")

Generate a matrix with various lags from a dataframe

Description

Generate a matrix with various lags from a dataframe

Usage

longitudinal_array(
  data,
  subj_var,
  vars,
  time_var,
  lags,
  label_length = 1,
  label_var = NULL,
  label_output = FALSE,
  time_var_output = FALSE
)

Arguments

data

A data frame, data frame extension (e.g. a tibble).

subj_var

A character string referring to the variable that specifies the "subject" variable.

vars

A character string referring to the variables that contain the variable values.

time_var

A character string referring to the variable that contains the time variable values (e.g. visit day, minutes, years). Important to get the sequences in the right order.

lags

The length of each sliced sequence.

label_length

How many values after are considered to be the label? Default to 1. If label_length = 1, the label value is always the value following the sliced sequence.

label_var

A character string referring to the variables that contain the label variable values.

label_output

logical. if TRUE a list including the matrix with the sliced sequences and a vector with the label is returned.

time_var_output

logical. Is time_var to be included in the final output. Default to FALSE.

Value

If label_output is FALSE, a 3D array with the sliced sequences is returned. The array dimensions are subject, time and variable. If label_output is TRUE, a list with the array and vector with the labels is returned.

Examples

longitudinal_array(alsfrs_data, "subjid", c("p1", "p2", "p3"), 
                   "visdy", lags = 3, label_output = FALSE)
longitudinal_array(alsfrs_data, "subjid", c("p1", "p2", "p3"),
                   "visdy", lags = 3, label_output = FALSE)[1,,]
longitudinal_array(alsfrs_data, "subjid", c("p1", "p2", "p3"), 
                  "visdy", lags = 3, label_output = FALSE)[,1,]
longitudinal_array(alsfrs_data, "subjid", c("p1", "p2", "p3"),
                  "visdy", lags = 3, label_output = FALSE)[,,1]

Generate a matrix with various lags from a sequence

Description

Generate a matrix with various lags from a sequence

Usage

slice_var_sequence(sequence, lags, label_length = 1, label_output = TRUE)

Arguments

sequence

A vector representing the sequence to be sliced into many rows.

lags

The length of each sliced sequence.

label_length

How many values after are considered to be the label? Default to 1. If label_length = 1, the label value is always the value following the sliced sequence.

label_output

logical. if TRUE a list including the matrix with the sliced sequences and a vector with the labels is returned.

Value

If label_output is FALSE, a matrix with the sliced sequences is returned. If label_output is TRUE, a list with the matrix and vector with the labels is returned.

Examples

slice_var_sequence(sequence = 1:30,
 lags = 3, label_length = 1,
 label_output = TRUE)
 
slice_var_sequence(sequence = 1:30, 
lags = 3, label_length = 1,
 label_output = FALSE)
 
slice_var_sequence(sequence = 1:30,
 lags = 3, label_length = 2,
  label_output = FALSE)