Create reference data from other data

Create reference data from almost any other data that has a datetime column and a data column. The reference data can even be created from subsets of the same data. Examples are that one participant can be used as a reference for all other participants, or that the first (second,...) day of every participant data is the reference for any other day. This function needs to be carefully handled, when the reference data time intervals are shorter than the data time intervals. In that case, use aggregate_Datetime() on the reference data beforehand to lengthen the interval.

Usage

data2reference(
  dataset,
  Reference.data = dataset,
  Datetime.column = Datetime,
  Data.column = MEDI,
  Id.column = Id,
  Reference.column = Reference,
  overwrite = FALSE,
  filter.expression.reference = NULL,
  across.id = FALSE,
  shift.start = FALSE,
  length.restriction.seconds = 60,
  shift.intervals = "auto",
  Reference.label = NULL
)

Arguments

dataset

A light logger dataset

Reference.data

The data that should be used as reference. By default the dataset will be used as reference.

Datetime.column

Datetime column of the dataset and Reference.data. Need to be the same in both sets. Default is Datetime.

Data.column

Data column in the Reference.data that is then converted to a reference. Default is MEDI.

Id.column

Name of the Id.column in both the dataset and the Reference.data.

Reference.column

Name of the reference column that will be added to the dataset. Default is Reference. Cannot be the same as any other column in the dataset and will throw an error if it is.

overwrite

If TRUE (defaults to FALSE), the function will overwrite the Reference.colname column if it already exists.

filter.expression.reference

Expression that is used to filter the Reference.data before it is used as reference. Default is NULL. See

across.id

Grouping variables that should be ignored when creating the reference data. Default is FALSE. If TRUE, all grouping variables are ignored. If FALSE, no grouping variables are ignored. If a vector of grouping variables is given, these are ignored.

shift.start

If TRUE, the reference data is shifted to the start of the respective group. Default is FALSE. The shift ignores the groups specified in across.id.

length.restriction.seconds

Restricts the application of reference data to a maximum length in seconds. Default is 60 seconds. This is useful to avoid reference data being applied to long periods of time, e.g., when there are gaps in the reference data

shift.intervals

Time shift in seconds, that is applied to every data point in the reference data. Default is "auto". If "auto", the shift is calculated by halving the most frequent time difference between two data points in the reference data. If a number is given, this number in seconds is used as the shift. Can also use lubridate::duration() to specify the shift.

Reference.label

Label that is added to the reference data. If NULL, no label is added.

Value

A dataset with a new column Reference that contains the reference data.

Details

To use subsets of data, use the filter.expression.reference argument to specify the subsets of data. The across.id argument specifies whether the reference data should be used across all or some grouping variables (e.g., across participants). The shift.start argument enables a shift of the reference data start time to the start of the respective group.

and @examples for more information. The expression is evaluated within dplyr::filter().

Examples

library(dplyr)
#> 
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:stats’:
#> 
#>     filter, lag
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, setdiff, setequal, union
library(lubridate)
#> 
#> Attaching package: ‘lubridate’
#> The following objects are masked from ‘package:base’:
#> 
#>     date, intersect, setdiff, union
library(ggplot2)

gg_reference <- function(dataset) {
dataset %>%
ggplot(aes(x = Datetime, y = MEDI, color = Id)) +
geom_line(linewidth = 1) +
geom_line(aes(y = Reference), color = "black", size = 0.25, linetype = "dashed") +
theme_minimal() + facet_wrap(~ Id, scales = "free_y")
}

#in this example, each data point is its own reference
sample.data.environment %>%
  data2reference() %>%
  gg_reference()
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.


#in this example, the first day of each ID is the reference for the other days
#this requires grouping of the Data by Day, which is then specified in across.id
#also, shift.start needs to be set to TRUE, to shift the reference data to the
#start of the groupings
sample.data.environment %>% group_by(Id, Day = as_date(Datetime)) %>%
data2reference(
  filter.expression.reference =  as_date(Datetime) == min(as_date(Datetime)),
  shift.start = TRUE,
  across.id = "Day") %>%
  gg_reference()
#> Joining with `by = join_by(Id, Day)`
#> Adding missing grouping variables: `Id`
#> Joining with `by = join_by(Id)`
#> Joining with `by = join_by(Id, Day)`
#> Joining with `by = join_by(Id, Day)`
#> Adding missing grouping variables: `Day`


#in this example, the Environment Data will be used as a reference
sample.data.environment %>%
data2reference(
  filter.expression.reference =  Id == "Environment",
  across.id = TRUE) %>%
  gg_reference()