Package 'eq5dsuite'

Title: Handling and Analysing EQ-5d Data
Description: The EQ-5D is a widely-used standarized instrument for measuring Health Related Quality Of Life (HRQOL), developed by the EuroQol group <https://euroqol.org/>. It assesses five dimensions; mobility, self-care, usual activities, pain/discomfort, and anxiety/depression, using either a three-level (EQ-5D-3L) or five-level (EQ-5D-5L) scale. Scores from these dimensions are commonly converted into a single utility index using country-specific value sets, which are critical in clinical and economic evaluations of healthcare and in population health surveys. The eq5dsuite package enables users to calculate utility index values for the EQ-5D instruments, including crosswalk utilities using the original crosswalk developed by van Hout et al. (2012) <doi:10.1016/j.jval.2012.02.008> (mapping EQ-5D-5L responses to EQ-5D-3L index values), or the recently developed reverse crosswalk by van Hout et al. (2021) <doi:10.1016/j.jval.2021.03.009> (mapping EQ-5D-3L responses to EQ-5D-5L index values). Users are allowed to add and/or remove user-defined value sets. Additionally, the package provides tools to analyze EQ-5D data according to the recommended guidelines outlined in "Methods for Analyzing and Reporting EQ-5D data" by Devlin et al. (2020) <doi:10.1007/978-3-030-47622-9>.
Authors: Kim Rand [aut, cre] (ORCID: <https://orcid.org/0000-0001-7692-4099>), Oliver Rivero-Arias [aut] (ORCID: <https://orcid.org/0000-0003-2233-6544>), Iryna Schlackow [aut] (ORCID: <https://orcid.org/0000-0002-4154-1431>), Anabel Estévez-Carrillo [aut] (ORCID: <https://orcid.org/0000-0001-8778-5055>)
Maintainer: Kim Rand <[email protected]>
License: GPL (>= 2)
Version: 2.0.0
Built: 2026-05-11 09:12:03 UTC
Source: https://github.com/mih-old/eq5dsuite

Help Index

Add utility values to a data frame

Description

This function adds utility values to a data frame based on a specified version of EQ-5D and a country name.

Usage

.add_utility(df, eq5d_version, country)

Arguments

df

A data frame containing the state data. The state must be included in the data frame as a character vector under the column named 'state'.
eq5d_version

A character string specifying the version of EQ-5D, i.e. 3L or 5L.
country

A character string representing the name of the country. This could be in a 2-letter format, full name or short name, as specified in the country_codes datasets.

Value

A data frame with an additional column named 'utility' containing the calculated utility values. If the input country name is not found in the country_codes dataset, a list of available codes is printed, and subsequentyl an error message is displayed and the function stops.

Examples

df <- data.frame(state = c("11111", "11123", "32541"))
.add_utility(df, "5L", "DK")

Check the uniqueness of groups This function takes a data frame 'df' and a vector of columns 'group_by', and checks whether the combinations of values in the columns specified by 'group_by' are unique. If the combinations are not unique, a warning message is printed.

Description

Check the uniqueness of groups This function takes a data frame 'df' and a vector of columns 'group_by', and checks whether the combinations of values in the columns specified by 'group_by' are unique. If the combinations are not unique, a warning message is printed.

Usage

.check_uniqueness(df, group_by)

Arguments

df

A data frame.
group_by

A character vector of column names in 'df' that specify the groups to check for uniqueness.

Value

No return value, called for side effects: it will stop with an error if any group combinations are not unique.

Examples

df <- data.frame(id = c(1, 1, 1, 1, 2, 2),
                 fu = rep(c("baseline", "follow-up"), 3),
                 value = rnorm(6))
.check_uniqueness(df, c("id", "fu"))

.EQxwrprob

Description

Takes a matrix of parameters for reverse crosswalk model, returns 243 x 25 matrix of state/level transition probabilities.

Usage

.EQxwrprob(par = NULL)

Arguments

par

Matrix of model parameters

Value

An 243 * 25 matrix with probabilities for state level transitions.

Helper function for frequency of levels by dimensions tables

Description

Helper function for frequency of levels by dimensions tables

Usage

.freqtab(
  df,
  names_eq5d = NULL,
  name_fu = NULL,
  levels_fu = NULL,
  eq5d_version = NULL,
  add_summary_problems_change = TRUE
)

Arguments

df

Data frame with the EQ-5D and follow-up columns
names_eq5d

Character vector of column names for the EQ-5D dimensions
name_fu

Character string for the follow-up column. If NULL, no grouping is used, and the table reports for the total population.
levels_fu

Character vector containing the order of the values in the follow-up column. If NULL (default value), the levels will be ordered in the order of appearance in df.
eq5d_version

Version of the EQ-5D instrument
add_summary_problems_change

If set to false, the resulting dataframe does not include a row on problems change.

Value

Summary data frame.

Generate colours for PCHC figures

Description

This internal function generates a vector of colours based on the specified base colour. Currently only green and orange colours are implemented. The wrapper is used in Figures 2.2-2.4.

Usage

.gen_colours(col, n)

Arguments

col

A character string specifying the base colour. Only "green" or "orange" is accepted.
n

A positive integer specifying the number of colours to generate.

Value

A vector of colours generated based on the specified base colour and number of colours.

Examples

# generate 10 colours for base colour "green"
.gen_colours("green", 10)
# generate 7 colours for base colour "orange"
.gen_colours("orange", 7)

Calculate the Level Frequency Score (LFS)

Description

This function calculates the Level Frequency Score (LFS) for a given EQ-5D state and a specified version of EQ-5D. If at least one domain contains a missing entry, the whole LFS is set to be NA.

Usage

.get_lfs(s, eq5d_version)

Arguments

s

A character vector representing the EQ-5D state, e.g. 11123.
eq5d_version

A character string specifying the version of EQ-5D, i.e. 3L or 5L.

Value

A character vector representing the calculated LFS.

Examples

.get_lfs("333", "3L") # returns 003
.get_lfs("333", "5L") # returns 00300
.get_lfs("12345", "5L") # returns 11111

Replace NULL names with default values

Description

This function takes in a list of parameters, which would be column names of the input data frame, and checks if they are null. Any nulls are replaced with default values, and the updated list of parameters is returned.

Usage

.get_names(df = NULL, ...)

Arguments

df

a data frame; only used/supplied if levels_fu needs to be defined
...

a list of parameters consisting of any/all of 'names_eq5d', 'name_fu', 'levels_fu', 'eq5d_version', and 'name_vas'.

Value

a list of parameters with null entries replaced with default values.

Examples

.get_names(names_eq5d = c("mo", "sc", "ua", "pd", "ad"))
.get_names(names_eq5d = NULL, eq5d_version = NULL, name_vas = NULL)

Get the mode of a vector.

Description

This function calculates the mode of a numeric or character vector. If there are multiple modes, the first one is returned. The code is taken from an R help page.

Usage

.getmode(v)

Arguments

v

A numeric or character vector.

Value

The mode of 'v'.

Examples

.getmode(c(1, 2, 3, 3))
.getmode(c("a", "b", "b", "c"))

Modify ggplot2 theme

Description

Modify ggplot2 theme

Usage

.modify_ggplot_theme(p)

Arguments

p

ggplot2 plot

Value

ggplot2 plot with modified theme

Wrapper to determine Paretian Classification of Health Change

Description

This internal function determines Paretian Classification of Health Change (PCHC) for each combination of the variables specified in the 'group_by' argument. It is used in the code for eq5d_profile_pchc_table, eq5d_profile_pchc_with_no_problems_table, eq5d_profile_dimension_change_table, and the eq5d_profile_*_by_group_plot functions. An EQ-5D health state is deemed to be 'better' than another if it is better on at least one dimension and is no worse on any other dimension. An EQ-5D health state is deemed to be 'worse' than another if it is worse in at least one dimension and is no better in any other dimension.

Usage

.pchc(df, level_fu_1, add_noprobs = FALSE)

Arguments

df

A data frame with EQ-5D states and follow-up variable. The dataset is assumed to be have been ordered correctly.
level_fu_1

Value of the first (i.e. earliest) follow-up. Would normally be defined as levels_fu[1].
add_noprobs

Logical value indicating whether to include a separate classification for those without problems (default is FALSE)

Value

A data frame with PCHC value for each combination of the grouping variables. If 'add_noprobs' is TRUE, a separate classification for those without problems is also included.

Examples

df <- data.frame(id = c(1, 1, 2, 2),
                 fu = c(1, 2, 1, 2),
                 mo = c(1, 1, 1, 1),
                 sc = c(1, 1, 5, 1),
                 ua = c(1, 1, 4, 3),
                 pd = c(1, 1, 1, 3),
                 ad = c(1, 1, 1, 1))
.pchc(df, level_fu_1 = 1, add_noprobs = TRUE)

Wrapper to generate Paretian Classification of Health Change plot by dimension

Description

This internal function plots Paretian Classification of Health Change (PCHC) by dimension. The input is a data frame containing the information to plot, and the plot will contain bars representing the proportion of the total data that falls into each dimension, stacked by covariate. The wrapper is used in Figures 2.2-2.4.

Usage

.pchc_plot_by_dim(plot_data, ylab, title, cols, text_rotate = FALSE)

Arguments

plot_data

A data frame containing information to plot, with columns for name (the dimensions to plot), p (the proportion of the total data falling into each dimension), and fu (the follow-up).
ylab

The label for the y-axis.
title

The plot title.
cols

A vector of colors to use for the bars.
text_rotate

A logical indicating whether to rotate the text labels for the bars.

Value

A ggplot object containing the PCHC plot.

Examples

df <- data.frame(
  name = rep(c("Dim1", "Dim2"), each = 2),
  p = c(0.6, 0.4, 0.7, 0.3),
  groupvar = rep(c("Group A", "Group B"), 2)
)
colors <- c("Group A" = "#1b9e77", "Group B" = "#d95f02")
.pchc_plot_by_dim(df, ylab = "Proportion", title = "Example Plot", cols = colors)

.pchctab: Changes in health according to the PCHC (Paretian Classification of Health Change)

Description

.pchctab: Changes in health according to the PCHC (Paretian Classification of Health Change)

Usage

.pchctab(
  df,
  name_id,
  name_groupvar,
  names_eq5d = NULL,
  name_fu = NULL,
  levels_fu = NULL,
  add_noprobs = FALSE
)

Arguments

df

Data frame with the EQ-5D, grouping, id and follow-up columns
name_id

Character string for the patient id column
name_groupvar

Character string for the grouping column
names_eq5d

Character vector of column names for the EQ-5D dimensions
name_fu

Character string for the follow-up column
levels_fu

Character vector containing the order of the values in the follow-up column. If NULL (default value), the levels will be ordered in the order of appearance in df.
add_noprobs

if set to TRUE, level corresponding to "no problems" will be added to the table

Value

Summary data frame

Examples

.pchctab(df = example_data,
  name_id = "id",
  name_groupvar = "procedure",
  name_fu = "time",
  levels_fu = c('Pre-op', 'Post-op')
)

Data checking/preparation: EQ-5D variables

Description

This function prepares a data frame for analysis by extracting, processing, and adding columns for EQ-5D variables, including state, LSS (Level Sum Score), LFS (Level Frequency Score) and utility.

Usage

.prep_eq5d(
  df,
  names,
  add_state = FALSE,
  add_lss = FALSE,
  add_lfs = FALSE,
  add_utility = FALSE,
  eq5d_version = NULL,
  country = NULL
)

Arguments

df

a data frame of EQ-5D scores
names

character vector of length 5 with names of EQ-5D variables in the data frame. The variables should be in an integer format.
add_state

logical indicating whether the EQ-5D state should be added
add_lss

logical indicating whether the LSS (Level Sum Score) should be added
add_lfs

logical indicating whether the LFS (Level Frequency Score) should be added
add_utility

logical indicating whether the utility should be added
eq5d_version

character indicating the version of the EQ-5D questionnaire to use (either "3L" or "5L")
country

character indicating the country to retrieve the quality of life score for

Value

a modified data frame with EQ-5D domain columns renamed to default names, and, if necessary, with added columns for state, LSS, LFS, and/or utility. If any of the checks fail (e.g. EQ-5D columns are not in an integer format), an error message is displayed and the function is stopping.

Examples

set.seed(1234)
df <- data.frame(mo = sample(1:5, 3), sc = sample(1:5, 3), 
  ua = sample(1:5, 3), pd = sample(1:5, 3), ad = sample(1:5, 3))
.prep_eq5d(df, names = c("mo", "sc", "ua", "pd", "ad"), 
  add_state = TRUE, add_lss = TRUE)
.prep_eq5d(df, names = c("mo", "sc", "ua", "pd", "ad"),
  add_state = TRUE, add_lss = TRUE, add_lfs = TRUE, add_utility = TRUE,
  eq5d_version = "5L", country = "ES")

Data checking/preparation: follow-up variable

Description

This function prepares the follow-up (FU) variable for analysis by giving it a default name ('fu') and factorising

Usage

.prep_fu(df, name = NULL, levels = NULL)

Arguments

df

A data frame.
name

Column name in the data frame that contains follow-up information.
levels

Levels to factorise the FU variable into.

Value

A data frame with the follow-up variable renamed as "fu" and factorised.

Examples

df <- data.frame(id = c(1, 1, 2, 2),
  visit = c("baseline", "follow-up", "baseline", "follow-up"))
.prep_fu(df = df, name = "visit", levels = c("baseline", "follow-up"))

Data checking/preparation: VAS variable

Description

The function prepares the data for VAS (Visual Analogue Scale) analyses.

Usage

.prep_vas(df, name)

Arguments

df

A data frame.
name

Column name in the data frame that holds the VAS score. The column can only contain integers or NAs

Value

A modified data frame with the VAS score renamed to "vas". If any checks fail (e.g. column is not numeric), an error message is displayed and the function is stopping.

Examples

df <- data.frame(vas_score = c(20, 50, 80, NA, 100))
.prep_vas(df = df, name = "vas_score")
df <- data.frame(vas_score = c(20.5, 50, 80, NA, 100))
.prep_vas(df = df, name = "vas_score")

.pstate3t5

Description

Takes a N x 25 matrix with probabilities per level/dimension, and creates an N * 3125 matrix with probabilities per state

Usage

.pstate3t5(PPP)

Arguments

PPP

N x 25 matrix with probabilities per level/dimension created by EQrxwprobs

Value

An N * 3125 matrix with probabilities per state

.pstate5t3

Description

Takes a 15 x 5 matrix with probabilities per level/dimension, and creates an 3125x243 matrix with probabilities per state

Usage

.pstate5t3(probs = .EQxwprob)

Arguments

probs

15 x 5 matrix with probabilities per level/dimension, typically saved in .EQxwprob

Value

An 3125x243 matrix with probabilities per state

Wrapper to summarise a continuous variable by follow-up (FU)

Description

This function summarizes a continuous variable for each follow-up (FU) and calculates various statistics such as mean, standard deviation, median, mode, kurtosis, skewness, minimum, maximum, range, and number of observations. It also reports the total sample size and the number (and proportion) of missing values for each FU. The input 'df' must contain an ordered FU variable and the continuous variable of interest. The name of the continuous variable must be specified using 'name_v'. The wrapper is used in Table 3.1 (for VAS) or Table 4.2 (for EQ-5D utility)

Usage

.summary_cts_by_fu(df, name_v)

Arguments

df

A data frame containing the FU and continuous variable of interest. The dataset must contain an ordered 'fu' variable.
name_v

A character string with the name of the continuous variable in 'df' to be summarised.

Value

Data frame with one row for each statistic and one column for each FU.

Examples

df <- data.frame(fu = c(1,1,2,2,3,3), 
                 vas = c(7,8,9,NA,7,6))
.summary_cts_by_fu(df, name_v = "vas")

Wrapper to calculate summary mean with 95% confidence interval

Description

This internal function calculates summary mean and 95% confidence interval of the utility variable, which can also be grouped. The function is used in Figures 4.2-4.4.

Usage

.summary_mean_ci(df, group_by)

Arguments

df

A data frame containing a 'utility' column.
group_by

A character vector of column names to group by.

Value

A data frame with the mean, lower bound, and upper bound of the 95

Examples

df <- data.frame(group = c("A", "A", "B", "B"), 
                 utility = c(0.5, 0.7, 0.8, 0.9))
.summary_mean_ci(df, group_by = "group")

Wrapper for the repetitive code in function_table_2_1. Data frame summary

Description

This internal function summarises a data frame by grouping it based on the variables specified in the 'group_by' argument and calculates the frequency of each group. The output is used in Table 2.1

Usage

.summary_table_2_1(df, group_by)

Arguments

df

A data frame
group_by

A character vector of variables in ‘df' to group by. Should contain ’eq5d' and 'fu'.

Value

A summarised data frame with groups defined by 'eq5d' and 'fu' variables, the count of observations in each group, and the frequency of each group.

Examples

set.seed(1234)
df <- data.frame(eq5d = rep(rnorm(5), 2),
                 fu = rep(c(1, 0, 1, 0, 1), 2))
.summary_table_2_1(df, c("eq5d", "fu"))

Summary wrapper for Table 4.3

Description

This internal function creates a summary of the data frame for Table 4.3. It groups the data by the variables specified in 'group_by' and calculates various summary statistics.

Usage

.summary_table_4_3(df, group_by)

Arguments

df

A data frame.
group_by

A character vector of names of variables by which to group the data.

Value

A data frame with the summary statistics.

Examples

df <- data.frame(group = c("A", "A", "B", "B"), 
                 utility = c(0.5, 0.7, 0.8, 0.9))
.summary_table_4_3(df, group_by = "group")

Summary wrapper for Table 4.4

Description

This internal function creates a summary of the data frame for Table 4.4. It groups the data by the variables specified in 'group_by' and calculates various summary statistics.

Usage

.summary_table_4_4(df, group_by)

Arguments

df

A data frame.
group_by

A character vector of names of variables by which to group the data.

Value

A data frame with the summary statistics.

Examples

df <- data.frame(group = c("A", "A", "B", "B"), 
                 utility = c(0.5, 0.7, 0.8, 0.9))
.summary_table_4_4(df, group_by = "group")

eq5d

Description

Get EQ-5D index values for the -3L, -5L, crosswalk (-3L value set applied to -5L health states), reverse crosswealk (-5L value set applied to -3L health states), and -Y-3L

Usage

eq5d(
  x,
  country = NULL,
  version = "5L",
  dim.names = c("mo", "sc", "ua", "pd", "ad")
)

Arguments

x

A vector of 5-digit EQ-5D-3L state indexes or a matrix/data.frame with columns corresponding to EQ-5D state dimensions
country

String vector indicating country names or ISO3166 Alpha 2 / 3 country codes.
version

String indicating which version to use. Options are '5L' (default), '3L', 'xw', 'xwr', and 'Y3L'.
dim.names

A vector of dimension names to identify dimension columns.

Value

A vector of values or data.frame with one column for each value set requested.

Examples

# US -3L value set
eq5d(c(11111, 12321, 32123, 33333), 'US', '3L') 
# Danish and US -5L value sets applied to -3L descriptives, i.e. reverse crosswalk
eq5d(make_all_EQ_states('3L'), c('DK', 'US'), 'XWR') 
# US -5L value set
eq5d(c(11111, 12321, 32153, 55555), 'US', '5L')

eq5d_profile_better_dimensions_by_group_plot: Percentage of Respondents Who Improved in Each EQ-5D Dimension, by Group This function calculates how many respondents improved in each dimension between two time points and summarizes the results for each group. The, it prodcuces a dimension-focused chart illustrating improvement percentages by dimension.

Description

eq5d_profile_better_dimensions_by_group_plot: Percentage of Respondents Who Improved in Each EQ-5D Dimension, by Group This function calculates how many respondents improved in each dimension between two time points and summarizes the results for each group. The, it prodcuces a dimension-focused chart illustrating improvement percentages by dimension.

Usage

eq5d_profile_better_dimensions_by_group_plot(
  df,
  name_id,
  name_groupvar = NULL,
  names_eq5d = NULL,
  name_fu = NULL,
  levels_fu = NULL
)

Arguments

df

Data frame containing EQ-5D columns, a grouping variable, an ID column, and a follow-up column
name_id

Character string for the patient ID column
name_groupvar

Character string for the grouping column (e.g. procedure). If NULL (default), the analysis is performed on the full population.
names_eq5d

Character vector of EQ-5D dimension names
name_fu

Character string for the follow-up column
levels_fu

Character vector of length 2, specifying the order of the follow-up levels (e.g. c("Pre-op","Post-op"))

Value

A list containing:

plot_data

A data frame of improvements by group and dimension
p

A ggplot2 object produced by '.pchc_plot_by_dim()'

Examples

result <- eq5d_profile_better_dimensions_by_group_plot(
  df = example_data,
  name_id = "id",
  name_groupvar = "procedure",
  names_eq5d = c("mo", "sc", "ua", "pd", "ad"),
  name_fu = "time",
  levels_fu = c("Pre-op","Post-op")
)
result$p
result$plot_data

eq5d_profile_change_summary: Frequency of levels by dimensions, by follow-up

Description

eq5d_profile_change_summary: Frequency of levels by dimensions, by follow-up

Usage

eq5d_profile_change_summary(
  df,
  names_eq5d = NULL,
  name_fu = NULL,
  levels_fu = NULL,
  eq5d_version = NULL
)

Arguments

df

Data frame with the EQ-5D and follow-up columns
names_eq5d

Character vector of column names for the EQ-5D dimensions
name_fu

Character string for the follow-up column. If NULL, the function will check if there is a column named "follow-up" or "fu", in which case the first of those will be used.
levels_fu

Character vector containing the order of the values in the follow-up column. If NULL (default value), the levels will be ordered in the order of appearance in df.
eq5d_version

Version of the EQ-5D instrument

Value

Summary data frame.

Examples

eq5d_profile_change_summary(
  df = example_data,
  names_eq5d = c("mo", "sc", "ua", "pd", "ad"),
  name_fu = "time",
  levels_fu = c("Pre-op" , "Post-op"),
  eq5d_version = "3L"
)

eq5d_profile_density_curve: Generate a Health State Density Curve (HSDC) for EQ-5D Data

Description

This function calculates and plots the Health State Density Curve (HSDC) for a given EQ-5D dataset. It concatenates dimension values to form health state profiles, filters out invalid states based on the specified EQ-5D version, then computes the cumulative distribution of profiles (profiles vs. observations). A diagonal reference line indicates a perfectly even distribution. The function also calculates the Health State Density Index (HSDI), representing how sharply the observed distribution deviates from the diagonal.

Usage

eq5d_profile_density_curve(df, names_eq5d, eq5d_version)

Arguments

df

Data frame with the EQ-5D columns
names_eq5d

Character vector of column names for the EQ-5D dimensions
eq5d_version

Version of the EQ-5D instrument

Value

A list containing:

plot_data

A data frame with the cumulative distribution of profiles
p

A ggplot2 object showing the Health State Density Index

Examples

figure <- eq5d_profile_density_curve(
            df = example_data, 
            names_eq5d = c("mo", "sc", "ua", "pd", "ad"), 
            eq5d_version = "3L"
          )
figure$plot_data
figure$p

eq5d_profile_dimension_change_table: Changes in levels in each dimension, percentages of total and of type of change

Description

eq5d_profile_dimension_change_table: Changes in levels in each dimension, percentages of total and of type of change

Usage

eq5d_profile_dimension_change_table(
  df,
  name_id,
  names_eq5d = NULL,
  name_fu = NULL,
  levels_fu = NULL
)

Arguments

df

Data frame with the EQ-5D, id and follow-up columns
name_id

Character string for the patient id column
names_eq5d

Character vector of column names for the EQ-5D dimensions
name_fu

Character string for the follow-up column
levels_fu

Character vector containing the order of the values in the follow-up column. If NULL (default value), the levels will be ordered in the order of appearance in df.

Value

Summary data frame

Examples

eq5d_profile_dimension_change_table(
  df = example_data,
  name_id = "id",
  names_eq5d = c("mo", "sc", "ua", "pd", "ad"),
  name_fu = "time",
  levels_fu = c("Pre-op" , "Post-op")
)

eq5d_profile_health_profile_grid: Health Profile Grid (HPG) for Two Time Points

Description

This function creates a Health Profile Grid (HPG) for EQ-5D data, plotting each individual's change in health states (ranked from best to worst) between two time points. A diagonal reference line indicates no change; points above the line reflect improvement, and points below indicate deterioration.

Usage

eq5d_profile_health_profile_grid(
  df,
  names_eq5d,
  name_fu,
  levels_fu = NULL,
  name_id,
  eq5d_version,
  country
)

Arguments

df

A data frame containing EQ-5D columns, a grouping variable, an ID column, and a follow-up column
names_eq5d

A character vector of EQ-5D dimension names
name_fu

A character string for the follow-up column
levels_fu

A character vector of length 2, specifying the order of the follow-up levels (e.g., c("Pre-op","Post-op"))
name_id

A character string for the patient ID column
eq5d_version

Version of the EQ-5D instrument
country

A character string representing the name of the country.

Value

A list with components:

plot_data

The plot data with ranks and classification.
p

A ggplot2 object displaying the HPG scatter plot.

Examples

tmp <- eq5d_profile_health_profile_grid(
           df = example_data, 
           names_eq5d = c("mo", "sc", "ua", "pd", "ad"), 
           name_fu = "time", 
           levels_fu = c("Pre-op", "Post-op"), 
           name_id = "id", 
           eq5d_version = "3L", 
           country = "UK"
       )

eq5d_profile_level_summary: Frequency of levels by dimensions, cross-sectional

Description

eq5d_profile_level_summary: Frequency of levels by dimensions, cross-sectional

Usage

eq5d_profile_level_summary(df, names_eq5d = NULL, eq5d_version = NULL)

Arguments

df

Data frame with the EQ-5D and follow-up columns
names_eq5d

Character vector of column names for the EQ-5D dimensions
eq5d_version

Version of the EQ-5D instrument

Value

Summary data frame.

Examples

eq5d_profile_level_summary(
 df = example_data[example_data$time == "Pre-op",],
 names_eq5d = c("mo", "sc", "ua", "pd", "ad"),
 eq5d_version = "3L"
)

eq5d_profile_level_summary_by_group: Frequency of levels by dimensions, separated by category

Description

eq5d_profile_level_summary_by_group: Frequency of levels by dimensions, separated by category

Usage

eq5d_profile_level_summary_by_group(
  df,
  names_eq5d = NULL,
  name_cat = NULL,
  levels_cat = NULL,
  eq5d_version = NULL
)

Arguments

df

Data frame with the EQ-5D and follow-up columns
names_eq5d

Character vector of column names for the EQ-5D dimensions
name_cat

Character string for the category column. If NULL, no grouping is used, and the table reports for the total population, i.e. equal to table 1.1.1.
levels_cat

Character vector containing the order of the values in the category column, if the wish is to have these presented in a particular order. If NULL (default value), unless the variable is a factor, the levels will be ordered in the order of appearance in df.
eq5d_version

Version of the EQ-5D instrument

Value

Summary data frame.

Examples

eq5d_profile_level_summary_by_group(
 df = example_data[example_data$time == "Pre-op",],
 names_eq5d = c("mo", "sc", "ua", "pd", "ad"),
 name_cat = "procedure",
 levels_cat = c("Hip Replacement", "Knee Replacement"),
 eq5d_version = "3L"
)

eq5d_profile_lfs_distribution: Distribution of the EQ-5D states by LFS (Level Frequency Score)

Description

eq5d_profile_lfs_distribution: Distribution of the EQ-5D states by LFS (Level Frequency Score)

Usage

eq5d_profile_lfs_distribution(df, names_eq5d = NULL, eq5d_version = NULL)

Arguments

df

Data frame with the EQ-5D columns
names_eq5d

Character vector of column names for the EQ-5D dimensions
eq5d_version

Version of the EQ-5D instrument

Value

Summary data frame

Examples

eq5d_profile_lfs_distribution(
  example_data, 
  names_eq5d = c("mo", "sc", "ua", "pd", "ad"), 
  eq5d_version = "3L"
)

eq5d_profile_lfs_mean_utility: Number of observations in the LFS (Level Frequency Score) according to the EQ-5D values

Description

eq5d_profile_lfs_mean_utility: Number of observations in the LFS (Level Frequency Score) according to the EQ-5D values

Usage

eq5d_profile_lfs_mean_utility(
  df,
  names_eq5d = NULL,
  eq5d_version = NULL,
  country
)

Arguments

df

Data frame with the EQ-5D columns
names_eq5d

Character vector of column names for the EQ-5D dimensions
eq5d_version

Version of the EQ-5D instrument
country

A character string representing the name of the country. This could be in a 2-letter format, full name or short name, as specified in the country_codes datasets.

Value

Summary data frame

Examples

eq5d_profile_lfs_mean_utility(
  example_data, 
  names_eq5d = c("mo", "sc", "ua", "pd", "ad"), 
  eq5d_version = "3L",
  country = "UK"
)

eq5d_profile_lfs_utility_plot: EQ-5D values plotted against LFS

Description

eq5d_profile_lfs_utility_plot: EQ-5D values plotted against LFS

Usage

eq5d_profile_lfs_utility_plot(
  df,
  names_eq5d = NULL,
  eq5d_version = NULL,
  country
)

Arguments

df

Data frame with the EQ-5D columns
names_eq5d

Character vector of column names for the EQ-5D dimensions
eq5d_version

Version of the EQ-5D instrument
country

A character string representing the name of the country. This could be in a 2-letter format, full name or short name, as specified in the country_codes datasets.

Value

Summary plot and data used for plotting

Examples

tmp <- eq5d_profile_lfs_utility_plot(
 example_data, 
 names_eq5d = c("mo", "sc", "ua", "pd", "ad"), 
 eq5d_version = "3L",
 country = "UK"
)
tmp$p
tmp$plot_data

eq5d_profile_lfs_utility_summary: Summary statistics of EQ-5D values by LFS (Level Frequency Score)

Description

eq5d_profile_lfs_utility_summary: Summary statistics of EQ-5D values by LFS (Level Frequency Score)

Usage

eq5d_profile_lfs_utility_summary(
  df,
  names_eq5d = NULL,
  eq5d_version = NULL,
  country
)

Arguments

df

Data frame with the EQ-5D columns
names_eq5d

Character vector of column names for the EQ-5D dimensions
eq5d_version

Version of the EQ-5D instrument
country

A character string representing the name of the country. This could be in a 2-letter format, full name or short name, as specified in the country_codes datasets.

Value

Summary data frame

Examples

eq5d_profile_lfs_utility_summary(
  example_data, 
  names_eq5d = c("mo", "sc", "ua", "pd", "ad"), 
  eq5d_version = "3L",
  country = "UK"
)

eq5d_profile_lss_utility_plot: EQ-5D values plotted against LSS

Description

eq5d_profile_lss_utility_plot: EQ-5D values plotted against LSS

Usage

eq5d_profile_lss_utility_plot(
  df,
  names_eq5d = NULL,
  eq5d_version = NULL,
  country
)

Arguments

df

Data frame with the EQ-5D columns
names_eq5d

Character vector of column names for the EQ-5D dimensions
eq5d_version

Version of the EQ-5D instrument
country

A character string representing the name of the country. This could be in a 2-letter format, full name or short name, as specified in the country_codes datasets.

Value

Summary plot and data used for plotting

Examples

df <- data.frame(make_all_EQ_states(version = "5L"))
tmp <- eq5d_profile_lss_utility_plot(
 df, 
 names_eq5d = c("mo", "sc", "ua", "pd", "ad"), 
 eq5d_version = "5L", 
 country = "US"
)
tmp$p
tmp$plot_data

eq5d_profile_lss_utility_summary: Summary statistics for the EQ-5D values by all the different LSSs (Level Sum Scores)

Description

eq5d_profile_lss_utility_summary: Summary statistics for the EQ-5D values by all the different LSSs (Level Sum Scores)

Usage

eq5d_profile_lss_utility_summary(
  df,
  names_eq5d = NULL,
  eq5d_version = NULL,
  country
)

Arguments

df

Data frame with the EQ-5D columns
names_eq5d

Character vector of column names for the EQ-5D dimensions
eq5d_version

Version of the EQ-5D instrument
country

A character string representing the name of the country. This could be in a 2-letter format, full name or short name, as specified in the country_codes datasets.

Value

Summary data frame

Examples

df <- data.frame(make_all_EQ_states(version = "5L"))
eq5d_profile_lss_utility_summary(
  df, 
  names_eq5d = c("mo", "sc", "ua", "pd", "ad"), 
  eq5d_version = "3L", 
  country = "US"
)

eq5d_profile_mixed_dimensions_by_group_plot: Percentage of Respondents Who Had a Mixed Change Overall, by Dimension Improved or Worsened, Grouped by Procedure (or Other Grouping)

Description

This function focuses on patients classified as having "Mixed change" overall (i.e., some dimensions improved, others worsened). It then examines which dimensions improved vs. worsened for each subject. Results are summarized by a grouping variable (e.g., procedure) and time points. The final output is a table plus a ggplot object.

Usage

eq5d_profile_mixed_dimensions_by_group_plot(
  df,
  name_id,
  name_groupvar = NULL,
  names_eq5d = NULL,
  name_fu = NULL,
  levels_fu = NULL
)

Arguments

df

Data frame containing columns for EQ-5D dimensions, a grouping variable, a patient ID, and a follow-up variable
name_id

Character string indicating the patient ID column
name_groupvar

Character string for the grouping column (e.g. "procedure"). If NULL (default), the analysis is performed on the full population.
names_eq5d

Character vector naming the EQ-5D dimensions (e.g. c("mo","sc","ua","pd","ad"))
name_fu

Character string for the follow-up column (e.g. "time")
levels_fu

Character vector of length 2 specifying the time order (e.g. c("Pre-op","Post-op"))

Value

A list with two elements:

plot_data

A wide-format data frame of dimension-specific improvements/worsenings for "Mixed change"
p

A ggplot2 object showing a dimension-level bar chart from .pchc_plot_by_dim

Examples

result <- eq5d_profile_mixed_dimensions_by_group_plot(
  df = example_data,
  name_id = "id",
  name_groupvar = "procedure",
  names_eq5d = c("mo","sc","ua","pd","ad"),
  name_fu = "time",
  levels_fu = c("Pre-op","Post-op")
)
result$plot_data
result$p

eq5d_profile_pchc_by_group_plot: Paretian Classification of Health Change (PCHC) by Group This function computes PCHC categories between two time points for each subject, stratifies them by a grouping variable, and produces a single bar chart with side-by-side bars showing the distribution of PCHC categories.

Description

eq5d_profile_pchc_by_group_plot: Paretian Classification of Health Change (PCHC) by Group This function computes PCHC categories between two time points for each subject, stratifies them by a grouping variable, and produces a single bar chart with side-by-side bars showing the distribution of PCHC categories.

Usage

eq5d_profile_pchc_by_group_plot(
  df,
  name_id,
  name_groupvar = NULL,
  names_eq5d = NULL,
  name_fu = NULL,
  levels_fu = NULL
)

Arguments

df

Data frame containing EQ-5D dimensions, a grouping variable, patient ID, and follow-up columns
name_id

Character string for the patient ID column
name_groupvar

Character string for the grouping column (e.g., procedure). If NULL (default), the analysis is performed on the full population.
names_eq5d

Character vector of column names for the EQ-5D dimensions
name_fu

Character string for the follow-up column
levels_fu

Character vector of length 2 indicating the order of follow-up time points (e.g., c("Pre-op", "Post-op"))

Value

A list with two elements:

plot_data

A tibble of PCHC percentages by group
p

A ggplot2 object showing a bar chart with side-by-side bars for each PCHC category

Examples

result <- eq5d_profile_pchc_by_group_plot(
  df = example_data,
  name_id = "id",
  name_groupvar = "procedure",
  names_eq5d = c("mo", "sc", "ua", "pd", "ad"),
  name_fu = "time",
  levels_fu = c("Pre-op", "Post-op")
)
result$p        # shows the plot
result$plot_data  # shows the summary table

eq5d_profile_pchc_table: Changes in health according to the PCHC (Paretian Classification of Health Change)

Description

eq5d_profile_pchc_table: Changes in health according to the PCHC (Paretian Classification of Health Change)

Usage

eq5d_profile_pchc_table(
  df,
  name_id,
  name_groupvar = NULL,
  names_eq5d = NULL,
  name_fu = NULL,
  levels_fu = NULL
)

Arguments

df

Data frame with the EQ-5D, grouping, id and follow-up columns
name_id

Character string for the patient id column
name_groupvar

Character string for the grouping column. If NULL (default), the analysis is performed on the full population.
names_eq5d

Character vector of column names for the EQ-5D dimensions
name_fu

Character string for the follow-up column
levels_fu

Character vector containing the order of the values in the follow-up column. If NULL (default value), the levels will be ordered in the order of appearance in df.

Value

Summary data frame

Examples

eq5d_profile_pchc_table(
  df = example_data,
  name_id = "id",
  name_groupvar = "procedure",
  names_eq5d = c("mo", "sc", "ua", "pd", "ad"),
  name_fu = "time",
  levels_fu = c("Pre-op" , "Post-op")
)

eq5d_profile_pchc_with_no_problems_table: Changes in health according to the PCHC, taking account of those with no problems

Description

eq5d_profile_pchc_with_no_problems_table: Changes in health according to the PCHC, taking account of those with no problems

Usage

eq5d_profile_pchc_with_no_problems_table(
  df,
  name_id,
  name_groupvar = NULL,
  names_eq5d = NULL,
  name_fu = NULL,
  levels_fu = NULL
)

Arguments

df

Data frame with the EQ-5D, grouping, id and follow-up columns
name_id

Character string for the patient id column
name_groupvar

Character string for the grouping column. If NULL (default), the analysis is performed on the full population.
names_eq5d

Character vector of column names for the EQ-5D dimensions
name_fu

Character string for the follow-up column
levels_fu

Character vector containing the order of the values in the follow-up column. If NULL (default value), the levels will be ordered in the order of appearance in df.

Value

Summary data frame

Examples

eq5d_profile_pchc_with_no_problems_table(
  df = example_data,
  name_id = "id",
  name_groupvar = "procedure",
  names_eq5d = c("mo", "sc", "ua", "pd", "ad"),
  name_fu = "time",
  levels_fu = c("Pre-op" , "Post-op")
)

eq5d_profile_top_states: Prevalence of the 10 most frequently observed self-reported health states

Description

eq5d_profile_top_states: Prevalence of the 10 most frequently observed self-reported health states

Usage

eq5d_profile_top_states(df, names_eq5d = NULL, eq5d_version = NULL, n = 10)

Arguments

df

Data frame with the EQ-5D columns
names_eq5d

Character vector of column names for the EQ-5D dimensions
eq5d_version

Version of the EQ-5D instrument
n

Number of most frequently observed states to display (default 10)

Value

Summary data frame

Examples

eq5d_profile_top_states(
  df = example_data[example_data$time == "Pre-op",],
  names_eq5d = c("mo", "sc", "ua", "pd", "ad"),
  eq5d_version = "3L",
  n = 10
)

This function identifies respondents with a "Worsen" PCHC state (i.e., overall health state got worse between levels_fu[1] and levels_fu[2]), checks dimension-specific changes (e.g., mo_diff < 0), and summarizes by a grouping variable (e.g., procedure) and time points. It returns a data table and a ggplot object.

Description

This function identifies respondents with a "Worsen" PCHC state (i.e., overall health state got worse between levels_fu[1] and levels_fu[2]), checks dimension-specific changes (e.g., mo_diff < 0), and summarizes by a grouping variable (e.g., procedure) and time points. It returns a data table and a ggplot object.

Usage

eq5d_profile_worse_dimensions_by_group_plot(
  df,
  name_id,
  name_groupvar = NULL,
  names_eq5d = NULL,
  name_fu = NULL,
  levels_fu = NULL
)

Arguments

df

A data frame containing EQ-5D columns, a grouping variable, an ID column, and a follow-up column
name_id

A character string for the patient ID column
name_groupvar

A character string for the grouping column (e.g., procedure). If NULL (default), the analysis is performed on the full population.
names_eq5d

A character vector of EQ-5D dimension names
name_fu

A character string for the follow-up column
levels_fu

A character vector of length 2, specifying the order of the follow-up levels (e.g., c("Pre-op","Post-op"))

Value

A list containing:

plot_data

A data frame of "Worsen" percentages by group and dimension
p

A ggplot2 object produced by '.pchc_plot_by_dim()'

Examples

result <- eq5d_profile_worse_dimensions_by_group_plot(
  df = example_data,
  name_id = "id",
  name_groupvar = "procedure",
  names_eq5d = c("mo", "sc", "ua", "pd", "ad"),
  name_fu = "time",
  levels_fu = c("Pre-op","Post-op")
)
result$p        # shows the plot
result$plot_data  # shows the summary table

eq5d_utility_by_group_plot: Mean EQ-5D values and 95% confidence intervals: all vs by groupvar

Description

eq5d_utility_by_group_plot: Mean EQ-5D values and 95% confidence intervals: all vs by groupvar

Usage

eq5d_utility_by_group_plot(
  df,
  names_eq5d = NULL,
  name_groupvar = NULL,
  eq5d_version = NULL,
  country
)

Arguments

df

Data frame with the EQ-5D and grouping columns
names_eq5d

Character vector of column names for the EQ-5D dimensions
name_groupvar

Character string for the grouping column. If NULL (default), the analysis is performed on the full population.
eq5d_version

Version of the EQ-5D instrument
country

A character string representing the name of the country. This could be in a 2-letter format, full name or short name, as specified in the country_codes datasets.

Value

Summary plot and data used for plotting

Examples

tmp <- eq5d_utility_by_group_plot(
 example_data,
 names_eq5d = c("mo", "sc", "ua", "pd", "ad"), 
 name_groupvar = "procedure",
 eq5d_version = "3L",
 country = "UK"
)
tmp$p
tmp$plot_data

eq5d_utility_change_by_group_plot: EQ-5D values: smoothed lines and confidence intervals by groupvar

Description

eq5d_utility_change_by_group_plot: EQ-5D values: smoothed lines and confidence intervals by groupvar

Usage

eq5d_utility_change_by_group_plot(
  df,
  names_eq5d = NULL,
  name_fu = NULL,
  levels_fu = NULL,
  name_groupvar = NULL,
  eq5d_version = NULL,
  country
)

Arguments

df

Data frame with the EQ-5D, follow-up and grouping columns
names_eq5d

Character vector of column names for the EQ-5D dimensions
name_fu

Character string for the follow-up column
levels_fu

Character vector containing the order of the values in the follow-up column. If NULL (default value), the levels will be ordered in the order of appearance in df.
name_groupvar

Character string for the grouping column. If NULL (default), the analysis is performed on the full population.
eq5d_version

Version of the EQ-5D instrument
country

A character string representing the name of the country. This could be in a 2-letter format, full name or short name, as specified in the country_codes datasets.

Value

Summary plot and data used for plotting

Examples

tmp <- eq5d_utility_change_by_group_plot(
 example_data,
 names_eq5d = c("mo", "sc", "ua", "pd", "ad"), 
 name_fu = "time",
 levels_fu = c('Pre-op', 'Post-op'),
 name_groupvar = "procedure",
 eq5d_version = "3L",
 country = "UK"
)
tmp$p
tmp$plot_data

eq5d_utility_distribution_plot: EQ-5D values: smoothed lines and confidence intervals by groupvar

Description

eq5d_utility_distribution_plot: EQ-5D values: smoothed lines and confidence intervals by groupvar

Usage

eq5d_utility_distribution_plot(
  df,
  names_eq5d = NULL,
  eq5d_version = NULL,
  country
)

Arguments

df

Data frame with the EQ-5D columns
names_eq5d

Character vector of column names for the EQ-5D dimensions
eq5d_version

Version of the EQ-5D instrument
country

A character string representing the name of the country. This could be in a 2-letter format, full name or short name, as specified in the country_codes datasets.

Value

Summary plot and data used for plotting

Examples

tmp <- eq5d_utility_distribution_plot(
 example_data,
 names_eq5d = c("mo", "sc", "ua", "pd", "ad"), 
 eq5d_version = "3L",
 country = "UK"
)
tmp$p
tmp$plot_data

eq5d_utility_norms_comparison:EQ-5D values: by age and groupvar

Description

eq5d_utility_norms_comparison:EQ-5D values: by age and groupvar

Usage

eq5d_utility_norms_comparison(
  df,
  names_eq5d = NULL,
  name_fu = NULL,
  levels_fu = NULL,
  name_groupvar = NULL,
  name_age,
  eq5d_version = NULL,
  country
)

Arguments

df

Data frame with the EQ-5D, age, follow-up and grouping columns
names_eq5d

Character vector of column names for the EQ-5D dimensions
name_fu

Character string for the follow-up column
levels_fu

Character vector containing the order of the values in the follow-up column. If NULL (default value), the levels will be ordered in the order of appearance in df.
name_groupvar

Character string for the grouping column. If NULL (default), the analysis is performed on the full population.
name_age

Character string for the age column
eq5d_version

Version of the EQ-5D instrument
country

A character string representing the name of the country. This could be in a 2-letter format, full name or short name, as specified in the country_codes datasets.

Value

Summary data frame

Examples

example_data$ageband <- factor(
  example_data$ageband,
  levels = c("20 to 29", "30 to 39", "40 to 49", "50 to 59", "60 to 69", "70 to 79", "80 to 89")
)
example_data <- example_data[example_data$gender %in% c("Male", "Female"),]
eq5d_utility_norms_comparison(
  example_data,
  names_eq5d = c("mo", "sc", "ua", "pd", "ad"),
  name_fu = "time",
  levels_fu = c('Pre-op', 'Post-op'),
  name_groupvar = "gender",
  name_age = "ageband",
  eq5d_version = "3L",
  country = "UK"
)

eq5d_utility_over_time_plot: EQ-5D values by timepoints: mean values and 95% confidence intervals

Description

eq5d_utility_over_time_plot: EQ-5D values by timepoints: mean values and 95% confidence intervals

Usage

eq5d_utility_over_time_plot(
  df,
  names_eq5d = NULL,
  name_fu = NULL,
  levels_fu = NULL,
  eq5d_version = NULL,
  country
)

Arguments

df

Data frame with the VAS columns
names_eq5d

Character vector of column names for the EQ-5D dimensions
name_fu

Character string for the follow-up column
levels_fu

Character vector containing the order of the values in the follow-up column. If NULL (default value), the levels will be ordered in the order of appearance in df.
eq5d_version

Version of the EQ-5D instrument
country

A character string representing the name of the country. This could be in a 2-letter format, full name or short name, as specified in the country_codes datasets.

Value

Summary plot and data used for plotting

Examples

tmp <- eq5d_utility_over_time_plot(
 example_data,
 names_eq5d = c("mo", "sc", "ua", "pd", "ad"), 
 name_fu = "time",
 levels_fu = c('Pre-op', 'Post-op'),
 eq5d_version = "3L",
 country = "UK"
)
tmp$p
tmp$plot_data

eq5d_utility_summary: EQ-5D values: by timepoints

Description

eq5d_utility_summary: EQ-5D values: by timepoints

Usage

eq5d_utility_summary(
  df,
  names_eq5d = NULL,
  name_fu = NULL,
  levels_fu = NULL,
  eq5d_version = NULL,
  country
)

Arguments

df

Data frame with the EQ-5D and follow-up columns
names_eq5d

Character vector of column names for the EQ-5D dimensions
name_fu

Character string for the follow-up column
levels_fu

Character vector containing the order of the values in the follow-up column. If NULL (default value), the levels will be ordered in the order of appearance in df.
eq5d_version

Version of the EQ-5D instrument
country

A character string representing the name of the country. This could be in a 2-letter format, full name or short name, as specified in the country_codes datasets.

Value

Summary data frame

Examples

eq5d_utility_summary(
  example_data,
  names_eq5d = c("mo", "sc", "ua", "pd", "ad"), 
  name_fu = "time",
  levels_fu = c('Pre-op', 'Post-op'),
  eq5d_version = "3L",
  country = "UK"
)

eq5d_utility_summary_by_group:EQ-5D values: by groupvar

Description

eq5d_utility_summary_by_group:EQ-5D values: by groupvar

Usage

eq5d_utility_summary_by_group(
  df,
  names_eq5d = NULL,
  name_groupvar = NULL,
  eq5d_version = NULL,
  country
)

Arguments

df

Data frame with the EQ-5D, follow-up and grouping columns
names_eq5d

Character vector of column names for the EQ-5D dimensions
name_groupvar

Character string for the grouping column. If NULL (default), the analysis is performed on the full population.
eq5d_version

Version of the EQ-5D instrument
country

A character string representing the name of the country.

Value

Summary data frame

Examples

eq5d_utility_summary_by_group(
  example_data,
  names_eq5d = c("mo", "sc", "ua", "pd", "ad"),
  name_groupvar = "procedure",
  eq5d_version = "3L",
  country = "UK"
)

eq5d_utility_vas_scatter_plot: EQ-5D values: smoothed lines and confidence intervals by groupvar

Description

eq5d_utility_vas_scatter_plot: EQ-5D values: smoothed lines and confidence intervals by groupvar

Usage

eq5d_utility_vas_scatter_plot(
  df,
  names_eq5d = NULL,
  name_vas = NULL,
  eq5d_version = NULL,
  country
)

Arguments

df

Data frame with the EQ-5D columns
names_eq5d

Character vector of column names for the EQ-5D dimensions
name_vas

Character string for the VAS column
eq5d_version

Version of the EQ-5D instrument
country

A character string representing the name of the country. This could be in a 2-letter format, full name or short name, as specified in the country_codes datasets.

Value

Summary plot and data used for plotting

Examples

tmp <- eq5d_utility_vas_scatter_plot(
   example_data,
   names_eq5d = c("mo", "sc", "ua", "pd", "ad"),
   name_vas = "vas",
   eq5d_version = "3L",
   country = "UK"
 )
tmp$p
tmp$plot_data

eq5d_vas_distribution_table: EQ VAS Scores frequency of mid-points

Description

eq5d_vas_distribution_table: EQ VAS Scores frequency of mid-points

Usage

eq5d_vas_distribution_table(df, name_vas = NULL, add_na_total = TRUE)

Arguments

df

Data frame with the VAS column
name_vas

Character string for the VAS column
add_na_total

Logical, whether to add summary of the missing, and across the Total, data

Value

Summary data frame

Examples

eq5d_vas_distribution_table(
  example_data,
  name_vas = 'vas', 
  add_na_total =  TRUE
  )

eq5d_vas_grouped_distribution_plot: Mid-point EQ VAS scores

Description

eq5d_vas_grouped_distribution_plot: Mid-point EQ VAS scores

Usage

eq5d_vas_grouped_distribution_plot(df, name_vas = NULL)

Arguments

df

Data frame with the VAS column
name_vas

Character string for the VAS column

Value

Summary plot and data used for plotting

Examples

tmp <- eq5d_vas_grouped_distribution_plot(example_data, name_vas = 'vas')
tmp$p
tmp$plot_data

eq5d_vas_histogram: EQ VAS scores

Description

eq5d_vas_histogram: EQ VAS scores

Usage

eq5d_vas_histogram(df, name_vas = NULL)

Arguments

df

Data frame with the VAS column
name_vas

Character string for the VAS column

Value

Summary plot and data used for plotting

Examples

tmp <- eq5d_vas_histogram(example_data, name_vas = 'vas')
tmp$p
tmp$plot_data

eq5d_vas_summary: EQ VAS Score by timepoints

Description

eq5d_vas_summary: EQ VAS Score by timepoints

Usage

eq5d_vas_summary(df, name_vas = NULL, name_fu = NULL, levels_fu = NULL)

Arguments

df

Data frame with the VAS and the follow-up columns
name_vas

Character string for the VAS column
name_fu

Character string for the follow-up column
levels_fu

Character vector containing the order of the values in the follow-up column.

Value

Summary data frame

Examples

eq5d_vas_summary(
  example_data,
  name_vas = 'vas', 
  name_fu = 'time', 
  levels_fu = c('Pre-op', 'Post-op')
)

eq5d3l

Description

Get EQ-5D-3L index values from individual responses to the five dimensions of the EQ-5D-3L.

Usage

eq5d3l(x, country = NULL, dim.names = c("mo", "sc", "ua", "pd", "ad"))

Arguments

x

A vector of 5-digit EQ-5D-3L state indexes, or a matrix/data.frame with columns corresponding to the EQ-5D-3L dimensions.
country

String vector indicating country names or ISO3166 Alpha 2 / 3 country codes.
dim.names

A character vector specifying the names of the EQ-5D-3L dimensions. Default is 'c("mo", "sc", "ua", "pd", "ad")'.

Value

A numeric vector of EQ-5D-3L values, or a data.frame with one column for each requested value set.

Examples

# Example 1: utility values from EQ-5D-3L profile codes
eq5d3l(c(11111, 12321, 32123, 33333), country = "US")

# Example 2: request multiple value sets
eq5d3l(make_all_EQ_states("3L"), country = c("DK", "CA"))

# Example 3: use a data.frame with dimension columns
df3l <- data.frame(
  mo = c(1, 2, 3),
  sc = c(1, 2, 2),
  ua = c(1, 3, 1),
  pd = c(2, 2, 3),
  ad = c(1, 1, 2)
)
eq5d3l(df3l, country = "US")

# Example 4: use custom dimension column names
df3l_named <- data.frame(
  mobility = c(1, 2, 3),
  self_care = c(1, 2, 2),
  usual_activities = c(1, 3, 1),
  pain_discomfort = c(2, 2, 3),
  anxiety_depression = c(1, 1, 2)
)
eq5d3l(
  df3l_named,
  country = "US",
  dim.names = c(
    "mobility", "self_care", "usual_activities",
    "pain_discomfort", "anxiety_depression"
  )
)

eq5d5l

Description

Get EQ-5D-5L index values from individual responses to the five dimensions of the EQ-5D-5L.

Usage

eq5d5l(x, country = NULL, dim.names = c("mo", "sc", "ua", "pd", "ad"))

Arguments

x

A vector of 5-digit EQ-5D-5L state indexes, or a matrix/data.frame with columns corresponding to the EQ-5D-5L dimensions.
country

String vector indicating country names or ISO3166 Alpha 2 / 3 country codes.
dim.names

A character vector specifying the names of the EQ-5D-5L dimensions. Default is 'c("mo", "sc", "ua", "pd", "ad")'.

Value

A numeric vector of EQ-5D-5L values, or a data.frame with one column for each requested value set.

Examples

# Example 1: utility values from EQ-5D-5L profile codes
eq5d5l(c(11111, 12321, 32423, 55555), country = "IT")

# Example 2: request multiple value sets
eq5d5l(make_all_EQ_states("5L"), country = c("ES", "DE"))

# Example 3: use a data.frame with dimension columns
df5l <- data.frame(
  mo = c(1, 2, 5),
  sc = c(1, 2, 4),
  ua = c(1, 3, 3),
  pd = c(2, 4, 2),
  ad = c(1, 5, 1)
)
eq5d5l(df5l, country = "ES")

# Example 4: use custom dimension column names from a real-world style dataset
df5l_named <- data.frame(
  mobility = c(1, 5, 3),
  self_care = c(2, 4, 2),
  usual_activities = c(3, 3, 1),
  pain_discomfort = c(4, 2, 2),
  anxiety_depression = c(5, 1, 3)
)
eq5d5l(
  df5l_named,
  country = "ES",
  dim.names = c(
    "mobility", "self_care", "usual_activities",
    "pain_discomfort", "anxiety_depression"
  )
)

eq5dy3l

Description

Get EQ-5D-Y-3L index values from individual responses to the five dimensions of the EQ-5D-Y-3L.

Usage

eq5dy3l(x, country = NULL, dim.names = c("mo", "sc", "ua", "pd", "ad"))

Arguments

x

A vector of 5-digit EQ-5D-Y-3L state indexes, or a matrix/data.frame with columns corresponding to the EQ-5D-Y-3L dimensions.
country

String vector indicating country names or ISO3166 Alpha 2 / 3 country codes.
dim.names

A character vector specifying the names of the EQ-5D-Y-3L dimensions. Default is 'c("mo", "sc", "ua", "pd", "ad")'.

Value

A numeric vector of EQ-5D-Y-3L values, or a data.frame with one column for each requested value set.

Examples

# Example 1: utility values from EQ-5D-Y-3L profile codes
eq5dy3l(x = c(11111, 12321, 33333), country = "SI")

# Example 2: request multiple value sets
eq5dy3l(make_all_EQ_states("3L"), country = c("ES", "DE"))

# Example 3: use a data.frame with dimension columns
dfy3l <- data.frame(
  mo = c(1, 2, 3),
  sc = c(1, 1, 2),
  ua = c(1, 2, 3),
  pd = c(2, 2, 3),
  ad = c(1, 3, 2)
)
eq5dy3l(dfy3l, country = "SI")

# Example 4: use custom dimension column names
dfy3l_named <- data.frame(
  mobility = c(1, 2, 3),
  self_care = c(1, 1, 2),
  usual_activities = c(1, 2, 3),
  pain_discomfort = c(2, 2, 3),
  anxiety_depression = c(1, 3, 2)
)
eq5dy3l(
  dfy3l_named,
  country = "SI",
  dim.names = c(
    "mobility", "self_care", "usual_activities",
    "pain_discomfort", "anxiety_depression"
  )
)

eqvs_add

Description

Add user-defined EQ-5D value set and corresponding crosswalk option.

Usage

eqvs_add(
  df,
  version = "5L",
  country = NULL,
  countryCode = NULL,
  VSCode = NULL,
  description = NULL,
  saveOption = 1,
  savePath = NULL
)

Arguments

df

A data.frame or file name pointing to csv file. The contents of the data.frame or csv file should be exactly two columns: state, containing a list of all 3125 (for 5L) or 243 (for 3L) EQ-5D health state vectors, and a column of corresponding utility values, with a suitable name.
version

Version of the EQ-5D instrument. Can take values 5L (default) or 3L.
country

Optional string. If not NULL, will be used as a country description for the user-defined value set.
countryCode

Optional string. If not NULL, will be used as the two-digit code for the value set. Must be different from any existing national value set code.
VSCode

Optional string. If not NULL, will be used as the three-digit code for the value set. Must be different from any existing national value set code.
description

Optional string. If not NULL, will be used as a descriptive text for the user-defined value set.
saveOption

Integer indicating how the cache data should be saved. 1: Do not save (default), 2: Save in package folder, 3: Save in another path.
savePath

A path where the cache data should be saved when 'saveOption' is 3. Please use 'eqvs_load' to load it in your next session.

Value

True/False, indicating success or error.

Examples

# make nonsense value set
new_df <- data.frame(state = make_all_EQ_indexes(), TEST = runif(3125))
# Add as value set for Fantasia
eqvs_add(
   new_df,
   version = "5L",
   country = 'Fantasia',
   countryCode = "MyCountry",
   VSCode = "FAN",
   saveOption = 1
)
eq5d5l(55555,country = "FAN")

eqvs_display

Description

Display available value sets, which can also be used as (reverse) crosswalks.

Usage

eqvs_display(version = "5L", return_df = FALSE)

Arguments

version

Version of the EQ-5D instrument. Can take values 5L (default), 3L or 3LY.
return_df

If set to TRUE, the function will return information on the names of the available value sets in a data.frame. Defaults to FALSE

Value

Default NULL, if return_df == TRUE, returns a data.frame with the displayed information.

Examples

# Display available value sets.
eqvs_display

eqvs_drop

Description

Drop user-defined EQ-5D value set to reverse crosswalk options.

Usage

eqvs_drop(country = NULL, version = "5L", saveOption = 1, savePath = NULL)

Arguments

country

Optional string. If NULL, a list of current user-defined value sets will be provided for selection. If set, and matching an existing user-defined value set, a prompt will be given as to whether the value set should be deleted.
version

Version of the EQ-5D instrument. Can take values 5L (default) or 3L.
saveOption

Integer indicating how the cache data should be saved. 1: Do not save (default), 2: Save in package folder, 3: Save in another path.
savePath

A path where the cache data should be saved when 'saveOption' is 3. Please use 'eqvs_load' to load it in your next session.

Value

True/False, indicating success or error.

Examples

# make nonsense value set
  new_df <- data.frame(state = make_all_EQ_indexes(), TEST = runif(3125))
  # Add as value set for Fantasia
  eqvs_add(
   new_df,
   version = "5L",
   country = 'Fantasia',
   countryCode = "MyCountry",
   VSCode = "FAN",
   saveOption = 1
  )
  # Test the new value set
  eq5d5l(55555,country = "FAN")
  # Drop value set for Fantasia
  eqvs_drop(country = 'FAN', saveOption = 1)

eqvs_load

Description

Load cache data from a specified path.

Usage

eqvs_load(loadPath)

Arguments

loadPath

The path from which to load the cache data.

Value

TRUE if loading is successful, FALSE otherwise.

eqxw

Description

Get crosswalk values

Usage

eqxw(x, country = NULL, dim.names = c("mo", "sc", "ua", "pd", "ad"))

Arguments

x

A vector of 5-digit EQ-5D-5L state indexes or a matrix/data.frame with columns corresponding to EQ-5D state dimensions
country

String vector indicating country names or ISO3166 Alpha 2 / 3 country codes.
dim.names

A vector of dimension names to identify dimension columns

Value

A vector of reverse crosswalk values or data.frame with one column per reverse crosswalk set requested.

Examples

eqxw(c(11111, 12521, 32123, 55555), 'US')
eqxw(make_all_EQ_states('5L'), c('DK', 'US'))

eqxw_UK

Description

Crosswalks EQ-5D-5L responses to EQ-5D-3L utilities using NICE's mapping.

Usage

eqxw_UK(x, age, male, dim.names = c("mo", "sc", "ua", "pd", "ad"), bwidth = 0)

Arguments

x

A vector of 5-digit EQ-5D-5L states (domain scores) or a summary score.
age

A numeric vector or column name (if 'x' is a data frame). Can be either: (1) a numeric age between 18 and 100, which will be automatically grouped into NICE-defined age bands (18-35, 35-45, 45-55, 55-65, +65), or (2) a factor/character/numeric vector already representing the NICE age bands with values 1-5 indicating age bands (18-35, 35-45, 45-55, 55-65, +65).
male

A numeric vector (1=male, 0=female) or column name indicating gender.
dim.names

A vector of dimension names for EQ-5D states (default: c("mo", "sc", "ua", "pd", "ad")).
bwidth

Numeric. Bandwidth for kernel smoothing when using summary scores.

Value

A vector or data frame with crosswalked EQ-5D-3L utilities.

Examples

eqxw_UK(c(11111, 12345, 32423, 55555), age = c(30, 40, 55, 70), male = c(1, 0, 1, 0))

eqxwr

Description

Get reverse crosswalk values

Usage

eqxwr(x, country = NULL, dim.names = c("mo", "sc", "ua", "pd", "ad"))

Arguments

x

A vector of 5-digit EQ-5D-3L state indexes or a matrix/data.frame with columns corresponding to EQ-5D state dimensions
country

String vector indicating country names or ISO3166 Alpha 2 / 3 country codes.
dim.names

A vector of dimension names to identify dimension columns

Value

A vector of reverse crosswalk values or data.frame with one column per reverse crosswalk set requested.

Examples

eqxwr(c(11111, 12321, 32123, 33333), 'US')
eqxwr(make_all_EQ_states('3L'), c('DK', 'US'))

example_data

Description

A dataset containing patient-level data in a long format.

Usage

data(example_data)

Format

A data frame with 10000 rows and 14 variables:

id

double Patient id

time

character Follow-up (Pre-op / Post-op)

mo

double EQ-5D-5L Mobility dimension

sc

double EQ-5D-5L Self-care dimension

ua

double EQ-5D-5L Usual activities dimension

pd

double EQ-5D-5L Pain / discomfort dimension

ad

double EQ-5D-5L Anxiety/depression dimension

vas

double Value of the VAS scale measurememnt

providercode

character Provider code

procedure

character Type of surgery

year

character Year of intervention

ageband

character Age in pre-defined ranges

gender

character Patient's gender (Female / Male)

make_all_EQ_indexes

Description

Make a vector containing all 5-digit EQ-5D indexes for -3L or -5L version.

Usage

make_all_EQ_indexes(
  version = "5L",
  dim.names = c("mo", "sc", "ua", "pd", "ad")
)

Arguments

version

Either "3L" or "5L", to signify whether 243 or 3125 states should be generated
dim.names

A vector of dimension names to be used as names for output columns.

Value

A vector with 5-digit state indexes for all 243 (-3L) or 3125 (-5L) EQ-5D health states

Examples

make_all_EQ_indexes('3L')

make_all_EQ_states

Description

Make a data.frame with all health states defined by dimensions

Usage

make_all_EQ_states(
  version = "5L",
  dim.names = c("mo", "sc", "ua", "pd", "ad"),
  append_index = FALSE
)

Arguments

version

Either "3L" or "5L", to signify whether 243 or 3125 states should be generated
dim.names

A vector of dimension names to be used as names for output columns.
append_index

Boolean to indicate whether a column of 5-digit EQ-5D health state indexes should be added to output.

Value

A data.frame with 5 columns and 243 (-3L) or 3125 (-5L) health states

Examples

make_all_EQ_states('3L')

EQ_dummies

Description

Make a data.frame of all EQ-5D dummies relevant for e.g. regression modeling.

Usage

make_dummies(
  df,
  version = "5L",
  dim.names = c("mo", "sc", "ua", "pd", "ad"),
  drop_level_1 = TRUE,
  add_intercept = FALSE,
  incremental = FALSE,
  prepend = NULL,
  append = NULL,
  return_df = TRUE
)

Arguments

df

data.frame containing EQ-5D health states.
version

Either "3L" or "5L", to signify EQ-5D instrument version
dim.names

A vector of dimension names to be used as names for output columns.
drop_level_1

If set to FALSE, dummies for level 1 will be included. Defaults to TRUE.
add_intercept

If set to TRUE, a column containing 1s will be appended. Defaults to FALSE.
incremental

If set to TRUE, incremental dummies will be produced (e.g. MO = 3 will give mo2 = 1, mo3 = 1). Defaults to FALSE.
prepend

Optional string to be prepended to column names.
append

Optional string to be appended to column names.
return_df

If set to TRUE, data.frame is returned, otherwise matrix. Defaults to TRUE.

Value

A data.frame of dummy variables

Examples

make_dummies(make_all_EQ_states('3L'), '3L')

make_dummies(df = make_all_EQ_states('3L'), 
             version =  '3L', 
             incremental = TRUE, 
             add_intercept = TRUE, 
             prepend = "d_")

Launch the eq5dsuite Shiny Application

Description

Opens an interactive Shiny application for uploading, processing, analysing, and exporting EQ-5D data using the eq5dsuite package.

Usage

run_app(...)

Arguments

...

Additional arguments passed to runApp, such as port or launch.browser.

Value

Called for its side effect of launching a Shiny application. Returns invisibly.

Examples

## Not run: 
  eq5dsuite::run_app()

## End(Not run)

toEQ5Ddims

Description

Generate dimension vectors based on state index

Usage

toEQ5Ddims(x, dim.names = c("mo", "sc", "ua", "pd", "ad"))

Arguments

x

A vector of 5-digit EQ-5D state indexes.
dim.names

A vector of dimension names to be used as names for output columns.

Value

A data.frame with 5 columns, one for each EQ-5D dimension, with names from dim.names argument.

Examples

toEQ5Ddims(c(12345, 54321, 12321))

Convert EQ-5D dimension scores to a five-digit profile index

Description

Convert EQ-5D dimension scores to a five-digit profile index

Usage

toEQ5Dindex(
  x,
  dim.names = c("mo", "sc", "ua", "pd", "ad"),
  na.rm = FALSE,
  quiet = FALSE
)

Arguments

x

A data.frame, matrix, or named numeric vector of EQ-5D dimension scores. Each dimension must contain integer values (typically 1–3 or 1–5).
dim.names

Character vector of length 5 giving the dimension names, in the conventional MO, SC, UA, PD, AD order.
na.rm

Logical. If FALSE (default), any NA in a row produces NA in the output. If TRUE, NA dimensions are treated as 0 — use with care, as this silently changes the index value.
quiet

Logical. Suppress informational messages about assumed column / name order. Default FALSE so existing scripts see the same messages; set TRUE inside pipelines.

Value

An integer vector with one element per row (data.frame/matrix input) or a single integer (vector input). Works inside dplyr::mutate() without rowwise().

Examples

# Named vector — scalar usage unchanged
toEQ5Dindex(c(mo=1, sc=2, ua=3, pd=1, ad=2))