suddengains
Sudden gains are large and stable improvements in an outcome variable
between consecutive measurements, for example during a psychological
intervention with multiple assessments (Tang and DeRubeis,
1999). The R package
suddengains
provides a set of tools to facilitate sudden gains
research. It identifies sudden gains or sudden losses while allowing to
apply adaptations of the standard criteria. It handles multiple gains by
creating two datasets, one structured by sudden gains and one by
participants. It also implements a function to specify which sudden
gains to choose in case of multiple gains (e.g. the earliest or largest
gain).
An interactive web application
shinygains
illustrates the main functions of this package and allows users to
explore and understand the impact of different methodological choices.
To learn more about the background of this package see our paper in PLOS ONE. We have also created an open Zotero group collecting all the literature looking at sudden gains in psychological therapies. Please let me know if I missed anything or join the group and add papers yourself.
Installation
You can install the released version of suddengains from CRAN with:
install.packages("suddengains")
And the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("milanwiedemann/suddengains")
Overview of the functions
The suddengains
package comes with a range of features which can be
categorised into:
- Functions to identify sudden gains:
select_cases()
: Select sample providing enough data to identify sudden gainsdefine_crit1_cutoff()
: Uses RCI formula to determine a cut-off value for criterion 1identify_sg()
: Identifies sudden gainsidentify_sl()
: Identifies sudden lossescheck_interval()
: Checks if a given interval is a sudden gain/loss
- Functions to create datasets for further analysis:
extract_values()
: Extracts values on a secondary measure around the sudden gain/losscreate_byperson()
: Creates a dataset with one row for each sudden gain/losscreate_bysg()
: Creates a dataset with one row for each person
- Helper functions to visualise and report sudden gains:
count_intervals()
: Count number of between-session intervals available to identify sudden gainsplot_sg()
: Creates plots of the average sudden gainplot_sg_trajectories()
: Creates plots of plots of individual case trajectoriesdescribe_sg()
: Shows descriptives for the sudden gains datasets
- Helper functions to export data sets to SPSS, Excel, Stata, and CSV:
write_bysg()
: Exports CSV, SPSS, Excel, or STATA files of the sudden gains data setswrite_byperson()
: Exports CSV, SPSS, Excel, or STATA files of the sudden gains data sets
A detailed illustration of all functions can be found in the vignette on CRAN. Note that the vignette is only available in R when you install the package from CRAN.
Examples
Below are some examples illustrating the suddengains package. More details can be found in the Vignette or in our PLOS ONE paper.
1. Functions to identify sudden gains
To identify sudden gains/losses you can use the identify_sg()
and
identify_sl()
functions. These functions return a data frame with
new variables indicating for each between-session interval whether a
sudden gain/loss was identified. For example the variable sg_2to3
holds information whether a sudden gains occurred from session two to
three, with two being the pregain and three being the postgain session.
Further functions to help with identifying sudden gains are listed
above.
identify_sg(data = sgdata,
sg_crit1_cutoff = 7,
sg_crit2_pct = 0.25,
sg_crit3 = TRUE,
id_var_name = "id",
sg_var_list = c("bdi_s1", "bdi_s2", "bdi_s3", "bdi_s4",
"bdi_s5", "bdi_s6", "bdi_s7", "bdi_s8",
"bdi_s9", "bdi_s10", "bdi_s11", "bdi_s12"),
identify_sg_1to2 = FALSE)
2. Functions to create datasets for further analysis
As participants may experience more than one gain, as in the present
example, and to allow for different subsequent analyses, the package
provides two options for output datasets: The create_bysg()
function creates a dataset structured with one row per sudden gain, and
the create_byperson()
function creates a dataset structured with
one row per person, indicating whether or not they experienced a sudden
gain. The create_bysg()
function is shown below. More functions to
help with creating datasets for further analyses are listed above.
# Create output dataset with one row per sudden gain
# and save as an object called "bysg" to use later
bysg <- create_bysg(data = sgdata,
sg_crit1_cutoff = 7,
id_var_name = "id",
tx_start_var_name = "bdi_s1",
tx_end_var_name = "bdi_s12",
sg_var_list = c("bdi_s1", "bdi_s2", "bdi_s3", "bdi_s4",
"bdi_s5", "bdi_s6", "bdi_s7", "bdi_s8",
"bdi_s9", "bdi_s10", "bdi_s11", "bdi_s12"),
sg_measure_name = "bdi",
identify = "sg")
#> First, second, and third sudden gains criteria were applied.
#> The critical value for the third criterion was adjusted for missingness.
#> Note: The vector specified in 'extract_var_list' must have the same number of repeated time points as the measure used to identify sudden gains.
3. Helper functions to visualise and report sudden gains
The plot_sg()
function plots the ‘average’ sudden gain, and can be
used to show changes around the sudden gain. The
plot_sg_trajectories()
can be used to visualise trajectories for a
selection of individual
cases.
# Create plot of average change in depression symptoms (BDI) around the gain
plot_sg(data = bysg,
id_var_name = "id",
tx_start_var_name = "bdi_s1",
tx_end_var_name = "bdi_s12",
sg_pre_post_var_list = c("sg_bdi_2n", "sg_bdi_1n", "sg_bdi_n",
"sg_bdi_n1", "sg_bdi_n2", "sg_bdi_n3"),
ylab = "BDI", xlab = "Session",
colour_single = "#239b89ff")
#> Warning: `fun.y` is deprecated. Use `fun` instead.
#> Warning: `fun.y` is deprecated. Use `fun` instead.
#> Warning: `fun.y` is deprecated. Use `fun` instead.
#> Warning: `fun.y` is deprecated. Use `fun` instead.
#> Warning: Removed 27 rows containing non-finite values (stat_summary).
#> Warning: Removed 27 rows containing non-finite values (stat_summary).
#> Warning: Removed 14 rows containing non-finite values (stat_summary).
#> Warning: Removed 8 rows containing non-finite values (stat_summary).
#> Warning: Removed 10 rows containing non-finite values (stat_summary).
# Visualise trajectories for a selection of individual cases
plot_sg_trajectories(data = sgdata,
id_var = "id",
select_id_list = c("2", "4", "5", "9"),
var_list = c("bdi_s1", "bdi_s2", "bdi_s3", "bdi_s4",
"bdi_s5", "bdi_s6", "bdi_s7", "bdi_s8",
"bdi_s9", "bdi_s10", "bdi_s11", "bdi_s12"),
show_id = TRUE,
id_label_size = 4,
label.padding = .2,
show_legend = TRUE,
colour = "viridis",
viridis_option = "D",
viridis_begin = 0,
viridis_end = 1,
connect_missing = TRUE,
scale_x_num = TRUE,
scale_x_num_start = 1,
apaish = TRUE,
xlab = "Session",
ylab = "BDI")
#> Warning: Removed 3 rows containing missing values (geom_point).
#> Warning: Removed 3 rows containing missing values (geom_label_repel).
4. Helper functions to export data sets to SPSS, Excel, Stata, and CSV
To continue working in another program (e.g. SPSS, STATA, Excel) the
functions write_bysg()
and write_byperson()
can be used to
export the datasets created in R as .sav, .dta, .xlsx, or .csv
files.
# Here is one example how to create a "bysg" data set and write a CSV file to the computer.
# Note that you have to change the file path and name in the argument 'path'
write_bysg(data = sgdata,
sg_crit1_cutoff = 7,
id_var_name = "id",
tx_start_var_name = "bdi_s1",
tx_end_var_name = "bdi_s12",
sg_var_list = c("bdi_s1", "bdi_s2", "bdi_s3", "bdi_s4",
"bdi_s5", "bdi_s6", "bdi_s7", "bdi_s8",
"bdi_s9", "bdi_s10", "bdi_s11", "bdi_s12"),
sg_measure_name = "bdi",
identify = "sg",
format = "CSV",
path = "~/Desktop/bysg_data.csv")