longitudinalcascade: Longitudinal cascade statistics and charts
In noahhaber/longitudinalcascade: Longitudinal Cascade
View source: R/longitudinalcascade.R
longitudinalcascade R Documentation
Longitudinal cascade statistics and charts
Description
This package generates a longitudinal cascade, including a graphical representation. This takes a long-formatted list of stage-by-stage events and transforms it into a longitudinal cascade, correcting the orders of events.
Usage
longitudinalcascade(
events.long,
stages.order,
groups.order = NA,
groups.date.breaks = NA,
groups.date.breaks.labels = NA,
death.indicator = NA,
censorship.indicator = NA,
censorship.date = "lastdate",
allow.sub.stages = FALSE,
allow.sub.stage.mortality = FALSE,
sub.stage.mortality.mode = "standard",
skip.mode = "none",
time.horizon = 365,
TTE.quantiles = c(0.25, 0.5, 0.75),
main.fill.colors = "#4472C4",
death.fill.color = "#FF6A6A",
chart.mode = "stage panels",
ts.indicator = NA,
ts.gap.time = 90,
ts.start.stage = 1,
ts.end.stage = NA,
ts.color = "#a2f2da",
risk.pool.size.line = FALSE,
risk.pool.fill.color = "#90dbb2",
background.prior.event = TRUE,
suppress.messages = FALSE,
x.axis.title = "Time (years) from start of stage"
)
Arguments
events.long
(required) The main dataframe input parameter. The data frame needs at least the following fields:
"ID": (required) A string-based individual identifier, indicating every person in the dataset.
"date": (required) Date-formatted date on which the event / stage occurred
"stage": (required) String indicating the stage achieved by the individual on the specified date. Stages must match the string in the stages.order parameter. Additonal events may be included in the "stage" category, including death, loss to follow up, and interstage events defined in the other parameters.
"group": (optional) String indicating any relevent groups of data.
stages.order
(required) stages.order is the parameter which defines the events to be considered in the main cascade and their order. This is a vector of strings matching items in the "Stage" column of the main data frame, e.g. c("Stage 1","Stage 2","Stage 3").
groups.order
(optional) This is a vector of groups, matching the "group" column of the main data frame. If left blank, no group comparisons will be performed. For the chart, each group will have its own row.
groups.date.breaks
(optional) If groups.date.breaks is filled in, the grouping will be defined by date range of entry event for each transition, rather than groups of individuals. Each transition will independently determine its own groups, based on the time in which the entrance event occurs. Times are determined by a vector of date breaks. Each group is defined as starting from a given date break value and continuing until it reaches the subsequent date break, not including data from that ending break value. For example, setting the break values to be January 1, 2011, January 1, 2012, and January 1, 2013 will create two groups. The first group will take individuals who entered each stage from January 1, 2011 to Dec 31, 2011, and the second will take individuals who entered into the stage from January 1, 2012 to Dec 31, 2012.
groups.date.breaks.labels
(optional) Changes the default labelling of the groups when you are using date break groupings. Entered as a vector of strings, and must be the same length as the number of groups.
death.indicator
(optional) This parameter is the string which indicates a death event in the dataset. If specified, between-stage mortality will be estimated and shown as a KM curve on the top of the chart(s). If left blank, death events will not be estimated.
censorship.indicator
(optional) This parameter is the string which indicates a right-censorship event. Most commonly, this will indicate permanent loss to follow up and/or end of data collection.
censorship.date
(optional) By default, censorship is set to the last date of data collection. If you would prefer to set a different date than that, enter it into censorship.date argument as a date.
allow.sub.stages
Sub-lines indicate subsequent transitions across the cascade. If TRUE, the main chart will show transitions to all possible subsequent events. For example, if there are 4 stages (1-4), the leftmost chart will show each transition from 1-2, 1-3, and 1-4, while the next chart will show 2-3 and 2-4, and the last chart will show only 3-4. If FALSE, the charts will only show transition to the subsequent stage.
allow.sub.stage.mortality
Sub-stage-mortality indicate subsequent mortality transitions across the cascade. If TRUE, the main chart will show transitions to all possible subsequent events. For example, if there are 4 stages (1-4), the leftmost chart will show each transition from 1-2, 1-3, and 1-4, while the next chart will show 2-3 and 2-4, and the last chart will show only 3-4. If FALSE, the charts will only show transition to the subsequent stage.
sub.stage.mortality.mode
By default, sub-stage mortality is shown as a transition underneath the main transition ("standard"). If set to "shifted" substage mortality will be shifted to the top of the chart, and all substages will be shifted downward accordingly
skip.mode
This option shows "skips" across the cascade in each chart, as indicated by the y intercept. If "none" (default) each stage will start only with people who have not moved on to a subsequent stage, i.e. the y intercept will always be 0. If set to "internal" an individual can enter into a stage even if they have "skipped" through it. For example, an individual may go straight from stage 1 to stage 3, skipping 2. If this indicator is FALSE, the stage transition chart from 2-3 will not contain this individual in the denomenator. If TRUE, this individual will be counted in the denomenator for this transition, but will be counted as having transitioned into stage 3 immediately upon entering stage 2. If "external" individuals contribute person-time and are in the y-axis of transitions even prior to their first recorded stage date.
time.horizon
This option shows the maximum range of each stage in days. Defaults to 365 days (1 year).
TTE.quantiles
This option sets the quantiles measured for the quantile time to event outputs, using a c() list. By default, this is set to 0.2, 0.5 (i.e. the median), and 0.75.
main.fill.colors
(optional) This defines the color scheme of the stage transition graphs, as a string indicator for color or a c() vector of colors. If the colors contain only one color, the color scheme will automatically generate progressively faded versions of the initial color provided for the remaining stage transitions. Otherwise, a list which is exactly one fewer than the # of stages must be provided, in the order of stage trasitions.
death.fill.color
(optional) This defines the color scheme for the death stage transition, as a string indicator for color.
chart.mode
By default, the chart is set to a stage-by-stage panel view ("stage panels"). Alternatively, it may be desirable to have only the first panel showing the overall experience from the first entry condition, as indicated by the "first transition" option.
ts.indicator
(experimental) (optional) This indicates the name of the events indicating the transient stage of interest. Can be either a single indicator, or a c() vector if there are multiple transient stages defined. Defaults to NA, disabling this feature.
ts.gap.time
(experimental) (optional) This indicates the time between events required until an indidual is considered "off" for the given transient stage. Can be either a single indicator, or a c() vector if there are multiple transient stages defined.
ts.start.stage
(experimental) (optional) This indicates the stage at which the transient stage of interest starts. Can be either a single indicator, or a c() vector if there are multiple transient stages defined.
ts.end.stage
(experimental) (optional) This indicates the stage at which the transient stage of interest ends Can be either a single indicator, or a c() vector if there are multiple transient stages defined.
ts.color
(experimental) (optional) Indicates the color used for transient stages
risk.pool.size.line
Setting to TRUE adds an indicator of risk pool remaining to the main charts as a line reflected beneath the main chart, showing the proportion of the original risk pool remaining at each time point. Defaults to FALSE.
risk.pool.fill.color
(optional) This defines the color scheme for the risk pool graphic, as a string indicator for color.
background.prior.event
(optional) This changes the background of the faceted chart to be the color for the prior event.
suppress.messages
(optional) Suppresses tips and messages about the dataset
x.axis.title
(optional) Changes the x axis label
Value
description All data are output to an object containing a the main chart ($chart), a survival-formatted dataset ($surv.dataset), the data underlying the main chart ($surv.dataset.chart), the underlying original dataset in long ($events.long) and wide ($events.wide), individual time to event data ($TTE.ind), TTE data by quantiles ($quantile.TTE), the equivalent functions for deat and transient events, and group difference tests
References
Haber et al. (2017) Lancet HIV 4(5):e223-e230
(PubMed)
Examples
# Pull in data from example simulated dataset
library(longitudinalcascade)
data(events_long)
# Set up options
stages.order <- c("First tested positive","Knows status","Linked to care","Eligible for ART",
"Initiated ART","Therapeutic response")
groups.order <- c("Group 1","Group 2","Group 3")
death.indicator <- "Death"
retention.indicator <- "Clinic visit"
censorship.indicator <- "LTFU"
allow.sub.stages <- TRUE
# Create cascade object
longitudinalcascade.sim <- longitudinalcascade(events_long,stages.order=stages.order,
groups.order=groups.order,death.indicator=death.indicator,
censorship.indicator=censorship.indicator,
allow.sub.stages=allow.sub.stages)
# Print/output main multipanel chart
longitudinalcascade.sim$chart
# Output full survival dataset generated, as a data frame
df.longitudainalcascade.survival <- longitudinalcascade.sim$surv.dataset
# Output heterogeneity test
longitudinalcascade.sim$surv.diffs
# Output original long-formatted list of events
df.events.long <- longitudinalcascade.sim$events.long
# Output generated wide-formatted list of events
df.events.wide <- longitudinalcascade.sim$events.wide
noahhaber/longitudinalcascade documentation built on May 24, 2023, 8:22 a.m.
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View source: R/longitudinalcascade.R
| longitudinalcascade | R Documentation |
Longitudinal cascade statistics and charts
Description
This package generates a longitudinal cascade, including a graphical representation. This takes a long-formatted list of stage-by-stage events and transforms it into a longitudinal cascade, correcting the orders of events.
Usage
longitudinalcascade(
events.long,
stages.order,
groups.order = NA,
groups.date.breaks = NA,
groups.date.breaks.labels = NA,
death.indicator = NA,
censorship.indicator = NA,
censorship.date = "lastdate",
allow.sub.stages = FALSE,
allow.sub.stage.mortality = FALSE,
sub.stage.mortality.mode = "standard",
skip.mode = "none",
time.horizon = 365,
TTE.quantiles = c(0.25, 0.5, 0.75),
main.fill.colors = "#4472C4",
death.fill.color = "#FF6A6A",
chart.mode = "stage panels",
ts.indicator = NA,
ts.gap.time = 90,
ts.start.stage = 1,
ts.end.stage = NA,
ts.color = "#a2f2da",
risk.pool.size.line = FALSE,
risk.pool.fill.color = "#90dbb2",
background.prior.event = TRUE,
suppress.messages = FALSE,
x.axis.title = "Time (years) from start of stage"
)
Arguments
events.long |
(required) The main dataframe input parameter. The data frame needs at least the following fields: "ID": (required) A string-based individual identifier, indicating every person in the dataset. "date": (required) Date-formatted date on which the event / stage occurred "stage": (required) String indicating the stage achieved by the individual on the specified date. Stages must match the string in the stages.order parameter. Additonal events may be included in the "stage" category, including death, loss to follow up, and interstage events defined in the other parameters. "group": (optional) String indicating any relevent groups of data. |
stages.order |
(required) stages.order is the parameter which defines the events to be considered in the main cascade and their order. This is a vector of strings matching items in the "Stage" column of the main data frame, e.g. c("Stage 1","Stage 2","Stage 3"). |
groups.order |
(optional) This is a vector of groups, matching the "group" column of the main data frame. If left blank, no group comparisons will be performed. For the chart, each group will have its own row. |
groups.date.breaks |
(optional) If groups.date.breaks is filled in, the grouping will be defined by date range of entry event for each transition, rather than groups of individuals. Each transition will independently determine its own groups, based on the time in which the entrance event occurs. Times are determined by a vector of date breaks. Each group is defined as starting from a given date break value and continuing until it reaches the subsequent date break, not including data from that ending break value. For example, setting the break values to be January 1, 2011, January 1, 2012, and January 1, 2013 will create two groups. The first group will take individuals who entered each stage from January 1, 2011 to Dec 31, 2011, and the second will take individuals who entered into the stage from January 1, 2012 to Dec 31, 2012. |
groups.date.breaks.labels |
(optional) Changes the default labelling of the groups when you are using date break groupings. Entered as a vector of strings, and must be the same length as the number of groups. |
death.indicator |
(optional) This parameter is the string which indicates a death event in the dataset. If specified, between-stage mortality will be estimated and shown as a KM curve on the top of the chart(s). If left blank, death events will not be estimated. |
censorship.indicator |
(optional) This parameter is the string which indicates a right-censorship event. Most commonly, this will indicate permanent loss to follow up and/or end of data collection. |
censorship.date |
(optional) By default, censorship is set to the last date of data collection. If you would prefer to set a different date than that, enter it into censorship.date argument as a date. |
allow.sub.stages |
Sub-lines indicate subsequent transitions across the cascade. If TRUE, the main chart will show transitions to all possible subsequent events. For example, if there are 4 stages (1-4), the leftmost chart will show each transition from 1-2, 1-3, and 1-4, while the next chart will show 2-3 and 2-4, and the last chart will show only 3-4. If FALSE, the charts will only show transition to the subsequent stage. |
allow.sub.stage.mortality |
Sub-stage-mortality indicate subsequent mortality transitions across the cascade. If TRUE, the main chart will show transitions to all possible subsequent events. For example, if there are 4 stages (1-4), the leftmost chart will show each transition from 1-2, 1-3, and 1-4, while the next chart will show 2-3 and 2-4, and the last chart will show only 3-4. If FALSE, the charts will only show transition to the subsequent stage. |
sub.stage.mortality.mode |
By default, sub-stage mortality is shown as a transition underneath the main transition ("standard"). If set to "shifted" substage mortality will be shifted to the top of the chart, and all substages will be shifted downward accordingly |
skip.mode |
This option shows "skips" across the cascade in each chart, as indicated by the y intercept. If "none" (default) each stage will start only with people who have not moved on to a subsequent stage, i.e. the y intercept will always be 0. If set to "internal" an individual can enter into a stage even if they have "skipped" through it. For example, an individual may go straight from stage 1 to stage 3, skipping 2. If this indicator is FALSE, the stage transition chart from 2-3 will not contain this individual in the denomenator. If TRUE, this individual will be counted in the denomenator for this transition, but will be counted as having transitioned into stage 3 immediately upon entering stage 2. If "external" individuals contribute person-time and are in the y-axis of transitions even prior to their first recorded stage date. |
time.horizon |
This option shows the maximum range of each stage in days. Defaults to 365 days (1 year). |
TTE.quantiles |
This option sets the quantiles measured for the quantile time to event outputs, using a c() list. By default, this is set to 0.2, 0.5 (i.e. the median), and 0.75. |
main.fill.colors |
(optional) This defines the color scheme of the stage transition graphs, as a string indicator for color or a c() vector of colors. If the colors contain only one color, the color scheme will automatically generate progressively faded versions of the initial color provided for the remaining stage transitions. Otherwise, a list which is exactly one fewer than the # of stages must be provided, in the order of stage trasitions. |
death.fill.color |
(optional) This defines the color scheme for the death stage transition, as a string indicator for color. |
chart.mode |
By default, the chart is set to a stage-by-stage panel view ("stage panels"). Alternatively, it may be desirable to have only the first panel showing the overall experience from the first entry condition, as indicated by the "first transition" option. |
ts.indicator |
(experimental) (optional) This indicates the name of the events indicating the transient stage of interest. Can be either a single indicator, or a c() vector if there are multiple transient stages defined. Defaults to NA, disabling this feature. |
ts.gap.time |
(experimental) (optional) This indicates the time between events required until an indidual is considered "off" for the given transient stage. Can be either a single indicator, or a c() vector if there are multiple transient stages defined. |
ts.start.stage |
(experimental) (optional) This indicates the stage at which the transient stage of interest starts. Can be either a single indicator, or a c() vector if there are multiple transient stages defined. |
ts.end.stage |
(experimental) (optional) This indicates the stage at which the transient stage of interest ends Can be either a single indicator, or a c() vector if there are multiple transient stages defined. |
ts.color |
(experimental) (optional) Indicates the color used for transient stages |
risk.pool.size.line |
Setting to TRUE adds an indicator of risk pool remaining to the main charts as a line reflected beneath the main chart, showing the proportion of the original risk pool remaining at each time point. Defaults to FALSE. |
risk.pool.fill.color |
(optional) This defines the color scheme for the risk pool graphic, as a string indicator for color. |
background.prior.event |
(optional) This changes the background of the faceted chart to be the color for the prior event. |
suppress.messages |
(optional) Suppresses tips and messages about the dataset |
x.axis.title |
(optional) Changes the x axis label |
Value
description All data are output to an object containing a the main chart ($chart), a survival-formatted dataset ($surv.dataset), the data underlying the main chart ($surv.dataset.chart), the underlying original dataset in long ($events.long) and wide ($events.wide), individual time to event data ($TTE.ind), TTE data by quantiles ($quantile.TTE), the equivalent functions for deat and transient events, and group difference tests
References
Haber et al. (2017) Lancet HIV 4(5):e223-e230 (PubMed)
Examples
# Pull in data from example simulated dataset
library(longitudinalcascade)
data(events_long)
# Set up options
stages.order <- c("First tested positive","Knows status","Linked to care","Eligible for ART",
"Initiated ART","Therapeutic response")
groups.order <- c("Group 1","Group 2","Group 3")
death.indicator <- "Death"
retention.indicator <- "Clinic visit"
censorship.indicator <- "LTFU"
allow.sub.stages <- TRUE
# Create cascade object
longitudinalcascade.sim <- longitudinalcascade(events_long,stages.order=stages.order,
groups.order=groups.order,death.indicator=death.indicator,
censorship.indicator=censorship.indicator,
allow.sub.stages=allow.sub.stages)
# Print/output main multipanel chart
longitudinalcascade.sim$chart
# Output full survival dataset generated, as a data frame
df.longitudainalcascade.survival <- longitudinalcascade.sim$surv.dataset
# Output heterogeneity test
longitudinalcascade.sim$surv.diffs
# Output original long-formatted list of events
df.events.long <- longitudinalcascade.sim$events.long
# Output generated wide-formatted list of events
df.events.wide <- longitudinalcascade.sim$events.wide
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