sts graph dialog: sts graph
-------------------------------------------------------------------------------
Title
[ST] sts graph -- Graph the survivor and cumulative hazard functions
Syntax
sts graph [if] [in] [, options]
options description
-------------------------------------------------------------------------
Main
survival graph Kaplan-Meier survivor
function; the default
failure graph Kaplan-Meier failure function
cumhaz graph Nelson-Aalen cumulative hazard
function
hazard graph smoothed hazard estimate
by(varlist) calculate separately on different
groups of varlist
adjustfor(varlist) adjust the estimates to zero values
of varlist
strata(varlist) stratify on different groups of
varlist
separate show curves on separate graphs;
default is to show curves one on
top of another
ci show pointwise confidence bands
At-risk table
risktable show table of number at risk beneath
graph
risktable(risk_spec) show customized table of number at
risk beneath graph
Options
level(#) set confidence level; default is
level(95)
per(#) units to be used in reported rates
noshow do not show st setting information
tmax(#) show graph for t <= #
tmin(#) show graph for t >= #
noorigin begin survival (failure) curve at
first exit time; default is begin
at t=0
width(#[#...]) override default bandwidth(s)
kernel(kernel) kernel function; use with hazard
noboundary no boundary correction; use with
hazard
lost show number lost
enter show number entered and number lost
atrisk show numbers at risk at beginning of
each interval
censored(single) show one hash mark at each censoring
time, no matter what number is
censored
censored(number) show one hash mark at each censoring
time and number censored above
hash mark
censored(multiple) show multiple hash marks for
multiple censoring at the same
time
censopts(hash_options) affect rendition of hash marks
lostopts(marker_label_options) affect rendition of numbers lost
atriskopts(marker_label_options) affect rendition of numbers at risk
Plot
plotopts(cline_options) affect rendition of plotted lines
plot#opts(cline_options) affect rendition of #th plotted
line; may not be combined with
separate
CI plot
ciopts(area_options) affect rendition of confidence bands
ci#opts(area_options) affect rendition of #th confidence
band; may not be combined with
separate
Add plots
addplot(plot) add other plots to the generated
graph
Y axis, X axis, Titles, Legend, Overall
twoway_options any options documented in
[G] twoway_options
byopts(byopts) how subgraphs are combined, labeled,
etc.
-------------------------------------------------------------------------
where risk_spec is
[numlist][, table_options group(group)]
numlist specifies the points at which the number at risk is to be
evaluated, table_options customizes the table of number at risk, and
group(group) specifies a specific group/row for table_options to be
applied.
table_options description
-------------------------------------------------------------------------
Main
axis_label_options control table by using axis labeling
options; seldom used
order(order_spec) select which rows appear and their
order
righttitles place titles on right side of the
table
failevents show number failed in the at-risk
table
text_options affect rendition of table elements
and titles
Row titles
rowtitle([text][, rtext_options]) change title for a row
Title
title([text][, ttext_options]) change overall table title
-------------------------------------------------------------------------
where order_spec is
# ["text" ["text" ...]] [...]
text_options description
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size(textsizestyle) size of text
color(colorstyle) color of text
justification(justificationstyle) text left-justified, centered,
right-justified
format(%fmt) format values per %fmt
topgap(relativesize) margin above rows
bottomgap(relativesize) margin beneath rows
+ style(textstyle) overall style of text
-------------------------------------------------------------------------
+ style() does not appear in the dialog box.
rtext_options description
-------------------------------------------------------------------------
size(textsizestyle) size of text
color(colorstyle) color of text
justification(justificationstyle) text left-justified, centered,
right-justified
at(#) override x position of titles
topgap(relativesize) margin above rows
+ style(textstyle) overall style of text
-------------------------------------------------------------------------
+ style() does not appear in the dialog box.
ttext_options description
-------------------------------------------------------------------------
size(textsizestyle) size of text
color(colorstyle) color of text
justification(justificationstyle) text left-justified, centered,
right-justified
at(#) override x position of titles
topgap(relativesize) margin above rows
bottomgap(relativesize) margin beneath rows
+ style(textstyle) overall style of text
-------------------------------------------------------------------------
+ style() does not appear in the dialog box.
group description
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#rownum specify group by row number in table
value specify group by value of group
label specify group by text of value label
associated with group
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hash_options description
-------------------------------------------------------------------------
line_options change look of dropped lines
marker_label_options add marker labels; any options
documented in [G]
marker_label_options, except
mlabel()
-------------------------------------------------------------------------
risktable() may be repeated and is merged-explicit group; see repeated
options.
You must stset your data before using sts graph; see [ST] stset.
fweights, iweights, and pweights may be specified using stset; see [ST]
stset.
Menu
Statistics > Survival analysis > Graphs > Survivor and cumulative hazard
functions
Description
sts graph graphs the estimated survivor (failure) function, the
Nelson-Aalen estimated cumulative (integrated) hazard function, or the
estimated hazard function.
sts graph can be used with single- or multiple-record or single- or
multiple-failure st data.
Options
+------+
----+ Main +-------------------------------------------------------------
survival, failure, cumhaz, and hazard specify the function to graph.
survival specifies that the Kaplan-Meier survivor function be
plotted. This option is the default if a function is not
specified.
failure specifies that the Kaplan-Meier failure function, 1 - S(t+0),
be plotted.
cumhaz specifies that the Nelson-Aalen estimate of the cumulative
hazard function be plotted.
hazard specifies that an estimate of the hazard function be plotted.
This estimate is calculated as a weighted kernel-density estimate
using the estimated hazard contributions. These hazard
contributions are the same as those obtained by sts generate
newvar = h.
by(varlist) produces separate survivor, cumulative hazard, or hazard
functions by making separate calculations for each group identified
by equal values of the variables in varlist and plots all the groups
on one graph. by() may not be combined with strata().
If you have more than one by() variable but need only one, use egen
to create it; see [D] egen.
adjustfor(varlist) adjusts the estimate of the survivor or hazard
functions to that for 0 values of varlist. If you want to adjust the
function to values different from 0, you need to center the variables
around those values before issuing the command. Say that you want to
plot survivor function adjusted to age of patients and the ages in
your sample are 40 to 60 years. Then
. sts graph, adjustfor(age)
will graph the survivor function adjusted to age 0. If you want to
adjust the function to age 40, type
. gen age40 = age - 40
. sts graph, adjustfor(age40)
adjustfor() is not available with cumhaz or ci.
If you specify adjustfor() with by(), sts fits separate Cox
regression models for each group, using the adjustfor() variables as
covariates. The separately calculated baseline survivor functions are
then retrieved.
If you specify adjustfor() with strata(), sts fits a
stratified-on-group Cox regression model using the adjustfor()
variables as covariates. The stratified, baseline survivor function
is then retrieved.
strata(varlist) produces estimates of the survivor (failure) or hazard
functions stratified on variables in varlist and plots all the groups
on one graph. It requires specifying adjustfor() and may not be
combined with by().
If you have more than one strata() varaible but need only one, use
egen to create it; see [D] egen.
separate is meaningful only with by() or strata(); it requests that each
group be placed on its own rather than one on top of the other.
Sometimes curves have to be placed on separate graphs -- such as when
you specify ci -- because otherwise it would be too confusing.
ci includes pointwise confidence bands. The default is not to produce
these bands. ci is not allowed with adjustfor() or pweights.
+---------------+
----+ At-risk table +----------------------------------------------------
risktable[([numlist][, table_options])] displays a table showing the
number at risk beneath the plot. risktable may not be used with
separate or adjustfor().
risktable displays the table in the default format with number at
risk shown for each time reported on the x axis.
risktable([numlist][, table_options]) specifies that the number at
risk be evaluated at the points specified in numlist or that the
rendition of the table be changed by table_options.
There are two ways to change the points at which the numbers at risk
are evaluated.
1. The x axis of the graph may be altered. For example:
. sts graph, xlabel(0(5)40) risktable
2. A numlist can be specified directly in the risktable() option,
which affects only the at-risk table. For example:
. sts graph, risktable(0(5)40)
The two examples produce the same at-risk table, but the first also
changes the time labels on the graph's x axis.
table_options affect the rendition of the at-risk table and may be
any of the following:
group(#rownum|value|label) specifies that all the suboptions
specified in the risktable() apply only to the specified
group. Because the risktable() option may be repeated, this
option allows different rows of the at-risk table to be
displayed with different colors, font sizes, etc.
When both a value and a value label are matched, the value
label takes precedence.
risktable() may be specified with or without the group()
suboption. When specified without group(), each suboption is
applied to all available groups or rows. risktable()
specified without group() is considered to be global and is
itself merged-explicit. See repeated options for more
information on how repeated options are merged.
Consider the following example:
. sts graph, by(drug) risktable(, color(red) size(small))
risktable(, color(navy))
The example above would produce a table where all rows are
colored navy with small text.
Combining global risktable() options with group-specific
risktable() options can be useful. When global options are
combined with group-specific options, group-specific options
always take precedence.
Consider the following example:
. sts graph, by(drug) risktable(, color(navy))
risktable(, color(red) group(#1))
The example above would produce a table with the first row
colored red and all remaining rows colored navy.
+------+
----+ Main +-----------------------------------------------------
axis_label_options control table by using axis labeling options.
These options are seldom used. See [G] axis_label_options.
order() specifies which and in what order rows are to appear in
the at-risk table. Optionally, order() can be used to
override the default text.
order(# # # ...) is the syntax used for identifying which
rows to display and their order. order(1 2 3) would specify
that row 1 is to appear first in the table, followed by row
2, followed by row 3. order(1 2 3) is the default if there
are three groups. If there were four groups, order(1 2 3 4)
would be the default, and so on. If there were four groups
and you specified order(1 2 3), the fourth row would not
appear in the at-risk table. If you specified order(2 1 3),
row 2 would appear first, followed by row 1, followed by row
3.
order(# "text" # "text" ...) is the syntax used for
specifying the row order and alternate row titles.
Consider the following at-risk table:
+------------------------------------+
| drug = 1 20 8 2 |
| drug = 2 14 10 4 1 |
| drug = 3 14 13 10 5 |
+------------------------------------+
Specifying order(1 "Placebo" 3 2) would produce
+------------------------------------+
| Placebo 20 8 2 |
| drug = 3 14 13 10 5 |
| drug = 2 14 10 4 1 |
+------------------------------------+
and specifying order(1 "Placebo" 3 "Drug 2" 2 "Drug 1") would
produce
+------------------------------------+
| Placebo 20 8 2 |
| Drug 2 14 13 10 5 |
| Drug 1 14 10 4 1 |
+------------------------------------+
righttitles specifies that row titles be placed to the right of
the at-risk values. The default is to place row titles to
the left of the at-risk values.
failevents specifies that the number of failure events be shown
in parentheses, after the time in which the risk values were
calculated.
text_options affect the rendition of both row titles and number
at risk and may be any of the following:
size(textsizestyle) specifies the size of text.
color(colorstyle) specifies the color of text.
justification(justificationstyle) specifies how text elements
are to be justified.
format(%fmt) specifies how numeric values are to be
formatted.
topgap(relativesize) specifies how much space is to be placed
above each row.
bottomgap(relativesize) specifies how much space is to be
placed beneath each row.
style(textstyle) specifies the style of text. This option
does not appear on the dialog box.
+------------+
----+ Row titles +-----------------------------------------------
rowtitle([text] [, rtext_options]) changes the default text or
rendition of row titles. Specifying rowtitle(, color(navy))
would change the color of all row titles to navy.
rowtitle() is often combined with group() to change the text
or rendition of a title. Specifying
rowtitle(Placebo) group(#2) would change the title of the
second row to Placebo. Specifying
rowtitle(, color(red)) group(#3) would change the color of
the row title for the third row to red.
Row titles may include more than one line. Lines are
specified one after the other, each enclosed in double
quotes. Specifying rowtitle("Experimental drug") group(#1)
would produce a one-line row title, and specifying
rowtitle("Experimental" "Drug") group(#1) would produce a
multiple-line row title.
rtext_options affect the rendition of both row titles and
number at risk and may be any of the following:
size(textsizestyle) specifies the size of text.
color(colorstyle) specifies the color of text.
justification(justificationstyle) specifies how text
elements are to be justified.
at(#) allows you to reposition row titles or the overall
table title to align with a specific location on the
x axis.
topgap(relativesize) specifies how much space is to be
placed above each row.
style(textstyle) specifies the style of text. This
option does not appear in the dialog box.
+-------+
----+ Title +----------------------------------------------------
title([title] [, ttext_options]) may be used to override the
default title for the at-risk table and affect the rendition
of its text.
Titles may include one line of text or multiple lines.
title("At-risk table") will produce a one-line title, and
title("At-risk" "table") will produce a multiple-line title.
ttext_options affect the rendition of both row titles and
number at risk and may be any of the following:
size(textsizestyle) specifies the size of text.
color(colorstyle) specifies the color of text.
justification(justificationstyle) specifies how text
elements are to be justified.
at(#) allows you to reposition row titles or the overall
table title to align with a specific location on the
x axis.
at(rowtitles) places the overall table title at the
default position calculated for the row titles. This
option is sometimes useful for alignment when the
default justification has not been used.
topgap(relativesize) specifies how much space is to be
placed above each row.
bottomgap(relativesize) specifies how much space is to be
placed beneath each row.
style(textstyle) specifies the style of text. This
option does not appear on the dialog box.
+---------+
----+ Options +----------------------------------------------------------
level(#) specifies the confidence level, as a percentage, for the
pointwise confidence interval around the survivor, failure, or
cumulative hazard function; see [R] level.
per(#) specifies the units used to report the survival or failure rates.
For example, if the analysis time is in years, specifying per(100)
results in rates per 100 person-years.
noshow prevents sts graph from showing the key st variables. This option
is seldom used because most people type stset, show or stset, noshow
to set whether they want to see these variables mentioned at the top
of the output of every st command; see [ST] stset.
tmax(#) specifies that the plotted curve be graphed only for t <= #.
This option does not affect the calculation of the function, rather
the portion that is displayed.
tmin(#) specifies that the plotted curve be graphed only for t >= #.
This option does not affect the calculation of the function, rather
the portion that is displayed.
noorigin requests that the plot of the survival (failure) curve begin at
the first exit time instead of beginning at t=0 (the default). This
option is ignored when cumhaz or hazard is specified.
width(# [# ...]) is for use with hazard and specifies the bandwidth to be
used in the kernel smooth used to plot the estimated hazard function.
If width() is not specified, a default bandwidth is used as described
in [R] kdensity. If it is used with by(), multiple bandwidths may be
specified, one for each group. If there are more groups than the k
bandwidths specified, the default bandwidth is used for the k+1, ...
remaining groups. If any bandwidth is specified as . (dot), the
default bandwidth is used for that group.
kernel(kernel) is for use with hazard and specifies the kernel function
to be used in calculating the weighted kernel-density estimate
required to produce a smoothed hazard-function estimator. The
default kernel is Epanechnikov, yet kernel may be any of the kernels
supported by kdensity; see [R] kdensity.
noboundary is for use with hazard. It specifies that no boundary-bias
adjustments are to be made when calculating the smoothed
hazard-function estimator. By default, the smoothed hazards are
adjusted near the boundaries. If the epan2, biweight, or rectangular
kernel is used, the bias correction near the boundary is performed
using boundary kernels. For other kernels, the plotted range of the
smoothed hazard function is restricted to be within one bandwidth of
each endpoint. For these other kernels, specifying noboundary merely
removes this range restriction.
lost specifies that the numbers lost be shown on the plot. These numbers
are shown as small numbers over the flat parts of the function.
If enter is not specified, the numbers displayed are the number
censored minus the number who enter. If you do specify enter, the
numbers displayed are the pure number censored. The underlying logic
is described in [ST] sts.
lost may not be used with hazard.
enter specifies that the number who enter be shown on the graph, as well
as the number lost. The number who enter are shown as small numbers
beneath the flat parts of the plotted function.
enter may not be used with hazard.
atrisk specifies that the numbers at risk at the beginning of each
interval be shown on the plot. The numbers at risk are shown as
small numbers beneath the flat parts of the plotted function.
atrisk may not be used with hazard.
censored(single | number | multiple) specifies that hash marks be placed
on the graph to indicate censored observations.
censored(single) places one hash mark at each censoring time,
regardless of the number of censorings at that time.
censored(number) places one hash mark at each censoring time and
displays the number of censorings about the hash mark.
censored(multiple) places multiple hash marks for multiple censorings
at the same time. For instance, if 3 observations are censored
at time 5, three hash marks are placed at time 5.
censored(multiple) is intended for use when there are few
censored observations; if there are too many censored
observations, the graph can look bad. In such cases, we
recommend that censored(number) be used.
censored() may not be used with hazard.
censopts(hash_options) specifies options that affect how the hash marks
for censored observations are rendered; see [G] line_options. When
combined with censored(number), censopts() also specifies how the
count of censoring is rendered; see [G] marker_label_options, except
mlabel() is not allowed.
lostopts(marker_label_options) specifies options that affect how the
numbers lost are rendered; see [G] marker_label_options. This option
implies the lost option.
atriskopts(marker_label_options) specifies options that affect how the
numbers at risk are rendered; see [G] marker_label_options. This
option implies the atrisk option.
+------+
----+ Plot +-------------------------------------------------------------
plotopts(cline_options) affects the rendition of the plotted lines; see
[G] cline_options. This option may not be combined with by(varlist)
or strata(varlist), unless separate is also specified.
plot#opts(cline_options) affects the rendition of the #th plotted line;
see [G] cline_options. This option may not be combined with
separate.
+---------+
----+ CI plot +----------------------------------------------------------
ciopts(area_options) affects the rendition of the confidence bands; see
[G] area_options. This option may not be combined with by(varlist)
or {opt strata(varlist), unless separate is also specified.
ci#opts(area_options) affects the rendition of the #th confidence band;
see [G] area_options. This option may not be combined with separate.
+-----------+
----+ Add plots +--------------------------------------------------------
addplot(plot) provides a way to add other plots to the generated graph;
see [G] addplot_option.
+-----------------------------------------+
----+ Y axis, X axis, Titles, Legend, Overall +--------------------------
twoway_options are any of the options documented in [G] twoway_options.
These include options for titling the graph (see [G] title_options)
and for saving the graph to disk (see [G] saving_option).
byopts(byopts) affects the appearance of the combined graph when by() or
adjustfor() is specified, including the overall graph title and the
organization of subgraphs. byopts() may not be specified with
separate. See [G] by_option.
Example: Including the number lost on the graph
Setup
. webuse drug2b
Graph the survivor functions for the two categories of drug and include
the number lost due to censoring as small numbers on the plots
. sts graph, by(drug) lost
Same as above, but show the number entered and the number lost
. sts graph, by(drug) enter
Example: Graphing the Nelson-Aalen cumulative hazard function
Setup
. webuse drug2
Graph the cumulative hazard functions for the two categories of drug
. sts graph, cumhaz by(drug)
Same as above, but include the number lost due to censoring as small
numbers on the plots
. sts graph, cumhaz by(drug) lost
Example: Graphing the hazard function
Graph the hazard functions for the two categories of drug
. sts graph, hazard by(drug)
Same as above, but use a Gaussian kernel with a bandwidth of 5 for drug =
0 and 7 for drug = 1
. sts graph, hazard by(drug) kernel(gauss) width(5 7)
Example: Adding an at-risk table
Graph the survivor functions for the two categories of drug in one plot,
including an at-risk table below the graph
. sts graph, by(drug) risktable
Same as above, but put the legend inside the plot rather than below it
. sts graph, by(drug) risktable legend(ring(0) position(2) rows(2))
Graph the survivor functions for the two categories of drug in one plot,
including an at-risk table below the graph and using the specified row
titles and order of rows for the at-risk table
. sts graph, by(drug) risktable(, order(1 "Placebo" 2 "Test drug"))
Same as above, but left-justify the row titles in the at-risk table
. sts graph, by(drug) risktable(, order(1 "Placebo" 2 "Test drug")
rowtitle(, justification(left)))
Same as above, but align the table title with the rwo titles
. sts graph, by(drug) risktable(, order(1 "Placebo" 2 "Test drug")
rowtitle(, justification(left)) title(, at(rowtitle)))
Also see
Manual: [ST] sts graph
Help: [ST] sts, [ST] sts generate, [ST] sts list, [ST] sts test, [ST]
stset; [R] kdensity
