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sts_graph_landmark.ado
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/*******************************************************************************
********************************************************************************
Name: sts_graph_landmark
Author: Arnaud Künzi (arnaud.kuenzi@ctu.unibe.ch)
Version: 1.1.3
Creation: 2020.09.01
Last edit: 2022.02.22
Description:
Comments:
Known bugs: stset options origin(), enter() and probably others
cause command 'streset' to fail in the program on a not found
temporary variable __00008.
Changelog:
-1.1.3 ON 2022.02.22
- Fixed bug in lcolor() where colors specified as other than a color name did not work
- Added support for lpattern()
-1.1.2 ON 2022.01.13
- Fixed bug where option symbol() could not be invoked without
labjustification() in risktableopts().
-1.1.1 ON 2022.01.13
- Fixed bug where execution failed when max follow-up time was not an integer.
- Fixed graphing bug when an observation time was below from the previous offset of 0.001
Offset was changed to epsilon = 1.0x-1b (see bulletpoint 9.6 at
https://blog.stata.com/2012/04/02/the-penultimate-guide-to-precision/#section9)
- Fixed bug where execution failed when numlist in at() had non-integer values
- Added undocumented keepplotdata option
-1.1.0 ON 2021.08.31
- Added risktableopts(). It is now possible to customize style and position of the elements of the
risktable (tbl_title, tbl_labels, tbl_content) as well as the symbol of the key
- 1.0.3 ON 30.11.2020
- fixed issues where custom axis labels such as
xlabel(0 "baseline" 30 "1 month" 60 "2 months")
caused problems for parsing the risktable numlist.
Added private program remove_non_numeric to do so.
- 1.0.2 ON 09.11.2020
- fixed issue where usercmd only worked when r(table) returned one column, so multiple covariates made the code crash. matrix _r now returns all covariates and landmark epochs are suffixed to the column names with a colon like so 'varname:0'
- 1.0.1 ON 22.10.2020
- fixed bug where content of local macros in option text() could not be delayed with backslash. (i.e. \`=something' or \`:something')
- 1.0 ON 10.09.2020:
- implemented risktables
- changed graph command from [if] to split variable (one for each line)
to improve clarity
- removed dependency on ssc colorpalette
- Option id() is now optional. It rests on the user to ensure that, if not specified, the data is actually single-record survival data.
- if data has already been stset, the program use the existing st settings.
if data is not stset, options failure() is required.
- Option by() is now optional: if missing, a default overall caregory is plotted instead
- 0.9 ON 2020.09.02: pre-release
from initial feedback
- fixed ytick() support
- fixed axis title support
********************************************************************************
*******************************************************************************/
cap program drop sts_graph_landmark
program define sts_graph_landmark
version 16
syntax [varlist(default=none)] [if] [in], [at(numlist >0) FAILure(varname) TItle(string) id(varname) by(varname) end(numlist max=1) YLABel(passthru) XLABel(passthru) LCOLors(passthru) LPATtern(passthru) RISKtable EVents risktableopts(string) SCale(real 0.8) FRFrom(string) usercmd(string) stsetopts(string) stslistopts(string) SHOWcmd KEEPplotdata *]
************* PARSING PARAMETERS AND SETTING DEFAULT VALUES *************
if ("`by'" == ""){
tempvar by
cap lab define ovlab 1 "Overall"
gen `by':ovlab = 1
local by_lvls
local nlevels 1
}
if ("`id'" == ""){
* create default id variable for stsplit. Makes the assumption st data is single-record
tempvar id
gen `id' = _n
local defaultid defaultid
}
*store levels of 'by' and 'at'
qui levelsof `by', local(by_lvls)
local nlevels `r(r)'
local nat `:word count `at''
*Default option values
local varname: word 1 of `varlist'
if ("`failure'" != "" & "`varname'" == "") local varname `failure'_days
else{
if ("`failure'" == "") local failure "`_dta[st_bd]'"
if ("`varname'" == "") local varname "`_dta[st_bt]'"
}
if ("`by'" != "") local byby by(`by')
local idid id(`id')
if ("`end'" == ""){
qui summ `varname'
local end `r(max)'
}
local atend "0 `at' `end'"
if ("`frframe'" == "") local frfrom default
*Default graphic options
local graphobs connect(J) sort
if !regexm(\`"`options'"', "ytitle\(") local options2 `"`options2' ytitle("Failure rate (%)")"'
if !regexm(\`"`options'"', "ytick\(") local options2 `"`options2' ytick(#10)"'
if !regexm("`ylabel'","angle") local ylabel `"`ylabel' ylabel(, angle(0))"'
if ("`xlabel'" == "") local xlabel `"xlabel(`atend')"'
if ("`title'" == ""){
if ("`failure'" != "" ){ //default title
local options2 `"`options2' title("K-M curves for `:variable label `failure''")"'
}
else if ("`_dta[st_bd]'" != ""){ //default title if data is already stset
local options2 `"`options2' title("K-M curves for `:variable label `_dta[st_bd]''")"'
}
} //user-defined title
else local options2 `"`options2' title("`title'")"'
if !regexm(\`"`options'"', "graphregion\("){
local options2 `"`options2' graphregion(color(white) lc(white) lw(thick) margin(5 5 5 5))"'
}
if (`"`risktableopts'"' != ""){
local risktable "risktable"
noi: di as text "{hi:risktableopts()} set -> option {hi:risktable} is implied."
}
if ("`legend'" == ""){
if ("`risktable'" == ""){
forvalues j = 1/`nlevels'{
local legendopts `"`legendopts' `j' "`:label (`by') `:word `j' of `by_lvls'''""'
}
local legendopts order(`legendopts')
}
else local legendopts "off"
local options2 `"`options2' legend(`legendopts')"'
}
*parse xlabel ticks
if "`risktable'" != "" {
gettoken discard keep: xlabel, parse("(")
gettoken keep discard: keep, match(parns)
*remove quoted labels. it outputs r(numlist)
remove_non_numeric `"`keep'"'
numlist `"`r(numlist)'"', sort
local risktabletimes `"0 `r(numlist)'"'
local risktabletimes: list uniq risktabletimes
}
*define K-M lines colors
if (`"`lcolors'"' == ""){
*Palette taken from the ssc colorpalette Set1
local default_palette `""55 126 184" "228 26 28" "77 175 74" "152 78 163" "255 127 0" "255 255 51" "166 86 40" "247 129 191" "153 153 153""'
local lcolors `"`default_palette'"'
}
else{
*This needs to get rid of "^lcolor(" and ")$" due to option mode passthru. option mode string was getting rid of the quotes which did not let us specify colors un RGB, HSV and YMCK.
gettoken discard lcolors: lcolors, parse("(") bind match(parns)
gettoken lcolors discard: lcolors, parse("(") bind match(parns)
}
if (`"`lpattern'"' != ""){
gettoken discard lpattern: lpattern, parse("(") bind match(parns)
gettoken lpattern discard: lpattern, parse("(") bind match(parns)
}
*parse xlabel formatting options for the risktable
while (`"`risktableopts'"' != ""){
gettoken crisktableopts risktableopts: risktableopts, bind match(parns)
gettoken cname copt: crisktableopts, parse("(") bind match(parns)
gettoken copt discard: copt, parse(",") match(parns)
if (regexm(`"`copt'"',",")){
gettoken cpos copt: copt, parse(",")
local copt: subinstr local copt "," "", count(local comma_replaced)
if ("`comma_replaced'" == "0"){
local cpos
}
}
else if real(`"`copt'"') != . {
local cpos `copt'
local copt
}
if inlist("`cname'","tbl_title","tbl_labels","tbl_content"){
*define justification if not defined in `cname'_opts
if (regexm(`"`copt'"',"labjustification\(left\)|labjustification\(right\)")){
local `cname'_just `=regexs(0)'
*remove the labjustification() parameter from the current option string as we have now parsed it.
local copt `=regexr(`"`copt'"',"labjustification\(left\)|labjustification\(right\)","")'
}
else{
local `cname'_just labjustification(right)
}
*define the symbol in the key
if ("`cname'" == "tbl_labels" ){
if (regexm(`"`copt'"',`"(symbol\()([^)]+)(\))"')){
local match `"`=regexs(2)'"'
local match: list clean match
*if it is a number, then it's the position in the following symbol list
if real(`"`match'"') != . {
local symbolnum = round(real("`match'"))
local symbol: word `symbolnum' of █ {&bull} ⬤ ⚫ //add here more symbols separated by space.
}
else{
*else we just take the content of `match' as the symbol.
local symbol `"`match'"'
}
*remove the symbol() parameter from the current option string as we have now parsed it.
local copt `"`=regexr(`"`copt'"',`"symbol\([^)]+\)"',"")'"'
}
else{
local symbol `"█"'
}
}
*store options and positions
local `cname'_opts `copt'
local `cname'_pos `cpos'
}
local copt
local cpos
local cname
}
if (`"`symbol'"' == ""){
local symbol `"█"'
}
if ("`tbl_title_pos'" == ""){
local tbl_title_pos = -20
}
if ("`tbl_labels_pos'" == "") {
local tbl_labels_pos = -20
}
if ("`tbl_labels_just'" == "") {
local tbl_labels_just labjustification(right)
}
************* GETTING A FRAME WITH RISK VALUES SPLIT AT LANDMARK TIME ******
*Get data
marksample touse
tempname frworking
frame copy `frfrom' `frworking'
frame `frworking' {
qui{
keep if `touse'
*if data is not already st
cap st_is 2
if _rc == 119 {
if "`failure'" != ""{
* set the data as survival
stset `varname', `idid' failure(`failure') `stsetopts'
}
else{
noi di as error _newline "Data not declared as survival-time." _newline "Run {cmd:stset} first or provide options {opt failure()}, {opt id()} (and {it:varname} if needed) to {cmd:sts_graph_landmark}. (see {stata help sts_graph_landmark})"
error 119
}
}
else{
//if data already stset
noi di as text _newline(1) "Current st settings:"
noi st_show
//has been stset with option id:
if ("`_dta[st_id]'" != ""){
//in case no id() option provided to sts_graph_landmark
if ("`defaultid'" == "defaultid"){
if("`stsetopts'" != ""){
noi di as text _newline(1) "Adding stsetops() to current st settings"
streset, `stsetopts'
}
else{
noi di as text _newline(1) "Using existing st settings."
}
*but still need to substitute internal variable with existing st settings:
drop `id' //drop the ad-hoc id tempvar to avoid confusion
local id "`_dta[st_id]'" //and use the stset id instead
local idid "id(`_dta[st_id]')"
}
else{
//in case user provided an override to stset id()
if ("`_dta[st_id]'" != "`id'"){
noi di as text _newline(1) "Override st id():"
streset, id(`id') `stsetopts'
noi st_show
}
}
}
else{
//if data already stset with option id:
*stsplit later require data to be id() set
if ("`defaultid'" == "defaultid") noi di as error _newline "Warning: data not {cmd:stset} with {opt id()} option." _newline " Data is reset as: .{cmd:streset, id(_n)} (->assumption that survival data is single-record. )" _newline "If data is multiple-record, please re-run either {cmd:stset} or {cmd:sts_graph_landmark} with the correct {opt id()} variable." _newline as text
else noi di as text _newline "Data not {cmd:stset} with {opt id()} option." _newline " Data is reset as: .{cmd:streset, id(`id')} as specified in option {opt id()}" _newline as text
noi di "`id'"
streset, id(`id') `stsetopts'
noi di as text _newline(1) "st settings used:"
noi st_show
}
}
*save label of failure variable
local fail_labvar: variable label `failure'
*if risktable, get at-risk populations:
if ("`risktable'" == "risktable"){
local nxlabel: word count `risktabletimes'
forval j = 1/`nlevels' {
local clevel : word `j' of `by_lvls'
forval i = 1/`nxlabel' {
local k : word `i' of `risktabletimes'
local k2 : word `=`i'+1' of `risktabletimes'
if `i' < `nxlabel'{
if (`k' == 0) local equal "="
else macro drop equal
count if _t>=`k' & `by' == `clevel' & _t0 <`equal' `k'
local atrisk `r(N)'
count if (_d & ~missing(_d) & _t >= `k' & _t < `k2' & `by'== `clevel' )
local events `r(N)'
/* add the at risk text */
local axislab`j' `"`axislab`j'' `k' "`atrisk'""'
if `"`showev'"' != "" {
/* add the events text */
local k2 = (`k' + `k2')/2.2
local axislab`j' `"`axislab`j'' `k2' "(`events')""'
}
}
else{ //last period is different (at the `end' timepoint)
quietly count if _t >= `k' & `by' == `clevel' & _t0 < `k'
local atrisk `r(N)'
local axislab`j' `"`axislab`j'' `k' "`atrisk'""'
*noi di `"`axislab`j''"'
}
}
}
}
*Landmark analyses for `nat' periods
stsplit indicator, at(`atend') trim nopreserve
*drop previous results of usedefined function
cap mat drop _r*
preserve
foreach i of numlist 0 `at' {
local ii: subinstr local i "." "pt" //necessary when at() numlist contains non-integers
tempfile lmfig_`ii'
keep if indicator == `i'
replace `failure' = 0 if `failure' != 1
/*previously:
stset, clear
stset `varname', `idid' failure(`failure') `stsetopts'
This is unneeded since we can simple re-apply stset like this:*/
pause
streset
*run user command:
if (`"`usercmd'"' != "" & ) {
noi di _newline(2) as text "{hline 80}" _newline "Landmark time `i'"
noi `usercmd'
mat _r_`i' = r(table)
add_fix `:colnames _r_`i'', prefix(`"""') suffix(`":`i'""')
mat colnames _r_`i' = `r(newlist)'
}
*save sts list
sts list, `byby' failure saving("`lmfig_`ii''", replace) `stslistopts'
restore, preserve
}
*store results from user command in same matrix
if (`"`usercmd'"' != "") {
local _r `:all matrices "_r_*"'
local _r "`:list sort local _r'"
local _r `"`:subinstr local _r " " ", ", all'"'
mat _r = `_r'
noi di _newline(2) as text "{hline 80}" _newline `"Available results from usercmd: "`usercmd'""'
noi mat list _r
}
restore, not
*coalesce data
use "`lmfig_0'", replace
local epsilon = 1.0x-1b
foreach i of numlist 0 `at' {
local ii: subinstr local i "." "pt" //necessary when at() numlist contains non-integers
foreach level of local by_lvls {
insobs 1, after(_N)
replace failure = 0 in l
replace time = cond(`i' == 0, 0, `i' + `epsilon') in l
replace `by' = `level' in l
}
if `i'> 0 append using "`lmfig_`ii''"
}
replace failure=failure*100
lab var failure "`fail_labvar'"
*separate KM curves per landmark-period and bygroups
forvalues i = 1/`=`nat'+1' { //for each `at' (landmark timepoints)
local lb = `:word `i' of `atend'' + `epsilon'
local ub = `:word `=`i'+1' of `atend'' + `epsilon'
if (`i'==1) local dis_cond time <= `ub'
else local dis_cond inrange(time,`lb', `ub')
forvalues j = 1/`nlevels' { //for each `level' (by groups)
local clevel : word `j' of `by_lvls'
gen failure`i'`j' = failure if `dis_cond' & ( (time == `lb' & missing(`by')) | `by' == `clevel')
replace failure`i'`j' = failure`i'`j'[_n-1] if failure`i'`j' == 0 & missing(failure`i'`j'[_n+1])
}
}
************* GRAPHING RESULTS AND BUILDING RISKTABLE ******************
*Build graphing command
forvalues i = 1/`=`nat'+1' { //for each `at' (landmark timepoints)
forvalues j = 1/`nlevels' { //for each `level' (by groups)
if (`j' > 1 | `nlevels' == 1) local twowaycmd `" || "'
local lmgraph `lmgraph' `twowaycmd' line failure`i'`j' time, `graphobs' lcolor("`:word `j' of `lcolors''") lpattern("`:word `j' of `lpattern''")
}
if (`i' > 1) local lmgraph `lmgraph' xline(`:word `i' of `atend'', lp(shortdash) lc(black)) //add landmark delimitation vertical line
}
*Add the risktable to the graph
if("`risktable'" == "risktable"){
local axisname 1
forvalues j = 0/`nlevels' {
local caxis `=`j'+10'
local axisname `"`axisname' `caxis'"'
local maxaxes `caxis'
*Remove all axis titles
local rtopts `rtopts' xtitle("", axis(`caxis'))
*Add risktable scheme to axis
local rtopts `rtopts' xscale(style(scheme sts_risktable) axis(`caxis'))
if `j'>0 {
*Add tbl_content: risktables content (numbers) as axis labels
local rtopts `rtopts' xlabel(`axislab`j'', custom axis(`caxis') `tbl_content_opts' /*labsize(vsmall)*/)
*Add tbl_labels: risktable labels (bygroup names)
local cbyname : label (`by') `:word `j' of `by_lvls'' 20
if (regexm("`tbl_labels_just'","left")){
local labeltxt1 `symbol'
local labeltxt2 `symbol' `cbyname'
}
else{
local labeltxt1 `symbol'
local labeltxt2 `cbyname' `symbol'
}
local tbl_label_ico xlabel(`tbl_labels_pos' `"`labeltxt1' "' , axis(`caxis') labcolor("`:word `j' of `lcolors''") `tbl_labels_just' `tbl_labels_opts' add custom)
local tbl_label xlabel(`tbl_labels_pos' `"`labeltxt2' "', axis(`caxis') add custom norescale `tbl_labels_just' `tbl_labels_opts' labstyle(sts_risktitle))
local rtopts `rtopts' `tbl_label' `tbl_label_ico'
}
else{
*Add tbl_title: risktable title (the table name (not an xtitle))
local rtopts `rtopts' xlabel(`tbl_title_pos' `"Number at risk"', custom norescale labstyle(sts_risktitle) axis(`caxis') `tbl_title_just' `tbl_title_opts')
}
}
local rtopts xaxis(`axisname') maxaxes(`maxaxes') `rtopts' xoverhang scale(`scale')
}
local lmgraph `"`lmgraph' `rtopts' `xlabel' `ylabel' `options' `options2'"' //add graph options
}
if "`showcmd'" != "" {
di as text _newline(2) `"`lmgraph'"'
}
************************ DISPLAY GRAPH *****************************
*Execute query
twoway `lmgraph'
}
*drop working frame
frame change default
*frame drop frworking
if("`keepplotdata'" != ""){
frame copy `frworking' sts_graph_data, replace
di "Plotting data available in frame sts_graph_data"
}
end
cap program drop add_fix
program define add_fix, rclass
syntax namelist [, PREFix(string) SUFfix(string)]
foreach word of local namelist {
local newlist "`newlist' `prefix'`word'`suffix'"
}
return local newlist = `"`newlist'"'
end
cap program drop remove_non_numeric
program define remove_non_numeric, rclass
*remove any non numeric element (not any character, any element) of list provided and returns a proper numlist
foreach word in `*' {
if regexm("`word'","[^0-9]") == 0 local numlist "`numlist' `word'"
}
return local numlist = `"`numlist'"'
end