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* ==============================================================================
* ciquartile: Creating spike plots with interquarterile range
* Author: Zong Huang
*
* Based off of Alexander Staudt's cibar
* ==============================================================================
* over1 : over-variable
* over2 : additional over-variable
* over3 : additional over-variable
* bar : plot spikes as bar; default is scatter
* horizontal : plot spikes horizontally; default is vertically
* reverse : reverse order of spikes
* missing : omit missing spikes (buggy)
* gap2 : specify gap between spike groups (over2); default is 67% (of a spike)
* gap3 : specify gap between spike groups (over3); default is 100% (of a spike)
* spikeopts : specify the look of the spikes (global)
* spikecolor : specify the color of the spikes, delimited by spaces
* spikegap : specify gap within spike groups; default is 0% (of a spike)
* spike : specify the look for each spike, delimited by ||
* spikegroup : specify the look for each spike group (over2), delimited by ||
* ciopts : specify the look of the confidence intervals (global)
* cicolor : specify the color of the confidence intervals, delimited by spaces
* ci : specify the look for each confidence interval, delimited by ||
* cigroup : specify the look for each confidence interval group (over2), delimited by ||
* graphopts : specify additional graph options
program define ciquartile
syntax anything(name = var) [if], ///
over1(string) [over2(string) over3(string) ///
bar horizontal missing reverse ///
gap2(integer 67) gap3(integer 100) ///
spikeopts(string asis) spikecolor(string asis) spikegap(integer 0) ///
spike(string asis) spikegroup(string asis) ///
ciopts(string asis) cicolor(string asis) ///
ci(string asis) cigroup(string asis) ///
graphopts(str asis)]
preserve
* ==========================================================================
* Parse options
* ==========================================================================
* If option
mark touse `if'
qui keep if touse == 1
* Direction option
if "`horizontal'" == "horizontal" {
local a1 "y"
local a2 "x"
local a1_angle "labgap(2) angle(0)"
local a1_order "s median"
}
else {
local a1 "x"
local a2 "y"
local a1_angle "labgap(2)"
local a1_order "median s"
}
* Group options
local bylist = "`over1' `over2' `over3'"
local n_over = wordcount("`bylist'")
local gap2 = `gap2' / 100 - 1
local gap3 = `gap3' / 100
* Spike options
local spikeopts = "fintensity(inten100) `a1'axis(1 2 3)" + " " + `"`spikeopts'"'
local sg = `spikegap' / 100
* Confidence interval options
local ciopts = "lcolor(gs8)" + " " + `"`ciopts'"'
* ==========================================================================
* Calculate mean and confidence interval
* ==========================================================================
* Calculate percentiles
bysort `bylist': egen lb = pctile(`var'), p(25)
bysort `bylist': egen median = mean(`var')
bysort `bylist': egen ub = pctile(`var'), p(75)
* Get percentiles
keep `bylist' lb median ub
duplicates drop
foreach x in `bylist' {
qui drop if `x' == . // Confidence intervals not calculated for missing groups
}
* ==========================================================================
* Get group labels
* ==========================================================================
if `n_over' == 2 {
capture confirm existence `over2'
if _rc == 6 {
local over2 = "`over3'"
display as txt "You specified over3() but not over2(). The value of over3() is used in over2() instead."
}
}
* Reindex group levels sequentially
forvalues i = 1/`n_over' {
qui tab `over`i''
local labels`i' = `r(r)'
qui levelsof(`over`i''), local(levels`i')
}
forvalues i = 1/`n_over' {
qui gen over`i'_n = .
tokenize "`levels`i''"
forvalues j = 1/`labels`i'' {
qui replace over`i'_n = `j' if `over`i'' == ``j''
}
}
* Label sequential group levels
forvalues i = 1/`n_over' {
tokenize "`levels`i''"
forvalues j = 1/`labels`i'' {
local ltext : label (`over`i'') ``j''
label define vlabel`i' `j' `"`ltext'"', add
if `j' == `labels`i'' label value over`i'_n vlabel`i'
}
}
forvalues i = 1/`n_over' {
qui levelsof(over`i'_n), local(levels`i'_n)
}
* ==========================================================================
* Generate graph labels (single group case)
* ==========================================================================
if `n_over' == 1 {
* Adjust spacing for spikegap
qui tab over1_n
qui gen s = over1_n
qui replace s = s * (1 + `sg')
* Reverse spacing if applicable
if "`reverse'" == "reverse" replace s = s * -1
* Get spacing for spikes
qui sum s
local s_min = `r(min)' - .75
local s_max = `r(max)' + .75
* Get labels for spikes
local axis = "`a1'label(`s_min'" + " " + `"" ""' + " " + "`s_max'" + " " + `"" ""' + ", noticks `a1_angle')"
}
* ==========================================================================
* Generate graph labels (two group case)
* ==========================================================================
if `n_over' == 2 {
* Add missing spikes
forvalues i = 1/`labels1' {
forvalues j = 1/`labels2' {
qui tab median if over1_n == `i' & over2_n == `j'
if `r(r)' == 0 {
local obsv = _N + 1
qui set obs `obsv'
qui replace over1_n = `i' in `obsv'
qui replace over2_n = `j' in `obsv'
}
}
}
sort over2_n over1_n
* Adjust spacing for spikegap
qui gen s = .
tokenize "`levels1_n'"
forvalues i = 1/`labels1' {
qui replace s = over1_n + (``i'' - 1) * (`sg') if over1_n == ``i''
}
* Adjust spacing for gap2
tokenize "`levels2_n'"
forvalues i = 1/`labels2' {
qui replace s = s + (`labels1' + 1 + `gap2' + `sg') * (`i' - 1) if over2_n == ``i''
}
* Get spacing for spikes
forvalues i = 1/`labels2' {
qui sum s if over2_n == `i'
local s_`i' = `r(mean)'
if `i' == `labels2' {
local s_min = 0
local s_max = `r(max)' + 1
}
}
* Reverse spacing if applicable
if "`reverse'" == "reverse" {
replace s = s * -1
forvalues i = 1/`labels2' {
local s_`i' = `s_`i'' * -1
}
local s_max = `s_max' * -1
}
* Get labels for spikes
local axis = "`a1'label(`s_min'" + " " + `"" ""'
forvalues i = 1/`labels2' {
local l_`i' : label (over2_n) `i'
local axis = `"`axis'"' + " " + "`s_`i''" + " " + `"`"`l_`i''"'"'
}
local axis = `"`axis'"' + " " + "`s_max'" + " " + `"" ""' + " " + ", noticks `a1_angle')"
}
* ==========================================================================
* Generate graph labels (three group case)
* ==========================================================================
if `n_over' == 3 {
* Add missing spikes
forvalues i = 1/`labels1' {
forvalues j = 1/`labels2' {
forvalues k = 1/`labels3' {
qui tab median if over1_n == `i' & over2_n == `j' & over3_n == `k'
if `r(r)' == 0 {
local obsv = _N+1
qui set obs `obsv'
qui replace over1_n = `i' in `obsv'
qui replace over2_n = `j' in `obsv'
qui replace over3_n = `k' in `obsv'
}
}
}
}
sort over3_n over2_n over1_n
* Drop missing cross-groups (if applicable)
qui egen over_cg = group(over3_n over2_n)
if "`missing'" == "missing" {
bysort over2_n over3_n: egen nonmissing = count(median)
qui drop if nonmissing == 0
}
sort over_cg `over1'
* Index cross-groupings
qui tab over_cg
local labels_cg = `r(r)'
qui levelsof(over_cg), local(levels_cg)
* Adjust spacing for spikegap
qui gen index = _n
qui gen over1_n2 = mod(index, `labels1')
qui replace over1_n2 = `labels1' if over1_n2 == 0
qui gen s = .
tokenize "`levels1_n'"
forvalues i = 1/`labels1' {
qui replace s = over1_n2 + (``i'' - 1) * (`sg') if over1_n2 == ``i''
}
* Adjust spacing for gap2
tokenize "`levels_cg'"
forvalues i = 1/`labels_cg' {
qui replace s = s + (`i' - 1) * (`labels1' + 1 + `gap2' + `sg') if over_cg == ``i''
}
* Adjust spacing for gap3
forvalues i = 1/`labels3' {
qui replace s = s + (-`gap2' + 1) * (`i' - 1) * `gap3' if over3_n == `i'
}
* Get spacing for spikes
tokenize "`levels_cg'"
forvalues i = 1/`labels_cg' {
qui sum s if over_cg == ``i''
local s_`i' = `r(mean)'
if `i' == `labels2' {
local s_min = 0
local s_max = `r(max)' + 1
}
}
* Reverse spacing if applicable
if "`reverse'" == "reverse" {
replace s = s * -1
forvalues i = 1/`labels_cg' {
local s_`i' = `s_`i'' * -1
}
local s_max = `s_max' * -1
}
* Get labels for cross-groupings
tokenize "`levels3_n'"
forvalues i = 1/`labels3' {
tokenize "`levels2_n'"
forvalues j = 1/`labels2' {
local l`j' : label (over2_n) ``j''
local y = `j' + (`i' - 1) * `labels2'
local y_l = "`y'" + " " + `"`"`l`j''"'"'
if `i' == 1 & `j' == 1 local vlabel = `"`y_l'"'
else local vlabel = `"`vlabel'"' + " " + `"`y_l'"'
}
}
qui label define vlabel `vlabel'
qui label value over_cg vlabel
* Get labels for spikes
tokenize "`levels_cg'"
local axis = "`a1'label(`s_min'" + " " + `"" ""'
forvalues i = 1/`labels_cg' {
local l_`i' : label (over_cg) ``i''
local axis = `"`axis'"' + " " + "`s_`i''" + " " + `"`"`l_`i''"'"'
}
local axis = `"`axis'"' + " " + "`s_max'" + " " + `"" ""' + " " + ", noticks `a1_angle')"
* Get labels for spike groupings
forvalues i = 1/`labels3' {
forvalues j = 1/`labels_cg' {
qui sum s if over3_n == `i'
}
local ss_`i' = `r(mean)'
local ll_`i' : label (over3_n) `i'
if `i' == 1 local l3 = "`ss_`i''" + " " + `"`"`ll_`i''"'"'
else local l3 = `"`l3'"' + " " + "`ss_`i''" + " " + `"`"`ll_`i''"'"'
if `i' == `labels3' {
local axis = `"`axis'"' + " " + "`a1'label(" + `"`l3'"' + ", noticks `a1_angle' axis(2))"
}
}
}
* ==========================================================================
* Generate graph components (single group case)
* ==========================================================================
if `n_over' == 1 {
* Generate graph components
forvalues j = 1/`labels1' {
if "`bar'" == "bar" {
qui gen spike`j' = "bar median s if over1_n == `j', `spikeopts' `horizontal'"
}
else {
qui gen spike`j' = "scatter `a1_order' if over1_n == `j', `spikeopts'"
}
qui gen rcap`j' = "rcap lb ub s if over1_n == `j', `ciopts' `horizontal'"
}
* Add colors to graph command
if wordcount(`"`spikecolor'"') > 0 {
qui gen scolors = `"`spikecolor'"'
qui split scolors, gen(scolor)
forvalues j = 1/`r(nvars)' {
cap qui replace spike`j' = spike`j' + " color(" + scolor`j' + ")"
}
}
if wordcount(`"`cicolor'"') > 0 {
qui gen rcolors = `"`cicolor'"'
qui split rcolors, gen(rcolor)
forvalues j = 1/`r(nvars)' {
cap qui replace rcap`j' = rcap`j' + " lcolor(" + rcolor`j' + ")"
}
}
* Add options to graph command
if wordcount(`"`spike'"') > 0 {
gen sopts = `"`spike'"'
qui split sopts, gen(sopt) p("||")
forvalues j = 1/`r(nvars)' {
cap qui replace spike`j' = spike`j' + " " + sopt`j'
}
}
if wordcount(`"`ci'"') > 0 {
gen ropts = `"`ci'"'
qui split ropts, gen(ropt) p("||")
forvalues j = 1/`r(nvars)' {
cap qui replace rcap`j' = rcap`j' + " " + ropt`j'
}
}
}
* ==========================================================================
* Generate graph components (multiple group case)
* ==========================================================================
if `n_over' > 1 {
* Generate graph components
forvalues i = 1/`labels1' {
forvalues j = 1/`labels2' {
if "`bar'" == "bar" {
qui gen spike`i'`j' = "bar median s if over1_n == `i' & over2_n == `j', `spikeopts' `horizontal'"
}
else {
qui gen spike`i'`j' = "scatter `a1_order' if over1_n == `i' & over2_n == `j', `spikeopts'"
}
qui gen rcap`i'`j' = "rcap lb ub s if over1_n == `i' & over2_n == `j', `ciopts' `horizontal'"
}
}
* Add colors to graph command
if wordcount(`"`spikecolor'"') > 0 {
qui gen scolors = `"`spikecolor'"'
qui split scolors, gen(scolor)
forvalues i = 1/`r(nvars)' {
forvalues j = 1/`labels2' {
cap qui replace spike`i'`j' = spike`i'`j' + " color(" + scolor`i' + ")"
}
}
}
if wordcount(`"`cicolor'"') > 0 {
qui gen rcolors = `"`cicolor'"'
qui split rcolors, gen(rcolor)
forvalues i = 1/`r(nvars)' {
forvalues j = 1/`labels2' {
cap qui replace rcap`i'`j' = rcap`i'`j' + " lcolor(" + rcolor`i' + ")"
}
}
}
* Add options to graph command
if wordcount(`"`spike'"') > 0 {
gen sopts = `"`spike'"'
qui split sopts, gen(sopt) p("||")
forvalues i = 1/`r(nvars)' {
forvalues j = 1/`labels2' {
cap qui replace spike`i'`j' = spike`i'`j' + " " + sopt`i'
}
}
}
if wordcount(`"`ci'"') > 0 {
gen ropts = `"`ci'"'
qui split ropts, gen(ropt) p("||")
forvalues i = 1/`r(nvars)' {
forvalues j = 1/`labels2' {
cap qui replace rcap`i'`j' = rcap`i'`j' + " " + ropt`i'
}
}
}
if wordcount(`"`spikegroup'"') > 0 {
gen sgopts = `"`spikegroup'"'
qui split sgopts, gen(sgopt) p("||")
forvalues i = 1/`labels1' {
forvalues j = 1/`r(nvars)' {
cap qui replace spike`i'`j' = spike`i'`j' + " " + sgopt`j'
}
}
}
if wordcount(`"`cigroup'"') > 0 {
gen rgopts = `"`cigroup'"'
qui split rgopts, gen(rgopt) p("||")
forvalues i = 1/`labels1' {
forvalues j = 1/`r(nvars)' {
cap qui replace rcap`i'`j' = rcap`i'`j' + " " + rgopt`j'
}
}
}
}
* ==========================================================================
* Generate graph
* ==========================================================================
* Concatenate graph components
if "`bar'" == "bar" {
qui egen graph = concat(spike* rcap*), punct(") (")
}
else {
qui egen graph = concat(rcap* spike*), punct(") (")
}
qui replace graph = "(" + graph + ")"
local graph = graph[1]
* ==========================================================================
* Get legend (single group case)
* ==========================================================================
if `n_over' == 1 {
forvalues j = 1/`labels1' {
local l`j' : label (over1_n) `j'
if "`bar'" == "bar" {
local v`j' = `j'
}
else {
local v`j' = `j' + `labels1'
}
if `j' == 1 {
local legend1 = `"`v`j'' "`l`j''""'
}
else {
local legend1 = `"`legend1'"' + " " + `"`v`j'' "`l`j''""'
}
}
local legend = `"legend(order(`legend1') region(lcolor(white)))"'
}
* ==========================================================================
* Get legend (multiple group case)
* ==========================================================================
if `n_over' > 1 {
forvalues j = 1/`labels1' {
local l`j' : label (over1_n) `j'
if "`bar'" == "bar" {
local v`j' = `j' * 2
}
else {
local v`j' = (`j' + `labels1') * 2
}
if `j' == 1 {
local legend1 = `"`v`j'' "`l`j''""'
}
else {
local legend1 = `"`legend1'"' + " " + `"`v`j'' "`l`j''""'
}
}
local legend = `"legend(order(`legend1') region(lcolor(white)))"'
}
* ==========================================================================
* Plot graph
* ==========================================================================
local format = `"`legend' plotregion(margin(bargraph)) graphregion(color(white))"' + " " + ///
`"`a2'title("") `a1'title("") `a1'title("", axis(2)) `a1'title("", axis(3))"' + " " + ///
`"`a1'scale(axis(2) noline) `a1'scale(axis(3) noline)"' + " " + ///
`"`a1'label(none, axis(2) noticks) `a1'label(none, axis(3) noticks)"' + " " + ///
`"`a1'label(, nogrid) `a2'label(, grid format(%9.3g))"'
dis `"`graph', `format' `axis' `graphopts'"'
twoway `graph', `format' `axis' `graphopts'
end
exit |