local v: di

video

7.1 summary

Lets recap the last 7 weeks in the spirit of a coda:

• help

  • the help command followed by any command you wish to further explore

  • e.g., h twoway

• tokenize

  • represent a numerical sequence (e.g. 1,2,3,…,6)

  • as a sequence of letters (e.g. a,b,c,…,z or A,B,C,…,Z)

• quietly

  • how to control what is displayed in the Stata terminal

  • Stata uses this e.g. with the neat regression output, and with profile.do

  • may very easily be changed to noisily if that suits your needs

• delimit

  • neat way to mimic SAS in defining the end of one “line” of code

  • especially useful when dealing with graphical output and numerous graphing options

  • absolutely necessary if ever you wish to translate .SAS code into .do

  • may make accessible what otherwise were inaccessible datasets (e.g. NHANES)

• rnormal()

  • simulating parametric distributions

  • you may develop this idea on your own in the future

  • but we lay the foundation for this developement somewhere below

  • runiform() & rnormal() are the only distributions demonstrated thus far

  • rbinomial() & rweibull() are introduced below in the context of time-to-event data

• pwd

  • pwd

  • di c(pwd)

  • di “text with embedded `c(pwd)’ for whatever reason”

  • global filepath c(pwd)

• r(mean)

  • creturn list

  • return list

  • ereturn list

• by

  • collapse (statistic) varname1, by(varname2)

  • egen varname1=statistic(varname2)

  • above commands are equivalent in many regards

  • one distorts the data; the other doesn’t do so at all

  • useful created twoway plots or other graphical output

• program define

  • rigid, specific programs (without syntax varlist or syntax, options)

  • flexible, generalizable programs (with syntax [varlist], [options])

    • table1_options.ado

    • ind_translator.ado

    • table_transplant.do

• capture

  • preventing error results and an arrested script

  • Stata is finicky, pernickety and this little preface to a command may spare you untold misery

  • we’ve used it most frequently before program define & log using

  • but, notably, we’ve used it as a parsimonous variant in syntax varlist if

• twoway

  • last weeks class, which we didn’t cover because of hw1-related issues

  • notes have been updated to give you the best bang for your buck

  • lookout for the following very important issues:

    • workflow;

    • open science; and,

    • chatGPTs take on these.

• on your own, please go walk step-by-step, command-by-command, through the twoway examples offered

• think about if macro { conditional code-blocks and your deployment of this artifice in future, very powerful Stata scripts!

7.2 macros

Today we’ll circle back to the method emplyed throughout this class:

• defining macros

• formatting them

• embedding them in strings, text, figures, and excel

• producing aesthically pleasing, richly informative output

7.3 science

But to what end?

• the advanced Stata Programming class answers that question thus:

  • open science

  • self-publication

  • collaboration

  • etc…

Show code cell source Hide code cell source

import networkx as nx
import matplotlib.pyplot as plt
#import numpy as np
#import sklearn as skl
# 

#plt.figure(figsize=[2, 2])
G = nx.DiGraph()
G.add_node("workflow",  pos = (0,700) )
G.add_node("jupyter",  pos = (-2000, 960) )
G.add_node("dofile",  pos = (2000, 950) )
G.add_node("python ", pos = (-3000, 550) )
G.add_node("stata", pos = (3000, 550) )
G.add_node("build", pos = (-1900, 150) )
G.add_node("dyndoc", pos = (1900, 150) )
G.add_node("html", pos = (0,0))
G.add_node("push", pos = (0, -475))
G.add_node("ghp", pos = (0, -950))
G.add_edges_from([ ("jupyter","python "), ("dofile", "stata")])
G.add_edges_from([("python ", "build"), ("stata", "dyndoc") ])
G.add_edges_from([("build", "html"), ("dyndoc", "html")])
G.add_edges_from([("html","push")])
G.add_edges_from([("push","ghp")])
nx.draw(G, 
        nx.get_node_attributes(G, 'pos'), 
        with_labels=True, 
        font_weight='bold', 
        node_size = 4500,
        node_color = "lightblue",
        linewidths = 3)
ax= plt.gca()
ax.collections[0].set_edgecolor("#000000")
ax.set_xlim([-5000, 5000])
ax.set_ylim([-1000, 1000])
plt.show()

If at all you’ve enjoyed the conveniences brought forth by this classbook, then it would be remiss of me not to let you know from whence this book comes:

• a data science class

• python environment

• jupyter notebooks

• vscode by miscrosoft

• dofiles

• stata

In the advanced class we merge these ideas and publish our analyses and documentation (roll over, annotation) online via gh-pages!!!

7.4 embed

Output

local macro: di %3.1f r(mean)*100

• Text

  • di “You may embed a macro in text”

• Figures

  • line y x, text(50 18 “macro”)

• Excel

  • putexcel set filename, replace

  • putexcel B2=(”macro”)

• Word

  • putdocx clear

  • putdocx begin

  • putdocx paragraph

  • putdocx text

  • putdocx save doc1.docx, replace

• Dataset

  • postfile regcoeffs b1 b2 b3 using regoutput, replace

  • postfile regcoeffs () () ()

  • postfile regcoeffs () () ()

  • postclose regcoeffs

  • ls *.dta //look for regoutput.dta in your pwd

• Markdown

  • dyndoc

  • .md

  • .html

  • LaTeX

  • .css

  • JavaScript

7.4.5 postfile

use transplants, clear
sum peak_pra,d
g highpra=peak_pra>r(p90)
sum wait_yrs,d
g longwait=wait_yrs>r(p50)
postutil clear 
postfile pp xaxis str80 coef double(result lb ub pvalue) using betas.dta, replace 
logistic highpra gender prev_ki bmi age wait_yrs don_ecd
local xaxis=1
qui foreach v of varlist gender prev_ki bmi age wait_yrs don_ecd {  
	lincom `v'
	return list 
	local est: di %3.2f r(estimate)
	local lb: di %3.2f r(lb)
	local ub: di %3.2f r(ub)
	local pval: di %3.2f r(p)
    post pp (`xaxis') ("`v'") (`est') (`lb') (`ub') (`pval')
	local xaxis=`xaxis' + 1
}

postclose pp

ls -l
use betas,clear
list 
#delimit ;
twoway (scatter result xaxis)
       (rcap lb ub xaxis, 
	       scale(log)
	       yline(1, 
	            lc(lime) 
			    lp(dash)
	            )
	       legend(off)
	       xlab(
	           1 "Gender" 
	           2 "Previous Tx"
	           3 "BMI"
		       4 "Age"
		       5 "Wait y"
	           6 "ECD"
	           )
	       ti("Association between High PRA and select risk factors", pos(11))
	       yti("OR", 
	           orientation(horizontal)
		      )
	       xti("")
	      )
        ;
#delimit cr
graph export logistic.png,replace 

7.4.6 alternative: coefplot

use transplants, clear
sum peak_pra,d
g highpra=peak_pra>r(p90)
sum wait_yrs,d
g longwait=wait_yrs>r(p50)
logistic highpra prev_ki bmi age wait_yrs don_ecd if gender==0
est store male
logistic highpra prev_ki bmi age wait_yrs don_ecd if gender==1
est store female
if 0 {
	lab var highpra "PRA>90th %"
	lab var longwait "Wait>50th %"
	lab var prev_ki "Previous Tx"
	lab var bmi "BMI, kg/m2"
	lab var age "Age, y"
	lab var don_ecd "ECD"
}
coefplot male female, drop(_cons) xline(0) 

7.6 counterfeiting

A word on simulation:

7.6.1 rigor vs. fraud

• worth developing skills

• making up data

• imaginary scenarios

• and why would one do that?

  • randomization (e.g. student -> TA in this class; study pop -> Rx group in clinical trial)

  • missing data (imputation)

  • bootstrap (the most robust way to estimate error for any statistic)

  • cryptography/disclosure risk

  • sample-size calculation (variant on missing data)

  • engineering, reverse engineering

  • counterfeiting reality for fraudulent purposes

  • adversarial training against sophisticated counterfeits

  • didactic purposes for any of the above :)

7.6.2 didactic

qui {
	clear 
	cls
	if c(N) { //background
		inspired by polack et al. nejm 2020
		NEJM2020;383:2603-15
		lets do some reverse engineering
		aka simulate, generate data 
		from results: reversed process!!
	}
	if c(os)=="Windows" { //methods
	    lobal workdir "`c(pwd)'\"
	}
	else {
	    global workdir "`c(pwd)'/"
	}
	capture log close
	log using ${workdir}simulation.log, replace 
	set seed 340600
	set obs 37706
	}
	if c(N)==37706 { //simulation 
	    #delimit ; 
		//row1
		g bnt=rbinomial(1,.5);
		lab define Bnt 
		    0 "Placebo"  
	        1 "BNT162b2" ;
		label values bnt Bnt ;
		tab bnt ; 
		//row2
		gen female=rbinomial(1, .494); 
		label define Female  
		    0 "Male"  
			1 "Female"; 
		label values female Female; 
		tab female;
		//row3 
		tempvar dem ;
		gen `dem'=round(runiform(0,100),.1); 
		recode `dem'  
		    (0/82.9=0)  
		    (83.0/92.1=1)  
		    (92.2/96.51=2)   
		    (96.52/97.0=3)  
		    (97.1/97.2=4)  
		    (97.3/99.41=5)  
		    (99.42/100=6)  
		         , gen(race);
		lab define Race  
			0 "White"    
		    1 "Black or African American" 
			2 "Asian" 
			3 "Native American or Alsak Native"  
			4 "Native Hawaiian or other Pacific Islander"  
			5 "Multiracial"  
			6 "Not reported"; 
		label values race Race; 
		tab race;
		//row4 
		gen ethnicity=rbinomial(1,0.28);
		tostring ethnicity, replace;
		replace ethnicity="Latinx" if ethnicity=="1";
		replace ethnicity="Other" if ethnicity=="0";
		//row5 
		tempvar country;
		gen `country'=round(runiform(0,100), .1);
		recode `country'   
		    (0/15.3=0)  
			(15.4/21.5=1)  
			(21.6/23.6=2)  
			(23.7/100=3) 
			    , gen(country) ;
		label define Country 
			0 "Argentina"  
		    1 "Brazil"  
			2 "South Africa"  
			3 "United States"; 
		label values country Country; 
		tab country;
		//row7 
		gen age=(rt(_N)*9.25)+52 ; 
		replace age=runiform(16,91)  
		    if !inrange(age,16,91); 
		summ age, d ;
		local age_med=r(p50); local age_lb=r(min); local age_ub=r(max);
		gen dob = d(27jul2020) -  
		          (age*365.25) ; 
		gen dor = dob + age*365.25 + runiform(0,4*30.25); 
		//row6 
		gen over55=age>55 ; tab over55;
		//row8 
		gen bmi=rbinomial(1, .351); tab bmi; 
		//figure 3 
		g days=rweibull(.7,17,0) if bnt==0 ;
		g covid=rbinomial(1, 162/21728) if bnt==0 ; 
		replace days=rweibull(.4,.8,0) if bnt==1 ;
		replace covid=rbinomial(1, 14/21772) if bnt==1; 
		//key dates 
		gen eft = dor + days;
		//date formats
		format dob %td; format dor %td; format eft %td;
		 //kaplan-meier curve
		 stset days, fail(covid) ;
		 sts graph,  
		    by(bnt)  
		    fail per(100)  
		    tmax(119)  
		    xlab(0(7)119) 
		    ylab(0(.4)2.4, 
		        angle(360)    
			    format("%3.1f")
				)  
		    xti("Days after Dose 1")  
		    legend(off) 
		    text(
			    2.3 100 
			    "Placebo",  
			     col(navy)
				 )  
		    text(
			    .5 100 
				"BNT162b2",  
			    col(maroon)
				) ;
		graph export BNT162b2.png, replace ;
		stcox bnt ;
		drop _* age over55 days ;
		g bnt_id=round(runiform(37,37+_N)) ;
		compress  ;
		#delimit cr
		//label variables
		lab var bnt_id "Participant Identifier"
		lab var bnt "Random treatment assignment"
		lab var female "Gender at birth"
		lab var race "Self-identified race"
		lab var ethnicity "Hispanic ethnicity"
		lab var country "Country where trial was conducted"
		lab var dob "Date of birth"
		lab var dor "Date of recruitment into BNT162b2 trial"
		lab var eft "Date of exit from BNT162b2 trial"
		lab var bmi "Obese"
		lab var covid  "Covid-19 status on eft date"
		//label data
		lab data "Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine"
		describe
		order bnt_id dob female race ethnicity country bmi bnt eft covid 
		*replace eft=. if eft>d(15dec2020) //some folks lost to followup
		save BNT162b2, replace 

	}
  log close 
}		

7.8 strings

• Handling strings such as:

  • data file names

  • generic drug names

  • all sorts of lists

• We’ll review a script I wrote 4 years ago:

  • 440 lines of code

• Then compare it with an update this spring:

  • 182 lines of code

• Finally compare it with a variant i wrote in the summer:

  • 139 lines of code

• In brief, there is a fundamental transformation in:

  • aesthetics, legibility, & brevity

  • what is repetitive is codified in a loop

  • loops always utilizes macros and conditional statements

7.8.1 wild-type

import excel "1-first gen antihisitamines.xlsx", sheet("de-duplicated list") clear
drop in 1/6
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="antihist"
keep *_gnn
gen group=1
save 01_antihistamines, replace

import excel "2-antiparkinsonian agents.xlsx", sheet("De-duplicated list") clear
drop in 1/6
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="antipark"
keep *_gnn
gen group=2
save 02_antiparkinsons,replace

import excel "3-Antispasmodics.xlsx", sheet("De-duplicated_list") clear
drop in 1/7
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="antispasm"
keep *_gnn
keep if !missing(drug)
gen group=3
save 03_antispasmodics,replace 

import excel "4-Antithrombotics", sheet("De-duplicated_results") clear
drop in 1/7
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="antithromb"
keep *_gnn
keep if !missing(drug)
gen group=4
save 04_antithrombotics,replace

import excel "5-antiinfective agents", sheet("Sheet2") clear
drop in 1/8
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="antiinfect"
keep *_gnn
keep if !missing(drug)
gen group=5
save 05_antiinfective,replace

import excel "6-Peripheral alpha-1 blockers", sheet("De-duplicated_results") clear
drop in 1/6
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="pera1block"
keep *_gnn
keep if !missing(drug)
gen group=6
save 06_peripheralalpha1blockers,replace

import excel "7-Central alpha-agonists", sheet("de-duplicated_list") clear
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="cena1ag"
keep *_gnn
keep if !missing(drug)
gen group=7
save 07_centralalpha1agonists,replace 

import excel "8-Other CNS alpha-agonists", sheet("De-duplicated_list") clear
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="otha1ag"
keep *_gnn
keep if !missing(drug)
gen group=8
save 08_otheralpha1agonists,replace 

import excel "9-Antidepressants", sheet("De-duplicated_results") clear
drop in 1/8
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="antidep"
keep *_gnn
keep if !missing(drug)
gen group=9
save 09_antidepressants,replace 

import excel "10-Antipsychotic agents", sheet("De-duplicated_results") clear
drop in 1/8
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="antipsy"
keep *_gnn
keep if !missing(drug)
gen group=10
save 10_antipsychotics,replace 

import excel "11-Barbituates", sheet("De-duplicated_results") clear
drop in 1/6
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="barb"
keep *_gnn
keep if !missing(drug)
gen group=11
save 11_barbiturates,replace 

import excel "12-Benzodiazepine lists", sheet("Short-acting") clear
drop in 1/7
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="benzoshort"
keep *_gnn
keep if !missing(drug)
tempfile benzoshort
save `benzoshort',replace

import excel "12-Benzodiazepine lists", sheet("Long-acting") clear
drop in 1/8
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="benzolong"
keep *_gnn
keep if !missing(drug)
tempfile benzolong
save `benzolong',replace

import excel "12-Benzodiazepine lists", sheet("Unknown") clear
drop in 1/7
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="benzounk"
keep *_gnn
keep if !missing(drug)
tempfile benzounk
save `benzounk',replace
         use `benzoshort',clear
append using `benzolong'
append using `benzounk'
gen group=12
save 12_benzodiazepines,replace 

import excel "13-Nonbenzodiazepines - Z-drugs", sheet("De-duplicated_results") clear
drop in 1/6
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="nonbenzo"
keep *_gnn
keep if !missing(drug)
gen group=13
save 13_nonbenzodiazepines,replace 

import excel "14-Ergoloid Mesylates", sheet("De-duplicated_results") clear
drop in 1/7
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="ergot"
keep *_gnn
keep if !missing(drug)
gen group=14
save 14_ergoloids,replace 

import excel "15-Androgens", sheet("De-duplicated_results") clear
drop in 1/7
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="andro"
keep *_gnn
keep if !missing(drug)
gen group=15
save 15_androgens,replace 

import excel "16-Estrogens", sheet("De-duplicated_results") clear
drop in 1/6
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="estro"
keep *_gnn
keep if !missing(drug)
gen group=16
save 16_estrogens,replace 

import excel "17-Growth hormone", sheet("De-duplicated_results") clear
drop in 1/7
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="growth"
keep *_gnn
keep if !missing(drug)
gen group=17
save 17_growthhormones,replace 

import excel "18-Insulin", sheet("De-duplicated_results") clear
drop in 1/8
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="insulin"
keep *_gnn
keep if !missing(drug)
gen group=18
save 18_insulin,replace 

import excel "19-Sulfonylureas", sheet("De-duplicated_results") clear
drop in 1/5
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="urea"
keep *_gnn
keep if !missing(drug)
gen group=19
save 19_sulfonylureas,replace 

import excel "20-38", sheet("20.Proton_Pump_Inhibitors") clear
drop in 1/1
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="ppi"
keep *_gnn
keep if !missing(drug)
gen group=20
save 20_protonpumpinh,replace 

import excel "20-38", sheet("21.non-selective NSAIDS") clear
drop in 1/1
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="nsnsaids"
keep *_gnn
keep if !missing(drug)
gen group=21
save 21_nonselectnsaids,replace 

import excel "20-38", sheet("22.Skeletal muscle relaxants") clear
drop in 1/2
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="muscle"
keep *_gnn
keep if !missing(drug)
gen group=22
save 22_musclerelaxants,replace 

import excel "20-38", sheet("23.non-DHP CCB") clear
drop in 1/1
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="ccb"
keep *_gnn
keep if !missing(drug)
gen group=23
save 23_nondhpccb,replace 

import excel "20-38", sheet("24.Thiazolidinediones") clear
drop in 1/1
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="thiazo"
keep *_gnn
keep if !missing(drug)
gen group=24
save 24_thiazolidinediones,replace 

import excel "20-38", sheet("25.Acetyl cholinesterase inhib") clear
drop in 1/1
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="achblock"
keep *_gnn
keep if !missing(drug)
gen group=25
save 25_acetylcholinesteraseinh,replace 

import excel "20-38", sheet("26.alpha-1 blockers") clear
drop in 1/1
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="a1block"
keep *_gnn
keep if !missing(drug)
gen group=26
save 26_alpha1blockers,replace 

import excel "20-38", sheet("27.ti-cyclic antidepressants") clear
drop in 1/1
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="tca"
keep *_gnn
keep if !missing(drug)
gen group=27
save 27_tca,replace 

import excel "20-38", sheet("28.corticosteroids") clear
drop in 1/1
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="steroids"
keep *_gnn
keep if !missing(drug)
gen group=28
save 28_corticosteroids,replace 

import excel "20-38", sheet("29.H2 receptor antagonists") clear
drop in 1/1
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="h2ant"
keep *_gnn
keep if !missing(drug)
gen group=29
save 29_h2rblockers,replace 

import excel "20-38", sheet("30.antiepileptics") clear
drop in 1/1
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="antiepi"
keep *_gnn
keep if !missing(drug)
gen group=30
save 30_antiepileptics,replace 

import excel "20-38", sheet("31.antiemetics") clear
drop in 1/1
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="antieme"
keep *_gnn
keep if !missing(drug)
gen group=31
save 31_antiemetics,replace 

import excel "20-38", sheet("32.NSAIDS") clear
drop in 1/1
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn 
gen class_gnn="nsaid"
keep *_gnn
keep if !missing(drug)
gen group=32
save 32_nsaids,replace 

import excel "20-38", sheet("33.Diuretics") clear
drop in 1/1
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="diuretics"
keep *_gnn
keep if !missing(drug)
gen group=33
save 33_diuretics,replace 

import excel "20-38", sheet("34.SNRIs") clear
drop in 1/1
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="snri"
keep *_gnn
keep if !missing(drug)
gen group=34
save 34_snri,replace 

import excel "20-38", sheet("35.SSRIs") clear
drop in 1/1
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="ssri"
keep *_gnn
keep if !missing(drug)
gen group=35
save 35_ssri,replace 

import excel "20-38", sheet("36.RAS Inhibitor") clear
drop in 1/2
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="ras"
keep *_gnn
keep if !missing(drug)
gen group=36
save 36_rasinhibitors,replace 

import excel "20-38", sheet("37.Opioids") clear
drop in 1/1
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="opioids"
keep *_gnn
keep if !missing(drug)
gen group=37
save 37_opioids,replace 

import excel "20-38", sheet("38.Anticholinergic") clear
drop in 1/1
replace A = strtrim(A)
replace A=ustrupper(A)
rename A drug_gnn
gen class_gnn="antich"
keep *_gnn
keep if !missing(drug)
gen group=38
save 38_anticholinergics,replace 

7.8.2 alpha-variant

qui {
	qui {
		clear
		cls
		if c(N) { //background
			we compiled a comprehensive list of medications within 
			each of the potentially inapporpriate medication (pim) 
			classes in a systematic manner.
			
			first, informaticists used micromedex, the control vocabularies of            medline and embase, and medication websites to generate 
			a trade and generic medication name list. 
			
			second, this list was curated to allow medications with multiple
            mechanisms of action to be represented in more than one pim class.
			we removed pims with topical or ocular routes of administration. 
			
			the final list was **imported into stata** to query 
			medicare part d claims for pims...
		} 
		if c(N)<1 { //methods
		    global workdir `c(pwd)' 
			if c(os)=="Windows" {
				global workdir "$workdir\"
			}
			else {
				global workdir "$workdir/"
			}
			#delimit ;
			global catalog1
			    "1-first gen antihisitamines"
				"2-antiparkinsonian agents"
				"3-Antispasmodics"
				"4-Antithrombotics"
				"5-antiinfective agents"
				"6-Peripheral alpha-1 blockers"
				"7-Central alpha-agonists"
				"8-Other CNS alpha-agonists"
				"9-Antidepressants"
				"10-Antipsychotic agents"
				"11-Barbituates"
				"12-Benzodiazepine lists"
				"12-Benzodiazepine lists"
				"12-Benzodiazepine lists"
				"13-Nonbenzodiazepines - Z-drugs"
				"14-Ergoloid Mesylates"
				"15-Androgens"
				"16-Estrogens"
				"17-Growth hormone"
				"18-Insulin"
				"19-Sulfonylureas"
				;  
			global catalog2
			    "20.Proton_Pump_Inhibitors"
				"21.non-selective NSAIDS"
				"22.Skeletal muscle relaxants"
				"23.non-DHP CCB"
				"24.Thiazolidinediones"
				"25.Acetyl cholinesterase inhib"
				"26.alpha-1 blockers"
				"27.ti-cyclic antidepressants"
				"28.corticosteroids"
				"29.H2 receptor antagonists"
				"30.antiepileptics"
				"31.antiemetics"
				"32.NSAIDS"
				"33.Diuretics"
				"34.SNRIs"
				"35.SSRIs"
				"36.RAS Inhibitor"
				"37.Opioids"
				"38.Anticholinergic";
			global namelist1
			    01_antihistamines
				02_antiparkinsons
				03_antispasmodics
				04_antithrombotics
				05_antiinfective
				06_peripheralalpha1blockers
				07_centralalpha1agonists
				08_otheralpha1agonists
				09_antidepressants
				10_antipsychotics
				11_barbiturates
			    benzoshort 
				benzolong
				benzounk 
				13_nonbenzodiazepines
				14_ergoloids
				15_androgens
				16_estrogens
				17_growthhormones
				18_insulin
				19_sulfonylureas;
			global namelist2
				20_protonpumpinh
				21_nonselectnsaids
				22_musclerelaxants
				23_nondhpccb
				24_thiazolidinediones
				25_acetylcholinesteraseinh
				26_alpha1blockers
				27_tca
				28_corticosteroids
				29_h2rblockers
				30_antiepileptics
				31_antiemetics
				32_nsaids
				33_diuretics
				34_snri
				35_ssri
				36_rasinhibitors
				37_opioids
				38_anticholinergics;
			#delimit cr 
			capture log close 
			log using "${workdir}01_bc050523.log",replace 
			set max_memory .
		}
		if c(N)==0 { //results
		    local group=1
			foreach class in "$catalog1" {  
			    import excel "${workdir}`class'.xlsx", clear
				drop in 1/6
				replace A=strtrim(A)
				replace A=ustrupper(A)
				rename A drug_gnn
				local class_tidy: di word("$namelist1",`group')
				g class_gnn="`class_tidy'"
				capture split class_gnn,p("_")
				capture keep drug_gnn class_gnn2
				if inrange(`group',1,11) {
					g group=`group'
				}
				else {
					g group=`group'-2
				}
				keep if !missing(drug)
				local filename: di word("$namelist1",`group')
				capture save "`filename'",replace  
				noi di "`filename'"
				local group=`group'+1 
			}
			use benzoshort,clear
			append using benzolong
			append using benzounk //debug
			replace group=12
			drop class_gnn
			rename class_gnn1 class_gnn2
			save 12_benzodiazepines,replace 
		}
		clear 
		if c(N)==0 {
			local group=1
			foreach class in "$catalog2" {
				import excel "${workdir}20-38.xlsx", /*
				    */ sheet("`class'") clear 
				drop in 1/1
				replace A=strtrim(A)
				replace A=ustrupper(A)
				rename A drug_gnn
				local class_tidy: di word("$namelist2",`group')
				g class_gnn="`class_tidy'"
				capture split class_gnn,p("_")
				capture keep drug_gnn class_gnn2
				g group=`group'+19
				keep if !missing(drug)
				local filename: di word("$namelist2",`group')
				capture save "`filename'",replace 
				noi di "`filename'"
				local group=`group'+1
				
			}
		}
	  cls
	  rm benzoshort.dta 
	  rm benzolong.dta
	  rm benzounk.dta 
      noi ls *.dta
	  timer list 
	  log close 
	}
}

7.8.3. beta-variant

qui {
	qui {
		clear
		cls
		if c(N) { //background
			we compiled a comprehensive list of medications within     
			each of the potentially inapporpriate medication (pim)     
			classes in a systematic manner.    
			
			first, informaticists used micromedex, the control vocabularies of                
			medline and embase, and medication websites to generate     
			a trade and generic medication name list.     
			
			second, this list was curated to allow medications with multiple        
            mechanisms of action to be represented in more than one pim class.     
			we removed pims with topical or ocular routes of administration.     
			
			the final list was **imported into stata** to query     
			medicare part d claims for pims...    
		} 
		if c(N)<1 { //methods
		    global workdir `c(pwd)' 
			if c(os)=="Windows" {
				global workdir "$workdir\"
			}
			else {
				global workdir "$workdir/"
			}
			#delimit ;   
			global catalog        
			    "1-first gen antihisitamines"     
				"2-antiparkinsonian agents"    
				"3-Antispasmodics"     
				"4-Antithrombotics"     
				"5-antiinfective agents"     
				"6-Peripheral alpha-1 blockers"    
				"7-Central alpha-agonists"    
				"8-Other CNS alpha-agonists"    
				"9-Antidepressants"    
				"10-Antipsychotic agents"    
				"11-Barbituates"    
				"12-Benzodiazepine lists"    
				"12-Benzodiazepine lists"    
				"12-Benzodiazepine lists"    
				"13-Nonbenzodiazepines - Z-drugs"    
				"14-Ergoloid Mesylates"    
				"15-Androgens"    
				"16-Estrogens"    
				"17-Growth hormone"    
				"18-Insulin"    
				"19-Sulfonylureas"    
			    "20.Proton_Pump_Inhibitors"    
				"21.non-selective NSAIDS"    
				"22.Skeletal muscle relaxants"    
				"23.non-DHP CCB"    
				"24.Thiazolidinediones"    
				"25.Acetyl cholinesterase inhib"    
				"26.alpha-1 blockers"    
				"27.ti-cyclic antidepressants"    
				"28.corticosteroids"    
				"29.H2 receptor antagonists"    
				"30.antiepileptics"    
				"31.antiemetics"    
				"32.NSAIDS"    
				"33.Diuretics"    
				"34.SNRIs"    
				"35.SSRIs"    
				"36.RAS Inhibitor"    
				"37.Opioids"    
				"38.Anticholinergic";    
			#delimit cr     
			capture log close     
			log using "${workdir}01_bc050523.log",replace     
			set max_memory .    
		}
		if c(N)==0 { //results
		    local group=1
		    foreach class in "$catalog" {
				if inrange(`group',1,9) {
					import excel "${workdir}`class'.xlsx", clear
					local class_tidy: di lower(substr("`class'",3,.))
					 g class_gnn="0`group'_`class_tidy'"
					 capture keep class_gnn
					 g group=`group'
					 keep if !missing(class_gnn)
					 capture save "0`group'_`class_tidy'",replace  
					 noi di "0`group'_`class_tidy'"
					local group=`group'+1
				}
				else if inrange(`group',10,11) {
					import excel "${workdir}`class'.xlsx", clear
					local class_tidy: di lower(substr("`class'",4,.))
					 g class_gnn="`group'_`class_tidy'"
					 capture keep class_gnn
					 g group=`group'
					 keep if !missing(class_gnn)
					 capture save "`group'_`class_tidy'",replace  
					 noi di "`group'_`class_tidy'"
					local group=`group'+1
				}	
				else if inrange(`group',12,21) {
					import excel "${workdir}`class'.xlsx", clear
					local class_tidy: di lower(substr("`class'",4,.))
					local group2=`group'-2
					 g class_gnn="`group2'_`class_tidy'"
					 capture keep class_gnn
					 g group=`group2'
					 keep if !missing(class_gnn)
					 capture save "`group2'_`class_tidy'",replace  
					 noi di "`group2'_`class_tidy'"
					local group=`group'+1
				}				
				else {
			   	    import excel "${workdir}20-38.xlsx", /*
				        */ sheet("`class'") clear 
					local class_tidy: di lower(substr("`class'",4,.))
					local group2=`group'-2
					 g class_gnn="`group2'_`class_tidy'"
					 capture keep class_gnn
					 g group=`group2'
					 keep if !missing(class_gnn)
					 capture save "`group2'_`class_tidy'",replace  
					 noi di "`group2'_`class_tidy'"
					local group=`group'+1
				}
			}
		}
	   clear 
	   forva i=10/12 {
	   	   append using "`i'_benzodiazepine lists"
		   rm "`i'_benzodiazepine lists.dta"
	   }
		   replace class_gnn="12_benzodiazepine"
		   replace group=12
           save 12_benzodiazepines,replace 
		   noi ls *.dta
		   log close 
	}
}			  	  

7.8.4 excel

Download these .xlsx files into the pwd for the above scripts to work:

1-first gen antihisitamines

2-antiparkinsonian agents

3-Antispasmodics

4-Antithrombotics

5-antiinfective agents

6-Peripheral alpha-1 blockers

7-Central alpha-agonists

8-Other CNS alpha-agonists

9-Antidepressants

10-Antipsychotic agents

11-Barbituates

12-Benzodiazepine lists

13-Nonbenzodiazepines - Z-drugs

14-Ergoloid Mesylates

15-Androgens

16-Estrogens

17-Growth hormone

18-Insulin

19-Sulfonylureas

20-38

7.8.5 commands

• strpos

• word

• strlen

• regexm

7.8.5.1 strpos

di "$S_TIME"
clear
set more off
tempfile pde_2013 pde_2014 pde2013bc pde2014bc 
use usrds_id srvc_dt gnn using "/dcs01/igm/segevlab/data/usrds2015/claims/pd/pde2013",clear
save `pde_2013',replace
use usrds_id srvc_dt gnn using "/dcs01/igm/segevlab/data/usrds2016/claims/pd/pde2014",clear
save `pde_2014',replace
local year "y=2013/2014"
forvalues `year' {
  capture use `pde_`y'',clear
	if _rc==0 {
		di "processing pde_`y'.dta ..."
        gen	antihist16=(strpos(gnn,"BROMPHENIRAMINE")!=0)
        gen	antihist19=(strpos(gnn,"CARBINOXAMINE")!=0)
        gen	antihist26=(strpos(gnn,"CHLORPHENIRAMINE")!=0)
        gen	antihist31=(strpos(gnn,"CLEMASTINE")!=0)
        gen	antihist36=(strpos(gnn,"CYPROHEPTADINE")!=0)
        gen	antihist39=(strpos(gnn,"DEXBROMPHENIRAMINE")!=0)
        gen	antihist40=(strpos(gnn,"DEXCHLORPHENIRAMINE")!=0)
        gen	antihist43=(strpos(gnn,"DIMENHYDRINATE")!=0)
        gen	antihist47=(strpos(gnn,"DIPHENHYDRAMINE")!=0)
        gen	antihist51=(strpos(gnn,"DOXYLAMINE")!=0)
        gen	antihist65=(strpos(gnn,"HYDROXYZINE")!=0)
        gen	antihist77=(strpos(gnn,"MECLIZINE")!=0)
        gen	antihist101=(strpos(gnn,"PROMETHAZINE")!=0)
        gen	antihist105=(strpos(gnn,"PYRILAMINE")!=0)
        gen	antihist127=(strpos(gnn,"TRIPROLIDINE")!=0)      
		gen  antihist_rx=( ///	
        antihist16+	///
        antihist19+	///
        antihist26+	///
        antihist31+	///
        antihist36+	///
        antihist39+	///
        antihist40+	///
        antihist43+	///
        antihist47+	///
        antihist51+	///
        antihist65+	///
        antihist77+	///
        antihist101+	///
        antihist105+	///
        antihist127	///
        >0)
        keep usrds_id srvc_dt antihist_rx 
        duplicates drop
        quietly compress
        save `pde`y'bc', replace  
	}
}

forvalues `year' {
		 capture append using `pde`y'bc'
}
save 01_antihistamines_expR.dta,replace
di "$S_TIME"        

7.8.5.2 others

//explore these commands sequentially, on your own
use transplants, clear
list extended_dgn in 1/5, clean
disp word("Hello, is there anybody in there?",4)
list extended_dgn if word(ext, 5) != "", clean noobs
disp strlen("Same as it ever was")
list extended_dgn if strlen(ext)< 6, clean
assert regexm("Earth", "art")
assert !regexm("team", "I")
tab ext if regexm(ext, "HTN")
list ext if regexm(ext, "^A")
//starts with A
list ext if regexm(ext, "X$")
//ends with X
tab ext if regexm(ext, "HIV.*Y")
//contains "HIV", then some otherstuff, then Y

7.9 dates

disp %td 19400 11feb2013
disp %td 366 01jan1961
disp %td -5 27dec1959
use transplants, clear
gen oneweek = transplant_date+7
list transplant_date oneweek in 1/3
format %td oneweek
list transplant_date oneweek in 1/3
disp td(04jul1976)
disp td(5may2021)
disp mdy(7,4,1976)
disp mdy(5,5,2021)
disp date("August 15, 1969", "MDY")
disp "$S_DATE"
di c(current_date)