5. Review of Weeks 1 - 4#
Show code cell source
import networkx as nx
import matplotlib.pyplot as plt
G = nx.DiGraph()
G.add_node("user", pos=(550, 500))
G.add_node("system", pos=(-550, 500))
G.add_node("program", pos=(-2000, 960))
G.add_node("syntax", pos=(2000, 950))
G.add_node("ado", pos=(-3000, 550))
G.add_node("do", pos=(3000, 550))
G.add_node("command", pos=(-1900, 150))
G.add_node("queue", pos=(1900, 150))
G.add_node("results", pos=(0, 0))
G.add_node("dta", pos=(0, -475))
G.add_node("log", pos=(-1900, -475))
G.add_node("excel", pos=(-4000, -475))
G.add_node("word", pos=(1900, -475))
G.add_node("html", pos=(4000, -475))
G.add_node("publish", pos=(0, -950))
G.add_edges_from([("program", "ado"), ("syntax", "do")])
G.add_edges_from([("ado", "command"), ("do", "queue")])
G.add_edges_from([("command", "results"), ("queue", "results"), ("results", "excel"), ("results", "word"), ("results", "html")])
G.add_edges_from([("results", "dta"), ("results", "log")])
G.add_edges_from([("dta", "publish"), ("log", "publish"), ("excel", "publish"), ("word", "publish"), ("html", "publish")])
pos = nx.get_node_attributes(G, 'pos')
node_colors = ["lightblue" if node not in ["results", "excel", "publish"] else "lightpink" if node == "excel" else "lavender" if node == "results" else "lightgreen" for node in G.nodes()]
nx.draw(G, pos, with_labels=True, font_weight='bold', node_size=4500, node_color=node_colors, linewidths=3)
ax = plt.gca()
ax.collections[0].set_edgecolor("#000000") # Set edge color to black for better contrast
ax.set_xlim([-5000, 5000])
ax.set_ylim([-1000, 1000])
plt.show()
qui {
if 0 { //background: ph340.600.01, 04/21/2023-04/22/2023
0. inspired by ~/applications/stata/ado/base/s/stcox.ado
1. lookout for a blank noi di "" + other innovations!
2. output not exactly as required or instructed for hw1
3. spot the subtle differences + their role in aesthetics...
4. parisimony & legibility, all steeped in tradition
5. will require next years' class to do it this way :)
}
if 1 { //methods: macros, logfile, settings
cls
noi di "What is your work directory?" _request(workdir)
if "$workdir" == "" {
di as err "No working directory provided. Exiting."
exit 340600
}
else {
cd "$workdir"
}
noi di "Is hw1.txt file in your work directory (yes/no)" _request(confirm)
if "$confirm" == "no" {
di as err "Please download at https://github.com/jhustata/basic/raw/main/hw1.txt and rerun program"
exit 340700
}
else {
global data "hw1.txt"
capture confirm file "$data"
if _rc == 0 {
noi di "hw1.txt file in your work directory is confirmed!"
noi di ""
noi di ""
noi di ""
noi di ""
noi di ""
noi di ""
}
else {
di as err "It appears that hw1.txt is not in your work directory"
exit 340800
}
}
capture log close
log using "${workdir}hw1.lastname.firstname.log", replace
set more off
}
if 2 { //results: data, shape, etc.
if 00 { //stata dropdown menu
1. with a mouse i selected (after trying other options)
2. file > import > text data (delimited...)
3. then i located hw1.txt in my `c(pwd)'
4. imported it and copied & pasted the syntax, edited...
5. from Stata's output window into this do file thus:
}
import delimited "hw1.txt", clear
}
if 3 { //conclusions: questions, code, output
//q1
noi di "Question 1: There are `c(N)' records in the dataset."
noi di ""
//q2
forvalues i=1/2 {
sum init_age if female==`i'-1, detail
#delimit ;
local m_iqr`i': di %2.0f r(p50)
" [" %2.0f r(p25)
"-" %2.0f r(p75)
"]"
;
#delimit cr
}
local q2p1: di "Question 2: The median [IQR] age is `m_iqr1'"
local q2p2: di "among males and `m_iqr2' among females."
noi di "`q2p1' `q2p2'"
noi di ""
//q3
forvalues i=1/2 {
sum prev if female==`i'-1, detail
local perc`i': di %2.1f r(mean)*100
}
local q2p1: di "Question 3: `perc1'% among males and `perc2'%"
noi di "`q2p1'" /*
*/ " among females have history of previous transplant."
noi di ""
//q4
g htn=dx=="4=Hypertensive"
label define htn_lab 0 "No" 1 "Yes"
label values htn htn_lab
noi di "Question 4:"
noi tab htn
noi di ""
//q5
capture program drop question5
program define question5
#delimit ; //use throughout program
qui { ; //line 1 quietly doesn't apply inside this program
//label variables with output in mind
lab var init_age "Age, median [IQR]";
local age_lab: var lab init_age;
lab var prev "Previous transplant, %" ;
local prev_lab: var lab prev;
forvalues i=1/2 { ; //columns 1 & 2
count if !missing(dx) & female==`i'-1;
//row1
count if female==`i'-1;
local female`i'_N=r(N);
local row1: di "Question 5"
_col(30) "Males (N=`female1_N')"
_col(50) "Females (N=`female2_N')"
;
//row2
sum init_age if female==`i'-1,
detail; //copy&paste from q2, edit
local m_iqr`i': di %2.0f r(p50)
" [" %2.0f r(p25)
"-" %2.0f r(p75)
"]"
;
local row2: di "`age_lab'"
_col(30) "`m_iqr1'"
_col(50) "`m_iqr2'"
;
//row3
sum prev if female==`i'-1 ;
local per_prev`i': di %2.1f r(mean)*100 ;
local row3: di "`prev_lab'"
_col(30) "`per_prev1'"
_col(50) "`per_prev2'"
;
} ;
//rows4_13
split dx, p("=") ; //from chapter: delimit
destring dx1, replace ;
lab var dx1 "Cause of ESRD, %" ;
local varlab: var lab dx1 ;
label def varlab
1 "Glomerular"
2 "Diabetes"
3 "PKD"
4 "Hypertensive"
5 "Renovascular"
6 "Congenital"
7 "Tubulo"
8 "Neoplasm"
9 "Other"
;
lab values dx1 varlab;
local row4: di "`varlab'" ;
local vallab: value label dx1
; //debug: chatGPT moved this from line 144 to 159!!!
forvalues i=1/2 { ; //columns 1 & 2
levelsof dx1 if female==`i'-1,
local(diagnosis) ; //variable-level
global N_`i'=r(N) ;
local row=5 ; //based on Q5. template
foreach l of numlist `diagnosis' { ;
local dxcat: lab `vallab' `l' ; //alliterative
sum dx1 if dx1==`l' & female==(`i'-1) ;
local col_`i'_`row': di %2.1f r(N)*100/${N_`i'} ;
//indent the lab `dxcat'
local row`row': di " `dxcat'"
_col(30) "`col_1_`row''"
_col(50) "`col_2_`row''"
;
local row = `row' + 1 ; //tracks rows 5-13
} ;
} ;
forvalues i=1/13 { ; //rows1-13
noi di "`row`i''";
} ;
} ;
#delimit cr
end
noi question5
//q6
logistic received_kt init_age female
matrix define m=r(table)
//row1
noi di ""
noi di "Question 6"
//row2
local row2: di "Variable" _col(30) "OR" _col(35) "(95% CI)"
noi di "`row2'"
//rows3-4
lab var init_age "Age"
local age_lab: var lab init_age
lab var female "Female"
local female_lab: var lab female
local row=3
local col=1
foreach v of varlist init_age female {
local `v'_lab: var lab `v'
#delimit ;
local row`col': di "``v'_lab'" %3.2f _col(30) m[1,`col']
%3.2f _col(35)
"(" %3.2f m[5,`col']
"-" %3.2f m[6,`col']
")"
;
#delimit cr
//noi di "`row`num''"
local row=`row' + 1
local col=`col' + 1
}
noi di "`row1'"
noi di "`row2'"
noi di ""
//q7
local q7p1: /*
*/di "Question 7: This regression included `e(N)' observations"
local q7p2: /*
*/di "whereas the study dataset has `c(N)' observations in total."
noi di "`q7p1' `q7p2'"
noi di ""
//q8
local q8p1: di "Question 8: I estimate that it took me 24 hours"
noi di "`q8p1' to complete this assignment."
noi di ""
}
log close
}
do https://github.com/jhustata/basic/raw/main/review.do
5.1 quietly#
qui {
//code
}
5.2 if 0#
if 0 {
- Annotation
- Non-Stata syntax
- Really, anything
}
5.3 //, *#
Avant-garde#
if 0 { //Background
- Annotation
- Non-Stata syntax
- Really, anything
}
Traditional#
/*
Background:
- Annotation
- Non-stata syntax
- Really, anything!
*/
5.3 display#
qui {
noi di "What is your work directory?" _request(workdir)
}
I’m going to use a relative path for this example: ~/downloads
5.4 log using#
Inspect the .log file created by your script
5.5 if 3 -> if 0#
5.6 Lab#
Please use this lab to review weeks 1 - 5 at your own pace.
5.7 Homework#
Answer these questions, which incorporate elements learned in weeks 1 - 5.