Making Tables and Figures with Stata Biostatistics 212 Lecture 6

Housekeeping Brackets indicate optional parts of a command (usually!) use vs. insheet Low p-value for heterogeneity ≠ important interaction “The strata never lie” Final projects –Read 1-page directions closely

Today Organizing your Stata files Making a table Making a figure

Today Organizing your Stata files Making a table  Lab practice = Final Project Making a figure  Lab practice = Lab 6

Organizing your Stata files Pitfalls –Proliferating dataset –Can’t remember what you did –Can’t remember why you did it –Can’t easily redo with new data

Organizing your Stata files My system (it’s not perfect) 1)Import data into Stata a)Using a Stata command (e.g., insheet or import ) within a do file b)Using other method (e.g., StatTransfer?) outside a do file, then SAVE the “raw” Stata file immediately 2) Write a do file that “cleans” your data, and saves it as a new clean dataset 3) Write do files for each component of your analysis

Raw data My organizational scheme

Raw data Raw data.csv Pre-process My organizational scheme

Raw data Raw data.csv In Stata My organizational scheme Pre-process

Raw data Raw data.csv In Stata Clean data.dta Data prep.doData prep.log My organizational scheme Pre-process

Raw data Raw data.csv In Stata Clean data.dta Data prep.doData prep.logTable 1.do Table 1.log My organizational scheme Pre-process

Raw data Raw data.csv In Stata Clean data.dta Data prep.doData prep.logTable 1.do Table 1.log Table 1.xls Cut and paste My organizational scheme Pre-process

Raw data Raw data.csv In Stata Clean data.dta Data prep.doData prep.logTable 1.do Table 1.log Table 1.xls Cut and paste My organizational scheme Table 1.doc Cut and paste Pre-process

Raw data Raw data.csv In Stata Clean data.dta Data prep.doData prep.logTable 1.do Table 2.do Table 1.log Table 2.log Table 1.xls Table 2.xls Cut and paste My organizational scheme Table 1.doc Table 2.doc Cut and paste Pre-process

Organizing your Stata files You will end up with: –1 or 2 Stata datasets Data, from Excel.dta (only if you import outside your do file) Data.dta –1 do file used for cleaning Data prep.do –1 do file to create each Table and Figure Table 1.do, Figure 1.do, Text data.do, etc –Matching log files (with the same names) for each do file Data prep.log, Table 1.log, Figure 2.log, Text data.log, etc

Organizing your Stata files Put them all in one folder called, “Stata files”, sort by file type. Example

Raw data Raw data.csv In Stata Clean data.dta Data prep.doData prep.logTable 1.do Table 2.do Table 1.log Table 2.log Table 1.xls Table 2.xls Cut and paste Any questions? Table 1.doc Table 2.doc Cut and paste Pre-process

Raw data Raw data.csv In Stata Clean data.dta Data prep.doData prep.logTable 1.do Table 2.do Table 1.log Table 2.log Table 1.xls Table 2.xls Cut and paste My organizational scheme Table 1.doc Table 2.doc Cut and paste Lecture 3 Pre-process

Raw data Raw data.csv In Stata Clean data.dta Data prep.doData prep.logTable 1.do Table 2.do Table 1.log Table 2.log Table 1.xls Table 2.xls Cut and paste My organizational scheme Table 1.doc Table 2.doc Cut and paste Lecture 3Lecture 5 Pre-process

Raw data Raw data.csv In Stata Clean data.dta Data prep.doData prep.logTable 1.do Table 2.do Table 1.log Table 2.log Table 1.xls Table 2.xls Cut and paste My organizational scheme Table 1.doc Table 2.doc Cut and paste Lecture 3Lecture 5 Lecture 7 Pre-process

Tables Two main purposes –Present the facts in a compact format –Provide side-by-side comparisons Six main components: –Data –Title, row heading, column headings –Row names –Footnotes Browner, W. Publishing and Presenting Clinical Research

5 Steps to Making a Table Step 1: Decide what the Table will be about –Sketch it out on paper Title, column headings, etc

5 Steps to Making a Table Step 2: Make the dummy table –Excel or Word –Makes you specify what you actually want! Row headings Decide on category cut-offs, labels Decide on reference categories for regression, etc Footnote liberally –Leave data cells blank

5 Steps to Making a Table Step 3: Write a do file that will produce each number you need –Iterative process, as you know

5 Steps to Making a Table Step 4: Copy and Paste the data in –Copy and Paste each number, or –“Copy Table” (under the “Edit” menu) –Minimize manual retyping, rounding –Use Excel to calculate and round for you

5 Steps to Making a Table Step 5: Format it so it looks nice –Standard, plain style – usually: Horizontal lines, not vertical Double-spaced Footnotes - *, †, ‡, §, ║, ¶ (or a,b,c,d,…) –Create a template for yourself

Word vs. Excel for Tables Stata  Word –Fewer steps, fewer files –But… Can’t cut and paste full tables Doesn’t do any calculations for you Formatting can become “corrupted”

Word vs. Excel for Tables Stata  Excel  Word –Can cut and paste values or whole tables –Set rounding, do calculations easily –Formatting easier? –Copy and Paste into Word (extra step)

Demo Table 1 for “Moderate drinking and coronary calcium in young adults: The CARDIA Study” –Basic content –Sketch –Generate numbers in Stata –Copy and paste into Word –Show final table –Demonstrate pasting a full table into Excel

Figures When use a figure? Making a figure with Excel Making a figure with Stata

When use a figure? When a graphical display of information more effectively conveys the intended message than words. “A picture is worth a thousand words”

Figures “A picture is worth a thousand words” How many words is this picture worth?

Figures “A picture is worth a thousand words” How many words is this picture worth? 48% of CARDIA participants consume alcohol moderately. Worth = 7 words

Figures “A picture is worth a thousand words” How many words is this picture worth?

Figures “A picture is worth a thousand words” How many words is this picture worth? WhiteBlack Drinks/dayn=1935n= %57% %26% %9% 2+8%8% Worth = 1 small table? (and avoid pie charts in general…)

Figures “A picture is worth a thousand words” How many words is this picture worth?

Figures “A picture is worth a thousand words” How many words is this picture worth? Proportion with CAC AbstainerMod drinker Black women White women Black men White men Can you see the interaction in this table without a figure? (Figures are good for illustrating interactions)

Figures “A picture is worth a thousand words” How many words is this picture worth?

Figures “A picture is worth a thousand words” How many words is this picture worth? Worth = 968 data points? Nice to show actual data points along with main effect, if possible!

Making a figure With Excel –First make a TABLE in Excel! Use Stata to generate numbers for the table –Create a figure from the Table using Excel tools With Stata –Use Stata commands to create the figure directly

Steps in making an Excel figure Sketch your figure Make a dummy TABLE Write a.do file to fill in the table Copy and paste from the log file or the results window into the Table Use the Chart Wizard to create the Figure Format, format, format until it looks nice

Example Figure 2 from Lipids paper

Steps in making an Excel figure Sketch your figure Make a dummy TABLE Write a.do file to fill in the table Copy and paste from the log file or the results window into the Table Use the Chart Wizard to create the Figure Format, format, format until it looks nice

Steps in making a Stata figure Sketch your figure Make a dummy TABLE Write a.do file with a graph command Copy and paste from the log file or the results window into the Table Use the Chart Wizard to create the Figure Format, format, format until it looks nice

Pay attention to… Formatting –Make it look nice and professional, but not gaudy Black and white, usually –The time-consuming part of making a figure is usually related to formatting.

Pay attention to… Labeling –Your figure should be understandable by itself, without the rest of the manuscript –All axes should be labeled. –Include important p-values

Pay attention to… The Figure Legend –Title, explanations, extra p-values, etc –Separate section in manuscript or at bottom of page – depends on journal

Stata vs. Excel for Figures Excel –Flexible and intuitive point-and-click figures Easy to create and modify Flexible, more options, error bars, adjusted estimates, good for bar graphs, etc –But… Requires an extra step – copy/pasting to Excel Harder to reproduce Much harder to do scatter plots

Stata vs. Excel for Figures Stata –Can create very customizable figures using 1 complex Stata command Easy to recreate – simple do file No error Scatter plots are MUCH easier with Stata –But… Harder to create the first time? - no point and click A little less flexible? Difficult to format: Graphic Editor helps address this

Stata vs. Excel for Figures Easiest tool Bar/Line* figuresExcel Confidence intervalsExcel Scatter plotsStata Box plotsStata Dot plotsStata * Where x-axis is categorical

Stata Demo Scatter plots: bmi vs. lipids –Iterative process of adding commands to do file –Cutting and pasting with substitution –Lowess smoother and linear fit lines –Post-graph editing

twoway (scatter dfev1 cumpy10 if menthol1==1, msymbol(plus) msize(small) mcolor(black)) /// (scatter dfev1 cumpy10 if menthol1==0, msymbol(circle_hollow)) /// (line m cumpy10 if menthol1==1, sort clcolor(black) clpat(dash) clwidth(thick)) /// (line nm cumpy10 if menthol1==0, sort clcolor(black) clpat(solid) clwidth(thick)) ///, ytitle(Change in FEV1 (milliliters), size(large)) yscale(titlegap(5)) /// xtitle(Pack-years of exposure to tobacco, size(large)) /// xscale(titlegap(3)) /// legend(order(1 "Menthol smokers" 2 "Non-menthol smokers" 3 "Menthol regression" /// 4 "Non-menthol regression")) /// scheme(s1mono) /// graphregion(fcolor(none) lcolor(none) ifcolor(none) ilcolor(none)) /// plotregion(fcolor(none) lcolor(none) ifcolor(none) ilcolor(none))

Key points It’s worth putting thought into your file organization Tables: –First sketch it on paper –Next make your dummy table –Only then write your do file Figures: –Make it with Stata if you can –Use dialog boxes to get the correct syntax, paste into your do file –Make bar charts with Excel Document everything you do!

Today’s Lab You will create 4 figures using stata. The focus will be on learning to use the dialog boxes to get the syntax right, and then transferring commands and options into a do file.