Basic syntax for commands.ppt

1、Computing for Research I Spring 2013,Primary Instructor: Elizabeth Garrett-Mayer,Stata Graphics February 12,Basic syntax for commands,prefix: command varlist, optionsExamples: regress y x, level(90) by race: sum y x, detail ttest y, by(x) unequal,Stata Graphics,Maybe we can just end class now! Check

2、 out these links: http:/www.ats.ucla.edu/stat/stata/library/GraphExamples/default.htm http:/www.ats.ucla.edu/stat/stata/topics/graphics.htm http:/data.princeton.edu/stata/graphics.html http:/ univariate displays,Boxplots Stem and leaf Histograms Density plots,Ceramide Data,Lets look at the ceramide

3、markers What are their distributions? Are there outliers? Should we consider taking logs, or using % change?Results of a phase II trial of gemcitabine plus doxorubicin in patients with recurrent head and neck cancers: serum C-ceramide as a novel biomarker for monitoring response. Saddoughi SA, Garre

4、tt-Mayer E, Chaudhary U, OBrien PE, Afrin LB, Day TA, Gillespie MB, Sharma AK, Wilhoit CS, Bostick R, Senkal CE, Hannun YA, Bielawski J, Simon GR, Shirai K, Ogretmen B. Clin Cancer Res. 2011 Sep 15;17(18):6097-105. Epub 2011 Jul 26.,Histogram,hist c18,Lets make it prettier,* prettier histograms hist

5、 c18 , freq xaxis(1 2) ylabel(0(2)24) xlabel(20 “Twenty“ 40 “Forty“)hist c18, title(“Histogram of C18 Ceramide“) subtitle(“PI: K. Shirai“)hist c18, ytitle(“number of patients“) freq yline(0(10)20)hist c18, xaxis(1 2) xlabel(19.6 “mean“ 11.9 “median“, axis(2) grid),finding help on these can sometimes

6、 be tricky! e.g. help axis_choice_options,Boxplots,graph box c18,Boxplots,graph box c18, by(cycle) graph box c18, over(cycle)tab cycle graph box c18 if cycle7, over(cycle)sort patient cycle merge m:1 patient using “Ptdata.GemDox.dta“ graph box c18 if cycle7, over(cycle) over(gender)graph hbox c18, o

7、ver(initial) capsize(5),graph hbox c18, over(initial) capsize(5),graph hbox c18, over(initial) medtype(marker)medmarker(msymbol(+) msize(large)graph hbox c18, over(initial) ytitle(“C18”),Labels,Sometimes xlabels cannot be applied (e.g. boxplots) need to label your values Example: cycle for boxplotsl

8、abel define cycle 1 “cycle 1“ 3 “cycle 3“ 5 “cycle 5“ 7 “cycle 7“ label values cycle cycle graph box c18 if cycle7, over(cycle) (Hint: use this on the homework!),Stem and Leaf,. stem c18Stem-and-leaf plot for c18ceramide (C18 ceramide)c18ceramide rounded to nearest multiple of .1 plot in units of .1

9、0* | 42,43,44,460* | 57,57,67,81,89,90,96,98,99,991* | 01,06,08,08,14,15,19,20,35,441* | 622* | 03,15,16,18,19,19,222* | 823* | 173* | 4* | 23,494* | 58,68,685* | 5* | 6* | 376* | 86,Dotplot,Excellent way to show data across groups when you have a relatively small dataset dotplot y, over(group) dotp

10、lot c18, over(cycle) dotplot c18, over(gender) dotplot c18, over(gender) nogroup dotplot c18, over(gender) nogroup jitter(3) dotplot c18, over(gender) nogroup median center,Dotplot, by gender,Scatterplots,Two way graph Syntax: graph twoway scatter y x1 x2 graph twoway scatter y x1 Example: graph two

11、way scatter c18 totalceramide,Regression example,Scatterplot Residual plots Leverage Fitted line with raw data,Code,graph twoway scatter c18 totalcer regress c18 totalcer* residual plot * (residual vs. fitted) rvfplot* the long way * 1. generate a new variable from the regression, residuals predict

12、resid, res * 2. generate a new variable from the regression, fitted values predict fit scatter res fit, yline(0) * leverage vs. residual plot lvr2plot* take transform of C18? gladder c18 boxcox c18,* generate new variable gen logc18=log(c18) scatter logc18 totalcer scatter logc18 totalcer, mlabel(ge

13、nder) scatter logc18 totalcer, mlabel(gender) s(i) scatter logc18 totalcer, s(Oh)* redo regression regress logc18 totalcer rvfplot, yline(0) lvr2plot predict logfit* make plot of fitted model and raw data scatter logfit logc18 totalcer scatter logfit logc18 totalcer, s(i o) c(l .) graph twoway scatt

14、er logfit totalcer, s(i) c(l) | scatter logc18 totalcer, s(o) c(.),The next graph to create,Fancier way to put regression lines,* data is described at http:/data.princeton.edu/wws509/datasets/infile str14 country setting effort change /using http:/data.princeton.edu/wws509/datasets/effort.rawgraph t

15、woway scatter change setting graph twoway (scatter change setting ) (lfit change setting ) graph twoway (scatter change setting ) (qfit change setting ) graph twoway (scatter change setting ) (lfitci change setting ),/ “continuation” comment scatter makes a scatterplot of the two variables lfit plot

16、s the regression line of y on x qfit plots a fitted quadratic model of y on x lfitci plots the line AND a confidence interval!,Fancier way to put regression lines,Plot using qfit,Plot using lfitci,One slight problem with the labels is the overlap of Costa Rica and Trinidad Tobago (and to a lesser ex

17、tent Panama and Nicaragua). We can solve this problem by specifying the position of the label relative to the marker using a 12-hour clock (so 12 is above, 3 is to the right, 6 is below and 9 is to the left) and the mlabv() option. We create a variable to hold the position set by default to 3 oclock

18、 and then move Costa Rica to 9 oclock and Trinidad Tobago to just a bit above that at 11 oclock (we can also move Nicaragua and Panama up a bit, say to 2 oclock).,graph twoway (lfitci change setting) (scatter change setting, mlabel(country) ),gen pos=3 replace pos = 11 if country = “TrinidadTobago“

19、replace pos = 9 if country = “CostaRica“ replace pos = 2 if country = “Panama“ | country = “Nicaragua“graph twoway (lfitci change setting) / (scatter change setting, mlabel(country) mlabv(pos) )* see marker_label_options in help,Legends,graph twoway (lfitci change setting) /(scatter change setting,

20、mlabel(country) mlabv(pos) ) /, title(“Fertility Decline by Social Setting“) /ytitle(“Fertility Decline“) /legend(pos(5) order(2 “linear fit“ 1 “95% CI“) graph twoway (lfitci change setting) /(scatter change setting, mlabel(country) mlabv(pos) ) /, title(“Fertility Decline by Social Setting“) /ytitl

21、e(“Fertility Decline“) /legend(off) * see help title_options for pos and ring in legend,Spaghetti plots,Command available from UCLA: spagplot* spaghetti plots clear insheet using “I:MUSC OncologyShirai, KeisukeOctober2010ceramide.csv“ findit spagplot spagplot c18 cycle, id(patient) spagplot c18 cycl

22、e, id(patient) nofit* remove patients who only have cycle=1 sort patient cycle by patient: gen visit=_n egen maxvis=max(visit), by(patient) spagplot c18 cycle if maxvis1, id(patient) nofit* or, use c(L) graph twoway scatter c18 cycle if maxvis1, c(L) help connectstyle,other neat stuff,graph matrix saving graphs: click and save as desired format saving and combining (see princeton site, section 3.3) http:/data.princeton.edu/stata/graphics.htmlSee GraphExamples on ucla site: http:/www.ats.ucla.edu/stat/stata/library/GraphExamples/,