On Wed, Oct 16, 2013 at 2:56 PM, Jorge Eduardo Prez Prez > Regards, "statalist@hsphsun2.harvard.edu" predict xb_predictor1 if e(sample), xb 3rd ed. * For searches and help try: However, you will need to do the work to compute the individual predicted outcome probabilities. pksumm Summarize pharmacokinetic data In Stata it is very easy to get the area under the ROC curve following either logit or logistic by using the lroc command. For example, we often wish to identify particular periods of recession or war or other distinct conditions. I just read Paul Seed's clarification of your question and it seems > > Department of Economics producutive path and so I shelved it. I am interested not only in the mean > I am not sure if I am understanding this correctly, but I think you logit outcome predictor2 * http://www.ats.ucla.edu/stat/stata/, http://www.stata.com/support/faqs/resources/statalist-faq/, st: Adjusting for individual clustering in pooled -svyset- data, st: Re: calculation of area under curve with Stata. > Gothenburg, Sweden -lroc-, which Joe Canner referred to, -roctab- roccomp- and -rocgold-. >> * For searches and help try: It is mainly used in pharmacokinetics, and it is clearly that which Elmir Omerovic is interested in. > Others can speak for themselves for Steve (Samuels) and I couldn't see why this would be interesting or useful. document.getElementById("ak_js_1").setAttribute("value",(new Date()).getTime()); Promote Code Transparency and Reusability in Accounting Research. roccomp outcome xb_predictor1 xb_predictor2, graph summary Wed, 16 Oct 2013 15:02:08 -0400 NB: as @Joris already pointed out you could use abs (y) if that would make more sense. > . sm_auc () calculates the AUC using the method of trapezoid integration; this is equivalent to trapz function in Matlab and numpy.trapz in Python. From RE: st: Calculating area under a curve. * > the area under each trapezoid for each measure and adding them: The pk commands are > The same idea is straightforwardly applied in a multi-level logistic regression framework. * http://www.stata.com/support/statalist/faq > gen area=(measure+measure[_n-1])*(time-time[_n-1])*0.5 Theme. > Hope this helps, Kernel density estimates are plotted by default in Stata as lines, meaning curves. Thanks for the clarification, which is very helpful. I did find the -cumul- and Graduate Student The twoway function plotting command is used to plot functions, such as y = mx + b. n.j.cox@durham.ac.uk On Thu, Dec 3, 2009 at 12:49 PM, Nick Cox wrote: > Graduate Student >> -- > On Fri, Nov 27, 2009 at 8:22 AM, Padmakumar Sivadasan To >> > Johns Hopkins University School of Medicine A better way of comparing the predictive ability of different models is to use the Receiver Operating Characteristic, or ROC curve (e.g., Hosmer and Lemeshow, 2000, Chapter 5). It is used as a cumulative measurement of drug effect in pharmacokinetics and as a means to compare peaks in chromatography. >> distributions at the local level to that at the national level. outside of your field who do not understand the jargon. To. >> this method? Subject. > statalist@hsphsun2.harvard.edu] On Behalf Of elmir term originates in signal detection theory. > Could you please explain why this is a good idea? Although the last invites confusion To >> * http://www.ats.ucla.edu/stat/stata/ Notice: On April 23, 2014, Statalist moved from an email list to a forum, based at statalist.org. x. Paul T Seed, Women's Health, KCL Nick n.j.cox@durham.ac.uk Padmakumar Sivadasan I realized after reading . >> * http://www.stata.com/support/faqs/resources/statalist-faq/ Only after that do you then even bother to show the ROC curve, and say we calculate the area under the curve (AUC) as a measure of how well the model can discriminate the two classes. Example 3: Find the Indicated Area Between Two Values. (Steve's at liberty to dissent if that's not his view.) "Seed, Paul" Elmir Omerovic is interested in. > . Fri, 27 Nov 2009 17:28:30 -0500. A value of 0.5 indicates no ability to discriminate (might as well toss a coin) while a value of 1 indicates perfect ability to discriminate, so the effective range of AUC is from 0.5 to 1.0. Next group. * For searches and help try: * http://www.stata.com/help.cgi?search > RE: st: Calculating area under a curve what is the formula to generate the area under the curve above the baseline (The incremental area under the curve). predict xb_predictor2 if e(sample), xb The first is the area under a dose concentration curve; or any other measurement taken repeatedly over time. > Elmir Omerovic MD, PhD BP was measured repeatedly in every animal at 10 > . Department of Geography. >> View this message in context: http://statalist.1588530.n2.nabble.com/calculation-of-area-under-curve-with-stata-tp7580438.html of mine. >> (1) Is there a way in Stata to calculate the area under cumulative A side question: whats the difference between logistic and logit regression? >> I am analyzing the blood pressure (BP) levels from the three different Re: st: calculation of area under curve with stata >> > One alternative and simple explanation of AUC though for binary models is to take the Harrells C index interpretation, which for binary predictions is equivalent to the AUC statistic. > A technical note from Stata: lroc requires that the current estimation results be from logistic, logit, probit, or ivprobit. Nick Coxs short answer is: same thing with different emphases in reporting. (something likeone gives you the odds ratios, the other gives you the log of the odds ratios. > ROC, by the way, stands for receiver operating characteristic; and the >> the area under the cumulative probability curve. Applied Logistic Regression. [Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index] Appropriate commands include -integ- functions ,that I was not aware of, useful for other projects Diagnostic or predictive test. > I understand that one way to compare the effect of the drugs on blood pressure Durham, UK. Brown University This curve plots the probability of detecting a true signal (sensitivity) and false signal (1specicity) for the entire range of possible cutpoints (p. 160, our emphasis). Advanced Criminology (Undergrad) Crim3302, Communities and Crime (Undergrad) Crim4323, Crim 7301 UT Dallas Seminar in Criminology Research andAnalysis, GIS in Criminology/Criminal Justice(Graduate), Crime Analysis (Special Topics) Undergrad, Text analysis, alt competition sites, andASC, I have no clue how to interview for data scientists | Andrew Wheeler, New paper: An Open Source Replication of a Winning Recidivism PredictionModel, Hot spots of crime in Raleigh and homebuying, Testing the equality of two regression coefficients, Git excluding specific files when merging branches. >> The samples are taken at 0, 30 min, 60 min, 90 min and 120 minutes. The area under the curve is an integrated measurement of a measurable effect or phenomenon. > You can also compare AUCs using: Thanks for the clarification, which is very helpful. >> probability curve? > >> >> performance. Required fields are marked *. New in Stata 17; Why Stata; All features; > To: statalist@hsphsun2.harvard.edu > You can compare more than two AUCs as desired; just repeat the -logit-, -lroc-, - > Elmir, One alternative and simple explanation of AUC though for binary models is to take the Harrell's C index interpretation, which for binary predictions is equivalent to the AUC statistic. > As suggested, I used -cumul- to calculate the cumulative distributions >> levels and then compare the area under the cumulative probability >> The -pk- suite of commands are "Nick Cox" > It's kind of you to thank us all but you do not distinguish between quite different comments. [Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index] >> Dear All, Often area-based graphs say in a complicated way what could be said much more simply. The area under the ROC curve (denoted AUC) provides a measure of the model's ability to discriminate. Change), You are commenting using your Facebook account. The formula for the total area under the curve is A = limx n i=1f (x).x lim x i = 1 n f ( x). [Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index] >> Kind regards > Kind regards Best wishes, Background shading of time series and other plots is a common need. One of the questions I often ask in data science interviews is How would you explain the area under the curve statistic to a business person?. > Brown University >> under the curve and to use this value in a linear mixed model. BP was measured repeatedly in every animal at 10 different time points * http://www.stata.com/support/faqs/resources/statalist-faq/ >> > . > Date: Mon, 14 Oct 2013 13:12:10 +0000 Jorge Eduardo Prez Prez > > (LogOut/ pkcross Analyze crossover experiments Solution: To answer this question, we simply need to subtract the area to the left of z = -1.81 from the area to the left of 1.26. > The animals were exposed to 3 different drugs (each group n=8). Stata: Data Analysis and Statistical Software PRODUCTS. > . > The official Stata -lroc- program has been around for a very long time, so it would be surprising if it had an uncorrected error. The Stata command to report AUC is as follows: The most recent edition of the book Kim and Skinner refer to isHosmer, D. W., Jr., S. A. Lemeshow, and R. X. Sturdivant. The area under the receiver operating characteristic (ROC) curve is a measure of discrimination ability used in diagnostic and prognostic research. > against time for each animal. For a curve y = f (x), it is broken into numerous rectangles of width x x. Change). Here we limit the number of rectangles up to infinity. I guess I should have read the clarification before answering. It has two arguments: - The first argument is . > One possibility, in addition to that already suggested is this: > - -----Original Message----- Padamakumar, Do you know whether the area under the curve is defined by a closed form integral? >> Elmir Omerovic MD, PhD > set obs 10 >> the cumulative probabilities but I couldn't find a method to calculate To > and -integ- to calculate the area under the curve.. On a small point of terminology, -cumul- and -integ- are to Stata commands, not functions. >> I would be very grateful if someone could help me with step-by-step n.j.cox@durham.ac.uk. The second is the area under a ROC curve. New models are often bench marked against established models using AUC. Accepted Answer: Mehmed Saad. >> v1. Subject Date. > > So while I try to do my best explaining technical statistical content, I often punt to simpler here are the end outcomes we care about (which dont technically answer the question) as opposed to here is how the sausage is made explanations. > set seed 1234 To avoid further confusion, can I explain that the term "area under the curve" So for this statistic you could say something like 'If I randomly sample a negative case and a positive case, the positive case will have a higher predicted . >> Gothenburg, Sweden >> I am analyzing the performance of companies indicated by a variable > On Mon, Oct 14, 2013 at 4:38 AM, elmir wrote: It is used as a convenient non-parametric measure of the performance of a Hello, I am struggling with shading area under the curve at the selected area. pkshape Reshape (pharmacokinetic) Latin-square data Hosmer-Lemeshow (2000, p. 162) indicate that AUC of 0.5 indicates no discrimination, AUC of between 0.7 and 0.8 indicates acceptable discrimination, AUC of between 0.8 and 0.9 indicates excellent discrimination, and AUC greater than 0.9 is considered outstanding discrimination. Date Subject Range and area plots : Stata. -------------------------------------------- It is mainly used in pharmacokinetics, and it is clearly that which Date. From twoway function y=normalden (x), range (-4 . or as a' (a-prime), or as the c-statistic. In the previous examples, we found that the area to the left of z = -1. . A value of 0.5 indicates no ability to discriminate (might as well toss a coin) while a value of 1 indicates perfect ability to discriminate, so the effective range of AUC is from 0.5 to 1.0. It is really helpful! < statalist@hsphsun2.harvard.edu >. And it is often good in a relative sense a model with an AUC of 0.8 is typically better than a model with and AUC of 0.75 (although not always, you need to draw the ROC curve and make sure the larger AUC curve dominates the other curve and that they do not cross). > Comparing AUCs of new and old models . Stata's built-in facilities for computing discrimination statistics (AUC, ROC tools, lroc and lsens, etc) are all intended to work with logistic regression. Has two completely different meanings in biostatistics. st: RE: calculation of area under curve with Stata > gen measure=uniform() The twoway function command. Your email address will not be published. > keep in mind that your posts are going to be read by Stata users statalist@hsphsun2.harvard.edu. twoway area d.gnp96 date [G-2] graph twoway area. > curve and to use this value in a linear mixed model. > -------------------------------------------- > animals. I am not familiar with the user-written program you are referring to, so I cannot comment why it gives a different result. Padmakumar Sivadasan Fri, 4 Dec 2009 08:55:00 -0000. >> to compute the cumulative probabilities at the national and local >> for the country as a whole and to that at the local level Durham University. It is elementary (meaning, fundamental) that area under the curve has an interpretation as probability. > > valuable suggestions! The variable subj_b_day1 now stores the data of subject b on Day 1. > I am analyzing the blood pressure (BP) levels from the three different groups of This effectively calculates the area using the trapezoidal method by taking the average of the "left" and "right" y-values. Stata. * The ROC plot is usually represented without additional information about decision thresholds used to generate the graph. > Subject: st: calculation of area under curve with stata >> You can also include graphing options available to twoway plots (e.g., xtitle ). Your email address will not be published. Variable v1 has a range 0-10 where higher values indicate poorer I wanted to fill the area over Body Weight line. I am attempting to compare the performance of companies logit outcome predictor1 Yes, the area under the ROC curve and the C-statistic are the same thing. If we want to evaluate the predictive ability of a logit or probit model,Kim and Skinner (2012, JAE, Measuring securities litigation risk) suggest that. On a small point of terminology, -cumul- and -integ- are to Stata commands, not functions. Notice: On April 23, 2014, Statalist moved from an email list to a forum, based at statalist.org. pkequiv Perform bioequivalence tests lroc Previous group. >> * Area Under the Curve - Definition, Types, and Examples. Date > * Add them > * Area of trapezoid for each time sample.mat. * http://www.ats.ucla.edu/stat/stata/, http://www.stata.com/support/statalist/faq, st: calculating p-values from pcorr's returned results, st: Fwd: Calculating weighted kappa for multiple raters. The first is the area under a dose concentration curve; . > Note that Prism also computes the area under a Receiver Operator Characteristic (ROC) curve as part of the separate ROC analysis. Tue, 15 Oct 2013 09:57:56 +0000 >> (2) Could someone point me to reference that I can use to read up on > Sahlgrenska University Hospital > wrote: 2013. But in any case, this shows that when you post to Statalist you should logit outcome predictors (LogOut/ > * http://www.ats.ucla.edu/stat/stata/, http://statalist.1588530.n2.nabble.com/calculation-of-area-under-curve-with-stata-tp7580438.html, http://www.stata.com/support/faqs/resources/statalist-faq/, st: calculation of area under curve with stata, Re: st: calculation of area under curve with stata, Re: st: Use of Stata project manager to make backing up and sharing more efficient, st: Regarding Kendall Coefficient of Concordance. > Joe Canner Abstract. RE: st: Calculating area under a curve Nick The solution for OP then reads as: sum (diff (strike) * (head (volatility,-1)+tail (volatility,-1)))/2. >> Area Under the Curve (AUC) In machine learning and diagnostic medicine the area under the receiver operating characteristic (ROC) curve or AUC is a common metric used to evaluate the predictive performance of a model or diagnostic test. > > . Why Stata Features New in Stata 17 Disciplines Stata/MP Which Stata is right for me? Re: st: calculation of area under curve with stata lroc or any other measurement taken repeatedly over time. In effect, you are integrating twice, as -cumul- is clearly numerical integration of the density function, even though not named as such, and you then integrate once more. From Department of Economics I did. >> I understand that one way to compare the effect of the drugs on blood >> Sent from the Statalist mailing list archive at Nabble.com. > want to calculate the area under the curve of a plot of BP measures https://andrewpwheeler.com/2021/11/19/how-to-interpret-the-area-under-the-curve-auc-stat/. Hoboken, NJ: Wiley. I realized after reading your initial post that what I was not on a #1 incremental area under the curve 28 Sep 2016, 20:00 Dear team, I am trying to compare the area under the curve of blood glucose results after the meal. > Dear All, > twoway area measure time > Jorge Eduardo Prez Prez > sum tarea Maybe it is too easy a question even for juniors, as I cant remember anyone getting it wrong. >> Dear All, * http://www.stata.com/support/faqs/resources/statalist-faq/ > From: owner-statalist@hsphsun2.harvard.edu [mailto:owner- >> (LogOut/ One suggestion I got was The most recent situation I remember this happened in real life, I actually said to the business rep that the AUC does not directly translate to revenue, but is a good indication that a model is good in an absolute sense (we know others have AUCs typically around 0.7 to 0.8 for this problem, and over 0.5 is better than random). -Steve On Fri, Nov 27, 2009 at 12:15 PM, Nick Cox <n.j.cox@durham.ac.uk> wrote: > Just to point out that -cumul- gives you the (cumulated) area under the density function. st: RE: calculation of area under curve with Stata > . > Nick * For searches and help try: Speaking Stata: Shading zones on time series and other plots. >> I understand that I can use the -cumul- function in Stata to calculate Date > how to calculate AUC in stata. >> groups of animals. Fill in your details below or click an icon to log in: You are commenting using your WordPress.com account. Question: Find the area under the standard normal curve between z = -1.81 and z = 1.26. pkexamine Calculate pharmacokinetic measures > The summation of the area of these rectangles gives the area under the curve. >> value of v1 but also the variability of v1. > Due to the irregular follow up times for different patients and some missing data at time=0, I need Stata to fit the spline and calculate the AUC under the spline for each patient for a consistent period say (day 0 to day +10) even if that particular patient has only data points at say day 0, 1, 4, 8, 12, 16 . designed to handle this: document.getElementById( "ak_js_1" ).setAttribute( "value", ( new Date() ).getTime() ); Enter your email address to follow this blog and receive notifications of new posts by email. >> The animals were exposed to 3 different drugs (each group n=8). * >> pressure within the whole experimental period would be to calculate the area >> instructions how to calculate AUC in stata. > clear > > Subject: st: RE: calculation of area under curve with stata )thanks to a post on Stack Overflow. Subject I have two questions > Main page. This could be achieved by calculating Thank you for providing such a clear and straightforward explanation of ROC evaluation. >> To avoid further confusion, can I explain that the term "area under the curve" Has two completely different meanings in biostatistics. > Padmakumar Sivadasan > . Nicholas J. Cox. Now let's calculate the area under a curve (AUC) from subj_b_day1 using sm_auc (). Fri, 4 Dec 2009 08:55:00 -0000 > within the whole experimental period would be to calculate the area under the Change), You are commenting using your Twitter account. The area under the ROC curve (denoted AUC) provides a measure of the models ability to discriminate. >> Sahlgrenska University Hospital with Harrell's C, which is another story . One of the most useful applications of integral calculus is learning how to calculate the area under the curve.Definite integrals and areas found under the curve are essential in physics, statistics, engineering, and other applied fields. > From: Joe Canner pkcollapse Generate pharmacokinetic measurement dataset > How to remove duplicate GVKEY-DATADATE when using Compustat Annual (FUNDA) and Quarterly (FUNDQ). > I would be very grateful if someone could help me with step-by-step instructions To avoid confusion with the other AUC, it is sometimes referred to as AUROC; I have attached my code and the screenshot of the plot. st: "no; data in memory would be lost" warning after preserve. * http://www.stata.com/help.cgi?search It is possible to do this using the logistic linear predictors and the roccomp command.Here is an example: > x = 0:2500; Lvy = (611 <= x)& (vgrf2 >= bw) & (x < 794); While there is no correct answer per se, the most logical response is you focus on discussing true positives and false positives, and how the predictive model can be tuned to capture more true positives at the expense of generating more false positives. this could be achieved by calculating > the area under each trapezoid for each measure and adding them: > > clear > set seed 1234 > set obs 10 > gen time=_n+uniform () > gen measure=uniform () > twoway area measure time > * area of trapezoid for each time > gen area= (measure+measure [_n-1])* (time-time [_n-1])*0.5 > * add them > egen tarea=total > n.j.cox@durham.ac.uk that you want an area under a ROC curve, completely unrelated to what > Thank you all (Martin, Philippe, Nick, Steve, Maarten, Bob) for your If we want to plot the density of a normal distribution across a range of x values, we type y=normalden (x). > within 90 minutes from the start of the experiment. >> different time points within 90 minutes from the start of the experiment. > egen tarea=total(area) > predict- sequence. > . > So for this statistic you could say something like If I randomly sample a negative case and a positive case, the positive case will have a higher predicted risk {AUC} percent of the time. I do like this interpretation, which illustrates that the AUC is all just about rank ordering the predictions, and a more discriminating model will have a higher AUC (although it says nothing about calibration). Subject. > To. > Sent: Monday, October 14, 2013 4:38 AM wrote: "statalist@hsphsun2.harvard.edu" Stata command to convert string GVKEY to numerical GVKEY or vice versa, A test on Stata running speed on MacBook Pro (M1 Pro chip) and old Macs, My thoughts on Python for accounting research, Use Stata to do propensity score matching (PSM), Export a SAS dataset to Stata with all variable names converted to lowercase, Use Python to download TXT-format SEC filings on EDGAR (Part I). >> (Metropolitan Statistical Area). >> in this regard * http://www.stata.com/help.cgi?search However, with lroc you cannot compare the areas under the ROC curve for two different models. > gen time=_n+uniform() Re: st: Calculating area under a curve. Jorge Eduardo Prez Prez Although areas under the cumulative probability curve F(t) are meaningless as far as I know, the total area under the survival curve S(t) = 1 - F(t) is equal to the mean. >> * http://www.stata.com/help.cgi?search lroc
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