From mboxrd@z Thu Jan 1 00:00:00 1970 X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on ip-172-31-74-118.ec2.internal X-Spam-Level: X-Spam-Status: No, score=-1.9 required=3.0 tests=BAYES_00,FREEMAIL_FROM autolearn=ham autolearn_force=no version=3.4.6 X-Received: by 2002:a05:620a:4495:: with SMTP id x21mr14074376qkp.633.1640677711877; Mon, 27 Dec 2021 23:48:31 -0800 (PST) X-Received: by 2002:a25:bcc3:: with SMTP id l3mr725717ybm.148.1640677711691; Mon, 27 Dec 2021 23:48:31 -0800 (PST) Path: eternal-september.org!reader02.eternal-september.org!news.misty.com!border2.nntp.dca1.giganews.com!nntp.giganews.com!news-out.google.com!nntp.google.com!postnews.google.com!google-groups.googlegroups.com!not-for-mail Newsgroups: comp.lang.ada Date: Mon, 27 Dec 2021 23:48:31 -0800 (PST) In-Reply-To: <87y2456071.fsf@bsb.me.uk> Injection-Info: google-groups.googlegroups.com; posting-host=213.166.55.173; posting-account=sDyr7QoAAAA7hiaifqt-gaKY2K7OZ8RQ NNTP-Posting-Host: 213.166.55.173 References: <7bede061-4b0f-4029-beb1-1056637e57d6n@googlegroups.com> <49538254-21ed-4fd0-8316-1bccc7d3c635n@googlegroups.com> <87sfue8a0v.fsf@bsb.me.uk> <31332c61-a370-43a5-bbe0-efe338ee6d8fn@googlegroups.com> <87fsqd7oz8.fsf@bsb.me.uk> <87y2456071.fsf@bsb.me.uk> User-Agent: G2/1.0 MIME-Version: 1.0 Message-ID: <7f50b560-9d28-4572-a90c-7488fb27582en@googlegroups.com> Subject: Re: Some advice required [OT] From: Laurent Injection-Date: Tue, 28 Dec 2021 07:48:31 +0000 Content-Type: text/plain; charset="UTF-8" Xref: reader02.eternal-september.org comp.lang.ada:63292 List-Id: On Tuesday, 28 December 2021 at 01:29:57 UTC+1, Ben Bacarisse wrote: > Laurent writes: > > > On Monday, 27 December 2021 at 21:49:18 UTC+1, Ben Bacarisse wrote: > >> Laurent writes: > >> > >> > On Monday, 27 December 2021 at 14:14:42 UTC+1, Ben Bacarisse wrote: > >> >> Laurent writes: > >> >> > >> >> > On Monday, 27 December 2021 at 12:16:27 UTC+1, Niklas Holsti wrote: > >> >> > > >> >> >> Sorry, but I found your problem description impossible to understand. > >> >> >> Try to describe more clearly the experiment that is done, the structure > >> >> >> of the data the experiment provides (the meaning of the Excel rows and > >> >> >> columns), and the statistic you want to compute. > >> >> > > >> >> > Sorry tried to keep it short, was too short. > >> >> > > >> >> > Columns are the antimicrobial drugs > >> >> > Rows are the microorganism. > >> >> > > >> >> > So every cell contains a result of S, I, R or simply an empty cell > >> >> > > >> >> > S = Sensible > >> >> > I = Intermediate > >> >> > R = Resistant > >> >> > > >> >> > empty cell >> >> > > >> >> > If a patient has 3 strains of the same microorganism but with > >> >> > different resistance profiles I have to find the most resistant > >> >> > one. Or if they are different I keep them all. > >> >> > > >> >> > I have no idea how to explain what I am doing to the compiler. > >> >> I think when you can explain it to people, you'll be able to code it. I > >> >> am still struggling to understand what you need. > >> >> > Why I would choose result from strain B over the result from strain A. > >> >> > > >> >> > strain A: SSSRSS > >> >> > strain B: SSRRRS > >> >> Let's space it out > >> >> > >> >> drug 1 drug 2 drug 3 drug 4 drug 5 drug 6 > >> >> strain A S S S R S S > >> >> strain B S S R R R S > >> >> > >> >> You want to choose B because it has is resistant to more drugs, yes? > >> >> > >> > > >> > Yes indeed > >> > > >> >> I think, from the ordering you give, you need a measure that treats an R > >> >> as "more important" that any "I" which is "more important" than an "S". > >> >> (We will come to empty cells later.) > >> >> > >> >> I think you need to treat the number of Rs, Is and Ss like digits in a > >> >> number. In base 10, the strains score > >> >> > >> >> R S I > >> >> strain A 1 5 0 = 150 > >> >> strain B 3 3 0 = 330 > >> >> > >> >> Now, in fact, you don't need to use base 10. The smallest base you can > >> >> use is one more than the maximum number of test results. If there can > >> >> be up to 16 tests (say) the score is > >> >> > >> >> n(R)*17*17 + n(S)*17 + n(I). > >> >> > >> >> If this suits your needs, we can consider empty cells later on. It's > >> >> not at all clear to me how to compare > >> >> > >> >> strain C R____ > >> >> strain D RRSSSS > >> >> > >> >> Strain C is "less resistant" but only because there is not enough > >> >> information. In fact it seems more serious as it is resistant to all > >> >> tested drugs. > >> >> > >> > > >> > Strain C is probably garbage and I would remove it. With a bit of luck I will have the result with the same sample Id which would be complete. > >> > > >> >> And then what about > >> >> > >> >> strain D SR > >> >> strain E RS > >> >> > >> > > >> > Yes those are the cases which are annoying me. > >> > > >> > That's why I came up withe idea of multiplying the value of the result > >> > (S=1, I=2 and R=3) with the position of the value. Tried it with > >> > triplets but there will still be cases where different results will > >> > give the same numeric value. Ignoring empty cell able tps for the moment. > >> > > >> > Strain F: SSR (1*1+2*1+3*3) =12 and Strain G: RRS (1*3+ 2*3+3*1) = 12 > >> > will be the same numerical value but they are different resistance > >> > profiles I would in this case keep both. > >> > > >> > How to prevent that from happening. > >> Can you first say why the suggestion I made is not helpful? > >> > >> -- > >> Ben. > > > > You mean that one: > > > >> >> I think you need to treat the number of Rs, Is and Ss like digits in a > >> >> number. In base 10, the strains score > >> >> > >> >> R S I > >> >> strain A 1 5 0 = 150 > >> >> strain B 3 3 0 = 330 > >> >> > > > > Different resistance profiles same result: > I don't yet understand the requirements so I am taking it in stages. > The first requirement seemed to be "more or less resistant". To do that > you can use digits in a large enough base but this will make the number > of Rs, Ss and Is paramount. Is that acceptable as a first step? > The requirements are one strain of a certain microorganism/patient The most resistant one or if they have different profiles SRS vs RRS => last one, more Rs SRS vs RSR = both, different profiles > In order to help people to be able to make further suggestions, maybe > you could give the relative ordering you would like to see between the > following sets of profiles. For example, between SSR, SRS and RSS, I > think the order you want is RSS > SRS > SSR. > > 1: SSR, SRS, RSS > > 2: RSI, RIS, SRI, SIR, IRS, ISR > > 3: SSSR, SSRS, SRSS, RSSS > > 4: RRSSS, RSSSR, RIIII, SRIII, RSIII, IIIRS, IIISR > The order of the results is given by the ID of the drug in the extraction tool. I could probably order them by family and hierarchy of potence but would that make a difference? > It's possible you could make do with an extra field (or digits) that > gives some measure of the relative ordering between otherwise similar > sequences. For example, using base 10 (for convenience of arithmetic) > both RRSSI and RSRSI would score 212xx but the last xx would reflect the > positioning of the results in the sequence. There are lots of way to do > this. One way would be use, as you were thinking, some sort of weighted > count. Using S=0, I=1 and R=2 with weights > > 54321 > RRSSI scores 2*10000 + 1*1000 + 2*100 + 2*(5+4) + 0*(3+2) + 1*1 = 21219 > RSRSI scores 2*10000 + 1*1000 + 2*100 + 2*(5+3) + 0*(4+2) + 1*1 = 21217 > So to be sure that I am following: 2*(5+4) = value of R (=2) * position of R(@5 and @4) 2*(5+3) = value of R (=2) * position of R(@5 and @3) 0*(3+2) = value of S (=0) * position of S(@3 and @2) 0*(4+2) = value of S (=0) * position of S(@4 and @2) 1*1 = value of I (=1) * position of I (@1) 2*10000 + 1*1000 + 2*100 Is just used as padding? So 212 could be any other number? But in this example I would have to keep both as drug 5,2 and 1 are common to both results but 4 and 3 are unique. The score would be completely misleading. So if my table has a width of 20 columns the first column would be 10^20, the next 10^19,.... +/- a few 0s off? I would have to implement it and see what I get as result. > If you absolutely must never get duplicate numbers, but you still want > to preserve a strict specified ordering, I think you will have much more > work to do. > > Getting a unique number for each case it trivial (but the ordering will > be wrong) and getting an ordering that rates every R > every S > every I > is also trivial, but there will be lots of duplicates. It's finding the > balance that's going to be hard. > > -- > Ben. I have prepared a cleaned up Excel workbook with only the duplicates which pose problems. The ones I would keep have an orange ID. I could upload it to Github. If that helps understanding the different cases. Thanks for your patience Laurent