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<p class="MsoNormal">Dear Traminer Users,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I would like to compute distances between sequences that belong to the same person for every person in my data.
<o:p></o:p></p>
<p class="MsoNormal">The code below seems to work: it calculates the distances between the expected and actual work schedule for each of the 10 people in the data.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">My code, however, is terribly inefficient. For instance, it calculates the entire pairwise distance matrix and then overwrites most of it with NA.
<o:p></o:p></p>
<p class="MsoNormal">This leaves me with two questions:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="mso-list:Ignore">1)<span style="font:7.0pt "Times New Roman"">
</span></span><![endif]>Does Traminer have a way to calculate just the distances between sequences that below to the same person?
<o:p></o:p></p>
<p class="MsoListParagraph"> (e.g., with clever use of the refseq option in the seqdist command or with the seqdistmc command for multi-channel sequence analysis)<o:p></o:p></p>
<p class="MsoListParagraph"><o:p> </o:p></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="mso-list:Ignore">2)<span style="font:7.0pt "Times New Roman"">
</span></span><![endif]>Is there a way to extract the elements just below the diagonal without overwriting all the other values with NA?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Jeremy<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="DE">mymat <- rbind(<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE"> c(1,1,0,0,1,1,1,1,1,0,0,0),c(1,2,0,0,1,1,1,1,1,1,0,0),<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE"> c(2,1,0,0,1,1,1,1,1,0,0,0),c(2,2,0,0,1,1,1,1,1,1,1,0),<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE"> c(3,1,0,0,1,1,1,1,1,0,0,0),c(3,2,0,0,1,1,1,1,1,1,1,1),<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE"> c(4,1,0,0,1,1,1,1,1,0,0,0),c(4,2,0,1,1,1,1,1,1,0,0,0),<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE"> c(5,1,0,0,1,1,1,1,1,0,0,0),c(5,2,1,1,1,1,1,1,1,0,0,0),<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE"> c(6,1,0,0,1,1,1,1,1,0,0,0),c(6,2,0,0,0,1,1,1,1,0,0,0),<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE"> c(7,1,0,0,1,1,1,1,1,0,0,0),c(7,2,0,0,0,0,1,1,1,0,0,0),<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE"> c(8,1,0,0,1,1,1,1,1,0,0,0),c(8,2,0,0,0,0,0,1,1,0,0,0),<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE"> c(9,1,0,0,1,1,1,1,1,0,0,0),c(9,2,0,0,0,0,0,0,1,0,0,0),<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE"> c(10,1,0,0,1,1,1,1,1,0,0,0),c(10,2,0,0,0,0,0,0,0,0,0,0)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE"> )<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="DE">colnames(mymat) <- c("ID", "sched", "t1", "t2", "t3", "t4", "t5", "t6", "t7", "t8", "t9", "t10")<o:p></o:p></span></p>
<p class="MsoNormal">mymat <- as.data.frame(mymat)<o:p></o:p></p>
<p class="MsoNormal">mymat$sched <- factor(mymat$sched,levels = c(1,2), labels = c("Expected", "Actual"))<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">library(TraMineR)<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"># make sequence object<o:p></o:p></p>
<p class="MsoNormal">labels <- c("working", "not working")<o:p></o:p></p>
<p class="MsoNormal"><span lang="DE">scode <- c("W", "N")<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE">seq <- seqdef(mymat, 3:12, states = scode, labels = labels)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE"><o:p> </o:p></span></p>
<p class="MsoNormal"># sequence index plot<o:p></o:p></p>
<p class="MsoNormal">seqIplot(seq, with.legend = T, main = "Expected and Actual Work Schedules of 5 People",border = NA)<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"># calculate dynamic hamming distances for every possible pair<o:p></o:p></p>
<p class="MsoNormal">distmat <- seqdist(seq, method = "DHD", indel = 1, sm = NULL)<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"># extract the elements just below the main diagonal<o:p></o:p></p>
<p class="MsoNormal">low <- 1<o:p></o:p></p>
<p class="MsoNormal">high <- 1<o:p></o:p></p>
<p class="MsoNormal">delta <- row(distmat) - col(distmat)<o:p></o:p></p>
<p class="MsoNormal">distmat[delta < low | delta > high] <- NA<o:p></o:p></p>
<p class="MsoNormal">distvec <- na.omit(as.data.frame(distmat[delta >= low | delta <= high]))<o:p></o:p></p>
<p class="MsoNormal">#repeat the last entry<o:p></o:p></p>
<p class="MsoNormal">distvec <- rbind(distvec,tail(distvec, n=1))<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">#attach the off diagonal to the data frame<o:p></o:p></p>
<p class="MsoNormal">colnames(distvec) <- "dist"<o:p></o:p></p>
<p class="MsoNormal">mymat <- cbind(mymat,distvec)<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div style="mso-element:para-border-div;border:none;border-bottom:solid windowtext 1.5pt;padding:0in 0in 1.0pt 0in">
<p class="MsoNormal" style="border:none;padding:0in"><o:p> </o:p></p>
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<p class="MsoNormal">Dr. Jeremy Reynolds<o:p></o:p></p>
<p class="MsoNormal">Professor<o:p></o:p></p>
<p class="MsoNormal">307 Stone Hall <o:p></o:p></p>
<p class="MsoNormal">Department of Sociology<o:p></o:p></p>
<p class="MsoNormal">700 W. State Street<o:p></o:p></p>
<p class="MsoNormal">Purdue University <o:p></o:p></p>
<p class="MsoNormal">West Lafayette, IN 47907 <o:p></o:p></p>
<p class="MsoNormal">Phone: (765) 496-3348 <o:p></o:p></p>
<p class="MsoNormal"><a href="https://cla.purdue.edu/directory/profiles/jeremy-reynolds.html">https://cla.purdue.edu/directory/profiles/jeremy-reynolds.html</a><o:p></o:p></p>
<p class="MsoNormal">Pronouns: he/him/his<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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