<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Caroline,<div><br></div><div> I have to admit that your case was like the perfect storm for BaSTA! We've sorted out the issues with the dataset you sent us. Here are some ways of dealing with it:</div><div><br></div><div> First, install the attached version of BaSTA which has several bug fixes that apply to your case. To install it just save it in a folder, say "C:/Documents/Temp/" and then run the following command on the R console:</div><div><br></div><div><div style="margin: 0px; font-size: 16px; font-family: Monaco; color: rgb(81, 87, 189); "><span style="color: #000000">install.packages</span><span style="color: #007900">(</span>"C:/Documents/Temp/BaSTA_1.9.1.tar.gz"<span style="color: #000000">, type = </span>"source"<span style="color: #007900">)</span></div></div><div><span style="color: #007900"><br></span></div><div> Then do the following: </div><div><br></div><div><div style="margin: 0px; font-size: 16px; font-family: Monaco; "> cv <- read.csv<span style="color: #007900">(</span>sprintf<span style="color: #007900">(</span><span style="color: #5157bd">"%sCaptHist.csv"</span>, path<span style="color: #007900">))</span></div><p style="margin: 0px; font-size: 16px; font-family: Monaco; min-height: 21px; "> <br class="webkit-block-placeholder"></p><div style="margin: 0px; font-size: 16px; font-family: Monaco; "> rd <- cv<span style="color: #006f00">$</span>ROBSDATES</div><div style="margin: 0px; font-size: 16px; font-family: Monaco; "> rd<-as.Date<span style="color: #007900">(</span>rd<span style="color: #007900">)</span></div><p style="margin: 0px; font-size: 16px; font-family: Monaco; min-height: 21px; "> <br class="webkit-block-placeholder"></p><div style="margin: 0px; font-size: 16px; font-family: Monaco; "> Y <- CensusToCaptHist<span style="color: #007900">(</span>ID = cv<span style="color: #006f00">[</span>,<span style="color: #011892">1</span><span style="color: #006f00">]</span>, d=rd, timeInt=<span style="color: #5157bd">"D"</span><span style="color: #007900">)</span></div><p style="margin: 0px; font-size: 16px; font-family: Monaco; min-height: 21px; "> <br class="webkit-block-placeholder"></p><div style="margin: 0px; font-size: 16px; font-family: Monaco; "> birthDeath <- read.csv<span style="color: #007900">(</span>sprintf<span style="color: #007900">(</span><span style="color: #5157bd">"%spenults_birthdeath.csv"</span>, path<span style="color: #007900">))</span></div><div style="margin: 0px; font-size: 16px; font-family: Monaco; "> birthDeath2 <- birthDeath</div><div style="margin: 0px; font-size: 16px; font-family: Monaco; "> birthDeath2<span style="color: #006f00">[</span>birthDeath <span style="color: #b05691">!=</span> <span style="color: #011892">0</span><span style="color: #006f00">]</span> <- birthDeath<span style="color: #006f00">[</span>birthDeath <span style="color: #b05691">!=</span> <span style="color: #011892">0</span><span style="color: #006f00">]</span> <span style="color: #b05691">+</span> <span style="color: #011892">100</span></div><div style="margin: 0px; font-size: 16px; font-family: Monaco; "> covarsRaw <- read.csv<span style="color: #007900">(</span>sprintf<span style="color: #007900">(</span><span style="color: #5157bd">"%sfixed_covars.csv"</span>, path<span style="color: #007900">))</span></div><div style="margin: 0px; font-size: 16px; font-family: Monaco; "> covars <- MakeCovMat<span style="color: #007900">(</span><span style="color: #b05691">~</span>SPECIES <span style="color: #b05691">+</span> CLADE, data = covarsRaw<span style="color: #007900">)</span></div><div style="margin: 0px; font-size: 16px; font-family: Monaco; "><span style="color: #007900"> # Change the colnames of two of the covariates that overlap with another two covariates:</span></div><div style="margin: 0px; font-size: 16px; font-family: Monaco; color: rgb(81, 87, 189); "><span style="color: #000000"> colnames</span><span style="color: #007900">(</span><span style="color: #000000">covars</span><span style="color: #007900">)</span><span style="color: #006f00">[</span><span style="color: #000000">c</span><span style="color: #007900">(</span><span style="color: #011892">21</span><span style="color: #000000">, </span><span style="color: #011892">31</span><span style="color: #007900">)</span><span style="color: #006f00">]</span><span style="color: #000000"> <- c</span><span style="color: #007900">(</span>"SPECIESmyrrh01"<span style="color: #000000">, </span>"CLADEA201"<span style="color: #007900">)</span></div><div style="margin: 0px; font-size: 16px; font-family: Monaco; color: rgb(78, 143, 98); "> dat <- data.frame<span style="color: rgb(0, 121, 0); ">(</span>birthDeath2, Y<span style="color: rgb(0, 111, 0); ">[</span>, <span style="color: rgb(176, 86, 145); ">-</span><span style="color: rgb(1, 24, 146); ">1</span><span style="color: rgb(0, 111, 0); ">]</span>, covars<span style="color: rgb(0, 111, 0); ">[</span>, <span style="color: rgb(176, 86, 145); ">-</span><span style="color: rgb(1, 24, 146); ">1</span><span style="color: rgb(0, 111, 0); ">]</span><span style="color: rgb(0, 121, 0); ">)</span></div><p style="margin: 0px; font-size: 16px; font-family: Monaco; min-height: 21px; "> <br class="webkit-block-placeholder"></p><div style="margin: 0px; font-size: 16px; font-family: Monaco; "> dat2 <- DataCheck<span style="color: #007900">(</span>dat, studyStart = <span style="color: #011892">101</span>, studyEnd = <span style="color: #011892">209</span>, autofix = rep<span style="color: #007900">(</span><span style="color: #011892">1</span>, <span style="color: #011892">7</span><span style="color: #007900">)</span>, </div><div style="margin: 0px; font-size: 16px; font-family: Monaco; "> silent = <span style="color: #932192">FALSE</span><span style="color: #007900">)</span></div><p style="margin: 0px; font-size: 16px; font-family: Monaco; min-height: 21px; "> out <- basta(dat2$newDat, studyStart = <span style="color: rgb(1, 24, 146); ">101</span>, studyEnd = <span style="color: rgb(1, 24, 146); ">209, thetaStart = c(-10, 0.001))</span></p><div><br></div><div><br></div><div> I hope this really solves it. If not please let us know. Best,</div><div><br></div><div> Fernando</div><div><br></div><div><br></div><div></div></div></body></html>