2012-03-06 V_0.0.7 Youyi Fong * add log.transform to rumi argument list * add est.conc, lb.conc, ub.conc to data frames returned by rumi 2012-03-22 V_0.0.8 Youyi Fong * add weighting to rumi argument list. Note that the power is -1.8 and it only works for non-transformed FI. * add drm.weights.var.power, a global variable that controls variance function 2012-04-09 V_0.0.9 Youyi Fong * add testing vcov is null due to a numerical exception from some dataset 2012-05-11 V_0.0.10 Youyi Fong * add incr and auto.detect.incr at the request of Maria 2012-05-21 V_0.0.11 Youyi Fong * bug fix for unknown sample concentration estimation when the curve is decreasing * prompted by Maria and Devin 2012-06-24 V_0.0.12 Youyi Fong * change the ordering of rows in data frame, this affects the numerical outcome of fitted curve because drm /5pl is sensitive * fix a bug for plot=F & find.LOD=T * if a sample has multiple replicates, fi in the returned data frame now equals exp(Y_bar), previously it equals exp(Y_1) * prompted by William 2012-08-11 V_0.0.13 Youyi Fong * add loq.30 * change how the default behavior of find.lod works. Previously it finds 95% CI by default, now it is 90%. This change is made to make it consistent with test.LOD, which defaults to 90%. Both defaults can be changed with a single parameter now, lod.ci * each curve will always have lod and loq. When se is bad, it will be NA 2012-08-22 V_0.0.14 Youyi Fong * use qt instead of qnorm for confidence interval and LODi testing/estimation 2012-08-30 V_0.0.15 Youyi Fong * change the column names of loq30 from rloq to rloq30, same for lloq * change the column names of lod from x.low to llodi, same for x.high * CI was defined on the t scale * LoDi was defined on the t scale, now the ci.scale.t parameter controls whether it is on t or x scale * LoQ was defined on the x scale using an usual definition of se * need to tell Devin LoDi.x=F * new feature in plots * Fix: if fi is 0 or less, things go wrong with no good error message (Tiffany). 2012-08-30 V_0.0.16 Youyi Fong * remove log.transform from the list of arguments * add rumi.formula, rumi.data.frame 2013-04-17 V_0.1-1 Youyi Fong, Krisztian Sebestyen * Rename Ruminex to nCal * improve fit.jags functional interface * add import functions * add Excel plugin * submit to CRAN * paper submission * remove drm.weights.var.power, a global variable that controls variance 2013-05-28 V_0.2-1 Youyi Fong * pass stringsAsFactors =FALSE to data.frame * repond to referee comments, add vignette, add tests, change package dependencies * fix bug in ncal.character * remove incr and auto.detect.incr and handle decreasing more smartly * framed.sty needs to be present where kpsewhich.exe locates * qpdf is downloaded and path added, ghostscrip 2013-05-28 V_0.2-2 Youyi Fong * making changes according to major revision comments * add additional.plot.func to ncal list of params * in ncal, when plotting drm fit, having xlim sometimes messes things up, not sure why 2013-05-28 V_0.3-1 Youyi Fong * remove some checkEqualsNumeric from nCal.Rd since they fail on some systems (drm optimization related) * making changes according to minor revision comments 2013-05-28 V_0.3-2 Youyi Fong * restrict unit testing to x86_64, mingw32 and x86_64, linux-gnu 2013-05-28 V_0.3-3 Youyi Fong * after bug fix to integrate(), some tests fail. move all testing from function help examples to unit testing files. change tolerance for those checks depending on integrate() to a large number for now. See email from Prof. Ripley on 7/16/13 2013-05-28 V_0.3-4 Youyi Fong * move unit testing code for read.luminex.xls to runit.ncal.R from function help * expand unit testing to all platforms with relaxed tolerance 2013-07-24 V_0.4-1 Youyi Fong * in drm.fit, use default ss.fct first so that the results will match drm call in most cases * add check.out.of.range parameter to ncal that supports two modes of checks. The default mode is a new mode which resets any estimated concentration that is outside the range of standard concentrations 2013-11-07 Youyi Fong * make fi 1 in ncal if fi is 0 or negative 2013-11-29 Youyi Fong * use a new copy of youtil.R that does not have getVarComponent.nlme to avoid a warning after a drc update 2014-03-31 Youyi Fong * change } else if(all(is.na(diag(vcov.)))) { to any at Doug Lowe's suggestion 2014-04-23 Xuesong Yu * add weighted ls implementation 2014-10-31 Youyi Fong * remove plot.crm. need to learn callNextMethod to use it, b/c it does not allow plot.drc or drc:::plot.drc 2018--8-17 * Change to use %.%