{"action":"created","issue":{"url":"https://api.github.com/repos/quantifish/TagGrowth/issues/20","labels_url":"https://api.github.com/repos/quantifish/TagGrowth/issues/20/labels{/name}","comments_url":"https://api.github.com/repos/quantifish/TagGrowth/issues/20/comments","events_url":"https://api.github.com/repos/quantifish/TagGrowth/issues/20/events","html_url":"https://github.com/quantifish/TagGrowth/issues/20","id":55408470,"number":20,"title":"Cant fit the ydev models","user":{"login":"quantifish","id":5566375,"avatar_url":"https://avatars.githubusercontent.com/u/5566375?v=3","gravatar_id":"","url":"https://api.github.com/users/quantifish","html_url":"https://github.com/quantifish","followers_url":"https://api.github.com/users/quantifish/followers","following_url":"https://api.github.com/users/quantifish/following{/other_user}","gists_url":"https://api.github.com/users/quantifish/gists{/gist_id}","starred_url":"https://api.github.com/users/quantifish/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/quantifish/subscriptions","organizations_url":"https://api.github.com/users/quantifish/orgs","repos_url":"https://api.github.com/users/quantifish/repos","events_url":"https://api.github.com/users/quantifish/events{/privacy}","received_events_url":"https://api.github.com/users/quantifish/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/quantifish/TagGrowth/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":28,"created_at":"2015-01-25T10:11:09Z","updated_at":"2015-01-28T21:50:01Z","closed_at":null,"body":"In the case study, the model estimating ydevs only is not pdHess. The model with random-effects for z and ydevs fits (see figs). The models for k and ydevs and k, z and ydevs do not work at all (getting bad alloc erros)."},"comment":{"url":"https://api.github.com/repos/quantifish/TagGrowth/issues/comments/71923739","html_url":"https://github.com/quantifish/TagGrowth/issues/20#issuecomment-71923739","issue_url":"https://api.github.com/repos/quantifish/TagGrowth/issues/20","id":71923739,"user":{"login":"James-Thorson","id":7989837,"avatar_url":"https://avatars.githubusercontent.com/u/7989837?v=3","gravatar_id":"","url":"https://api.github.com/users/James-Thorson","html_url":"https://github.com/James-Thorson","followers_url":"https://api.github.com/users/James-Thorson/followers","following_url":"https://api.github.com/users/James-Thorson/following{/other_user}","gists_url":"https://api.github.com/users/James-Thorson/gists{/gist_id}","starred_url":"https://api.github.com/users/James-Thorson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/James-Thorson/subscriptions","organizations_url":"https://api.github.com/users/James-Thorson/orgs","repos_url":"https://api.github.com/users/James-Thorson/repos","events_url":"https://api.github.com/users/James-Thorson/events{/privacy}","received_events_url":"https://api.github.com/users/James-Thorson/received_events","type":"User","site_admin":false},"created_at":"2015-01-28T21:50:01Z","updated_at":"2015-01-28T21:50:01Z","body":"Makes sense! And yes, our results in hand should be publishable.\r\n\r\nSent from my iPhone\r\n\r\n> On Jan 28, 2015, at 12:31 PM, Darcy Webber <notifications@github.com> wrote:\r\n> \r\n> OK, I've changed my mind for two reasons: I have 2 months to finish my \r\n> PhD and I'm pushing it, and I'd like to revisit this stuff later this \r\n> year anyway (adding in cohort slicing or suchlike to get at the growth \r\n> retardation due to tagging). So if you reckon we have a publishable unit \r\n> as it stands lets just stick with that for now. Sorry to fluff around in \r\n> making up my mind Jim.\r\n> \r\n> So that being said, you'll be waiting on me to rip into the results, \r\n> I'll get to this later today.\r\n> \r\n> Cheers\r\n> Darcy\r\n> \r\n> \r\n> On 28/01/15 18:09, Jim Thorson wrote:\r\n> > Ok, happy to contribute some coding too. basically I envision that the\r\n> > z_sd is constant for all years and individuals (instead of that \r\n> > complicated\r\n> > function from Ole's paper). And, looking at it again, we'll need a random\r\n> > effect for each year between Year0, Year1, and Year2 for each individual.\r\n> > Then the length will just be calculated recursively for a given \r\n> > individual\r\n> > from Year0 to Year1, and Year1 to Year2. finally, ln_ydev, ln_xdev,\r\n> > ln_bdev, and ln_zdev (or whatever we call the new z for each year and\r\n> > individual) will enter via lognormal variation in gamma.\r\n> >\r\n> > finally, as I said before, I think we have a publishable unit as-is, and\r\n> > don't mind abandoning time-variation now or later.\r\n> >\r\n> > jim\r\n> >\r\n> > On Tue, Jan 27, 2015 at 7:12 PM, Darcy Webber <notifications@github.com>\r\n> > wrote:\r\n> >\r\n> > > Yep so right you are, that didn't help.\r\n> > >\r\n> > > OK, so do you reckon we give option 2 a go? I am happy to change the\r\n> > > code to try this out, I can do a little tonight and the rest tomo \r\n> > morning.\r\n> > >\r\n> > >\r\n> > >\r\n> > >\r\n> > > On 28/01/15 15:14, Jim Thorson wrote:\r\n> > > > We could try it if you want. I'm skeptical it'll solve it but it \r\n> > would\r\n> > > > be quick to try\r\n> > > >\r\n> > > > Sent from my iPhone\r\n> > > >\r\n> > > > > On Jan 27, 2015, at 2:01 PM, Darcy Webber \r\n> > <notifications@github.com>\r\n> > > > wrote:\r\n> > > > >\r\n> > > > > Might placing a prior penalty on sd_ydev help keep this in line?\r\n> > > > > Something that pushes sd_ydev towards smaller values, like a\r\n> > > > > gamma/exponential, e.g. Ga(1, 500). I can derive and justify this\r\n> > > > > properly based on an assumption that we would not expect growth to\r\n> > > > > change by more than 10% due to annual effects...or something \r\n> > like that.\r\n> > > > >\r\n> > > > >\r\n> > > > > On 28/01/15 10:34, Jim Thorson wrote:\r\n> > > > > > Yes v3 (year random) is non-pd because ln_bmean goes to -20 \r\n> > and the\r\n> > > > > > gradient wrt it is small but nonzero\r\n> > > > > >\r\n> > > > > > Sent from my iPhone\r\n> > > > > >\r\n> > > > > > > On Jan 27, 2015, at 1:19 PM, Darcy Webber\r\n> > > > <notifications@github.com>\r\n> > > > > > wrote:\r\n> > > > > > >\r\n> > > > > > > Ah right. OK so being a pain on one more issue, we still can't\r\n> > > > get a\r\n> > > > > > pdH\r\n> > > > > > > model for ydev random-effects only, this influences option 2 \r\n> > right?\r\n> > > > > > >\r\n> > > > > > >\r\n> > > > > > >\r\n> > > > > > > On 28/01/15 10:07, Jim Thorson wrote:\r\n> > > > > > > > Because it would require reserving the equation that we \r\n> > got from\r\n> > > > > > ole's\r\n> > > > > > > > paper (currently in the appendix) whereas number 2 we can do\r\n> > > > > > > > numerically in TMB without adding any coefficients\r\n> > > > > > > >\r\n> > > > > > > > Sent from my iPhone\r\n> > > > > > > >\r\n> > > > > > > > > On Jan 27, 2015, at 12:14 PM, Darcy Webber\r\n> > > > > > > > <notifications@github.com> wrote:\r\n> > > > > > > > >\r\n> > > > > > > > > Mmmm ok. Why would option 3 be the hardest?\r\n> > > > > > > > >\r\n> > > > > > > > >\r\n> > > > > > > > > On 28/01/15 07:58, Jim Thorson wrote:\r\n> > > > > > > > > > OK, on further thought, I think the problem is a \r\n> > fundamental\r\n> > > > > > issue\r\n> > > > > > > > when\r\n> > > > > > > > > > including time-varying in gamma, but individual \r\n> > variation in\r\n> > > > > > beta,\r\n> > > > > > > > where\r\n> > > > > > > > > > the model can more-easily explain variation in data via\r\n> > > > > > variation in\r\n> > > > > > > > > > gamma,\r\n> > > > > > > > > > and hence when time-variation in gamma is available, it\r\n> > > > > > essentially\r\n> > > > > > > > > > \"turns\r\n> > > > > > > > > > off\" beta and variation therein.\r\n> > > > > > > > > >\r\n> > > > > > > > > > There's three ways to proceed (two are relatively \r\n> > feasible):\r\n> > > > > > > > > >\r\n> > > > > > > > > > 1. Leave as-is and don't deal with time-variation \r\n> > (this is\r\n> > > > the\r\n> > > > > > > > easiest\r\n> > > > > > > > > > obviously)\r\n> > > > > > > > > > 2. Change our code to put all components in gamma and\r\n> > > > hence on an\r\n> > > > > > > > even\r\n> > > > > > > > > > footing (this requires a rebuild of the code, but \r\n> > nothing too\r\n> > > > > > > > serious. it\r\n> > > > > > > > > > would also require re-running all case study and sim\r\n> > > > results, and\r\n> > > > > > > > > > re-writing parts of the methods).\r\n> > > > > > > > > > 3. change our code to put all components in beta (this is\r\n> > > > > > hardest,\r\n> > > > > > > > and I\r\n> > > > > > > > > > don't really propose it seriously)\r\n> > > > > > > > > >\r\n> > > > > > > > > > thoughts and preferences?\r\n> > > > > > > > > >\r\n> > > > > > > > > > jim\r\n> > > > > > > > > >\r\n> > > > > > > > > > On Tue, Jan 27, 2015 at 8:57 AM, James Thorson\r\n> > > > > > <jamest.esq@gmail.com>\r\n> > > > > > > > > > wrote:\r\n> > > > > > > > > >\r\n> > > > > > > > > > > Darcy,\r\n> > > > > > > > > > >\r\n> > > > > > > > > > > 1. Sorry about asking you to do that Year2 included\r\n> > > > thing! as\r\n> > > > > > > > you point\r\n> > > > > > > > > > > out, its not clear how to use it. I didn't think \r\n> > carefully\r\n> > > > > > about it\r\n> > > > > > > > > > last\r\n> > > > > > > > > > > night.\r\n> > > > > > > > > > >\r\n> > > > > > > > > > > 2. The problem with v3 is that, with year effects, the\r\n> > > > bmean\r\n> > > > > > wants\r\n> > > > > > > > > > to go\r\n> > > > > > > > > > > negative, and so ln_bmean -> -Inf. The problem with v5\r\n> > > > is that\r\n> > > > > > > > the same\r\n> > > > > > > > > > > thing happens, and when ln_bmean -> -Inf, bmean -> \r\n> > 0, which\r\n> > > > > > means\r\n> > > > > > > > > > that the\r\n> > > > > > > > > > > ln_bdev has no effect, which means that the hessian of\r\n> > > > random\r\n> > > > > > > > effects\r\n> > > > > > > > > > > becomes singular and non-pD.\r\n> > > > > > > > > > >\r\n> > > > > > > > > > > 3. I tried adding in bias-correction for the lognormal\r\n> > > > ln_ydev\r\n> > > > > > > > effect:\r\n> > > > > > > > > > >\r\n> > > > > > > > > > > for (int y = 0; y < Nyears; y++) { ans -= dnorm(\r\n> > > > ln_ydev(y),\r\n> > > > > > > > > > > -0.5*pow(sd_ydev,2), sd_ydev, true ); }\r\n> > > > > > > > > > >\r\n> > > > > > > > > > > in line 96 of the CPP, and this didn't fix the \r\n> > problem of\r\n> > > > > > > > ln_bmean ->\r\n> > > > > > > > > > > -Inf. I'll think more about the problem. If nothing\r\n> > > > else, we\r\n> > > > > > > > should go\r\n> > > > > > > > > > > ahead with the individual and individual-by-year\r\n> > > > deviations (4\r\n> > > > > > > > > > candidate\r\n> > > > > > > > > > > models) that we have working already, which should \r\n> > still be\r\n> > > > > > > > > > publishable.\r\n> > > > > > > > > > >\r\n> > > > > > > > > > > cheers,\r\n> > > > > > > > > > > jim\r\n> > > > > > > > > > >\r\n> > > > > > > > > > > On Tue, Jan 27, 2015 at 1:22 AM, Darcy Webber\r\n> > > > > > > > > > <notifications@github.com>\r\n> > > > > > > > > > > wrote:\r\n> > > > > > > > > > >\r\n> > > > > > > > > > >> Hey Jim\r\n> > > > > > > > > > >>\r\n> > > > > > > > > > >> The calculation of Year2 and Time2 etc is all done by\r\n> > > > the R\r\n> > > > > > code\r\n> > > > > > > > > > >> already, the R function time_step does all this. I've\r\n> > > > > > passed both\r\n> > > > > > > > > > >> directly into TMB, but I'm not sure what you want \r\n> > me to do\r\n> > > > > > with\r\n> > > > > > > > it.\r\n> > > > > > > > > > >>\r\n> > > > > > > > > > >> The deal is that our model is working on weekly\r\n> > > > time-steps (or\r\n> > > > > > > > > > whatever\r\n> > > > > > > > > > >> the user specifies in the R function). But our \r\n> > effects are\r\n> > > > > > annual.\r\n> > > > > > > > > > So to\r\n> > > > > > > > > > >> line the weeks up with the years I am using the \r\n> > vectors\r\n> > > > > > \"Time0\"\r\n> > > > > > > > and\r\n> > > > > > > > > > >> \"Time1\". These vectors are the number of weeks since\r\n> > > > year0,\r\n> > > > > > the\r\n> > > > > > > > first\r\n> > > > > > > > > > >> week that any individual was born. Each weekly\r\n> > > > time-step in\r\n> > > > > > the\r\n> > > > > > > > model\r\n> > > > > > > > > > >> increments this time (i.e. since Time0 and Time1). \r\n> > When\r\n> > > > the\r\n> > > > > > time\r\n> > > > > > > > > > becomes\r\n> > > > > > > > > > >> a multiple of 52 we increment the year which \r\n> > started at\r\n> > > > Year0\r\n> > > > > > > > or Year1\r\n> > > > > > > > > > >> for each individual.\r\n> > > > > > > > > > >>\r\n> > > > > > > > > > >> The other thing is that the model with ydevs only\r\n> > > > works, its\r\n> > > > > > > > just not\r\n> > > > > > > > > > >> pdH, and the model with z and ydevs works and is pdH.\r\n> > > > > > Weirdly now\r\n> > > > > > > > > > the z\r\n> > > > > > > > > > >> and ydev model doesnt work on my machine. I'm going to\r\n> > > > bed,\r\n> > > > > > > > will think\r\n> > > > > > > > > > >> about this again tomo.\r\n> > > > > > > > > > >>\r\n> > > > > > > > > > >> Cheers\r\n> > > > > > > > > > >> D\r\n> > > > > > > > > > >>\r\n> > > > > > > > > > >>\r\n> > > > > > > > > > >>\r\n> > > > > > > > > > >>\r\n> > > > > > > > > > >> On 27/01/15 17:24, Jim Thorson wrote:\r\n> > > > > > > > > > >> > actually just checked the new code. could you \r\n> > also add\r\n> > > > > > > > > > calculation of\r\n> > > > > > > > > > >> > Year2 (the year of recapture) in R and pass it \r\n> > directly\r\n> > > > > > to TMB\r\n> > > > > > > > > > instead\r\n> > > > > > > > > > >> of\r\n> > > > > > > > > > >> > calculating it via incrementing in the loop from \r\n> > Year1?\r\n> > > > > > > > That'd be my\r\n> > > > > > > > > > >> > guess\r\n> > > > > > > > > > >> > for the problem, and would also ease debugging.\r\n> > > > > > > > > > >> >\r\n> > > > > > > > > > >> > thanks for helping. obviously I welcome you \r\n> > sleuthing\r\n> > > > for\r\n> > > > > > the\r\n> > > > > > > > > > solution\r\n> > > > > > > > > > >> > too, but if I'm gonna dive in, I gotta try and be\r\n> > > > efficient.\r\n> > > > > > > > > > >> >\r\n> > > > > > > > > > >> > jim\r\n> > > > > > > > > > >> >\r\n> > > > > > > > > > >> > On Mon, Jan 26, 2015 at 8:12 PM, James Thorson\r\n> > > > > > > > > > <jamest.esq@gmail.com>\r\n> > > > > > > > > > >> > wrote:\r\n> > > > > > > > > > >> >\r\n> > > > > > > > > > >> > > Sure thing I'll check this week\r\n> > > > > > > > > > >> > >\r\n> > > > > > > > > > >> > > Sent from my iPhone\r\n> > > > > > > > > > >> > >\r\n> > > > > > > > > > >> > > On Jan 26, 2015, at 8:10 PM, Darcy Webber\r\n> > > > > > > > > > <notifications@github.com>\r\n> > > > > > > > > > >> > > wrote:\r\n> > > > > > > > > > >> > >\r\n> > > > > > > > > > >> > > Hi Jim,\r\n> > > > > > > > > > >> > >\r\n> > > > > > > > > > >> > > So I have changed ADREPORT(Linf) to REPORT(Linf),\r\n> > > > > > included the\r\n> > > > > > > > > > >> gradient\r\n> > > > > > > > > > >> > > in all nlminb calls and calculated Nyear from \r\n> > the R\r\n> > > > > > generated\r\n> > > > > > > > > > Year1\r\n> > > > > > > > > > >> > etc.\r\n> > > > > > > > > > >> > >\r\n> > > > > > > > > > >> > > But, still not getting anywhere with the ydev\r\n> > > > models. The\r\n> > > > > > > > > > version with\r\n> > > > > > > > > > >> > > ydevs as the only RE (v3/) is still not pdH, \r\n> > the other\r\n> > > > > > > > versions\r\n> > > > > > > > > > for\r\n> > > > > > > > > > >> > k, y\r\n> > > > > > > > > > >> > > and k, y, z simply crash. Initially I'd changed \r\n> > the\r\n> > > > Nyears\r\n> > > > > > > > from\r\n> > > > > > > > > > 40 to\r\n> > > > > > > > > > >> > > something else to test if this was the issue. Can\r\n> > > > you run\r\n> > > > > > > > perhaps\r\n> > > > > > > > > > >> > v5/ in\r\n> > > > > > > > > > >> > > case_study and see what happens your end?\r\n> > > > > > > > > > >> > >\r\n> > > > > > > > > > >> > > Cheers\r\n> > > > > > > > > > >> > > D\r\n> > > > > > > > > > >> > >\r\n> > > > > > > > > > >> > >\r\n> > > > > > > > > > >> > > On 27/01/15 08:16, Jim Thorson wrote:\r\n> > > > > > > > > > >> > > > Sorry, I meant to say that we should put the\r\n> > > > > > calculation of\r\n> > > > > > > > > > Year1\r\n> > > > > > > > > > >> and\r\n> > > > > > > > > > >> > > > Year2\r\n> > > > > > > > > > >> > > > in R in teh data prep function. that way, in R,\r\n> > > > we can\r\n> > > > > > > > make sure\r\n> > > > > > > > > > >> > > > Nyears is\r\n> > > > > > > > > > >> > > > correct.\r\n> > > > > > > > > > >> > > >\r\n> > > > > > > > > > >> > > > jim\r\n> > > > > > > > > > >> > > >\r\n> > > > > > > > > > >> > > > On Mon, Jan 26, 2015 at 10:31 AM, Darcy Webber\r\n> > > > > > > > > > >> > <notifications@github.com\r\n> > > > > > > > > > >> > > >\r\n> > > > > > > > > > >> > > > wrote:\r\n> > > > > > > > > > >> > > >\r\n> > > > > > > > > > >> > > > > Jim,\r\n> > > > > > > > > > >> > > > >\r\n> > > > > > > > > > >> > > > > I remember thinking about this and reckoned \r\n> > that I\r\n> > > > > > > > would put\r\n> > > > > > > > > > >> > > > integrating\r\n> > > > > > > > > > >> > > > > these date calculations into the C++ code \r\n> > in the\r\n> > > > > > too hard\r\n> > > > > > > > > > >> > basket. We're\r\n> > > > > > > > > > >> > > > > using a weekly time-step and the year/ydev\r\n> > > > stuff is\r\n> > > > > > > > obviously\r\n> > > > > > > > > > >> > > > annual, so\r\n> > > > > > > > > > >> > > > > yet another vector needs to be calculated \r\n> > called\r\n> > > > > > > > \"Time1\" and\r\n> > > > > > > > > > >> > \"Time2\"\r\n> > > > > > > > > > >> > > > > that tells us which year matches up with which\r\n> > > > > > > > time-step. This\r\n> > > > > > > > > > >> > > > vector is\r\n> > > > > > > > > > >> > > > > calculated from an actual datetime field in \r\n> > the\r\n> > > > > > data so\r\n> > > > > > > > > > that the\r\n> > > > > > > > > > >> > proper\r\n> > > > > > > > > > >> > > > > number of weeks are incremented (i.e. not all\r\n> > > > fish are\r\n> > > > > > > > > > tagged at\r\n> > > > > > > > > > >> > the\r\n> > > > > > > > > > >> > > > > beginning of the year). These sorts of \r\n> > datetime\r\n> > > > > > > > operations go\r\n> > > > > > > > > > >> > beyond my\r\n> > > > > > > > > > >> > > > > C++ capabilities unfortunately. I think that's\r\n> > > > how it\r\n> > > > > > > > is, I'll\r\n> > > > > > > > > > >> look\r\n> > > > > > > > > > >> > > > into\r\n> > > > > > > > > > >> > > > > it again and have a think... does that all \r\n> > make\r\n> > > > sense?\r\n> > > > > > > > > > >> > > > >\r\n> > > > > > > > > > >> > > > > Also, yes I'll make sure the gradient info \r\n> > is in\r\n> > > > > > all the\r\n> > > > > > > > > > >> > optimization\r\n> > > > > > > > > > >> > > > > calls and take a look at the \r\n> > REPORT()/ADREPORT()\r\n> > > > > > for Linf.\r\n> > > > > > > > > > >> > > > >\r\n> > > > > > > > > > >> > > > > Cheers Jim\r\n> > > > > > > > > > >> > > > > D\r\n> > > > > > > > > > >> > > > >\r\n> > > > > > > > > > >> > > > >\r\n> > > > > > > > > > >> > > > > On 27/01/15 06:08, Jim Thorson wrote:\r\n> > > > > > > > > > >> > > > > > Darcy,\r\n> > > > > > > > > > >> > > > > >\r\n> > > > > > > > > > >> > > > > > I'll upload in a minute my files that I \r\n> > used to\r\n> > > > > > > > > > investigate the\r\n> > > > > > > > > > >> > > > problem.\r\n> > > > > > > > > > >> > > > > >\r\n> > > > > > > > > > >> > > > > > Basically you had the number of years\r\n> > > > pre-specified\r\n> > > > > > > > at 33\r\n> > > > > > > > > > and\r\n> > > > > > > > > > >> its\r\n> > > > > > > > > > >> > > > > > actually\r\n> > > > > > > > > > >> > > > > > 40, so the model over-ran the length of \r\n> > vector\r\n> > > > > > ln_ydev\r\n> > > > > > > > > > and would\r\n> > > > > > > > > > >> > > > crash.\r\n> > > > > > > > > > >> > > > > >\r\n> > > > > > > > > > >> > > > > > The best solution is to calculate a new\r\n> > > > data-vector\r\n> > > > > > > > > > \"Year1\" and\r\n> > > > > > > > > > >> > > > \"Year2\"\r\n> > > > > > > > > > >> > > > > > which give the year for length measurements\r\n> > > > > > Length1 and\r\n> > > > > > > > > > >> > Length2. This\r\n> > > > > > > > > > >> > > > > > would replace the code for incrementing \r\n> > \"year\"\r\n> > > > > > > > internally\r\n> > > > > > > > > > to the\r\n> > > > > > > > > > >> > > > CPP, and\r\n> > > > > > > > > > >> > > > > > would make it easier to ensure that \r\n> > there's no\r\n> > > > > > mismatch\r\n> > > > > > > > > > of the\r\n> > > > > > > > > > >> > > > length of\r\n> > > > > > > > > > >> > > > > > ln_ydev and the number of years.\r\n> > > > > > > > > > >> > > > > > 1. does this make sense?\r\n> > > > > > > > > > >> > > > > > 2. you willing to make this change in the \r\n> > CPP?\r\n> > > > > > > > > > >> > > > > >\r\n> > > > > > > > > > >> > > > > > cheers,\r\n> > > > > > > > > > >> > > > > > jim\r\n> > > > > > > > > > >> > > > > >\r\n> > > > > > > > > > >> > > > > >\r\n> > > > > > > > > > >> > > > > > On Sun, Jan 25, 2015 at 8:15 PM, Darcy \r\n> > Webber\r\n> > > > > > > > > > >> > > > <notifications@github.com>\r\n> > > > > > > > > > >> > > > > > wrote:\r\n> > > > > > > > > > >> > > > > >\r\n> > > > > > > > > > >> > > > > > > Done.\r\n> > > > > > > > > > >> > > > > > >\r\n> > > > > > > > > > >> > > > > > >\r\n> > > > > > > > > > >> > > > > > >\r\n> > > > > > > > > > >> > > > > > > On 26/01/15 16:50, Jim Thorson wrote:\r\n> > > > > > > > > > >> > > > > > > > Good idea tell me when I should try \r\n> > again,\r\n> > > > > > thanks!\r\n> > > > > > > > > > >> > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > Sent from my iPhone\r\n> > > > > > > > > > >> > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > On Jan 25, 2015, at 6:07 PM, Darcy \r\n> > Webber\r\n> > > > > > > > > > >> > > > > > <notifications@github.com>\r\n> > > > > > > > > > >> > > > > > > > wrote:\r\n> > > > > > > > > > >> > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > Jim,\r\n> > > > > > > > > > >> > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > Ah yes, that data file isn't in the\r\n> > > > repo yet\r\n> > > > > > > > (we still\r\n> > > > > > > > > > >> > don't\r\n> > > > > > > > > > >> > > > have\r\n> > > > > > > > > > >> > > > > > > > > permission to make it public yet). \r\n> > To get\r\n> > > > > > around\r\n> > > > > > > > > > this I\r\n> > > > > > > > > > >> > suggest\r\n> > > > > > > > > > >> > > > > > we make\r\n> > > > > > > > > > >> > > > > > > > > the repo private for now and upload\r\n> > > > > > everything.\r\n> > > > > > > > Sound\r\n> > > > > > > > > > >> > ok? I'll\r\n> > > > > > > > > > >> > > > > > let you\r\n> > > > > > > > > > >> > > > > > > > > know when this is done.\r\n> > > > > > > > > > >> > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > Cheers\r\n> > > > > > > > > > >> > > > > > > > > D\r\n> > > > > > > > > > >> > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > On 26/01/15 14:51, Jim Thorson wrote:\r\n> > > > > > > > > > >> > > > > > > > > > Darcy,\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > when I try to run:\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > devtools::install_github(\"quantifish/TagGrowth\")\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > to install the package, I get an \r\n> > error\r\n> > > > > > message:\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > Downloading github repo\r\n> > > > > > > > quantifish/TagGrowth@master\r\n> > > > > > > > > > >> > > > > > > > > > Installing TagGrowth\r\n> > > > > > > > > > >> > > > > > > > > > \"C:/PROGRA~1/R/R-31~1.1/bin/x64/R\"\r\n> > > > > > --vanilla CMD\r\n> > > > > > > > > > >> > INSTALL \\\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > >\r\n> > > > > > > > > > >> > > > > > >\r\n> > > > > > > > > > >> > > > > >\r\n> > > > > > > > > > >> > > > >\r\n> > > > > > > > > > >> > > >\r\n> > > > > > > > > > >> > >\r\n> > > > > > > > > > >> >\r\n> > > > > > > > > > >>\r\n> > > > > > > > > >\r\n> > > > > > > >\r\n> > > > > >\r\n> > > >\r\n> > > \r\n> > \"C:\\Users\\James.Thorson\\AppData\\Local\\Temp\\1\\Rtmp6DNpZS\\devtools1f947b001530\\quantifish-TagGrowth-3d606db\"\r\n> > > > > > > > > > >> > > > > > >\r\n> > > > > > > > > > >> > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > \\\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > >\r\n> > > > > > > > \r\n> > --library=\"C:/Users/James.Thorson/Documents/R/win-library/3.1\"\r\n> > > > > > > > > > >> > > > > > > > > > --install-tests\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > * installing *source* package\r\n> > > > 'TagGrowth'\r\n> > > > > > ...\r\n> > > > > > > > > > >> > > > > > > > > > ** R\r\n> > > > > > > > > > >> > > > > > > > > > ** data\r\n> > > > > > > > > > >> > > > > > > > > > ** inst\r\n> > > > > > > > > > >> > > > > > > > > > ** preparing package for lazy \r\n> > loading\r\n> > > > > > > > > > >> > > > > > > > > > Warning: package 'ggplot2' was built\r\n> > > > under R\r\n> > > > > > > > version\r\n> > > > > > > > > > >> > 3.1.2\r\n> > > > > > > > > > >> > > > > > > > > > ** help\r\n> > > > > > > > > > >> > > > > > > > > > *** installing help indices\r\n> > > > > > > > > > >> > > > > > > > > > ** building package indices\r\n> > > > > > > > > > >> > > > > > > > > > Warning in readChar(con, 5L, \r\n> > useBytes =\r\n> > > > > > TRUE) :\r\n> > > > > > > > > > >> > > > > > > > > > cannot open compressed file \r\n> > 'AGE.RData',\r\n> > > > > > > > probable\r\n> > > > > > > > > > reason\r\n> > > > > > > > > > >> > > > 'No such\r\n> > > > > > > > > > >> > > > > > > > file or\r\n> > > > > > > > > > >> > > > > > > > > > directory'\r\n> > > > > > > > > > >> > > > > > > > > > Error in readChar(con, 5L, \r\n> > useBytes =\r\n> > > > > > TRUE) :\r\n> > > > > > > > cannot\r\n> > > > > > > > > > >> > open the\r\n> > > > > > > > > > >> > > > > > > > connection\r\n> > > > > > > > > > >> > > > > > > > > > ERROR: installing package indices \r\n> > failed\r\n> > > > > > > > > > >> > > > > > > > > > * removing\r\n> > > > > > > > > > >> > > > > > > >\r\n> > > > > > > > > > >> >\r\n> > > > > > 'C:/Users/James.Thorson/Documents/R/win-library/3.1/TagGrowth'\r\n> > > > > > > > > > >> > > > > > > > > > Error: Command failed (1)\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > and a quick scan of AGE.RData \r\n> > doesn't\r\n> > > > > > show where\r\n> > > > > > > > > > it is\r\n> > > > > > > > > > >> > > > referenced\r\n> > > > > > > > > > >> > > > > > > > in the\r\n> > > > > > > > > > >> > > > > > > > > > installation instructions, or housed\r\n> > > > in the\r\n> > > > > > > > repo.\r\n> > > > > > > > > > >> > Could you\r\n> > > > > > > > > > >> > > > > > try to\r\n> > > > > > > > > > >> > > > > > > > debug\r\n> > > > > > > > > > >> > > > > > > > > > this installation issue?\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > Alternatively, the first thing \r\n> > I'd check\r\n> > > > > > for the\r\n> > > > > > > > > > ydev\r\n> > > > > > > > > > >> > case\r\n> > > > > > > > > > >> > > > is,\r\n> > > > > > > > > > >> > > > > > if you\r\n> > > > > > > > > > >> > > > > > > > > > turn\r\n> > > > > > > > > > >> > > > > > > > > > off all random effects using:\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > Obj = ADMakeFun(..., random=NULL)\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > are all the gradients non-zero:\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > min( abs(Obj$gr( Obj$par ) ) )\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > if not, then it can result in\r\n> > > > non-pdHess. If\r\n> > > > > > > > this\r\n> > > > > > > > > > is not\r\n> > > > > > > > > > >> > > > it, then\r\n> > > > > > > > > > >> > > > > > > > what\r\n> > > > > > > > > > >> > > > > > > > > > about when you calculate the\r\n> > > > > > finite-difference\r\n> > > > > > > > > > hessian\r\n> > > > > > > > > > >> of\r\n> > > > > > > > > > >> > > > fixed\r\n> > > > > > > > > > >> > > > > > > > effects\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > Hess = optimHess(par=Opt$par, \r\n> > fn=Obj$fn,\r\n> > > > > > > > gr=Obj$gr)\r\n> > > > > > > > > > >> > > > > > > > > > eigen(Hess)$values\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > cheers,\r\n> > > > > > > > > > >> > > > > > > > > > jim\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > cheers,\r\n> > > > > > > > > > >> > > > > > > > > > jim\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > On Sun, Jan 25, 2015 at 11:48 AM, \r\n> > Darcy\r\n> > > > > > Webber\r\n> > > > > > > > > > >> > > > > > > > <notifications@github.com>\r\n> > > > > > > > > > >> > > > > > > > > > wrote:\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > > This has been done.\r\n> > > > > > > > > > >> > > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > > Cheers Jim\r\n> > > > > > > > > > >> > > > > > > > > > > D\r\n> > > > > > > > > > >> > > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > > On 26/01/15 07:02, Jim Thorson \r\n> > wrote:\r\n> > > > > > > > > > >> > > > > > > > > > > > Darcy,\r\n> > > > > > > > > > >> > > > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > > > could you please add to GitHub a\r\n> > > > folder\r\n> > > > > > > > called\r\n> > > > > > > > > > >> > > > testing_ydevs,\r\n> > > > > > > > > > >> > > > > > > > which\r\n> > > > > > > > > > >> > > > > > > > > > > > has an\r\n> > > > > > > > > > >> > > > > > > > > > > > R script for these cases but\r\n> > > > > > configured to\r\n> > > > > > > > > > >> > estimating the\r\n> > > > > > > > > > >> > > > > > > > > > only-ydevs case\r\n> > > > > > > > > > >> > > > > > > > > > > > by default? I imagine it being\r\n> > > > set up\r\n> > > > > > > > where I\r\n> > > > > > > > > > can\r\n> > > > > > > > > > >> > > > change a\r\n> > > > > > > > > > >> > > > > > single\r\n> > > > > > > > > > >> > > > > > > > > > switch\r\n> > > > > > > > > > >> > > > > > > > > > > > to estimate one of the bad alloc\r\n> > > > models.\r\n> > > > > > > > I could\r\n> > > > > > > > > > >> then\r\n> > > > > > > > > > >> > > > try to\r\n> > > > > > > > > > >> > > > > > > > > > sleuth out\r\n> > > > > > > > > > >> > > > > > > > > > > > the issue.\r\n> > > > > > > > > > >> > > > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > > > cheers,\r\n> > > > > > > > > > >> > > > > > > > > > > > jim\r\n> > > > > > > > > > >> > > > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > > > On Sun, Jan 25, 2015 at 2:11 AM,\r\n> > > > Darcy\r\n> > > > > > > > Webber\r\n> > > > > > > > > > >> > > > > > > > > > <notifications@github.com>\r\n> > > > > > > > > > >> > > > > > > > > > > > wrote:\r\n> > > > > > > > > > >> > > > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > > > > In the case study, the model\r\n> > > > > > estimating\r\n> > > > > > > > > > ydevs only\r\n> > > > > > > > > > >> > > > is not\r\n> > > > > > > > > > >> > > > > > > > > > pdHess. The\r\n> > > > > > > > > > >> > > > > > > > > > > > > model with random-effects \r\n> > for z\r\n> > > > and\r\n> > > > > > > > ydevs fits\r\n> > > > > > > > > > >> (see\r\n> > > > > > > > > > >> > > > > > figs). The\r\n> > > > > > > > > > >> > > > > > > > > > > > models for k\r\n> > > > > > > > > > >> > > > > > > > > > > > > and ydevs and k, z and \r\n> > ydevs do\r\n> > > > not\r\n> > > > > > > > work at\r\n> > > > > > > > > > all\r\n> > > > > > > > > > >> > > > (getting\r\n> > > > > > > > > > >> > > > > > bad\r\n> > > > > > > > > > >> > > > > > > > alloc\r\n> > > > > > > > > > >> > > > > > > > > > > > erros).\r\n> > > > > > > > > > >> > > > > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > > > > —\r\n> > > > > > > > > > >> > > > > > > > > > > > > Reply to this email \r\n> > directly or\r\n> > > > > > view it on\r\n> > > > > > > > > > GitHub\r\n> > > > > > > > > > >> > > > > > > > > > > > >\r\n> > > > > > > > > > >> > <https://github.com/quantifish/TagGrowth/issues/20>.\r\n> > > > > > > > > > >> > > > > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > > > —\r\n> > > > > > > > > > >> > > > > > > > > > > > Reply to this email directly \r\n> > or view\r\n> > > > > > it on\r\n> > > > > > > > > > GitHub\r\n> > > > > > > > > > >> > > > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > >\r\n> > > > > > > > > > >> > > > > >\r\n> > > > > > > > > > >> > > >\r\n> > > > > > > > > > >> > <\r\n> > > > > > > > > > >>\r\n> > > > > > > > > >\r\n> > > > > > > >\r\n> > > > > >\r\n> > > > \r\n> > https://github.com/quantifish/TagGrowth/issues/20#issuecomment-71383623\r\n> > > > > > > > > > >> > > > > > > > > > > >.\r\n> > > > > > > > > > >> > > > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > > --\r\n> > > > > > > > > > >> > > > > > > > > > >\r\n> > > > > > > > --------------------------------------------------\r\n> > > > > > > > > > >> > > > > > > > > > > Darcy Webber\r\n> > > > > > > > > > >> > > > > > > > > > > Quantifish | Quantitative Marine\r\n> > > > Science\r\n> > > > > > > > Solutions\r\n> > > > > > > > > > >> > > > > > > > > > > P: 021 0233 0163\r\n> > > > > > > > > > >> > > > > > > > > > > E: darcy@quantifish.co.nz\r\n> > > > > > > > > > >> > > > > > > > > > > W: www.quantifish.co.nz\r\n> > > > > > > > > > >> > > > > > > > > > >\r\n> > > > > > > > --------------------------------------------------\r\n> > > > > > > > > > >> > > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > > Visit the ADMB project\r\n> > > > > > > > http://admb-project.org/\r\n> > > > > > > > > > >> > > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > > —\r\n> > > > > > > > > > >> > > > > > > > > > > Reply to this email directly or\r\n> > > > view it on\r\n> > > > > > > > GitHub\r\n> > > > > > > > > > >> > > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > >\r\n> > > > > > > > > > >> > > > > >\r\n> > > > > > > > > > >> > > >\r\n> > > > > > > > > > >> > <\r\n> > > > > > > > > > >>\r\n> > > > > > > > > >\r\n> > > > > > > >\r\n> > > > > >\r\n> > > > \r\n> > https://github.com/quantifish/TagGrowth/issues/20#issuecomment-71388882\r\n> > > > > > > > > > >> > > > > > > >.\r\n> > > > > > > > > > >> > > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > > —\r\n> > > > > > > > > > >> > > > > > > > > > Reply to this email directly or view\r\n> > > > it on\r\n> > > > > > > > GitHub\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > >\r\n> > > > > > > > > > >> > > > > >\r\n> > > > > > > > > > >> > > >\r\n> > > > > > > > > > >> > <\r\n> > > > > > > > > > >>\r\n> > > > > > > > > >\r\n> > > > > > > >\r\n> > > > > >\r\n> > > > \r\n> > https://github.com/quantifish/TagGrowth/issues/20#issuecomment-71405777\r\n> > > > > > > > > > >> > > > > > > >.\r\n> > > > > > > > > > >> > > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > --\r\n> > > > > > > > > > >> > > > > > > > >\r\n> > > > > > --------------------------------------------------\r\n> > > > > > > > > > >> > > > > > > > > Darcy Webber\r\n> > > > > > > > > > >> > > > > > > > > Quantifish | Quantitative Marine \r\n> > Science\r\n> > > > > > Solutions\r\n> > > > > > > > > > >> > > > > > > > > P: 021 0233 0163\r\n> > > > > > > > > > >> > > > > > > > > E: darcy@quantifish.co.nz\r\n> > > > > > > > > > >> > > > > > > > > W: www.quantifish.co.nz\r\n> > > > > > > > > > >> > > > > > > > >\r\n> > > > > > --------------------------------------------------\r\n> > > > > > > > > > >> > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > > Visit the ADMB project\r\n> > > > > > http://admb-project.org/\r\n> > > > > > > > > > >> > > > > > > > > —\r\n> > > > > > > > > > >> > > > > > > > > Reply to this email directly or \r\n> > view it on\r\n> > > > > > GitHub.\r\n> > > > > > > > > > >> > > > > > > > >\r\n> > > > > > > > > > >> > > > > > > >\r\n> > > > > > > > > > >> > > > > > > > —\r\n> > > > > > > > > > >> > > > > > > > Reply to this email directly or view \r\n> > it on\r\n> > > > > > GitHub\r\n> > > > > > > > > > >> > > > > > > >\r\n> > > > > > > > > > >> > > > > >\r\n> > > > > > > > > > >> > > >\r\n> > > > > > > > > > >> > <\r\n> > > > > > > > > > >>\r\n> > > > > > > > > >\r\n> > > > > > > >\r\n> > > > > >\r\n> > > > \r\n> > https://github.com/quantifish/TagGrowth/issues/20#issuecomment-71411905\r\n> > > > > > > > > > >> > > > > > > >.\r\n> > > > > > > > > > >> > > > > > > >\r\n> > > > > > > > > > >> > > > > > >\r\n> > > > > > > > > > >> > > > > > > --\r\n> > > > > > > > > > >> > > > > > >\r\n> > > > --------------------------------------------------\r\n> > > > > > > > > > >> > > > > > > Darcy Webber\r\n> > > > > > > > > > >> > > > > > > Quantifish | Quantitative Marine Science\r\n> > > > Solutions\r\n> > > > > > > > > > >> > > > > > > P: 021 0233 0163\r\n> > > > > > > > > > >> > > > > > > E: darcy@quantifish.co.nz\r\n> > > > > > > > > > >> > > > > > > W: www.quantifish.co.nz\r\n> > > > > > > > > > >> > > > > > >\r\n> > > > --------------------------------------------------\r\n> > > > > > > > > > >> > > > > > >\r\n> > > > > > > > > > >> > > > > > > Visit the ADMB project\r\n> > > > http://admb-project.org/\r\n> > > > > > > > > > >> > > > > > >\r\n> > > > > > > > > > >> > > > > > > —\r\n> > > > > > > > > > >> > > > > > > Reply to this email directly or view it on\r\n> > > > GitHub\r\n> > > > > > > > > > >> > > > > > >\r\n> > > > > > > > > > >> > > > > >\r\n> > > > > > > > > > >> > > >\r\n> > > > > > > > > > >> > <\r\n> > > > > > > > > > >>\r\n> > > > > > > > > >\r\n> > > > > > > >\r\n> > > > > >\r\n> > > > \r\n> > https://github.com/quantifish/TagGrowth/issues/20#issuecomment-71413080\r\n> > > > > > > > > > >> > > > > >.\r\n> > > > > > > > > > >> > > > > > >\r\n> > > > > > > > > > >> > > > > >\r\n> > > > > > > > > > >> > > > > > —\r\n> > > > > > > > > > >> > > > > > Reply to this email directly or view it on\r\n> > > > GitHub\r\n> > > > > > > > > > >> > > > > >\r\n> > > > > > > > > > >> > > >\r\n> > > > > > > > > > >> > <\r\n> > > > > > > > > > >>\r\n> > > > > > > > > >\r\n> > > > > > > >\r\n> > > > > >\r\n> > > > \r\n> > https://github.com/quantifish/TagGrowth/issues/20#issuecomment-71496413\r\n> > > > > > > > > > >> > > > > >.\r\n> > > > > > > > > > >> > > > > >\r\n> > > > > > > > > > >> > > > >\r\n> > > > > > > > > > >> > > > > --\r\n> > > > > > > > > > >> > > > > \r\n> > --------------------------------------------------\r\n> > > > > > > > > > >> > > > > Darcy Webber\r\n> > > > > > > > > > >> > > > > Quantifish | Quantitative Marine Science \r\n> > Solutions\r\n> > > > > > > > > > >> > > > > P: 021 0233 0163\r\n> > > > > > > > > > >> > > > > E: darcy@quantifish.co.nz\r\n> > > > > > > > > > >> > > > > W: www.quantifish.co.nz\r\n> > > > > > > > > > >> > > > > \r\n> > --------------------------------------------------\r\n> > > > > > > > > > >> > > > >\r\n> > > > > > > > > > >> > > > > Visit the ADMB project \r\n> > http://admb-project.org/\r\n> > > > > > > > > > >> > > > >\r\n> > > > > > > > > > >> > > > > —\r\n> > > > > > > > > > >> > > > > Reply to this email directly or view it on \r\n> > GitHub\r\n> > > > > > > > > > >> > > > >\r\n> > > > > > > > > > >> > > >\r\n> > > > > > > > > > >> > <\r\n> > > > > > > > > > >>\r\n> > > > > > > > > >\r\n> > > > > > > >\r\n> > > > > >\r\n> > > > \r\n> > https://github.com/quantifish/TagGrowth/issues/20#issuecomment-71511379\r\n> > > > > > > > > > >> > > >.\r\n> > > > > > > > > > >> > > > >\r\n> > > > > > > > > > >> > > >\r\n> > > > > > > > > > >> > > > —\r\n> > > > > > > > > > >> > > > Reply to this email directly or view it on \r\n> > GitHub\r\n> > > > > > > > > > >> > > >\r\n> > > > > > > > > > >> > <\r\n> > > > > > > > > > >>\r\n> > > > > > > > > >\r\n> > > > > > > >\r\n> > > > > >\r\n> > > > \r\n> > https://github.com/quantifish/TagGrowth/issues/20#issuecomment-71519198\r\n> > > > > > > > > > >> > > >.\r\n> > > > > > > > > > >> > > >\r\n> > > > > > > > > > >> > >\r\n> > > > > > > > > > >> > > --\r\n> > > > > > > > > > >> > > --------------------------------------------------\r\n> > > > > > > > > > >> > > Darcy Webber\r\n> > > > > > > > > > >> > > Quantifish | Quantitative Marine Science Solutions\r\n> > > > > > > > > > >> > > P: 021 0233 0163\r\n> > > > > > > > > > >> > > E: darcy@quantifish.co.nz\r\n> > > > > > > > > > >> > > W: www.quantifish.co.nz\r\n> > > > > > > > > > >> > > --------------------------------------------------\r\n> > > > > > > > > > >> > >\r\n> > > > > > > > > > >> > > Visit the ADMB project http://admb-project.org/\r\n> > > > > > > > > > >> > >\r\n> > > > > > > > > > >> > > —\r\n> > > > > > > > > > >> > > Reply to this email directly or view it on GitHub\r\n> > > > > > > > > > >> > >\r\n> > > > > > > > > > >> > <\r\n> > > > > > > > > > >>\r\n> > > > > > > > > >\r\n> > > > > > > >\r\n> > > > > >\r\n> > > > \r\n> > https://github.com/quantifish/TagGrowth/issues/20#issuecomment-71587071\r\n> > > >.\r\n> > > > > > > > > > >> > >\r\n> > > > > > > > > > >> > >\r\n> > > > > > > > > > >> >\r\n> > > > > > > > > > >> > —\r\n> > > > > > > > > > >> > Reply to this email directly or view it on GitHub\r\n> > > > > > > > > > >> > <\r\n> > > > > > > > > > >>\r\n> > > > > > > > > >\r\n> > > > > > > >\r\n> > > > > >\r\n> > > > \r\n> > https://github.com/quantifish/TagGrowth/issues/20#issuecomment-71587890\r\n> > > >.\r\n> > > > > > > > > > >> >\r\n> > > > > > > > > > >>\r\n> > > > > > > > > > >> --\r\n> > > > > > > > > > >> --------------------------------------------------\r\n> > > > > > > > > > >> Darcy Webber\r\n> > > > > > > > > > >> Quantifish | Quantitative Marine Science Solutions\r\n> > > > > > > > > > >> P: 021 0233 0163\r\n> > > > > > > > > > >> E: darcy@quantifish.co.nz\r\n> > > > > > > > > > >> W: www.quantifish.co.nz\r\n> > > > > > > > > > >> --------------------------------------------------\r\n> > > > > > > > > > >>\r\n> > > > > > > > > > >> Visit the ADMB project http://admb-project.org/\r\n> > > > > > > > > > >>\r\n> > > > > > > > > > >> —\r\n> > > > > > > > > > >> Reply to this email directly or view it on GitHub\r\n> > > > > > > > > > >>\r\n> > > > > > > > > >\r\n> > > > > > > >\r\n> > > > > >\r\n> > > > \r\n> > <https://github.com/quantifish/TagGrowth/issues/20#issuecomment-71614566\r\n> > > >\r\n> > > > > > > > > > >> .\r\n> > > > > > > > > > >>\r\n> > > > > > > > > > >\r\n> > > > > > > > > > >\r\n> > > > > > > > > >\r\n> > > > > > > > > > —\r\n> > > > > > > > > > Reply to this email directly or view it on GitHub\r\n> > > > > > > > > >\r\n> > > > > > > >\r\n> > > > > >\r\n> > > > \r\n> > <https://github.com/quantifish/TagGrowth/issues/20#issuecomment-71705748\r\n> > > >.\r\n> > > > > > > > > >\r\n> > > > > > > > >\r\n> > > > > > > > > --\r\n> > > > > > > > > --------------------------------------------------\r\n> > > > > > > > > Darcy Webber\r\n> > > > > > > > > Quantifish | Quantitative Marine Science Solutions\r\n> > > > > > > > > P: 021 0233 0163\r\n> > > > > > > > > E: darcy@quantifish.co.nz\r\n> > > > > > > > > W: www.quantifish.co.nz\r\n> > > > > > > > > --------------------------------------------------\r\n> > > > > > > > >\r\n> > > > > > > > > Visit the ADMB project http://admb-project.org/\r\n> > > > > > > > > —\r\n> > > > > > > > > Reply to this email directly or view it on GitHub.\r\n> > > > > > > > >\r\n> > > > > > > >\r\n> > > > > > > > —\r\n> > > > > > > > Reply to this email directly or view it on GitHub\r\n> > > > > > > >\r\n> > > > > >\r\n> > > > \r\n> > <https://github.com/quantifish/TagGrowth/issues/20#issuecomment-71727938\r\n> > > >.\r\n> > > > > > > >\r\n> > > > > > >\r\n> > > > > > > --\r\n> > > > > > > --------------------------------------------------\r\n> > > > > > > Darcy Webber\r\n> > > > > > > Quantifish | Quantitative Marine Science Solutions\r\n> > > > > > > P: 021 0233 0163\r\n> > > > > > > E: darcy@quantifish.co.nz\r\n> > > > > > > W: www.quantifish.co.nz\r\n> > > > > > > --------------------------------------------------\r\n> > > > > > >\r\n> > > > > > > Visit the ADMB project http://admb-project.org/\r\n> > > > > > > —\r\n> > > > > > > Reply to this email directly or view it on GitHub.\r\n> > > > > > >\r\n> > > > > >\r\n> > > > > > —\r\n> > > > > > Reply to this email directly or view it on GitHub\r\n> > > > > >\r\n> > > > \r\n> > <https://github.com/quantifish/TagGrowth/issues/20#issuecomment-71732555\r\n> > > >.\r\n> > > > > >\r\n> > > > >\r\n> > > > > --\r\n> > > > > --------------------------------------------------\r\n> > > > > Darcy Webber\r\n> > > > > Quantifish | Quantitative Marine Science Solutions\r\n> > > > > P: 021 0233 0163\r\n> > > > > E: darcy@quantifish.co.nz\r\n> > > > > W: www.quantifish.co.nz\r\n> > > > > --------------------------------------------------\r\n> > > > >\r\n> > > > > Visit the ADMB project http://admb-project.org/\r\n> > > > > —\r\n> > > > > Reply to this email directly or view it on GitHub.\r\n> > > > >\r\n> > > >\r\n> > > > —\r\n> > > > Reply to this email directly or view it on GitHub\r\n> > > > \r\n> > <https://github.com/quantifish/TagGrowth/issues/20#issuecomment-71769263\r\n> > > >.\r\n> > > >\r\n> > >\r\n> > > --\r\n> > > --------------------------------------------------\r\n> > > Darcy Webber\r\n> > > Quantifish | Quantitative Marine Science Solutions\r\n> > > P: 021 0233 0163\r\n> > > E: darcy@quantifish.co.nz\r\n> > > W: www.quantifish.co.nz\r\n> > > --------------------------------------------------\r\n> > >\r\n> > > Visit the ADMB project http://admb-project.org/\r\n> > >\r\n> > > —\r\n> > > Reply to this email directly or view it on GitHub\r\n> > > \r\n> > <https://github.com/quantifish/TagGrowth/issues/20#issuecomment-71774014>.\r\n> > >\r\n> >\r\n> > —\r\n> > Reply to this email directly or view it on GitHub \r\n> > <https://github.com/quantifish/TagGrowth/issues/20#issuecomment-71781898>.\r\n> >\r\n> \r\n> -- \r\n> --------------------------------------------------\r\n> Darcy Webber\r\n> Quantifish | Quantitative Marine Science Solutions\r\n> P: 021 0233 0163\r\n> E: darcy@quantifish.co.nz\r\n> W: www.quantifish.co.nz\r\n> --------------------------------------------------\r\n> \r\n> Visit the ADMB project http://admb-project.org/\r\n> —\r\n> Reply to this email directly or view it on GitHub.\r\n> "}}