new data pushed; check your code and output

@dbuona @MoralesCastilla @DeirdreLoughnan

Per issue #456 I found some undead data issues and @cchambe12 updated our data. This should lead to super tiny changes in the data, but Rangers and Traitors leads should re-run their code and report on any issues that we may need to address collectively.

@MoralesCastilla I feel this is TOO close to submission to ask you to re run everything especially given how small the changes are. But to check this plan is okay, I ran the new data through the model code TODAY and got:

> fitsum <- summary(fit, pars = list("a_z", "sigma_interceptsa", 
+                             "b_zf", "sigma_interceptsbf", "lam_interceptsbf", 
+                             "b_zc", "sigma_interceptsbc", "lam_interceptsbc",
+                             "b_zp", "sigma_interceptsbp", "lam_interceptsbp","sigma_y"))$summary
> 
> fitsumdf <- as.data.frame(fitsum)
> 
> fitsumdf
                         mean     se_mean        sd         2.5%        25%        50%        75%      97.5%      n_eff      Rhat
a_z                30.8586682 0.028573744 3.1244238  24.51378922 28.8510482 30.9100918 32.9134772 36.9707825 11956.5415 0.9997377
sigma_interceptsa  16.4032640 0.013520373 1.1306062  14.36984450 15.6115147 16.3320844 17.1107664 18.8473343  6992.7079 1.0010554
b_zf               -6.3024881 0.031805261 2.0737783 -10.46721666 -7.6489843 -6.3282862 -4.9868448 -2.1141416  4251.3488 1.0005100
sigma_interceptsbf  5.7748029 0.030416760 0.9696763   4.06810743  5.1012319  5.6989239  6.3686916  7.9131733  1016.3135 1.0030444
lam_interceptsbf    0.6223089 0.008655771 0.2002112   0.21300106  0.4803805  0.6300961  0.7768827  0.9664451   535.0142 1.0125460
b_zc               -7.2670938 0.024889245 1.9620888 -10.94684732 -8.5397330 -7.3565534 -6.0779262 -3.0851419  6214.6097 1.0002233
sigma_interceptsbc  6.9990807 0.019314387 0.8381182   5.47448700  6.4096666  6.9550539  7.5358519  8.7669682  1882.9929 1.0035526
lam_interceptsbc    0.4239742 0.003315223 0.1539723   0.12748266  0.3145403  0.4241792  0.5322667  0.7228370  2157.0470 1.0013300
b_zp               -1.1996242 0.014203022 0.7348214  -2.62612523 -1.6716790 -1.2048925 -0.7433664  0.2830247  2676.7144 1.0012982
sigma_interceptsbp  2.3491887 0.013897395 0.3892646   1.62960607  2.0838420  2.3259870  2.5970540  3.1891705   784.5543 1.0064588
lam_interceptsbp    0.3650651 0.011153318 0.2425485   0.01752335  0.1639508  0.3298353  0.5365562  0.8942912   472.9213 1.0075544
sigma_y            12.6006235 0.001580200 0.1741199  12.26435219 12.4823298 12.5992414 12.7163680 12.9502436 12141.5033 0.9999141

... on quick glance this look identical to what you have (given MCMC errors) so I feel okay.

To get the code to run (as there is now a Juglans_spp that seems new) I added one line:

bb.stan <- subset(bb.stan, species!="spp") Around line 104 so those lines look like:

bb.stan <- subset(bb.stan, species!="spp")
namesdat <- unique(paste(bb.stan$genus,bb.stan$species,sep="_"))
bb.stan$spps <- paste(bb.stan$genus,bb.stan$species,sep="_")
bb.stan$phylo <- paste(bb.stan$genus,bb.stan$species,sep="_")

I think once at the requested revision stage it would be good to re-run everything if you think that's possible.

lizzieinvancouver / ospree

new data pushed; check your code and output #459