kapelner
commented
1 year ago Yeah it's an error in the new version. I'll have to figure it out. The following code works.
options(java.parameters = c("-Xmx20000m")) install.packages(" https://cran.r-project.org/src/contrib/Archive/bartMachine/bartMachine_1.2.7.tar.gz ", repos = NULL, type="source",dependancies=TRUE) library(bartMachine) n = 50 X = data.frame(cippa=rnorm(n), lippa=rnorm(n), pasqualino=rnorm(n))
y = rnorm(n) bm = bartMachine(X, y) ss = get_sigsqs(bm, plot_hist=T) print(ss)
On Wed, Dec 28, 2022 at 9:31 AM Giacomo Petrillo @.***> wrote:
The vector of posterior samples on the error variance returned by get_sigsqs contains many zeroes. Minimal example:
library(bartMachine)n = 50X = data.frame(cippa=rnorm(n), lippa=rnorm(n), pasqualino=rnorm(n))y = rnorm(n)bm = bartMachine(X, y)ss = get_sigsqs(bm, plot_hist=T) print(ss)
Output:
Loading required package: rJava Loading required package: bartMachineJARs Loading required package: randomForest randomForest 4.7-1.1 Type rfNews() to see new features/changes/bug fixes. Loading required package: missForest Welcome to bartMachine v1.3.2! You have 0.54GB memory available.
If you run out of memory, restart R, and use e.g. 'options(java.parameters = "-Xmx5g")' for 5GB of RAM before you call 'library(bartMachine)'.
bartMachine initializing with 50 trees... bartMachine vars checked... bartMachine java init... bartMachine factors created... bartMachine before preprocess... bartMachine after preprocess... 3 total features... bartMachine sigsq estimated... bartMachine training data finalized... Now building bartMachine for regression... evaluating in sample data...done [1] 0.6738567 0.6823280 0.3963788 0.5420501 0.5526897 0.4949011 0.6561506 [8] 0.4309214 0.6297360 0.6574286 0.8740465 0.6049023 0.7190190 0.6186070 [15] 0.4147947 0.5096590 0.3854179 0.3236273 0.6343288 0.7104224 0.5492379 [22] 0.5403672 0.7041673 0.5576870 0.6404842 0.4569708 0.7032812 0.6057967 [29] 0.4068528 0.6529362 0.4497582 0.5405523 0.5146371 0.5606146 0.7231270 [36] 0.4251352 0.5017961 0.4039385 0.4185928 0.5516639 0.5349040 0.6444614 [43] 0.4168752 0.4755697 0.4472841 0.6164776 0.5950383 0.6032409 0.4814202 [50] 0.3817277 0.4124045 0.6495234 0.6515946 0.6564860 0.5243605 0.4625689 [57] 0.5676971 0.5400568 0.3962279 0.3540788 0.4758006 0.4983467 0.4925431 [64] 0.5626715 0.9368755 0.7203849 0.4467512 0.5900052 0.2964828 0.6399533 [71] 0.4715198 0.7480451 0.5043543 0.5348309 0.4169205 0.3890896 0.5225142 [78] 0.5893633 0.6248662 0.4411586 0.5316090 0.5906821 0.6600916 0.6358257 [85] 0.5430974 0.4191855 0.4234045 0.6401893 0.6160910 0.6149260 0.5239037 [92] 0.7346262 0.7927698 0.8559771 0.8564749 0.6399547 0.6617545 0.4862764 [99] 0.5218394 0.5361528 0.4645625 0.4862391 0.4249653 0.4966983 0.5722455 [106] 0.5756632 0.5889968 0.7468448 0.7112704 0.4752701 0.4422910 0.6224502 [113] 0.7478145 0.6917788 0.6593739 0.5041079 0.5702368 0.4908382 0.5388601 [120] 0.6565747 0.7446141 0.4281959 0.8973551 0.5082524 0.6022598 0.6682022 [127] 0.6210314 0.6441824 0.4827757 0.7639993 0.4104385 0.8480981 0.7278081 [134] 0.6674551 0.7050705 0.5499230 0.7574979 0.6489151 0.7373134 0.5471537 [141] 0.5827605 0.5526380 0.5107312 0.4410340 0.4361805 0.3881677 0.6540108 [148] 0.4434175 0.5201778 0.7684820 0.6036935 0.7783705 0.8112201 0.5085767 [155] 0.4166957 0.5891744 0.8272326 0.8059974 0.6039739 0.4926725 0.5685766 [162] 0.4819520 0.4345115 0.7241730 0.5001127 0.6093101 0.8074775 0.6211340 [169] 0.7598558 0.6495594 0.5982428 0.6298588 0.7029029 0.5206628 0.6280212 [176] 0.5671791 0.4642438 0.9423288 0.6641100 0.5236050 0.4615422 0.5714215 [183] 0.6319731 0.5353613 0.4966538 0.5876032 0.6829575 0.5461618 0.3516722 [190] 0.4463553 0.4113644 0.7175616 0.7268501 0.9897334 0.5659359 0.5467450 [197] 0.3853242 0.4799703 0.4543558 0.3864065 0.3867739 0.4059116 0.4904520 [204] 0.4990398 0.5829876 0.6681405 0.5245365 0.4816886 0.7247148 0.4489095 [211] 0.4673745 0.5346889 0.5267316 0.5896845 0.7151791 0.4212330 0.6294356 [218] 0.7690222 0.6634902 0.6094897 0.5036922 0.5318404 0.4286724 0.4636125 [225] 0.3526284 0.4528986 0.3979473 0.6440758 0.4455897 0.4236689 0.5220958 [232] 0.5161978 0.6882160 0.5583662 0.6369836 0.4804866 0.5249673 0.3036010 [239] 0.3186854 0.3680794 0.3473360 0.3445205 0.3993789 0.6134708 0.5605042 [246] 0.4203016 0.5262919 0.7055306 0.4151140 0.3950877 0.4945300 0.3403064 [253] 0.6336636 0.5760601 0.5937295 0.7816578 0.5743999 0.5130912 0.3211351 [260] 0.4333243 0.4532728 0.8836527 0.5542467 0.5189086 0.3853733 0.5863797 [267] 0.6456744 0.5490664 0.6830404 0.5591154 0.6707948 0.7266904 0.8191645 [274] 0.6519134 0.4418197 0.6754014 0.6498065 0.6172073 0.6850096 0.7220211 [281] 0.4933638 0.3720437 0.5880862 0.4299151 0.5928170 0.6562778 0.8242513 [288] 0.4299219 0.4942766 0.5546288 0.4497238 0.5144395 0.8645564 0.5358512 [295] 0.6815332 0.4826089 0.5361426 0.6610768 0.4361343 0.7495521 0.8360831 [302] 0.6435257 0.4058136 0.3989772 0.7589361 0.6532333 0.6084130 0.6920568 [309] 0.4990992 0.7679044 0.6186806 0.7343711 0.7986024 0.5366567 0.4798369 [316] 0.6301960 0.4961707 0.5888135 0.4025134 0.5232452 0.6341495 0.5325702 [323] 0.5920682 0.4763510 0.7678790 0.3672965 0.8628438 0.5431980 0.5667032 [330] 0.4591356 0.5990987 0.5662614 0.4698281 0.6696803 0.5874177 0.5867314 [337] 0.5061874 0.4649711 0.6824143 0.4890839 0.5424590 0.3392641 0.3994007 [344] 0.3851744 0.5515101 0.5159149 0.4030643 0.6579546 0.5439394 0.4285955 [351] 0.5869903 0.4381423 0.8446627 0.3845370 0.5609957 0.4207567 0.6653356 [358] 0.4841911 0.4964988 0.4404760 0.5421151 0.3389921 0.7477354 0.9128842 [365] 0.6247109 0.4614823 0.6427378 0.4976938 0.7045662 0.4602396 0.4469913 [372] 0.5559259 0.5829157 0.4815411 0.4331116 0.6426673 0.0000000 0.0000000 [379] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [386] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [393] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [400] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [407] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [414] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [421] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [428] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [435] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [442] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [449] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [456] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [463] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [470] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [477] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [484] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [491] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [498] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [505] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [512] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [519] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [526] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [533] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [540] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [547] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [554] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [561] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [568] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [575] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [582] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [589] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [596] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [603] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [610] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [617] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [624] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [631] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [638] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [645] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [652] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [659] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [666] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [673] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [680] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [687] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [694] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [701] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [708] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [715] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [722] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [729] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [736] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [743] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [750] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [757] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [764] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [771] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [778] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [785] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [792] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [799] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [806] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [813] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [820] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [827] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [834] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [841] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [848] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [855] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [862] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [869] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [876] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [883] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [890] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [897] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [904] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [911] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [918] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [925] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [932] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [939] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [946] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [953] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [960] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [967] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [974] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [981] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [988] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 [995] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 building BART with mem-cache speedup... Iteration 100/1250 Iteration 200/1250 Iteration 300/1250 Iteration 400/1250 Iteration 500/1250 Iteration 600/1250 Iteration 700/1250 Iteration 800/1250 Iteration 900/1250 Iteration 1000/1250 Iteration 1100/1250 Iteration 1200/1250 done building BART in 0.217 sec
burning and aggregating chains from all threads... done
[image: image] https://user-images.githubusercontent.com/9684110/209827127-1f799768-cb0c-4ab8-add8-d8e155c137df.png
Versions:
- macOS 13.1, M1 processor
- R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid" Platform: aarch64-apple-darwin20 (64-bit)
- openjdk-19.0.1_macos-aarch64_bin
- bartMachine 1.3.2 installed from CRAN
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-- Adam Kapelner, Ph.D. Associate Professor of Mathematics Director of the Undergraduate Data Science and Statistics Program Queens College, City University of New York 65-30 Kissena Blvd., Kiely Hall Room 604 Flushing, NY, 11367 M: 516-435-6795 kapelner.com (CV http://kapelner.com/adk_cv_07_21_22.pdf | scholar https://scholar.google.com/citations?user=TzgMmnoAAAAJ | publons https://publons.com/wos-op/researcher/431881/adam-kapelner/peer-review/ | github https://github.com/kapelner | linkedin https://www.linkedin.com/in/adam-kapelner/)
Gattocrucco
The vector of posterior samples on the error variance returned by
get_sigsqscontains many zeroes. Minimal example:Output:
Versions: