MCMC sample

Description

Returns the chains of the MCMC process

Usage

MCMCsample(object)

Arguments

Examples

# Not run
data(sensory)

Consumer <- factor(sensory$consumer)
Sacarose <- factor(sensory$sacarose)

#### Model 
# Not run
dex1 <- Bayesthresh(cor ~ (1|Consumer) + Sacarose, burn = 0, Write=TRUE,
																			jump = 1, ef.iter = 10, data=sensory) 
MCMCsample(dex1)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Bayesthresh)
Loading required package: lme4
Loading required package: Matrix
Loading required package: MASS
Loading required package: VGAM
Loading required package: stats4
Loading required package: splines
Loading required package: mvtnorm
Loading required package: matrixcalc
Loading required package: coda

Attaching package: 'coda'

The following object is masked from 'package:VGAM':

    nvar

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/Bayesthresh/MCMCsample.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MCMCsample
> ### Title: MCMC sample
> ### Aliases: MCMCsample
> 
> ### ** Examples
> 
> # Not run
> data(sensory)
> 
> Consumer <- factor(sensory$consumer)
> Sacarose <- factor(sensory$sacarose)
> 
> #### Model 
> # Not run
> dex1 <- Bayesthresh(cor ~ (1|Consumer) + Sacarose, burn = 0, Write=TRUE,
+ 																			jump = 1, ef.iter = 10, data=sensory) 
> MCMCsample(dex1)
$Theta
   (Intercept) Sacarose40 Sacarose50           1           2           3
1     1.659453  0.2592687  0.2251945 -1.39259756 -0.25732727 -1.59892276
2     1.070319 -0.3755148 -0.2613930 -0.67697798 -0.04897321  0.23597423
3     1.164538 -0.2457032 -0.3757067 -1.09110812  0.08051257 -0.65170693
4     1.504559 -0.3366595 -0.1743436 -0.64400321 -0.47583751 -0.11849832
5     1.401691 -0.8092481 -0.7561218 -0.02123257  0.44663436 -0.54933096
6     1.288894 -0.4457274 -0.5421982 -0.34655587 -0.20279099  0.16009961
7     1.231644 -0.3853975 -0.4768351 -0.53922291 -0.10294153 -0.11376472
8     1.258223 -0.4377803 -0.5016109 -0.80814050 -0.56723406 -0.44343741
9     1.025128 -0.2048109 -0.3115317 -0.65398029 -0.19684703  0.02379575
10    1.409705 -0.6769978 -0.4838927 -0.92045139  0.08283118  0.16166414
            4          5           6           7         8           9
1   0.1487977 -1.5314022 -1.67383341 -0.81497604 0.1184235 -1.16333915
2  -0.5576815 -0.4669797  0.90837232 -0.06905258 1.2934480 -0.13446331
3  -0.5698059 -0.5737632  1.26890077  0.11853651 1.0344983 -0.25766853
4  -0.8168649 -0.8117551  0.80952820 -0.18900782 1.0365804  0.12497625
5   0.1349225 -0.2538882  0.74888094 -0.32615307 1.4394654  0.44646869
6  -0.3497061 -0.4573096  1.39359656  0.06086275 1.0036572 -0.01210549
7  -0.1799161 -0.1161542  0.38450522 -0.78078203 0.1300947  0.76314100
8  -0.1336971 -0.4056037 -0.01002707  0.08757246 0.2030099  0.36576731
9  -0.4623620 -0.4511317  0.38611664  0.57012915 0.4697120 -0.17112904
10 -0.1223439 -0.1342483  0.77364030 -0.04173058 0.5023798  0.08632401
             10          11          12         13         14         15
1   0.202424141 -0.51160904 -1.19104500 -0.6599946 -1.7679214 -1.6447757
2  -0.927263897 -0.01773203 -0.02829106  0.7327560 -0.5878292  1.0474741
3   0.008025633 -0.04140601 -0.19185584  0.5455516 -0.9013865  0.4872299
4  -1.058449323 -0.18880980 -0.99658496 -0.4107193 -0.6002097 -0.1900864
5  -0.472739369  0.15551572 -0.51338320  0.2210011 -0.2564991  0.1785879
6  -0.558286657  0.02348982  0.10571542  0.7299597 -0.3890319  0.5773515
7  -0.554999241  0.54427535  0.08397802  0.6702547 -0.7695422  0.6058146
8  -0.051070611 -0.01179895 -0.57945962  0.6126357 -0.4683273  0.5285738
9  -0.358215853  0.25206600 -0.12853307  0.4230076 -0.2839995  0.3539621
10 -0.257964092 -0.09537912  0.17486145  0.2160789 -0.5396752  0.8018073
            16          17          18         19          20         21
1  -0.82369489 -1.28942397 -0.87544422 -0.9527924 -1.16283839 -0.6362338
2  -0.17747445  0.61888317  0.38952487 -0.4977019  0.54747969 -0.5383902
3   0.01470687 -0.30275632 -0.44868322 -0.2455093  0.40923439 -0.1727636
4  -0.53061453 -0.81592718 -0.26224021 -0.8299504  0.66950948 -0.7412881
5  -0.77458078 -0.03928845 -0.07850912  0.1259229  0.35993518 -0.3510683
6  -0.06380956 -0.14847294 -0.31761397  0.2638838  0.05914258 -0.3562234
7  -0.42960630  0.25499710 -0.07448040 -0.4910211  0.17030845 -0.4567786
8  -0.32897591 -0.13588587 -0.05251898 -0.1526157  0.02097141 -0.2957930
9   0.14488519 -0.05958309  0.26028986 -0.1123485  0.41091836 -0.5076394
10 -0.12267153 -0.24742044 -0.38794519 -0.2889199  0.36083595 -0.3775368
           22          23          24           25           26           27
1  -0.7344832 -0.77854222 -0.72045466 -0.835246387 -0.320681709 -0.030507316
2  -0.6741746  0.54722429 -0.56009335 -0.006645107 -0.184163568  0.726986114
3  -0.4965464  0.07421053  0.30339380  0.437723873 -0.264106759  0.671706886
4  -0.4734992  0.61623315 -0.34468194 -0.181323275  0.007574089  0.954432464
5  -0.1274782  0.29270665 -0.47060099  0.133066284  0.619390329  0.866160831
6  -0.4116350  0.95693670 -0.34131302 -0.105524302 -0.034867642  0.580570805
7  -0.2349282  0.27990777  0.62634076 -0.351886200 -0.213425450  1.054031358
8  -0.3048819  0.23552979 -0.15483276  0.292110578 -0.172445934  0.002763626
9   0.2001252 -0.22336824  0.09433907  0.326518805 -0.239489170  0.961267555
10 -0.4426109  0.22285872  0.16608134  0.314487910  0.019140613 -0.025233145
            28         29          30         31          32           33
1  -0.81298143 -0.3963508 -0.77639206 -0.7187668 -1.59437261 -2.057838698
2  -0.04330846 -0.7668345  0.01100751 -0.5323957 -0.17541151  0.087387246
3  -0.42163892 -0.8186103  0.30559374 -0.2050024 -0.27611742  0.005830188
4  -0.35152394 -0.2753680  0.01729449 -0.7358471 -0.16508796 -0.350876589
5  -0.52150103  0.1631798  0.86182062  0.2157510 -0.51823512  0.171085448
6  -0.63970496 -0.3338758 -0.13535402 -0.6398268 -0.12572671  0.384110969
7  -0.08135056 -0.5930081  1.03637172  0.5261080  0.38042645  0.298487591
8  -0.52858942 -0.8981177  0.63956140 -0.2265808  0.07465249 -0.007523045
9  -0.25889808 -0.4152917  0.56764738 -0.4986450 -0.02488804  0.088402652
10  0.52764658 -0.1849549  0.58797438 -0.4068035  0.32894687 -0.871970328
            34         35          36
1  -0.05538570 -0.7918498 -2.62607672
2  -0.75244830 -0.9543785  0.97212057
3   0.08431164 -0.9309969 -0.10057774
4  -0.02975161 -1.2540221 -0.34723742
5  -0.06502101 -0.4580058 -0.20341095
6   0.58770268 -0.8375750 -0.09043747
7   0.12392003 -0.5956081  0.17022173
8  -0.76713049 -0.1445395  0.05198127
9  -0.09128876 -0.1358970 -0.09157391
10 -0.48199983 -0.4210811 -0.20045792

$Variance
    Consumer
1  0.9884116
2  0.3857163
3  0.2601074
4  0.2864667
5  0.1375545
6  0.2113716
7  0.2190426
8  0.1740188
9  0.1741706
10 0.2380117

$cutpoints
      [,1]        [,2]        [,3]       [,4]      [,5]      [,6]      [,7]
 [1,]    0 0.001926563 0.034019654 0.05812782 0.1937560 0.3032111 0.4720779
 [2,]    0 0.007961982 0.025911868 0.02652676 0.1638365 0.2462879 0.4188698
 [3,]    0 0.002418858 0.003182459 0.01714649 0.1060064 0.2472921 0.3896242
 [4,]    0 0.002418858 0.003182459 0.01714649 0.1060064 0.2472921 0.3896242
 [5,]    0 0.002418858 0.003182459 0.01714649 0.1060064 0.2472921 0.3896242
 [6,]    0 0.038721501 0.048126513 0.05099769 0.1344852 0.2085541 0.3441084
 [7,]    0 0.038721501 0.048126513 0.05099769 0.1344852 0.2085541 0.3441084
 [8,]    0 0.025289437 0.047294286 0.05034566 0.2526861 0.3015496 0.4744833
 [9,]    0 0.025289437 0.047294286 0.05034566 0.2526861 0.3015496 0.4744833
[10,]    0 0.025289437 0.047294286 0.05034566 0.2526861 0.3015496 0.4744833
      [,8]
 [1,]    1
 [2,]    1
 [3,]    1
 [4,]    1
 [5,]    1
 [6,]    1
 [7,]    1
 [8,]    1
 [9,]    1
[10,]    1

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>