Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ---- message=FALSE-----------------------------------------------------------
library(BANOVA)
data(colorad)
head(colorad)
## ---- message=FALSE, eval=FALSE-----------------------------------------------
# library(rstan)
# set.seed(700)
# model <- BANOVA.model(model_name = 'Binomial')
# banova_fit <- BANOVA.build(model)
# res <- BANOVA.run(y~typic, ~color*blur, data = colorad, fit = banova_fit,
# id = 'id', num_trials = as.integer(16), iter = 1000, thin = 1, chains = 2)
## ---- message=FALSE, eval=FALSE-----------------------------------------------
# res_alt <- BANOVA.run(y~typic, ~color*blur, data = colorad, model_name = 'Binomial',
# id = 'id', num_trials = as.integer(16), iter = 1000, thin = 1, chains = 2)
## ---- message=FALSE, eval=FALSE-----------------------------------------------
# summary(res)
# #> Call:
# #> BANOVA.run(l1_formula = y ~ typic, l2_formula = ~color * blur,
# #> fit = banova_fit, data = colorad, id = 'id', iter = 1000,
# #> num_trials = as.integer(16), thin = 1, chains = 2)
# #>
# #> Convergence diagnostics:
# #> Geweke Diag. & Heidelberger and Welch's Diag.
# #> Geweke stationarity test
# #> (Intercept) : (Intercept) passed
# #> (Intercept) : color1 passed
# #> (Intercept) : blur passed
# #> (Intercept) : color1:blur passed
# #> typic1 : (Intercept) passed
# #> typic1 : color1 passed
# #> typic1 : blur passed
# #> typic1 : color1:blur passed
# #> Geweke convergence p value
# #> (Intercept) : (Intercept) 0.1409
# #> (Intercept) : color1 0.9288
# #> (Intercept) : blur 0.4537
# #> (Intercept) : color1:blur 0.9024
# #> typic1 : (Intercept) 0.9642
# #> typic1 : color1 0.9105
# #> typic1 : blur 0.1451
# #> typic1 : color1:blur 0.4603
# #> H. & W. stationarity test
# #> (Intercept) : (Intercept) passed
# #> (Intercept) : color1 passed
# #> (Intercept) : blur passed
# #> (Intercept) : color1:blur passed
# #> typic1 : (Intercept) passed
# #> typic1 : color1 passed
# #> typic1 : blur passed
# #> typic1 : color1:blur passed
# #> H. & W. convergence p value
# #> (Intercept) : (Intercept) 0.4819
# #> (Intercept) : color1 0.6041
# #> (Intercept) : blur 0.7871
# #> (Intercept) : color1:blur 0.4488
# #> typic1 : (Intercept) 0.8005
# #> typic1 : color1 0.8028
# #> typic1 : blur 0.1004
# #> typic1 : color1:blur 0.6634
# #>
# #> The Chain has converged.
# #>
# #> Table of sum of squares & effect sizes:
# #>
# #> Table of sum of squares:
# #> (Intercept) color blur color:blur Residuals Total
# #> (Intercept) 59.5532 2.3591 26.1587 9.0749 138.4249 229.8047
# #> typic1 21.9510 1.9610 5.4139 7.0553 20.1769 50.6221
# #>
# #> Table of effect sizes (95% credible interval):
# #> (Intercept) color
# #> (Intercept) 0.3014 (0.249,0.358) 0.0159 (-0.015,0.104)
# #> typic1 0.5215 (0.402,0.638) 0.0781 (-0.015,0.34)
# #> blur color:blur
# #> (Intercept) 0.1590 (0.108,0.21) 0.0581 (-0.006,0.199)
# #> typic1 0.2114 (0.088,0.362) 0.2352 (0.006,0.521)
# #>
# #> Table of p-values (Multidimensional):
# #> (Intercept) color blur color:blur
# #> (Intercept) <0.0001 0.9560 <0.0001 0.1400
# #> typic <0.0001 0.4180 <0.0001 0.0280
# #>
# #> Table of coefficients:
# #> mean SD Quantile0.025 Quantile0.975
# #> (Intercept) : (Intercept) 0.4975 0.0572 0.3881 0.6101
# #> (Intercept) : color1 -0.0069 0.1245 -0.2605 0.2413
# #> (Intercept) : blur -0.1716 0.0307 -0.2333 -0.1133
# #> (Intercept) : color1:blur 0.0410 0.0291 -0.0171 0.1001
# #> typic1 : (Intercept) 0.3011 0.0313 0.2374 0.3580
# #> typic1 : color1 -0.0596 0.0736 -0.2062 0.0781
# #> typic1 : blur -0.0767 0.0170 -0.1087 -0.0439
# #> typic1 : color1:blur 0.0384 0.0178 0.0052 0.0733
# #> p.value Signif.codes
# #> (Intercept) : (Intercept) <0.0001 ***
# #> (Intercept) : color1 0.9560
# #> (Intercept) : blur <0.0001 ***
# #> (Intercept) : color1:blur 0.1400
# #> typic1 : (Intercept) <0.0001 ***
# #> typic1 : color1 0.4180
# #> typic1 : blur <0.0001 ***
# #> typic1 : color1:blur 0.0280 *
# #> ---
# #> Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1
# #>
# #> Multiple R-squared: 0.0664
# #>
# #> Table of predictions:
# #>
# #> Grand mean:
# #> 9.95
# #> 2.5% 97.5%
# #> 9.5332 10.3673
# #>
# #>
# #> typic mean 2.5% 97.5%
# #> 0 11.035 10.5818 11.4579
# #> 1 8.7829 8.2705 9.2933
# #>
# #>
# #> color mean 2.5% 97.5%
# #> 0 9.924 8.7817 10.9414
# #> 1 9.9759 9.0196 10.8926
# #>
# #>
# #> typic color mean 2.5% 97.5%
# #> 0 0 10.8042 9.4812 11.9297
# #> 0 1 11.26 10.202 12.271
# #> 1 0 8.9913 7.7188 10.2174
# #> 1 1 8.5735 7.4431 9.6343
## ---- message=FALSE, eval=FALSE-----------------------------------------------
# library(rstan)
# set.seed(900)
# res_fac <- BANOVA.run(y~typic, ~color*blurfac, data = colorad, fit = banova_fit,
# id = 'id', num_trials = as.integer(16), iter = 2000, thin = 1, chains = 2)
## ---- message=FALSE, eval=FALSE-----------------------------------------------
# summary(res_fac)
# #> Call:
# #> BANOVA.run(l1_formula = y ~ typic, l2_formula = ~color * blurfac,
# #> fit = banova_fit, data = colorad, id = 'id', iter = 2000,
# #> num_trials = as.integer(16), thin = 1, chains = 2)
# #>
# #> Convergence diagnostics:
# #> Geweke Diag. & Heidelberger and Welch's Diag.
# #> Geweke stationarity test
# #> (Intercept) : (Intercept) passed
# #> (Intercept) : color1 passed
# #> (Intercept) : blurfac1 passed
# #> (Intercept) : blurfac2 passed
# #> (Intercept) : blurfac3 passed
# #> (Intercept) : blurfac4 passed
# #> (Intercept) : color1:blurfac1 passed
# #> (Intercept) : color1:blurfac2 passed
# #> (Intercept) : color1:blurfac3 passed
# #> (Intercept) : color1:blurfac4 passed
# #> typic1 : (Intercept) passed
# #> typic1 : color1 passed
# #> typic1 : blurfac1 passed
# #> typic1 : blurfac2 passed
# #> typic1 : blurfac3 passed
# #> typic1 : blurfac4 passed
# #> typic1 : color1:blurfac1 passed
# #> typic1 : color1:blurfac2 passed
# #> typic1 : color1:blurfac3 passed
# #> typic1 : color1:blurfac4 passed
# #> Geweke convergence p value
# #> (Intercept) : (Intercept) 0.0217
# #> (Intercept) : color1 0.4861
# #> (Intercept) : blurfac1 0.7050
# #> (Intercept) : blurfac2 0.5498
# #> (Intercept) : blurfac3 0.4843
# #> (Intercept) : blurfac4 0.6209
# #> (Intercept) : color1:blurfac1 0.9840
# #> (Intercept) : color1:blurfac2 0.6900
# #> (Intercept) : color1:blurfac3 0.2931
# #> (Intercept) : color1:blurfac4 0.7919
# #> typic1 : (Intercept) 0.0159
# #> typic1 : color1 0.5622
# #> typic1 : blurfac1 0.0594
# #> typic1 : blurfac2 0.1408
# #> typic1 : blurfac3 0.0534
# #> typic1 : blurfac4 0.3087
# #> typic1 : color1:blurfac1 0.3151
# #> typic1 : color1:blurfac2 0.4267
# #> typic1 : color1:blurfac3 0.1776
# #> typic1 : color1:blurfac4 0.8341
# #> H. & W. stationarity test
# #> (Intercept) : (Intercept) passed
# #> (Intercept) : color1 passed
# #> (Intercept) : blurfac1 passed
# #> (Intercept) : blurfac2 passed
# #> (Intercept) : blurfac3 passed
# #> (Intercept) : blurfac4 passed
# #> (Intercept) : color1:blurfac1 passed
# #> (Intercept) : color1:blurfac2 passed
# #> (Intercept) : color1:blurfac3 passed
# #> (Intercept) : color1:blurfac4 passed
# #> typic1 : (Intercept) passed
# #> typic1 : color1 passed
# #> typic1 : blurfac1 passed
# #> typic1 : blurfac2 passed
# #> typic1 : blurfac3 passed
# #> typic1 : blurfac4 passed
# #> typic1 : color1:blurfac1 passed
# #> typic1 : color1:blurfac2 passed
# #> typic1 : color1:blurfac3 passed
# #> typic1 : color1:blurfac4 passed
# #> H. & W. convergence p value
# #> (Intercept) : (Intercept) 0.2829
# #> (Intercept) : color1 0.8963
# #> (Intercept) : blurfac1 0.5252
# #> (Intercept) : blurfac2 0.8212
# #> (Intercept) : blurfac3 0.5227
# #> (Intercept) : blurfac4 0.9169
# #> (Intercept) : color1:blurfac1 0.5844
# #> (Intercept) : color1:blurfac2 0.4926
# #> (Intercept) : color1:blurfac3 0.7559
# #> (Intercept) : color1:blurfac4 0.8684
# #> typic1 : (Intercept) 0.0515
# #> typic1 : color1 0.0775
# #> typic1 : blurfac1 0.2471
# #> typic1 : blurfac2 0.1948
# #> typic1 : blurfac3 0.0845
# #> typic1 : blurfac4 0.0610
# #> typic1 : color1:blurfac1 0.1983
# #> typic1 : color1:blurfac2 0.2473
# #> typic1 : color1:blurfac3 0.2181
# #> typic1 : color1:blurfac4 0.8831
# #>
# #> The Chain has converged.
# #>
# #> Table of sum of squares & effect sizes:
# #>
# #> Table of sum of squares:
# #> (Intercept) color blurfac color:blurfac Residuals Total
# #> (Intercept) 59.3470 5.1145 29.5136 1.0276 136.9923 231.8971
# #> typic1 21.3932 2.0202 13.6640 1.9275 16.7336 55.6143
# #>
# #> Table of effect sizes (95% credible interval):
# #> (Intercept) color blurfac
# #> (Intercept) 0.3028 (0.25,0.36) 0.0361 (0.01,0.066) 0.1774 (0.123,0.232)
# #> typic1 0.5602 (0.444,0.67) 0.1075 (0.017,0.231) 0.4476 (0.315,0.585)
# #> color:blurfac
# #> (Intercept) 0.0075 (-0.028,0.038)
# #> typic1 0.1023 (0.009,0.231)
# #>
# #> Table of p-values (Multidimensional):
# #> (Intercept) color blurfac color:blurfac
# #> (Intercept) <0.0001 0.0100 <0.0001 0.1590
# #> typic <0.0001 0.0010 <0.0001 0.0200
# #>
# #> Table of coefficients:
# #> mean SD Quantile0.025 Quantile0.975
# #> (Intercept) : (Intercept) 0.4981 0.0574 0.3840 0.6115
# #> (Intercept) : color1 0.1532 0.0567 0.0404 0.2683
# #> (Intercept) : blurfac1 0.5591 0.1139 0.3470 0.7807
# #> (Intercept) : blurfac2 0.0554 0.1168 -0.1731 0.2883
# #> (Intercept) : blurfac3 0.0193 0.1036 -0.1775 0.2226
# #> (Intercept) : blurfac4 -0.0565 0.1094 -0.2689 0.1672
# #> (Intercept) : color1:blurfac1 -0.1586 0.1146 -0.3897 0.0724
# #> (Intercept) : color1:blurfac2 0.1137 0.1162 -0.1094 0.3347
# #> (Intercept) : color1:blurfac3 -0.0774 0.1096 -0.2961 0.1376
# #> (Intercept) : color1:blurfac4 0.0125 0.1114 -0.2098 0.2329
# #> typic1 : (Intercept) 0.3092 0.0318 0.2481 0.3742
# #> typic1 : color1 0.0906 0.0311 0.0296 0.1532
# #> typic1 : blurfac1 0.1621 0.0634 0.0379 0.2901
# #> typic1 : blurfac2 0.3612 0.0692 0.2138 0.4951
# #> typic1 : blurfac3 -0.0260 0.0642 -0.1543 0.0996
# #> typic1 : blurfac4 -0.1653 0.0625 -0.2830 -0.0409
# #> typic1 : color1:blurfac1 -0.1443 0.0645 -0.2727 -0.0231
# #> typic1 : color1:blurfac2 0.0344 0.0671 -0.1041 0.1637
# #> typic1 : color1:blurfac3 -0.0238 0.0597 -0.1456 0.0915
# #> typic1 : color1:blurfac4 0.0956 0.0619 -0.0272 0.2211
# #> p.value Signif.codes
# #> (Intercept) : (Intercept) <0.0001 ***
# #> (Intercept) : color1 0.0100 **
# #> (Intercept) : blurfac1 <0.0001 ***
# #> (Intercept) : blurfac2 0.6400
# #> (Intercept) : blurfac3 0.8430
# #> (Intercept) : blurfac4 0.5910
# #> (Intercept) : color1:blurfac1 0.1590
# #> (Intercept) : color1:blurfac2 0.3360
# #> (Intercept) : color1:blurfac3 0.4850
# #> (Intercept) : color1:blurfac4 0.8890
# #> typic1 : (Intercept) <0.0001 ***
# #> typic1 : color1 0.0010 ***
# #> typic1 : blurfac1 0.0080 **
# #> typic1 : blurfac2 <0.0001 ***
# #> typic1 : blurfac3 0.6920
# #> typic1 : blurfac4 0.0060 **
# #> typic1 : color1:blurfac1 0.0200 *
# #> typic1 : color1:blurfac2 0.5940
# #> typic1 : color1:blurfac3 0.6940
# #> typic1 : color1:blurfac4 0.1150
# #> ---
# #> Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1
# #>
# #> Multiple R-squared: 0.0856
# #>
# #> Table of predictions:
# #>
# #> Grand mean:
# #> 9.9522
# #> 2.5% 97.5%
# #> 9.5174 10.3726
# #>
# #>
# #> typic mean 2.5% 97.5%
# #> 0 11.0645 10.5896 11.4879
# #> 1 8.7534 8.2242 9.2339
# #>
# #>
# #> color mean 2.5% 97.5%
# #> 0 10.5167 9.9177 11.0551
# #> 1 9.3662 8.7386 9.9471
# #>
# #> blurfac mean 2.5% 97.5%
# #> 1 11.8745 11.0664 12.6146
# #> 2 10.1591 9.1897 11.1158
# #> 3 10.0247 9.1808 10.8356
# #> 4 9.7383 8.8491 10.6451
# #> 5 7.6834 6.6721 8.65
# #>
# #>
# #> typic color mean 2.5% 97.5%
# #> 0 0 11.8558 11.2628 12.3795
# #> 0 1 10.1961 9.521 10.8499
# #> 1 0 9.0004 8.262 9.6717
# #> 1 1 8.5049 7.8023 9.2008
# #>
# #> typic blurfac mean 2.5% 97.5%
# #> 0 1 13.1487 12.3854 13.7718
# #> 0 2 12.3638 11.4074 13.14
# #> 0 3 11.0416 10.0703 11.8974
# #> 0 4 10.2774 9.2503 11.2558
# #> 0 5 7.5923 6.4556 8.7182
# #> 1 1 10.2786 9.1893 11.2832
# #> 1 2 7.533 6.3988 8.7
# #> 1 3 8.9327 7.9134 9.9488
# #> 1 4 9.1821 8.1045 10.2629
# #> 1 5 7.7745 6.6116 8.9589
# #>
# #>
# #> color blurfac mean 2.5% 97.5%
# #> 0 1 11.8576 10.7518 12.8309
# #> 1 1 11.8912 10.7507 12.8908
# #> 0 2 11.1088 9.6862 12.2988
# #> 1 2 9.1388 7.7334 10.5106
# #> 0 3 10.3056 9.0203 11.4538
# #> 1 3 9.7384 8.5515 10.9235
# #> 0 4 10.3571 8.9993 11.6076
# #> 1 4 9.0969 7.7976 10.4325
# #> 0 5 8.7333 7.3643 10.1124
# #> 1 5 6.6442 5.314 8.0042
# #>
# #>
# #> typic color blurfac mean 2.5% 97.5%
# #> 0 0 1 13.0075 11.8829 13.8698
# #> 0 1 1 13.2845 12.2295 14.1165
# #> 0 0 2 13.3472 12.179 14.2525
# #> 0 1 2 11.1483 9.6802 12.4133
# #> 0 0 3 11.5161 10.1419 12.6794
# #> 0 1 3 10.5408 9.1534 11.8042
# #> 0 0 4 11.4974 10.0861 12.6792
# #> 0 1 4 8.9302 7.4175 10.3435
# #> 0 0 5 9.1508 7.5622 10.651
# #> 0 1 5 6.0642 4.63 7.6654
# #> 1 0 1 10.4543 8.9691 11.7715
# #> 1 1 1 10.1005 8.5915 11.5018
# #> 1 0 2 8.0995 6.3761 9.7681
# #> 1 1 2 6.9711 5.4889 8.5847
# #> 1 0 3 8.9678 7.3996 10.3327
# #> 1 1 3 8.8976 7.5123 10.3464
# #> 1 0 4 9.1014 7.5952 10.681
# #> 1 1 4 9.2626 7.7261 10.8305
# #> 1 0 5 8.3118 6.8199 9.9193
# #> 1 1 5 7.2393 5.6957 8.8424
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