## ----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