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From: <chr...@us...> - 2010-05-17 19:57:35
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Revision: 157
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=157&view=rev
Author: chris-jackson
Date: 2010-05-17 19:57:28 +0000 (Mon, 17 May 2010)
Log Message:
-----------
Added new tests: examples.R (a selection of the official examples which take a few seconds in total to run - posterior means are compared to the results in examples.stats.R) and functions.R (including assertion tests for all of the user-visible functions).
Added Paths:
-----------
trunk/BRugs/tests/examples.R
trunk/BRugs/tests/examples.stats.R
trunk/BRugs/tests/functions.R
Added: trunk/BRugs/tests/examples.R
===================================================================
--- trunk/BRugs/tests/examples.R (rev 0)
+++ trunk/BRugs/tests/examples.R 2010-05-17 19:57:28 UTC (rev 157)
@@ -0,0 +1,40 @@
+library(BRugs)
+
+## Selected examples which take a few seconds in total to run
+
+test.models <- c("Air", "Asia", "Beetles", "BiRats", "Camel",
+ "Dugongs", "Dyes", "Equiv", "Eyes",
+ "Line", "OtreesMVN", "Rats", "Stacks",
+ "Surgical", "Surgicalrand")
+
+test.params <- list(Air = c("X", "theta"),
+ Asia = c("bronchitis", "either", "lung.cancer"),
+ Beetles = c("alpha", "beta", "rhat"),
+ BiRats = c("mu.beta", "sigma"),
+ Camel = c("Sigma2", "rho", "tau"),
+ Dugongs = c("U3","alpha", "beta", "gamma", "sigma"),
+ Dyes = c("sigma2.btw", "sigma2.with", "theta"),
+ Equiv = c("equiv", "mu", "phi", "pi","sigma1", "sigma2", "theta"),
+ Eyes = c("P", "lambda", "sigma"),
+ Line = c("alpha", "beta", "sigma"),
+ OtreesMVN = c("mu","sigma", "sigmaC"),
+ Rats = c("alpha0", "beta.c", "sigma"),
+ Stacks = c("b", "b0", "outlier[21]","outlier[3]", "outlier[4]", "sigma"),
+ Surgical = "p",
+ Surgicalrand = c("p","pop.mean", "sigma")
+ )
+
+test.modelfile = paste(test.models,"model.txt",sep="")
+test.datafile = paste(test.models,"data.txt",sep="")
+test.inits = paste(test.models,"inits.txt",sep="")
+
+### Test for posterior means within 1 percent of previously saved values
+
+res.true <- dget(file="examples.stats.R")
+for (i in seq(along=test.models)) {
+ fit <- BRugsFit(data=test.datafile[i], inits=test.inits[i], modelFile=test.modelfile[i], para=test.params[[test.models[i]]],
+ nBurnin=5000, nIter=20000, nThin=1, numChains=1, seed=1,
+ working.directory=system.file("OpenBUGS", "Examples", package = "BRugs")
+ )
+ stopifnot(isTRUE(all.equal(fit$Stats$mean, res.true[[i]]$Stats$mean, tol=1e-02)))
+}
Added: trunk/BRugs/tests/examples.stats.R
===================================================================
--- trunk/BRugs/tests/examples.stats.R (rev 0)
+++ trunk/BRugs/tests/examples.stats.R 2010-05-17 19:57:28 UTC (rev 157)
@@ -0,0 +1,215 @@
+list(structure(list(Stats = structure(list(mean = c(13.45, 27.41,
+40.91, -0.8844, 0.0448), sd = c(8.677, 7.465, 8.811, 2.831, 0.1047
+), MC_error = c(0.143, 0.08436, 0.1297, 0.04967, 0.001829), val2.5pc = c(-3.828,
+12.88, 23.57, -4.62, -0.01401), median = c(13.52, 27.32, 40.89,
+-0.67, 0.03728), val97.5pc = c(30.29, 42.38, 58.25, 0.6397, 0.1856
+), start = c(5001L, 5001L, 5001L, 5001L, 5001L), sample = c(20000L,
+20000L, 20000L, 20000L, 20000L)), .Names = c("mean", "sd", "MC_error",
+"val2.5pc", "median", "val97.5pc", "start", "sample"), row.names = c("X[1]",
+"X[2]", "X[3]", "theta[1]", "theta[2]"), class = "data.frame"),
+ DIC = structure(list(Dbar = c(14.2, 14.2), Dhat = c(11.62,
+ 11.62), DIC = c(16.79, 16.79), pD = c(2.583, 2.583)), .Names = c("Dbar",
+ "Dhat", "DIC", "pD"), class = "data.frame", row.names = c("y",
+ "total"))), .Names = c("Stats", "DIC")), structure(list(Stats = structure(list(
+ mean = c(1.808, 1.177, 1.095), sd = c(0.3942, 0.3816, 0.293
+ ), MC_error = c(0.004268, 0.004489, 0.003713), val2.5pc = c(1,
+ 1, 1), median = c(2, 1, 1), val97.5pc = c(2, 2, 2), start = c(5001L,
+ 5001L, 5001L), sample = c(20000L, 20000L, 20000L)), .Names = c("mean",
+"sd", "MC_error", "val2.5pc", "median", "val97.5pc", "start",
+"sample"), row.names = c("bronchitis", "either", "lung.cancer"
+), class = "data.frame"), DIC = NULL), .Names = c("Stats", "DIC"
+)), structure(list(Stats = structure(list(mean = c(-60.79, 34.31,
+3.567, 9.951, 22.51, 33.9, 50.05, 53.22, 59.15, 58.69), sd = c(5.147,
+2.894, 0.9514, 1.676, 2.09, 1.761, 1.662, 1.114, 0.7424, 0.4299
+), MC_error = c(0.0498, 0.02805, 0.008182, 0.01405, 0.01656,
+0.01414, 0.01468, 0.01026, 0.006914, 0.004009), val2.5pc = c(-71.1,
+28.75, 1.994, 6.945, 18.48, 30.4, 46.66, 50.84, 57.51, 57.7),
+ median = c(-60.69, 34.26, 3.465, 9.858, 22.48, 33.91, 50.09,
+ 53.29, 59.22, 58.74), val97.5pc = c(-50.91, 40.14, 5.707,
+ 13.5, 26.67, 37.27, 53.16, 55.19, 60.38, 59.36), start = c(5001L,
+ 5001L, 5001L, 5001L, 5001L, 5001L, 5001L, 5001L, 5001L, 5001L
+ ), sample = c(20000L, 20000L, 20000L, 20000L, 20000L, 20000L,
+ 20000L, 20000L, 20000L, 20000L)), .Names = c("mean", "sd",
+"MC_error", "val2.5pc", "median", "val97.5pc", "start", "sample"
+), row.names = c("alpha", "beta", "rhat[1]", "rhat[2]", "rhat[3]",
+"rhat[4]", "rhat[5]", "rhat[6]", "rhat[7]", "rhat[8]"), class = "data.frame"),
+ DIC = structure(list(Dbar = c(39.42, 39.42), Dhat = c(37.43,
+ 37.43), DIC = c(41.4, 41.4), pD = c(1.987, 1.987)), .Names = c("Dbar",
+ "Dhat", "DIC", "pD"), class = "data.frame", row.names = c("r",
+ "total"))), .Names = c("Stats", "DIC")), structure(list(Stats = structure(list(
+ mean = c(106.6, 6.187, 6.147), sd = c(2.352, 0.1061, 0.4781
+ ), MC_error = c(0.02256, 0.0009468, 0.006136), val2.5pc = c(101.9,
+ 5.978, 5.301), median = c(106.5, 6.187, 6.112), val97.5pc = c(111.2,
+ 6.398, 7.173), start = c(5001L, 5001L, 5001L), sample = c(20000L,
+ 20000L, 20000L)), .Names = c("mean", "sd", "MC_error", "val2.5pc",
+"median", "val97.5pc", "start", "sample"), row.names = c("mu.beta[1]",
+"mu.beta[2]", "sigma"), class = "data.frame"), DIC = structure(list(
+ Dbar = c(969.6, 969.6), Dhat = c(919.6, 919.6), DIC = c(1020,
+ 1020), pD = c(50.01, 50.01)), .Names = c("Dbar", "Dhat",
+"DIC", "pD"), class = "data.frame", row.names = c("Y", "total"
+))), .Names = c("Stats", "DIC")), structure(list(Stats = structure(list(
+ mean = c(3.242, 0.008511, 0.008511, 3.199, 0.001476, 0.8453,
+ -0.004605, -0.004605, 0.8579), sd = c(2.101, 2.492, 2.492,
+ 2.104, 0.6561, 0.5059, 0.7047, 0.7047, 0.509), MC_error = c(0.0255,
+ 0.08255, 0.08255, 0.02649, 0.02443, 0.007006, 0.02403, 0.02403,
+ 0.007312), val2.5pc = c(1.14, -4.754, -4.754, 1.104, -0.9073,
+ 0.2191, -1.398, -1.398, 0.2237), median = c(2.691, -0.01866,
+ -0.01866, 2.652, -0.007769, 0.7261, 0.003158, 0.003158, 0.7381
+ ), val97.5pc = c(8.551, 4.769, 4.769, 8.537, 0.9089, 2.119,
+ 1.398, 1.398, 2.163), start = c(5001L, 5001L, 5001L, 5001L,
+ 5001L, 5001L, 5001L, 5001L, 5001L), sample = c(20000L, 20000L,
+ 20000L, 20000L, 20000L, 20000L, 20000L, 20000L, 20000L)), .Names = c("mean",
+"sd", "MC_error", "val2.5pc", "median", "val97.5pc", "start",
+"sample"), row.names = c("Sigma2[1,1]", "Sigma2[1,2]", "Sigma2[2,1]",
+"Sigma2[2,2]", "rho", "tau[1,1]", "tau[1,2]", "tau[2,1]", "tau[2,2]"
+), class = "data.frame"), DIC = NULL), .Names = c("Stats", "DIC"
+)), structure(list(Stats = structure(list(mean = c(1.859, 2.651,
+0.9713, 0.8622, 0.09894), sd = c(0.265, 0.07082, 0.07689, 0.03177,
+0.01488), MC_error = c(0.0146, 0.00389, 0.002055, 0.001754, 0.0002341
+), val2.5pc = c(1.332, 2.53, 0.8227, 0.7911, 0.07493), median = c(1.853,
+2.642, 0.9703, 0.8645, 0.09724), val97.5pc = c(2.374, 2.803,
+1.124, 0.9148, 0.133), start = c(5001L, 5001L, 5001L, 5001L,
+5001L), sample = c(20000L, 20000L, 20000L, 20000L, 20000L)), .Names = c("mean",
+"sd", "MC_error", "val2.5pc", "median", "val97.5pc", "start",
+"sample"), row.names = c("U3", "alpha", "beta", "gamma", "sigma"
+), class = "data.frame"), DIC = structure(list(Dbar = c(-49.1,
+-49.1), Dhat = c(-52.96, -52.96), DIC = c(-45.25, -45.25), pD = c(3.852,
+3.852)), .Names = c("Dbar", "Dhat", "DIC", "pD"), class = "data.frame", row.names = c("Y",
+"total"))), .Names = c("Stats", "DIC")), structure(list(Stats = structure(list(
+ mean = c(2380, 2981, 1527), sd = c(8162, 1091, 22.42), MC_error = c(121.4,
+ 36.99, 0.3445), val2.5pc = c(0.01265, 1549, 1483), median = c(1382,
+ 2753, 1526), val97.5pc = c(10210, 5686, 1571), start = c(5001L,
+ 5001L, 5001L), sample = c(20000L, 20000L, 20000L)), .Names = c("mean",
+"sd", "MC_error", "val2.5pc", "median", "val97.5pc", "start",
+"sample"), row.names = c("sigma2.btw", "sigma2.with", "theta"
+), class = "data.frame"), DIC = structure(list(Dbar = c(323.4,
+323.4), Dhat = c(316.9, 316.9), DIC = c(329.9, 329.9), pD = c(6.475,
+6.475)), .Names = c("Dbar", "Dhat", "DIC", "pD"), class = "data.frame", row.names = c("y",
+"total"))), .Names = c("Stats", "DIC")), structure(list(Stats = structure(list(
+ mean = c(0.9978, 1.434, -0.008588, -0.1801, 0.1104, 0.1406,
+ 0.9928), sd = c(0.04685, 0.05495, 0.05196, 0.05179, 0.03345,
+ 0.05436, 0.05167), MC_error = c(0.0003252, 0.001275, 0.0003669,
+ 0.0003675, 0.0006507, 0.0009669, 0.0003686), val2.5pc = c(1,
+ 1.325, -0.1124, -0.2828, 0.06491, 0.04493, 0.8937), median = c(1,
+ 1.434, -0.008368, -0.1805, 0.1032, 0.1355, 0.9917), val97.5pc = c(1,
+ 1.542, 0.09495, -0.0747, 0.1924, 0.2671, 1.1), start = c(5001L,
+ 5001L, 5001L, 5001L, 5001L, 5001L, 5001L), sample = c(20000L,
+ 20000L, 20000L, 20000L, 20000L, 20000L, 20000L)), .Names = c("mean",
+"sd", "MC_error", "val2.5pc", "median", "val97.5pc", "start",
+"sample"), row.names = c("equiv", "mu", "phi", "pi", "sigma1",
+"sigma2", "theta"), class = "data.frame"), DIC = structure(list(
+ Dbar = c(-33.27, -33.27), Dhat = c(-45.21, -45.21), DIC = c(-21.32,
+ -21.32), pD = c(11.94, 11.94)), .Names = c("Dbar", "Dhat",
+"DIC", "pD"), class = "data.frame", row.names = c("Y", "total"
+))), .Names = c("Stats", "DIC")), structure(list(Stats = structure(list(
+ mean = c(0.6032, 0.3968, 536.8, 548.9, 3.758), sd = c(0.08391,
+ 0.08391, 0.9152, 1.209, 0.6041), MC_error = c(0.00113, 0.00113,
+ 0.01592, 0.01913, 0.01316), val2.5pc = c(0.4339, 0.2372,
+ 535.1, 546.5, 2.919), median = c(0.6042, 0.3958, 536.7, 548.9,
+ 3.653), val97.5pc = c(0.7628, 0.5662, 538.6, 551.2, 5.259
+ ), start = c(5001L, 5001L, 5001L, 5001L, 5001L), sample = c(20000L,
+ 20000L, 20000L, 20000L, 20000L)), .Names = c("mean", "sd",
+"MC_error", "val2.5pc", "median", "val97.5pc", "start", "sample"
+), row.names = c("P[1]", "P[2]", "lambda[1]", "lambda[2]", "sigma"
+), class = "data.frame"), DIC = NULL), .Names = c("Stats", "DIC"
+)), structure(list(Stats = structure(list(mean = c(2.995, 0.7968,
+1.022), sd = c(0.5625, 0.3953, 0.7287), MC_error = c(0.004086,
+0.002512, 0.009658), val2.5pc = c(1.916, 0.05661, 0.4119), median = c(2.997,
+0.7993, 0.8279), val97.5pc = c(4.059, 1.541, 2.789), start = c(5001L,
+5001L, 5001L), sample = c(20000L, 20000L, 20000L)), .Names = c("mean",
+"sd", "MC_error", "val2.5pc", "median", "val97.5pc", "start",
+"sample"), row.names = c("alpha", "beta", "sigma"), class = "data.frame"),
+ DIC = structure(list(Dbar = c(12.97, 12.97), Dhat = c(9.063,
+ 9.063), DIC = c(16.87, 16.87), pD = c(3.903, 3.903)), .Names = c("Dbar",
+ "Dhat", "DIC", "pD"), class = "data.frame", row.names = c("Y",
+ "total"))), .Names = c("Stats", "DIC")), structure(list(Stats = structure(list(
+ mean = c(5.264, 2.198, -5.881, 0.2585, 0.2708, 0.2283, 7.837
+ ), sd = c(0.1339, 0.1666, 0.1437, 0.1155, 0.1379, 0.1102,
+ 1.19), MC_error = c(0.002003, 0.00395, 0.003601, 0.001239,
+ 0.002355, 0.002098, 0.02413), val2.5pc = c(4.996, 1.879,
+ -6.172, 0.1275, 0.1199, 0.1086, 5.91), median = c(5.264,
+ 2.196, -5.879, 0.2317, 0.2399, 0.2018, 7.699), val97.5pc = c(5.532,
+ 2.535, -5.602, 0.5434, 0.6071, 0.5034, 10.57), start = c(5001L,
+ 5001L, 5001L, 5001L, 5001L, 5001L, 5001L), sample = c(20000L,
+ 20000L, 20000L, 20000L, 20000L, 20000L, 20000L)), .Names = c("mean",
+"sd", "MC_error", "val2.5pc", "median", "val97.5pc", "start",
+"sample"), row.names = c("mu[1]", "mu[2]", "mu[3]", "sigma[1]",
+"sigma[2]", "sigma[3]", "sigmaC"), class = "data.frame"), DIC = structure(list(
+ Dbar = c(242.7, 242.7), Dhat = c(229.9, 229.9), DIC = c(255.6,
+ 255.6), pD = c(12.83, 12.83)), .Names = c("Dbar", "Dhat",
+"DIC", "pD"), class = "data.frame", row.names = c("Y", "total"
+))), .Names = c("Stats", "DIC")), structure(list(Stats = structure(list(
+ mean = c(106.6, 6.186, 6.097), sd = c(3.629, 0.1074, 0.4656
+ ), MC_error = c(0.02738, 0.0008775, 0.005451), val2.5pc = c(99.38,
+ 5.975, 5.271), median = c(106.6, 6.187, 6.065), val97.5pc = c(113.6,
+ 6.395, 7.094), start = c(5001L, 5001L, 5001L), sample = c(20000L,
+ 20000L, 20000L)), .Names = c("mean", "sd", "MC_error", "val2.5pc",
+"median", "val97.5pc", "start", "sample"), row.names = c("alpha0",
+"beta.c", "sigma"), class = "data.frame"), DIC = structure(list(
+ Dbar = c(967, 967), Dhat = c(912.7, 912.7), DIC = c(1021,
+ 1021), pD = c(54.36, 54.36)), .Names = c("Dbar", "Dhat",
+"DIC", "pD"), class = "data.frame", row.names = c("Y", "total"
+))), .Names = c("Stats", "DIC")), structure(list(Stats = structure(list(
+ mean = c(0.7154, 1.294, -0.1516, -39.93, 0.0104, 0.05455,
+ 0.3221, 3.389), sd = c(0.1418, 0.3861, 0.1655, 12.65, 0.1014,
+ 0.2271, 0.4673, 0.6247), MC_error = c(0.002215, 0.005965,
+ 0.001676, 0.1113, 0.0006987, 0.001789, 0.004462, 0.005228
+ ), val2.5pc = c(0.4371, 0.5286, -0.4804, -65.13, 0, 0, 0,
+ 2.423), median = c(0.7154, 1.292, -0.1516, -39.98, 0, 0,
+ 0, 3.297), val97.5pc = c(0.9979, 2.062, 0.1764, -14.65, 0,
+ 1, 1, 4.841), start = c(5001L, 5001L, 5001L, 5001L, 5001L,
+ 5001L, 5001L, 5001L), sample = c(20000L, 20000L, 20000L,
+ 20000L, 20000L, 20000L, 20000L, 20000L)), .Names = c("mean",
+"sd", "MC_error", "val2.5pc", "median", "val97.5pc", "start",
+"sample"), row.names = c("b[1]", "b[2]", "b[3]", "b0", "outlier[3]",
+"outlier[4]", "outlier[21]", "sigma"), class = "data.frame"),
+ DIC = structure(list(Dbar = c(110.3, 110.3), Dhat = c(105,
+ 105), DIC = c(115.5, 115.5), pD = c(5.265, 5.265)), .Names = c("Dbar",
+ "Dhat", "DIC", "pD"), class = "data.frame", row.names = c("Y",
+ "total"))), .Names = c("Stats", "DIC")), structure(list(Stats = structure(list(
+ mean = c(0.02045, 0.1263, 0.07463, 0.05796, 0.04218, 0.0707,
+ 0.06664, 0.1475, 0.07183, 0.09073, 0.1164, 0.06897), sd = c(0.01989,
+ 0.02722, 0.02387, 0.008142, 0.01376, 0.01815, 0.02014, 0.02405,
+ 0.01783, 0.02867, 0.01986, 0.01338), MC_error = c(0.0001314,
+ 0.0001809, 0.0001651, 5.562e-05, 0.000104, 0.0001297, 0.0001363,
+ 0.000159, 0.0001341, 0.0002174, 0.0001431, 7.827e-05), val2.5pc = c(0.0005114,
+ 0.07791, 0.03489, 0.04312, 0.01952, 0.03918, 0.03277, 0.1033,
+ 0.04117, 0.04322, 0.08045, 0.04527), median = c(0.01431,
+ 0.1245, 0.07223, 0.05761, 0.0408, 0.06934, 0.06457, 0.1462,
+ 0.07045, 0.08807, 0.1156, 0.0682), val97.5pc = c(0.07349,
+ 0.1833, 0.1272, 0.0748, 0.07277, 0.1099, 0.1107, 0.1975,
+ 0.1112, 0.1546, 0.158, 0.09749), start = c(5001L, 5001L,
+ 5001L, 5001L, 5001L, 5001L, 5001L, 5001L, 5001L, 5001L, 5001L,
+ 5001L), sample = c(20000L, 20000L, 20000L, 20000L, 20000L,
+ 20000L, 20000L, 20000L, 20000L, 20000L, 20000L, 20000L)), .Names = c("mean",
+"sd", "MC_error", "val2.5pc", "median", "val97.5pc", "start",
+"sample"), row.names = c("p[1]", "p[2]", "p[3]", "p[4]", "p[5]",
+"p[6]", "p[7]", "p[8]", "p[9]", "p[10]", "p[11]", "p[12]"), class = "data.frame"),
+ DIC = structure(list(Dbar = c(62.74, 62.74), Dhat = c(52.3,
+ 52.3), DIC = c(73.17, 73.17), pD = c(10.43, 10.43)), .Names = c("Dbar",
+ "Dhat", "DIC", "pD"), class = "data.frame", row.names = c("r",
+ "total"))), .Names = c("Stats", "DIC")), structure(list(Stats = structure(list(
+ mean = c(0.05316, 0.103, 0.07054, 0.05926, 0.05167, 0.06909,
+ 0.06683, 0.1232, 0.07, 0.07816, 0.1021, 0.0685, 0.07273,
+ 0.4024), sd = c(0.01955, 0.02166, 0.0174, 0.00791, 0.01315,
+ 0.01487, 0.01597, 0.02253, 0.01458, 0.01988, 0.01755, 0.01166,
+ 0.01016, 0.1546), MC_error = c(0.0002498, 0.0002237, 0.0001453,
+ 8.046e-05, 0.0001714, 0.0001062, 0.0001437, 0.0002708, 0.0001184,
+ 0.0001472, 0.000178, 9.045e-05, 0.0001177, 0.002699), val2.5pc = c(0.01832,
+ 0.06674, 0.03992, 0.0446, 0.02813, 0.04269, 0.03834, 0.08309,
+ 0.04398, 0.04431, 0.07166, 0.04735, 0.05325, 0.1627), median = c(0.05232,
+ 0.101, 0.06922, 0.059, 0.05099, 0.0683, 0.06583, 0.1216,
+ 0.0691, 0.07615, 0.1009, 0.06801, 0.07254, 0.3812), val97.5pc = c(0.09456,
+ 0.1511, 0.1088, 0.07551, 0.07896, 0.1011, 0.1011, 0.1711,
+ 0.1012, 0.1223, 0.14, 0.09294, 0.0937, 0.7632), start = c(5001L,
+ 5001L, 5001L, 5001L, 5001L, 5001L, 5001L, 5001L, 5001L, 5001L,
+ 5001L, 5001L, 5001L, 5001L), sample = c(20000L, 20000L, 20000L,
+ 20000L, 20000L, 20000L, 20000L, 20000L, 20000L, 20000L, 20000L,
+ 20000L, 20000L, 20000L)), .Names = c("mean", "sd", "MC_error",
+"val2.5pc", "median", "val97.5pc", "start", "sample"), row.names = c("p[1]",
+"p[2]", "p[3]", "p[4]", "p[5]", "p[6]", "p[7]", "p[8]", "p[9]",
+"p[10]", "p[11]", "p[12]", "pop.mean", "sigma"), class = "data.frame"),
+ DIC = structure(list(Dbar = c(65.97, 65.97), Dhat = c(57.49,
+ 57.49), DIC = c(74.45, 74.45), pD = c(8.479, 8.479)), .Names = c("Dbar",
+ "Dhat", "DIC", "pD"), class = "data.frame", row.names = c("r",
+ "total"))), .Names = c("Stats", "DIC")))
Added: trunk/BRugs/tests/functions.R
===================================================================
--- trunk/BRugs/tests/functions.R (rev 0)
+++ trunk/BRugs/tests/functions.R 2010-05-17 19:57:28 UTC (rev 157)
@@ -0,0 +1,109 @@
+library(BRugs)
+setwd(system.file("OpenBUGS", "Examples", package="BRugs"))
+
+### TEST ALL USER-LEVEL FUNCTIONS USING RATS EXAMPLE
+
+### Basic model setup and stats
+modelCheck("ratsmodel.txt")
+modelData("ratsdata.txt")
+modelCompile(numChains=2)
+modelSetRN(4)
+stopifnot(modelGetRN()==4)
+modelInits(rep("ratsinits.txt", 2))
+modelUpdate(1000)
+samplesSet(c("alpha0", "alpha"))
+summarySet(c("alpha0","alpha"))
+ranksSet("alpha")
+dicSet()
+modelUpdate(1000)
+stopifnot(samplesMonitors("*")[31]=="alpha0")
+stopifnot(isTRUE(all.equal(samplesStats("*")["alpha0","mean"], 106.6)))
+stopifnot(isTRUE(all.equal(dicStats()["total","DIC"],1021)))
+stopifnot(isTRUE(all.equal(summaryStats("alpha0")["alpha0","mean"], 106.6)))
+stopifnot(isTRUE(all.equal(as.numeric(ranksStats("alpha")[1,]), c(10,12,18))))
+
+### Utilities
+samplesSetBeg(1200); stopifnot(samplesGetBeg()==1200)
+samplesSetEnd(1500); stopifnot(samplesGetEnd()==1500)
+samplesSetFirstChain(2); stopifnot(samplesGetFirstChain()==2)
+samplesSetLastChain(2); stopifnot(samplesGetLastChain()==2)
+samplesSetThin(2); stopifnot(samplesGetThin()==2)
+samplesSetBeg(1000)
+samplesSetEnd(1000000)
+samplesSetFirstChain(1)
+samplesSetLastChain(2)
+samplesSetThin(1)
+stopifnot(samplesSize("alpha0")==2*1000)
+stopifnot(length(samplesSample("alpha0"))==2*1000)
+stopifnot(length(infoNodeValues("alpha"))==30)
+stopifnot(BRugs:::dimensions("alpha")==1)
+stopifnot(BRugs:::dimensions("alpha0")==0)
+stopifnot(modelIteration()==2000)
+stopifnot(all.equal(sort(modelNames()),sort(c("N", "T", "Y", "alpha", "alpha.c", "alpha.tau", "alpha0", "beta","beta.c", "beta.tau", "deviance", "mu", "sigma", "tau.c", "x","xbar"))))
+modelPrecision(8)
+stopifnot(nchar(as.character(samplesStats("alpha0")$mean))==9)
+modelPrecision(4)
+x <- infoNodeValues("alpha")
+setValues("alpha", x-1)
+stopifnot(isTRUE(all.equal(infoNodeValues("alpha"), x-1)))
+stopifnot(modelAdaptivePhase()==-1)
+
+### Plots
+stopifnot(all(dim(samplesHistory("alpha0", plot=interactive())[[1]])==c(1000,2)))
+stopifnot(isTRUE(all.equal(samplesAutoC("alpha0", 1, plot=interactive())$alpha0$acf[1], 1)))
+stopifnot(all(dim(samplesBgr("alpha0", plot=interactive())$alpha0)==c(50,4)))
+stopifnot(isTRUE(all.equal(samplesCorrel("alpha[1]", "alpha[2]")[1,1], 0.007215)))
+stopifnot(all(dim(samplesDensity("alpha", plot=interactive()))==c(7,30)))
+stopifnot(all(dim(plotHistory("alpha0", plot=interactive())[[1]])==c(1000,2)))
+stopifnot(isTRUE(all.equal(plotAutoC("alpha0", 1, plot=interactive())$acf[1], 1)))
+stopifnot(all(dim(plotBgr("alpha0", plot=interactive()))==c(50,4)))
+stopifnot(length(plotDensity("alpha0",plot=FALSE))==7)
+
+### Clearing
+samplesClear("alpha")
+stopifnot(samplesMonitors("*")=="alpha0")
+stopifnot(samplesSize("alpha")==0)
+dicClear()
+summaryClear("*")
+
+## External and file access
+samplesCoda("*" ,stem="rats")
+modelSaveState(stem="rats")
+require(coda)
+rats.coda <- buildMCMC("alpha0")
+stopifnot(length(rats.coda[[1]])==1000)
+modelCheck("ratsmodel.txt")
+dat <- dget("Ratsdata.txt")
+modelData(bugsData(dat))
+modelCompile(numChains=2)
+inits <- dget("Ratsinits.txt")
+modelInits(bugsInits(list(inits,inits), numChains=2))
+# writeModel() # tested in help page example
+
+## Manuals
+if (interactive()) help.BRugs() # todo remove link from doc
+if (interactive()) help.WinBUGS()
+
+## Gen inits
+modelCheck("ratsmodel.txt")
+modelData("ratsdata.txt")
+modelCompile(numChains=2)
+inits <- dget("Ratsinits.txt"); inits[c("alpha","beta")] <- NULL
+modelInits(bugsInits(list(inits,inits), numChains=2))
+modelGenInits()
+
+## Functions to tune updaters. Just make sure their interfaces are correct
+#modelSetAP()
+#modelSetIts()
+#modelSetOR()
+#modelEnable()
+#modelDisable()
+
+## Info functions
+stopifnot(infoNodeMethods("alpha")[,"Type"] == "UpdaterNormal.StdUpdater")
+stopifnot(infoNodeTypes("alpha")[1,"Type"]=="GraphNormal.StdNode")
+stopifnot(infoUpdatersbyName()["alpha.c","Type"]=="conjugatenormalupdater")
+stopifnot(infoUpdatersbyDepth()["alpha.c","Type"]=="conjugatenormalupdater")
+mem <- infoMemory()
+stopifnot(is.numeric(mem) && mem > 0)
+stopifnot(any(infoModules()[,"Module"] == "Kernel"))
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|
|
From: <li...@us...> - 2011-12-30 15:55:58
|
Revision: 230
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=230&view=rev
Author: ligges
Date: 2011-12-30 15:55:52 +0000 (Fri, 30 Dec 2011)
Log Message:
-----------
reflect changed StartupMessage from rev 211 in Rout.save files
Revision Links:
--------------
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=211&view=rev
Modified Paths:
--------------
trunk/BRugs/tests/BRugs.Rout.save
trunk/BRugs/tests/examples.Rout.save
trunk/BRugs/tests/functions.Rout.save
Modified: trunk/BRugs/tests/BRugs.Rout.save
===================================================================
--- trunk/BRugs/tests/BRugs.Rout.save 2011-12-23 03:17:03 UTC (rev 229)
+++ trunk/BRugs/tests/BRugs.Rout.save 2011-12-30 15:55:52 UTC (rev 230)
@@ -75,7 +75,7 @@
+ }
Loading required package: coda
Loading required package: lattice
-Welcome to BRugs running on OpenBUGS version 3.2.1
+Welcome to BRugs connected to OpenBUGS version 3.2.1
model is syntactically correct
data loaded
model compiled
Modified: trunk/BRugs/tests/examples.Rout.save
===================================================================
--- trunk/BRugs/tests/examples.Rout.save 2011-12-23 03:17:03 UTC (rev 229)
+++ trunk/BRugs/tests/examples.Rout.save 2011-12-30 15:55:52 UTC (rev 230)
@@ -66,7 +66,7 @@
+ }
Loading required package: coda
Loading required package: lattice
-Welcome to BRugs running on OpenBUGS version 3.2.1
+Welcome to BRugs connected to OpenBUGS version 3.2.1
model is syntactically correct
data loaded
model compiled
Modified: trunk/BRugs/tests/functions.Rout.save
===================================================================
--- trunk/BRugs/tests/functions.Rout.save 2011-12-23 03:17:03 UTC (rev 229)
+++ trunk/BRugs/tests/functions.Rout.save 2011-12-30 15:55:52 UTC (rev 230)
@@ -149,7 +149,7 @@
+ }
Loading required package: coda
Loading required package: lattice
-Welcome to BRugs running on OpenBUGS version 3.2.1
+Welcome to BRugs connected to OpenBUGS version 3.2.1
model is syntactically correct
data loaded
model compiled
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <li...@us...> - 2011-12-30 18:33:29
|
Revision: 237
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=237&view=rev
Author: ligges
Date: 2011-12-30 18:33:23 +0000 (Fri, 30 Dec 2011)
Log Message:
-----------
check for success on file.copy
Modified Paths:
--------------
trunk/BRugs/tests/BRugs.R
trunk/BRugs/tests/BRugs.Rout.save
trunk/BRugs/tests/examples.R
trunk/BRugs/tests/examples.Rout.save
trunk/BRugs/tests/functions.R
trunk/BRugs/tests/functions.Rout.save
Modified: trunk/BRugs/tests/BRugs.R
===================================================================
--- trunk/BRugs/tests/BRugs.R 2011-12-30 17:36:42 UTC (rev 236)
+++ trunk/BRugs/tests/BRugs.R 2011-12-30 18:33:23 UTC (rev 237)
@@ -7,8 +7,13 @@
## Prepare the example files in a temporary directory
exfiles <- dir(options()$OpenBUGSExamples, pattern="^Rats.*txt$", full.names=TRUE)
ok <- file.copy(exfiles, tempdir())
+if(!all(ok))
+ stop("Some files could not be copied from OpenBUGS examples to the temporary directory")
+
exfiles <- dir(options()$OpenBUGSExamples, pattern="^Beetles.*txt$", full.names=TRUE)
ok <- file.copy(exfiles, tempdir())
+if(!all(ok))
+ stop("Some files could not be copied from OpenBUGS examples to the temporary directory")
BRugsFit(data = "Ratsdata.txt", inits = "Ratsinits.txt",
Modified: trunk/BRugs/tests/BRugs.Rout.save
===================================================================
--- trunk/BRugs/tests/BRugs.Rout.save 2011-12-30 17:36:42 UTC (rev 236)
+++ trunk/BRugs/tests/BRugs.Rout.save 2011-12-30 18:33:23 UTC (rev 237)
@@ -1,5 +1,5 @@
-R version 2.13.1 Patched (2011-07-20 r56455)
+R version 2.14.1 (2011-12-22)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i386-pc-mingw32/i386 (32-bit)
@@ -25,8 +25,13 @@
+ ## Prepare the example files in a temporary directory
+ exfiles <- dir(options()$OpenBUGSExamples, pattern="^Rats.*txt$", full.names=TRUE)
+ ok <- file.copy(exfiles, tempdir())
++ if(!all(ok))
++ stop("Some files could not be copied from OpenBUGS examples to the temporary directory")
++
+ exfiles <- dir(options()$OpenBUGSExamples, pattern="^Beetles.*txt$", full.names=TRUE)
+ ok <- file.copy(exfiles, tempdir())
++ if(!all(ok))
++ stop("Some files could not be copied from OpenBUGS examples to the temporary directory")
+
+
+ BRugsFit(data = "Ratsdata.txt", inits = "Ratsinits.txt",
Modified: trunk/BRugs/tests/examples.R
===================================================================
--- trunk/BRugs/tests/examples.R 2011-12-30 17:36:42 UTC (rev 236)
+++ trunk/BRugs/tests/examples.R 2011-12-30 18:33:23 UTC (rev 237)
@@ -38,6 +38,8 @@
for (i in seq(along=test.models)) {
exfiles <- dir(options()$OpenBUGSExamples, pattern=test.pattern[i], full.names=TRUE)
ok <- file.copy(exfiles, tempdir())
+ if(!all(ok))
+ stop("Some files could not be copied from OpenBUGS examples to the temporary directory")
fit <- BRugsFit(data=test.datafile[i], inits=test.inits[i],
modelFile=test.modelfile[i], para=test.params[[test.models[i]]],
nBurnin=5000, nIter=20000, nThin=1, numChains=1, seed=1,
Modified: trunk/BRugs/tests/examples.Rout.save
===================================================================
--- trunk/BRugs/tests/examples.Rout.save 2011-12-30 17:36:42 UTC (rev 236)
+++ trunk/BRugs/tests/examples.Rout.save 2011-12-30 18:33:23 UTC (rev 237)
@@ -1,5 +1,5 @@
-R version 2.13.1 Patched (2011-07-20 r56455)
+R version 2.14.1 (2011-12-22)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i386-pc-mingw32/i386 (32-bit)
@@ -56,6 +56,8 @@
+ for (i in seq(along=test.models)) {
+ exfiles <- dir(options()$OpenBUGSExamples, pattern=test.pattern[i], full.names=TRUE)
+ ok <- file.copy(exfiles, tempdir())
++ if(!all(ok))
++ stop("Some files could not be copied from OpenBUGS examples to the temporary directory")
+ fit <- BRugsFit(data=test.datafile[i], inits=test.inits[i],
+ modelFile=test.modelfile[i], para=test.params[[test.models[i]]],
+ nBurnin=5000, nIter=20000, nThin=1, numChains=1, seed=1,
@@ -176,7 +178,7 @@
monitor set for variable 'sigma1'
monitor set for variable 'sigma2'
monitor set for variable 'theta'
-20000 updates took 1 s
+20000 updates took 0 s
model is syntactically correct
data loaded
model compiled
@@ -269,5 +271,5 @@
monitor set for variable 'p'
monitor set for variable 'pop.mean'
monitor set for variable 'sigma'
-20000 updates took 2 s
+20000 updates took 1 s
>
Modified: trunk/BRugs/tests/functions.R
===================================================================
--- trunk/BRugs/tests/functions.R 2011-12-30 17:36:42 UTC (rev 236)
+++ trunk/BRugs/tests/functions.R 2011-12-30 18:33:23 UTC (rev 237)
@@ -5,6 +5,8 @@
library("BRugs")
exfiles <- dir(options()$OpenBUGSExamples, pattern="^Rats.*txt$", full.names=TRUE)
ok <- file.copy(exfiles, tempdir())
+if(!all(ok))
+ stop("Some files could not be copied from OpenBUGS examples to the temporary directory")
setwd(tempdir())
## .onLoad(lib=.libPaths()[1], pkg="BRugs") # if developing without using namespace
Modified: trunk/BRugs/tests/functions.Rout.save
===================================================================
--- trunk/BRugs/tests/functions.Rout.save 2011-12-30 17:36:42 UTC (rev 236)
+++ trunk/BRugs/tests/functions.Rout.save 2011-12-30 18:33:23 UTC (rev 237)
@@ -1,5 +1,5 @@
-R version 2.13.1 Patched (2011-07-20 r56455)
+R version 2.14.1 (2011-12-22)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i386-pc-mingw32/i386 (32-bit)
@@ -23,6 +23,8 @@
+ library("BRugs")
+ exfiles <- dir(options()$OpenBUGSExamples, pattern="^Rats.*txt$", full.names=TRUE)
+ ok <- file.copy(exfiles, tempdir())
++ if(!all(ok))
++ stop("Some files could not be copied from OpenBUGS examples to the temporary directory")
+ setwd(tempdir())
+ ## .onLoad(lib=.libPaths()[1], pkg="BRugs") # if developing without using namespace
+
@@ -141,8 +143,8 @@
+ ## Info functions
+ stopifnot(infoNodeMethods("alpha")[,"Type"] == "UpdaterNormal.StdUpdater")
+ stopifnot(infoNodeTypes("alpha")[1,"Type"]=="GraphNormal.Node")
-+ stopifnot(infoUpdatersbyName()["alpha.c","Type"]=="conjugatenormalupdater")
-+ stopifnot(infoUpdatersbyDepth()["alpha.c","Type"]=="conjugatenormalupdater")
++ stopifnot(infoUpdatersbyName()["alpha.c","Type"]=="conjugate normal updater")
++ stopifnot(infoUpdatersbyDepth()["alpha.c","Type"]=="conjugate normal updater")
+ mem <- infoMemory()
+ stopifnot(is.numeric(mem) && mem > 0)
+ stopifnot(any(infoModules()[,"Module"] == "Kernel"))
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