Added code from README to test (#8)

tests/testthat/test-pinferunemjmcmc-example-match-1.4.3.R

@@ -1,4 +1,63 @@
 # TODO #8: fill empty tests
+
+# inference
+
+X <- read.csv("inst/extdata/exa1.csv")
+data.example <- as.data.frame(X)
+
+# specify the initial formula
+formula1 <- as.formula(
+  paste(colnames(X)[5], "~ 1 +", paste0(colnames(X)[-5], collapse = "+"))
+)
+
+# a set of nonlinearities that will be used in the DBRM model
+sini <- function(x) sin(x / 180 * pi)
+expi <- function(x) exp(-abs(x))
+logi <- function(x) log(abs(x) + 1)
+troot <- function(x) abs(x)^(1 / 3)
+to23 <- function(x) abs(x)^(2.3)
+to35 <- function(x) abs(x)^(3.5)
+
+# define the number or cpus
+M <- 4
+# define the size of the simulated samples
+NM <- 1000
+# define \k_{max} + 1 from the paper
+compmax <- 16
+# define treshold for preinclusion of the tree into the analysis
+th <- (10)^(-5)
+# define a final treshold on the posterior marginal probability for reporting a
+# tree
+thf <- 0.05
+# specify tuning parameters of the algorithm for exploring DBRM of interest
+# notice that allow_offsprings=3 corresponds to the GMJMCMC runs and
+# allow_offsprings=4 -to the RGMJMCMC runs
+res1 <- pinferunemjmcmc(
+  n.cores = M, report.level = 0.5, num.mod.best = NM, simplify = TRUE,
+  runemjmcmc.params = list(
+    formula = formula1, data = data.example, estimator = estimate.gamma.cpen,
+    estimator.args = list(data = data.example), recalc_margin = 249,
+    save.beta = FALSE, interact = TRUE, outgraphs = FALSE,
+    relations = c("to23", "expi", "logi", "to35", "sini", "troot", "sigmoid"),
+    relations.prob = c(0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1),
+    interact.param = list(allow_offsprings = 3, mutation_rate = 250,
+    last.mutation = 10000, max.tree.size = 5, Nvars.max = 15,
+    p.allow.replace = 0.9, p.allow.tree = 0.01, p.nor = 0.9, p.and = 0.9),
+    n.models = 10000, unique = TRUE, max.cpu = 4, max.cpu.glob = 4,
+    create.table = FALSE, create.hash = TRUE, pseudo.paral = TRUE,
+    burn.in = 100, print.freq = 1000,
+    advanced.param = list(
+      max.N.glob = as.integer(10),
+      min.N.glob = as.integer(5),
+      max.N = as.integer(3),
+      min.N = as.integer(1),
+      printable = FALSE
+    )
+  )
+)
+
+print(res1$feat.stat)
+
 test_that("pinferunemjmcmc output matches version 1.4.3", {
 
 })