Package check result: ERROR Check: examples, Result: ERROR Running examples in ‘micd-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: getSuff > ### Title: Obtain 'suffStat' for conditional independence testing > ### Aliases: getSuff > > ### ** Examples > > > # Example 1: continuous variables, no missing values ===================== > data(windspeed) > dat1 <- as.matrix(windspeed) > > ## analyse data > gaussCItest(1, 2, NULL, suffStat = getSuff(windspeed, test = "gaussCItest")) [1] 1.219773e-90 > mixCItest(1, 2, NULL, suffStat = windspeed) [1] 1.219773e-90 > > ## Example 2: continuous variables, multiple imputation =================== > dat2 <- mice::ampute(windspeed)$amp > > ## delete some observations > set.seed(123) > > ## Impute missing values under normal model > imp2 <- mice(dat2, method = "norm", printFlag = FALSE) > > ## analyse imputed data > gaussMItest(1, 2, c(4,5), suffStat = getSuff(imp2, test="gaussMItest")) [1] 9.956884e-17 > mixMItest(1, 2, c(4,5), suffStat = getSuff(imp2, test="mixMItest")) [1] 9.956884e-17 > mixMItest(1, 2, c(4,5), suffStat = mice::complete(imp2, action="all")) [1] 9.956884e-17 > flexMItest(1, 2, c(4,5), suffStat = getSuff(imp2, test="flexMItest")) [1] 9.956884e-17 > > ## Example 3: discrete variables, multiple imputation ===================== > ## simulate factor variables > n <- 200 > set.seed(789) > x <- factor(sample(0:2, n, TRUE)) # factor, 3 levels > y <- factor(sample(0:3, n, TRUE)) # factor, 4 levels > z <- factor(sample(0:1, n, TRUE)) # factor, 2 levels > dat3 <- data.frame(x,y,z) > > ## delete some observations of z > dat3[sample(1:n, 40), 3] <- NA > > ## impute missing values under saturated model > form <- make.formulas.saturated(dat3) > imp3 <- mice::mice(dat3, method = "logreg", formulas = form, printFlag = FALSE) > > ## analyse imputed data > disMItest(1, 3, 2, suffStat = getSuff(imp3, test="disMItest")) [1] 0.9449046 > disMItest(1, 3, 2, suffStat = mice::complete(imp3, action = "all")) [1] 0.9449046 > mixMItest(1, 3, 2, suffStat = getSuff(imp3, test="mixMItest")) [1] 0.9449046 > mixMItest(1, 3, 2, suffStat = mice::complete(imp3, action = "all")) [1] 0.9449046 > flexMItest(1, 3, 2, suffStat = getSuff(imp3, test="flexMItest")) [1] 0.9449046 > > # Example 4: mixed variables, multiple imputation ========================= > dat4 <- toenail2[1:400, ] > set.seed(123) > dat4[sample(400, 20), 2] <- NA > dat4[sample(400, 30), 4] <- NA > > ## impute missing values using random forests > imp4 <- mice(dat4, method="rf", m = 3, printFlag = FALSE) Error in loadNamespace(x) : there is no package called ‘ranger’ Calls: mice ... sampler -> sampler.univ -> do.call -> mice.impute.rf -> f Execution halted