Running examples in 'sensiPhy-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: intra_clade_phyglm
> ### Title: Interaction between intraspecific variability and influential
> ###   clade detection - Phylogenetic Logistic Regression
> ### Aliases: intra_clade_phyglm
> 
> ### ** Examples
> 
> ## Not run: 
> ##D set.seed(6987)
> ##D phy = rtree(100)
> ##D x = rTrait(n=1,phy=phy,parameters=list(ancestral.state=2,optimal.value=2,sigma2=1,alpha=1))
> ##D X = cbind(rep(1,100),x)
> ##D y = rbinTrait(n=1,phy=phy, beta=c(-1,0.5), alpha=.7 ,X=X)
> ##D z = rnorm(n = length(x),mean = mean(x),sd = 0.1*mean(x))
> ##D cla <- rep(c("A","B","C","D"), each = 25)
> ##D dat = data.frame(y, x, z, cla)
> ##D intra_clade <- intra_clade_phyglm(formula=y ~ x, data = dat, phy = phy,
> ##D                                   clade.col = "cla", n.sim = 30, n.intra = 3,
> ##D                                   x.transf = log, Vx = "z", distrib="normal")
> ##D sensi_plot(intra_clade)
> ##D sensi_plot(intra_clade, clade = "B", graphs = 2)
> ## End(Not run)
> ## Don't show: 
> set.seed(6987)
> phy = rtree(100)
> x = rTrait(n=1,phy=phy,parameters=list(ancestral.state=2,optimal.value=2,sigma2=1,alpha=1))
> X = cbind(rep(1,100),x)
> y = rbinTrait(n=1,phy=phy, beta=c(-1,0.5), alpha=.7 ,X=X)
> z = rnorm(n = length(x),mean = mean(x),sd = 0.1*mean(x))
> cla <- rep(c("A","B","C","D"), each = 25)
> dat = data.frame(y, x, z, cla)
> intra_clade <- intra_clade_phyglm(formula=y ~ x, data = dat, phy = phy,
+                                  clade.col = "cla", n.sim = 1, n.intra = 1,
+                                  x.transf = log, Vx = "z", distrib="normal")
Warning in intra_clade_phyglm(formula = y ~ x, data = dat, phy = phy, clade.col = "cla",  :
  distrib=normal: make sure that standard deviation is provided for Vx
Used dataset has  100  species that match data and phylogeny

  |                                                                            
  |                                                                      |   0%
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  |======================================================================| 100%
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
sensiPhy
 --- call from context --- 
recombine(intra.clade, slot1 = 3, slot2 = 1)
 --- call from argument --- 
if (class(x[[1]]) == "data.frame" | class(x[[1]]) == "matrix" | 
    class(x[[1]]) == "numeric") {
    n.rows <- nrow(x[[1]])
    if (is.null(n.rows)) {
        nam <- as.numeric(names(sensi.list))
        n.rows <- length(x[[1]])
        est.name <- names(sensi.list[[1]][[slot1]])[[slot2]]
        N <- rep(nam, each = n.rows)
        res <- data.frame(iteration = N, do.call("rbind", x))
        colnames(res)[2] <- est.name
        return(res)
    }
    else res <- data.frame(iteration = rep(names(x), sapply(x, 
        nrow)), do.call(rbind, x))
    res$info <- unlist(lapply(x, rownames))
    return(res)
} else stop("Check if slot indexing returns a valid data.frame or numeric value withn your list")
 --- R stacktrace ---
where 1: recombine(intra.clade, slot1 = 3, slot2 = 1)
where 2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
where 3: suppressWarnings(recombine(intra.clade, slot1 = 3, slot2 = 1))
where 4: intra_clade_phyglm(formula = y ~ x, data = dat, phy = phy, clade.col = "cla", 
    n.sim = 1, n.intra = 1, x.transf = log, Vx = "z", distrib = "normal")

 --- value of length: 2 type: logical ---
[1]  TRUE FALSE
 --- function from context --- 
function (sensi.list, slot1, slot2 = NULL) 
{
    is <- NULL
    if (is.null(slot2)) {
        x <- lapply(sensi.list, function(x) x[[slot1]])
        if (is(x[[1]], "list")) 
            stop("Please also provide a value for slot2")
        if (is.na(match(class(x[[1]]), c("data.frame", "matrix")))) 
            stop("Check if slot indexing returns a valid data.frame or numeric value withn your list")
        res <- data.frame(iteration = rep(names(x), sapply(x, 
            nrow)), do.call(rbind, x))
        res$info <- unlist(lapply(x, rownames))
        return(res)
    }
    if (is.null(slot2) == FALSE) {
        x <- lapply(sensi.list, function(x) x[[slot1]][[slot2]])
        if (class(x[[1]]) == "data.frame" | class(x[[1]]) == 
            "matrix" | class(x[[1]]) == "numeric") {
            n.rows <- nrow(x[[1]])
            if (is.null(n.rows)) {
                nam <- as.numeric(names(sensi.list))
                n.rows <- length(x[[1]])
                est.name <- names(sensi.list[[1]][[slot1]])[[slot2]]
                N <- rep(nam, each = n.rows)
                res <- data.frame(iteration = N, do.call("rbind", 
                  x))
                colnames(res)[2] <- est.name
                return(res)
            }
            else res <- data.frame(iteration = rep(names(x), 
                sapply(x, nrow)), do.call(rbind, x))
            res$info <- unlist(lapply(x, rownames))
            return(res)
        }
        else stop("Check if slot indexing returns a valid data.frame or numeric value withn your list")
    }
}
<bytecode: 0x11d990d8>
<environment: namespace:sensiPhy>
 --- function search by body ---
Function recombine in namespace sensiPhy has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1