R help - Sep 2022 - Error in if (class(networks) == "matrix") from a function

Dear R-Help community,

This is a crosspost on SO but I've had no luck so far. So I have a function
which computes a centrality index for the nodes in a network or matrix.
Here is the function:

library(igraph) #load package igraph
centrality <- function (networks, type = c("indegree",
"outdegree", "freeman",
    "betweenness", "flow", "closeness",
"eigenvector", "information",
    "load", "bonpow"), directed = TRUE, lag = 0, rescale =
FALSE,
    center = FALSE, coefname = NULL, ...) {
    if (is.null(directed) || !is.logical(directed)) {
        stop("'directed' must be TRUE or FALSE.")
    }
    else if (length(directed) != 1) {
        stop("The 'directed' argument must contain a single logical
value only.")
    }
    else if (directed == FALSE) {
        gmode <- "graph"
    }
    else {
        gmode <- "digraph"
    }
    objects <- checkDataTypes(y = NULL, networks = networks,
        lag = lag)
    centlist <- list()
    for (i in 1:objects$time.steps) {
        if (type[1] == "indegree") {
            cent <- degree(objects$networks[[i]], gmode = gmode,
                cmode = "indegree", rescale = rescale, ...)
        }
        else if (type[1] == "outdegree") {
            cent <- degree(objects$networks[[i]], gmode = gmode,
                cmode = "outdegree", rescale = rescale, ...)
        }
        else if (type[1] == "freeman") {
            cent <- degree(objects$networks[[i]], gmode = gmode,
                cmode = "freeman", rescale = rescale, ...)
        }
        else if (type[1] == "betweenness") {
            cent <- betweenness(objects$networks[[i]], gmode = gmode,
                rescale = rescale, ...)
        }
        else if (type[1] == "flow") {
            cent <- flowbet(objects$networks[[i]], gmode = gmode,
                rescale = rescale, ...)
        }
        else if (type[1] == "closeness") {
            cent <- closeness(objects$networks[[i]], gmode = gmode,
                rescale = rescale, ...)
        }
        else if (type[1] == "eigenvector") {
            cent <- evcent(objects$networks[[i]], gmode = gmode,
                rescale = rescale, ...)
        }
        else if (type[1] == "information") {
            cent <- infocent(objects$networks[[i]], gmode = gmode,
                rescale = rescale, ...)
        }
        else if (type[1] == "load") {
            cent <- loadcent(objects$networks[[i]], gmode = gmode,
                rescale = rescale, ...)
        }
        else if (type[1] == "bonpow") {
            cent <- bonpow(objects$networks[[i]], gmode = gmode,
                rescale = rescale, tol = 1e-20, ...)
        }
        else {
            stop("'type' argument was not recognized.")
        }
        centlist[[i]] <- cent
    }
    time <- numeric()
    y <- numeric()
    for (i in 1:objects$time.steps) {
        time <- c(time, rep(i, objects$n[[i]]))
        if (is.null(centlist[[i]])) {
            y <- c(y, rep(NA, objects$n[[i]]))
        }
        else {
            if (center == TRUE) {
                centlist[[i]] <- centlist[[i]] - mean(centlist[[i]],
                  na.rm = TRUE)
            }
            y <- c(y, centlist[[i]])
        }
    }
    if (is.null(coefname) || !is.character(coefname) || length(coefname) >
        1) {
        coeflabel <- ""
    }
    else {
        coeflabel <- paste0(".", coefname)
    }
    if (lag == 0) {
        laglabel <- ""
    }
    else {
        laglabel <- paste0(".lag", paste(lag, collapse =
"."))
    }
    label <- paste0(type[1], coeflabel, laglabel)
    dat <- data.frame(y, time = time, node = objects$nodelabels)
    dat$node <- as.character(dat$node)
    colnames(dat)[1] <- label
    attributes(dat)$lag <- lag
    return(dat)}

Here is the matrix:

dat <- read.table(text="A B #this is edgelist
1 2
1 3
1 2
2 1
2 3
3 1
3 2
3 1", header=TRUE)
datmat <- as.matrix(get.adjacency(graph.edgelist(as.matrix(dat),
directed=TRUE))) #this is the matrix
colnames(datmat) <- c("1", "2", "3") #rename
the columns

When I applied the function to a matrix
centrality(datmat,type="flow",center=TRUE), it returns the error:

Error in if (class(networks) == "matrix") { :
  the condition has length > 1

What is the cause of this error? How to fix it? Any help will be greatly
appreciated!


Best,

Chao

	[[alternative HTML version deleted]]

In R 4.2.0 there is a significant change. When you use an if() statement
with a condition of length > 1 this now reports an error.
e.g. this link mentions it as a change
https://www.jumpingrivers.com/blog/new-features-r420/

In your case this is because class(obj) can return a character vector of
length > 1 (all the classes).
One possible workaround would be:

if ( "matrix" %in% class(networks) ) ...

HTH,
Eric


On Wed, Sep 21, 2022 at 10:21 PM Chao Liu <psychaoliu at gmail.com> wrote:
> Dear R-Help community,
>
> This is a crosspost on SO but I've had no luck so far. So I have a
function
> which computes a centrality index for the nodes in a network or matrix.
> Here is the function:
>
> library(igraph) #load package igraph
> centrality <- function (networks, type = c("indegree",
"outdegree",
> "freeman",
>     "betweenness", "flow", "closeness",
"eigenvector", "information",
>     "load", "bonpow"), directed = TRUE, lag = 0,
rescale = FALSE,
>     center = FALSE, coefname = NULL, ...) {
>     if (is.null(directed) || !is.logical(directed)) {
>         stop("'directed' must be TRUE or FALSE.")
>     }
>     else if (length(directed) != 1) {
>         stop("The 'directed' argument must contain a single
logical
> value only.")
>     }
>     else if (directed == FALSE) {
>         gmode <- "graph"
>     }
>     else {
>         gmode <- "digraph"
>     }
>     objects <- checkDataTypes(y = NULL, networks = networks,
>         lag = lag)
>     centlist <- list()
>     for (i in 1:objects$time.steps) {
>         if (type[1] == "indegree") {
>             cent <- degree(objects$networks[[i]], gmode = gmode,
>                 cmode = "indegree", rescale = rescale, ...)
>         }
>         else if (type[1] == "outdegree") {
>             cent <- degree(objects$networks[[i]], gmode = gmode,
>                 cmode = "outdegree", rescale = rescale, ...)
>         }
>         else if (type[1] == "freeman") {
>             cent <- degree(objects$networks[[i]], gmode = gmode,
>                 cmode = "freeman", rescale = rescale, ...)
>         }
>         else if (type[1] == "betweenness") {
>             cent <- betweenness(objects$networks[[i]], gmode = gmode,
>                 rescale = rescale, ...)
>         }
>         else if (type[1] == "flow") {
>             cent <- flowbet(objects$networks[[i]], gmode = gmode,
>                 rescale = rescale, ...)
>         }
>         else if (type[1] == "closeness") {
>             cent <- closeness(objects$networks[[i]], gmode = gmode,
>                 rescale = rescale, ...)
>         }
>         else if (type[1] == "eigenvector") {
>             cent <- evcent(objects$networks[[i]], gmode = gmode,
>                 rescale = rescale, ...)
>         }
>         else if (type[1] == "information") {
>             cent <- infocent(objects$networks[[i]], gmode = gmode,
>                 rescale = rescale, ...)
>         }
>         else if (type[1] == "load") {
>             cent <- loadcent(objects$networks[[i]], gmode = gmode,
>                 rescale = rescale, ...)
>         }
>         else if (type[1] == "bonpow") {
>             cent <- bonpow(objects$networks[[i]], gmode = gmode,
>                 rescale = rescale, tol = 1e-20, ...)
>         }
>         else {
>             stop("'type' argument was not recognized.")
>         }
>         centlist[[i]] <- cent
>     }
>     time <- numeric()
>     y <- numeric()
>     for (i in 1:objects$time.steps) {
>         time <- c(time, rep(i, objects$n[[i]]))
>         if (is.null(centlist[[i]])) {
>             y <- c(y, rep(NA, objects$n[[i]]))
>         }
>         else {
>             if (center == TRUE) {
>                 centlist[[i]] <- centlist[[i]] - mean(centlist[[i]],
>                   na.rm = TRUE)
>             }
>             y <- c(y, centlist[[i]])
>         }
>     }
>     if (is.null(coefname) || !is.character(coefname) || length(coefname)
>
>         1) {
>         coeflabel <- ""
>     }
>     else {
>         coeflabel <- paste0(".", coefname)
>     }
>     if (lag == 0) {
>         laglabel <- ""
>     }
>     else {
>         laglabel <- paste0(".lag", paste(lag, collapse =
"."))
>     }
>     label <- paste0(type[1], coeflabel, laglabel)
>     dat <- data.frame(y, time = time, node = objects$nodelabels)
>     dat$node <- as.character(dat$node)
>     colnames(dat)[1] <- label
>     attributes(dat)$lag <- lag
>     return(dat)}
>
> Here is the matrix:
>
> dat <- read.table(text="A B #this is edgelist
> 1 2
> 1 3
> 1 2
> 2 1
> 2 3
> 3 1
> 3 2
> 3 1", header=TRUE)
> datmat <- as.matrix(get.adjacency(graph.edgelist(as.matrix(dat),
> directed=TRUE))) #this is the matrix
> colnames(datmat) <- c("1", "2", "3")
#rename the columns
>
> When I applied the function to a matrix
> centrality(datmat,type="flow",center=TRUE), it returns the error:
>
> Error in if (class(networks) == "matrix") { :
>   the condition has length > 1
>
> What is the cause of this error? How to fix it? Any help will be greatly
> appreciated!
>
>
> Best,
>
> Chao
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
	[[alternative HTML version deleted]]

In general, you should be using inherits(netwotks, "matrix") or
is(networks, "matrix") instead of class() =
Your function fails because your object has multiple classes so class=returns
multiple logical values so if will fail.

But inherits or is will return one logical value, so if will not raise an
error.

On Wed., Sep. 21, 2022, 15:21 Chao Liu, <psychaoliu at gmail.com> wrote:
> Dear R-Help community,
>
> This is a crosspost on SO but I've had no luck so far. So I have a
function
> which computes a centrality index for the nodes in a network or matrix.
> Here is the function:
>
> library(igraph) #load package igraph
> centrality <- function (networks, type = c("indegree",
"outdegree",
> "freeman",
>     "betweenness", "flow", "closeness",
"eigenvector", "information",
>     "load", "bonpow"), directed = TRUE, lag = 0,
rescale = FALSE,
>     center = FALSE, coefname = NULL, ...) {
>     if (is.null(directed) || !is.logical(directed)) {
>         stop("'directed' must be TRUE or FALSE.")
>     }
>     else if (length(directed) != 1) {
>         stop("The 'directed' argument must contain a single
logical
> value only.")
>     }
>     else if (directed == FALSE) {
>         gmode <- "graph"
>     }
>     else {
>         gmode <- "digraph"
>     }
>     objects <- checkDataTypes(y = NULL, networks = networks,
>         lag = lag)
>     centlist <- list()
>     for (i in 1:objects$time.steps) {
>         if (type[1] == "indegree") {
>             cent <- degree(objects$networks[[i]], gmode = gmode,
>                 cmode = "indegree", rescale = rescale, ...)
>         }
>         else if (type[1] == "outdegree") {
>             cent <- degree(objects$networks[[i]], gmode = gmode,
>                 cmode = "outdegree", rescale = rescale, ...)
>         }
>         else if (type[1] == "freeman") {
>             cent <- degree(objects$networks[[i]], gmode = gmode,
>                 cmode = "freeman", rescale = rescale, ...)
>         }
>         else if (type[1] == "betweenness") {
>             cent <- betweenness(objects$networks[[i]], gmode = gmode,
>                 rescale = rescale, ...)
>         }
>         else if (type[1] == "flow") {
>             cent <- flowbet(objects$networks[[i]], gmode = gmode,
>                 rescale = rescale, ...)
>         }
>         else if (type[1] == "closeness") {
>             cent <- closeness(objects$networks[[i]], gmode = gmode,
>                 rescale = rescale, ...)
>         }
>         else if (type[1] == "eigenvector") {
>             cent <- evcent(objects$networks[[i]], gmode = gmode,
>                 rescale = rescale, ...)
>         }
>         else if (type[1] == "information") {
>             cent <- infocent(objects$networks[[i]], gmode = gmode,
>                 rescale = rescale, ...)
>         }
>         else if (type[1] == "load") {
>             cent <- loadcent(objects$networks[[i]], gmode = gmode,
>                 rescale = rescale, ...)
>         }
>         else if (type[1] == "bonpow") {
>             cent <- bonpow(objects$networks[[i]], gmode = gmode,
>                 rescale = rescale, tol = 1e-20, ...)
>         }
>         else {
>             stop("'type' argument was not recognized.")
>         }
>         centlist[[i]] <- cent
>     }
>     time <- numeric()
>     y <- numeric()
>     for (i in 1:objects$time.steps) {
>         time <- c(time, rep(i, objects$n[[i]]))
>         if (is.null(centlist[[i]])) {
>             y <- c(y, rep(NA, objects$n[[i]]))
>         }
>         else {
>             if (center == TRUE) {
>                 centlist[[i]] <- centlist[[i]] - mean(centlist[[i]],
>                   na.rm = TRUE)
>             }
>             y <- c(y, centlist[[i]])
>         }
>     }
>     if (is.null(coefname) || !is.character(coefname) || length(coefname)
>
>         1) {
>         coeflabel <- ""
>     }
>     else {
>         coeflabel <- paste0(".", coefname)
>     }
>     if (lag == 0) {
>         laglabel <- ""
>     }
>     else {
>         laglabel <- paste0(".lag", paste(lag, collapse =
"."))
>     }
>     label <- paste0(type[1], coeflabel, laglabel)
>     dat <- data.frame(y, time = time, node = objects$nodelabels)
>     dat$node <- as.character(dat$node)
>     colnames(dat)[1] <- label
>     attributes(dat)$lag <- lag
>     return(dat)}
>
> Here is the matrix:
>
> dat <- read.table(text="A B #this is edgelist
> 1 2
> 1 3
> 1 2
> 2 1
> 2 3
> 3 1
> 3 2
> 3 1", header=TRUE)
> datmat <- as.matrix(get.adjacency(graph.edgelist(as.matrix(dat),
> directed=TRUE))) #this is the matrix
> colnames(datmat) <- c("1", "2", "3")
#rename the columns
>
> When I applied the function to a matrix
> centrality(datmat,type="flow",center=TRUE), it returns the error:
>
> Error in if (class(networks) == "matrix") { :
>   the condition has length > 1
>
> What is the cause of this error? How to fix it? Any help will be greatly
> appreciated!
>
>
> Best,
>
> Chao
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
	[[alternative HTML version deleted]]

Hello,

Check what class(datmat) returns and use ?inherits instead.


class(datmat)
#[1] "matrix" "array"
inherits(datmat, "matrix")
#[1] TRUE


Also, the error the posted code gives is

centrality(datmat,type="flow",center=TRUE)
Error in checkDataTypes(y = NULL, networks = networks, lag = lag) :
   could not find function "checkDataTypes"


but I assume you have function checkDataTypes somewhere in your session, 
the problem should be solved with inherits().

Hope this helps,

Rui Barradas

?s 20:20 de 21/09/2022, Chao Liu escreveu:
> Dear R-Help community,
> 
> This is a crosspost on SO but I've had no luck so far. So I have a
function
> which computes a centrality index for the nodes in a network or matrix.
> Here is the function:
> 
> library(igraph) #load package igraph
> centrality <- function (networks, type = c("indegree",
"outdegree", "freeman",
>      "betweenness", "flow", "closeness",
"eigenvector", "information",
>      "load", "bonpow"), directed = TRUE, lag = 0,
rescale = FALSE,
>      center = FALSE, coefname = NULL, ...) {
>      if (is.null(directed) || !is.logical(directed)) {
>          stop("'directed' must be TRUE or FALSE.")
>      }
>      else if (length(directed) != 1) {
>          stop("The 'directed' argument must contain a single
logical
> value only.")
>      }
>      else if (directed == FALSE) {
>          gmode <- "graph"
>      }
>      else {
>          gmode <- "digraph"
>      }
>      objects <- checkDataTypes(y = NULL, networks = networks,
>          lag = lag)
>      centlist <- list()
>      for (i in 1:objects$time.steps) {
>          if (type[1] == "indegree") {
>              cent <- degree(objects$networks[[i]], gmode = gmode,
>                  cmode = "indegree", rescale = rescale, ...)
>          }
>          else if (type[1] == "outdegree") {
>              cent <- degree(objects$networks[[i]], gmode = gmode,
>                  cmode = "outdegree", rescale = rescale, ...)
>          }
>          else if (type[1] == "freeman") {
>              cent <- degree(objects$networks[[i]], gmode = gmode,
>                  cmode = "freeman", rescale = rescale, ...)
>          }
>          else if (type[1] == "betweenness") {
>              cent <- betweenness(objects$networks[[i]], gmode = gmode,
>                  rescale = rescale, ...)
>          }
>          else if (type[1] == "flow") {
>              cent <- flowbet(objects$networks[[i]], gmode = gmode,
>                  rescale = rescale, ...)
>          }
>          else if (type[1] == "closeness") {
>              cent <- closeness(objects$networks[[i]], gmode = gmode,
>                  rescale = rescale, ...)
>          }
>          else if (type[1] == "eigenvector") {
>              cent <- evcent(objects$networks[[i]], gmode = gmode,
>                  rescale = rescale, ...)
>          }
>          else if (type[1] == "information") {
>              cent <- infocent(objects$networks[[i]], gmode = gmode,
>                  rescale = rescale, ...)
>          }
>          else if (type[1] == "load") {
>              cent <- loadcent(objects$networks[[i]], gmode = gmode,
>                  rescale = rescale, ...)
>          }
>          else if (type[1] == "bonpow") {
>              cent <- bonpow(objects$networks[[i]], gmode = gmode,
>                  rescale = rescale, tol = 1e-20, ...)
>          }
>          else {
>              stop("'type' argument was not recognized.")
>          }
>          centlist[[i]] <- cent
>      }
>      time <- numeric()
>      y <- numeric()
>      for (i in 1:objects$time.steps) {
>          time <- c(time, rep(i, objects$n[[i]]))
>          if (is.null(centlist[[i]])) {
>              y <- c(y, rep(NA, objects$n[[i]]))
>          }
>          else {
>              if (center == TRUE) {
>                  centlist[[i]] <- centlist[[i]] - mean(centlist[[i]],
>                    na.rm = TRUE)
>              }
>              y <- c(y, centlist[[i]])
>          }
>      }
>      if (is.null(coefname) || !is.character(coefname) || length(coefname)
>
>          1) {
>          coeflabel <- ""
>      }
>      else {
>          coeflabel <- paste0(".", coefname)
>      }
>      if (lag == 0) {
>          laglabel <- ""
>      }
>      else {
>          laglabel <- paste0(".lag", paste(lag, collapse =
"."))
>      }
>      label <- paste0(type[1], coeflabel, laglabel)
>      dat <- data.frame(y, time = time, node = objects$nodelabels)
>      dat$node <- as.character(dat$node)
>      colnames(dat)[1] <- label
>      attributes(dat)$lag <- lag
>      return(dat)}
> 
> Here is the matrix:
> 
> dat <- read.table(text="A B #this is edgelist
> 1 2
> 1 3
> 1 2
> 2 1
> 2 3
> 3 1
> 3 2
> 3 1", header=TRUE)
> datmat <- as.matrix(get.adjacency(graph.edgelist(as.matrix(dat),
> directed=TRUE))) #this is the matrix
> colnames(datmat) <- c("1", "2", "3")
#rename the columns
> 
> When I applied the function to a matrix
> centrality(datmat,type="flow",center=TRUE), it returns the error:
> 
> Error in if (class(networks) == "matrix") { :
>    the condition has length > 1
> 
> What is the cause of this error? How to fix it? Any help will be greatly
> appreciated!
> 
> 
> Best,
> 
> Chao
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.