[R] Error in if (class(networks) == "matrix") from a function

[Rui Barradas]

Hello,

In my previous I forgot that this, for matrices to have 2 classes , is 
relatively new. It was introduced in R 4.0.0. From the News file [1], 
point 2:


R News
[R logo] CHANGES IN 4.0.0
SIGNIFICANT USER-VISIBLE CHANGES

matrix objects now also inherit from class "array", so e.g., 
class(diag(1)) is c("matrix", "array"). This invalidates code 
incorrectly assuming that class(matrix_obj)) has length one.


So the R Core Team did an excelent job once again and warned R users. 
This was a major R version, where changes like this generally happen and 
are anounced with antecipation. (I remeber to have seen it but cannot 
place it.) Old code needs to be changed, it might break.


[1] https://cran.r-project.org/bin/windows/base/old/4.0.0/NEWS.R-4.0.0.html

Hope this helps,

Rui Barradas

Às 20:35 de 21/09/2022, Rui Barradas escreveu:
> 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
> 
> Às 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 using r-project.org mailing list -- To UNSUBSCRIBE and more, see
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>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
> 
> ______________________________________________
> R-help using 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.