all comments were addressed, except -behavior- as a vector.

Author: aoliveram

R/adjmat.r

@@ -491,7 +491,6 @@ toa_mat <- function(obj, labels=NULL, t0=NULL, t1=NULL) {
             }
   } else {
     for (q in 1:num_of_behaviors) {
-      #cls <- class(obj[,q])
       ans[[q]] <- if ("matrix" %in% class(obj)) {
               if ("integer" %in% class(obj[,q])){
                 toa_mat.integer(obj[,q], labels, t0, t1)

R/diffnet-class.r

@@ -638,6 +638,8 @@ new_diffnet <- function(graph, toa, t0=min(toa, na.rm = TRUE), t1=max(toa, na.rm
 
       # This should be reviewed !! (here the graph becomes 'dynamic')
 
+      warning("here the graph becomes 'dynamic' for multiple")
+
       graph <- lapply(1:ncol(mat[[1]]$adopt), function(x) methods::as(graph, "dgCMatrix"))
       meta  <- classify_graph(graph)
     }

R/diffnet-methods.r

@@ -95,7 +95,7 @@ print.diffnet <- function(x, ...) {
                      ifelse(meta$n>8, ", ...", "") ,")")
 
     # Computing prevalence for multi-diff
-    single <- class(cumadopt)[1]!='list'
+    single <- !inherits(cumadopt, "list")
     if (!single) {
       prevalence_all <- character(length(cumadopt))
       for (q in 1:length(cumadopt)) {
@@ -214,7 +214,7 @@ summary.diffnet <- function(
   }))
 
   # identify single-diff from multi-diff
-  single <- class(object$cumadopt)[1]!='list'
+  single <- !inherits(object$cumadopt, "list")
 
   # Computing moran's I
   if (single) {

R/rdiffnet.r

@@ -332,12 +332,12 @@ rdiffnet <- function(
   if (!length(exposure.args[["valued"]])) exposure.args[["valued"]] <- getOption("diffnet.valued", FALSE)
   if (!length(exposure.args[["normalized"]])) exposure.args[["normalized"]] <- TRUE
 
-  if (class(exposure.args[["attrs"]])[1] == "matrix") {
+  if (inherits(exposure.args[["attrs"]], "matrix")) {
     # Checking if the attrs matrix is has dims n x t
     if (any(dim(exposure.args[["attrs"]]) != dim(matrix(NA, nrow = n, ncol = t)))) {
       stop("Incorrect size for -attrs- in rdiffnet. Does not match n dim or t dim.")}
     attrs_arr <- exposure.args[["attrs"]]
-    if (class(seed.p.adopt) == 'list'){
+    if (inherits(seed.p.adopt, "list")){
       attrs_arr <- array(attrs_arr, dim = c(n, t, length(seed.p.adopt)))
     } else {attrs_arr <- array(attrs_arr, dim = c(n, t, 1))}
   }
@@ -511,14 +511,14 @@ rdiffnet_validate_args <- function(seed.p.adopt, seed.nodes, behavior) {
 
   # The class of seed.p.adopt determines if is a single or multiple diff pross.
 
-  if (class(seed.p.adopt) == "list") {
+  if (inherits(seed.p.adopt, "list")) {
 
     message(paste("Message: Multi-diffusion behavior simulation selected.",
                   "Number of behaviors: ", length(seed.p.adopt)))
 
     multi <- TRUE
 
-  } else if (class(seed.p.adopt) == "numeric") {
+  } else if (inherits(seed.p.adopt, "numeric")) {
 
     if (length(seed.p.adopt)>1) {
       stop(paste("length(seed.p.adopt) =", length(seed.p.adopt),
@@ -539,7 +539,7 @@ rdiffnet_validate_args <- function(seed.p.adopt, seed.nodes, behavior) {
 
     # For multi-diff.
 
-    if (class(seed.nodes) == "list") {
+    if (inherits(seed.nodes, "list")) {
       if (length(seed.nodes) != length(seed.p.adopt)) {
         stop("Length of lists -seed.nodes- and -seed.p.adopt- must be the same for multi diffusion.")
       }
@@ -563,12 +563,12 @@ rdiffnet_validate_args <- function(seed.p.adopt, seed.nodes, behavior) {
       } else {
         stop("All elements of the list seed.nodes must be either -character- or -numeric-.")
       }
-    } else if (class(seed.nodes) == "numeric") {
+    } else if (inherits(seed.nodes, "numeric")) {
       message("Message: Object -seed.nodes- converted to a -list-.",
               "All behaviors will have the same -", seed.nodes, "- seed nodes.")
 
       seed.nodes <- replicate(length(seed.p.adopt), seed.nodes, simplify = FALSE)
-    } else if (class(seed.nodes) == "character") {
+    } else if (inherits(seed.nodes, "character")) {
       if (length(seed.nodes)==length(seed.p.adopt)) {
         seed.nodes <- as.list(seed.nodes)
         message("Message: Object -seed.nodes- converted to a -list-.",
@@ -583,17 +583,17 @@ rdiffnet_validate_args <- function(seed.p.adopt, seed.nodes, behavior) {
       stop("Unsupported -seed.nodes- value. See the manual for references.")
     }
 
-    if (class(behavior) == "list") {
+    if (inherits(behavior, "list")) {
       if (length(seed.p.adopt)!=length(behavior)) {
         stop("If -behavior- is a list, it must be of the same length as -seed.p.adopt-.")
       }
-    } else if (class(behavior) == "character" && length(behavior) > 1) {
+    } else if (inherits(behavior, "character") && length(behavior) > 1) {
       if (length(behavior) != length(seed.p.adopt)) {
         stop("Mismatch between length(behavior) and length(seed.p.adopt)")
       } else {
         behavior <- as.list(behavior)
       }
-    } else if (class(behavior) == "character" && length(behavior) == 1) {
+    } else if (inherits(behavior, "character") && length(behavior) == 1) {
       message(paste("Message: Name of 1 behavior provided, but", length(seed.p.adopt), "are needed. "),
               "Names generalized to 'behavior'_1, 'behavior'_2, etc.")
       behaviors <- list()
@@ -609,7 +609,7 @@ rdiffnet_validate_args <- function(seed.p.adopt, seed.nodes, behavior) {
 
     # For Single-diff.
 
-    if (length(seed.nodes) == 1 && class(seed.nodes)=="character") {
+    if (length(seed.nodes) == 1 && inherits(seed.nodes, "character")) {
 
       if (!seed.nodes %in% c("marginal", "central", "random")) {
         stop("Object -seed.nodes- is a -character- different from 'marginal', 'central', or 'random'.")

tests/testthat/test-rdiffnet-parameters.R

@@ -11,18 +11,18 @@ test_that(
   behavior <- c("random behavior")
   rdiffnet_args <- rdiffnet_validate_args(seed.p.adopt, seed.nodes, behavior)
 
-  class(rdiffnet_args$seed.p.adopt) == "list"
-  class(rdiffnet_args$seed.nodes) == "list"
-  class(rdiffnet_args$behavior) == "list"
+  expect_type(rdiffnet_args$seed.p.adopt, "list")
+  expect_type(rdiffnet_args$seed.nodes, "list")
+  expect_type(rdiffnet_args$behavior, "list")
 
   seed.p.adopt <- 0.14
   seed.nodes <- 'random'
   behavior <- "random behavior"
   rdiffnet_args <- rdiffnet_validate_args(seed.p.adopt, seed.nodes, behavior)
 
-  class(rdiffnet_args$seed.p.adopt) == "list"
-  class(rdiffnet_args$seed.nodes) == "list"
-  class(rdiffnet_args$behavior) == "list"
+  expect_type(rdiffnet_args$seed.p.adopt, "list")
+  expect_type(rdiffnet_args$seed.nodes, "list")
+  expect_type(rdiffnet_args$behavior, "list")
 
   # Must show ERROR
 
@@ -104,40 +104,42 @@ test_that("Multi diff models rdiff args work", {
   seed.nodes <- "random"
   behavior <- "random behavior"
   rdiffnet_args <- rdiffnet_validate_args(seed.p.adopt, seed.nodes, behavior)
+  expect_type(rdiffnet_args$seed.p.adopt, "list")
+  expect_type(rdiffnet_args$seed.nodes, "list")
+  expect_type(rdiffnet_args$behavior, "list")
 
   seed.nodes <- c(1,3,5)
   rdiffnet_args <- rdiffnet_validate_args(seed.p.adopt, seed.nodes, behavior)
+  expect_type(rdiffnet_args$seed.nodes, "list")
 
   seed.nodes <- c('marginal',"central")
   rdiffnet_args <- rdiffnet_validate_args(seed.p.adopt, seed.nodes, behavior)
+  expect_type(rdiffnet_args$seed.nodes, "list")
 
-  seed.p.adopt <- list(0.14,0.05)
-  seed.nodes <- list('random', "central")
   behavior <- list("random behavior_1", "random behavior_2")
   rdiffnet_args <- rdiffnet_validate_args(seed.p.adopt, seed.nodes, behavior)
-  class(rdiffnet_args$seed.p.adopt) == "list"
-  class(rdiffnet_args$seed.nodes) == "list"
-  class(rdiffnet_args$behavior) == "list"
+  expect_type(rdiffnet_args$behavior, "list")
 
   behavior <- c("random behavior_1", "random behavior_2")
   rdiffnet_args <- rdiffnet_validate_args(seed.p.adopt, seed.nodes, behavior)
-  class(rdiffnet_args$behavior) == "list"
+  expect_type(rdiffnet_args$behavior, "list")
 
   behavior <- "random behavior" #Default
   rdiffnet_args <- rdiffnet_validate_args(seed.p.adopt, seed.nodes, behavior)
-  class(rdiffnet_args$behavior) == "list"
+  expect_type(rdiffnet_args$behavior, "list")
+
+  behavior <- c("random behavior_1")
+  rdiffnet_args <- rdiffnet_validate_args(seed.p.adopt, seed.nodes, behavior)
+  expect_type(rdiffnet_args$behavior, "list")
 
   seed.nodes <- c(1,3,5)
   behavior <- list("random behavior_1", "random behavior_2")
   rdiffnet_args <- rdiffnet_validate_args(seed.p.adopt, seed.nodes, behavior)
-  class(rdiffnet_args$seed.nodes) == 'list'
+  expect_type(rdiffnet_args$seed.nodes, "list")
 
   seed.nodes <- list('marginal',"central")
   rdiffnet_args <- rdiffnet_validate_args(seed.p.adopt, seed.nodes, behavior)
-  class(rdiffnet_args$seed.nodes) == 'list'
-
-  behavior <- c("random behavior_1")
-  rdiffnet_args <- rdiffnet_validate_args(seed.p.adopt, seed.nodes, behavior)
+  expect_type(rdiffnet_args$seed.nodes, "list")
 
   # Must show ERROR
 

tests/testthat/test-rdiffnet.R

@@ -107,9 +107,35 @@ test_that("Simulation study", {
 
 })
 
-# Test for multi diffusion ---
+# Testing diffnet class across several inputs (single)
+test_that("rdiffnet must run across several inputs (single)", {
+  expect_s3_class(rdiffnet(100, 5), "diffnet")
+  expect_s3_class(rdiffnet(100, 5, seed.p.adopt = 0.1), "diffnet")
+  expect_s3_class(rdiffnet(100, 5, seed.p.adopt = 0.1, seed.nodes = 'random'), "diffnet")
+  expect_s3_class(rdiffnet(100, 5, seed.nodes = c(1, 3, 5)), "diffnet")
+
+  # summary
+  net_1 <- rdiffnet(100, 5, seed.nodes = c(1,3,5))
+  expect_s3_class(summary(net_1), "data.frame")
+})
+
+# Testing diffnet class across several inputs (multiple)
+test_that("rdiffnet must run across several inputs (multiple)", {
+  expect_s3_class(rdiffnet(100, 5, seed.p.adopt = list(0.1, 0.08)), "diffnet")
+  expect_s3_class(rdiffnet(100, 5, seed.p.adopt = list(0.1, 0.08), behavior = c('tabacco', 'alcohol')), "diffnet")
+  expect_s3_class(rdiffnet(100, 5, seed.p.adopt = list(0.1, 0.08), seed.nodes = 'random'), "diffnet")
+  expect_s3_class(rdiffnet(100, 5, seed.p.adopt = list(0.1, 0.08), seed.nodes = c('random', 'central')), "diffnet")
+  expect_s3_class(rdiffnet(100, 5, seed.p.adopt = list(0.1, 0.08), threshold.dist = 0.3), "diffnet")
+  expect_s3_class(rdiffnet(100, 5, seed.p.adopt = list(0.1, 0.08), threshold.dist = list(0.1, 0.2)), "diffnet")
+  expect_s3_class(rdiffnet(100, 5, seed.p.adopt = list(0.1, 0.08), threshold.dist = rexp(100)), "diffnet")
+  expect_s3_class(rdiffnet(100, 5, seed.p.adopt = list(0.1, 0.08), threshold.dist = list(rexp(100), runif(100))), "diffnet")
+  expect_s3_class(rdiffnet(100, 5, seed.p.adopt = list(0.1, 0.08), threshold.dist = function(x) 0.3), "diffnet")
+  expect_s3_class(rdiffnet(100, 5, seed.p.adopt = list(0.1, 0.08), threshold.dist = list(function(x) 0.3, function(x) 0.2)), "diffnet")
+
+  net_2 <- rdiffnet(100, 5, seed.p.adopt = list(0.05,0.05), seed.nodes = c(1,3,5))
+  expect_s3_class(summary(net_2), "data.frame")
+})
 
-# Seed of first adopters
 test_that("All should be equal! (multiple)", {
   set.seed(12131)
   n            <- 50
@@ -131,31 +157,6 @@ test_that("All should be equal! (multiple)", {
 })
 
 
-#single
-rdiffnet(100, 5)
-rdiffnet(100, 5, seed.p.adopt = 0.1)
-rdiffnet(100, 5, seed.p.adopt = 0.1, seed.nodes = 'random')
-rdiffnet(100, 5, seed.nodes = c(1,3,5))
-net_1 <- rdiffnet(100, 5, seed.nodes = c(1,3,5))
-summary(net_1)
-
-#multi
-rdiffnet(100, 5, seed.p.adopt = list(0.1,0.08))
-rdiffnet(100, 5, seed.p.adopt = list(0.1,0.08), behavior = c('tabacco', 'alcohol'))
-rdiffnet(100, 5, seed.p.adopt = list(0.1,0.08), seed.nodes = 'random')
-rdiffnet(100, 5, seed.p.adopt = list(0.1,0.08), seed.nodes = c('random', 'central'))
-rdiffnet(100, 5, seed.p.adopt = list(0.1,0.08), threshold.dist = 0.3)
-rdiffnet(100, 5, seed.p.adopt = list(0.1,0.08), threshold.dist = list(0.1,0.2))
-rdiffnet(100, 5, seed.p.adopt = list(0.1,0.08), threshold.dist = rexp(100))
-rdiffnet(100, 5, seed.p.adopt = list(0.1,0.08), threshold.dist = list(rexp(100),runif(100)))
-rdiffnet(100, 5, seed.p.adopt = list(0.1,0.08), threshold.dist = function(x) 0.3)
-rdiffnet(100, 5, seed.p.adopt = list(0.1,0.08), threshold.dist = list(function(x) 0.3, function(x) 0.2))
-
-net_1 <- rdiffnet(100, 5, seed.nodes = c(1,3,5))
-summary(net_1)
-net_2 <- rdiffnet(100, 5, seed.p.adopt = list(0.05,0.05), seed.nodes = c(1,3,5))
-summary(net_2)
-
 #rdiffnet(100, 5, seed.p.adopt = 0.9, threshold.dist = 2, exposure.args = list(normalized=FALSE))
 
 # set.seed(1234)