Merge pull request #61 from jhollway/develop

* Renamed twomode_netlm() to netlm2()
* Fixed various printing issues with netlm2()
* Added tests for netlm2()
* Added tests for create_random()
* Added opensecrets data
* Added powerelite data

Author: jhollway

.Rbuildignore

@@ -2,3 +2,4 @@
 ^LICENSE\.md$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^working$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: roctopus
 Title: Utility functions for multimode and multilevel network analysis
-Version: 0.2.5
+Version: 0.2.6
 Description: This package assembles a number of utility functions for 
    loading, visualising, and analysing multimode, multiplex, and multilevel networks.
 URL: https://github.com/jhollway/roctopus

NAMESPACE

@@ -7,6 +7,7 @@ export(create_nest)
 export(create_poles)
 export(create_random)
 export(df_to_mat)
+export(netlm2)
 export(plot_2x2)
 export(plot_globalnet)
 export(plot_multilevel)
@@ -23,7 +24,6 @@ export(twomode_components)
 export(twomode_constraint)
 export(twomode_dominance)
 export(twomode_modularity)
-export(twomode_netlm)
 export(twomode_smallworld)
 import(geosphere)
 import(ggplot2)

NEWS.md

@@ -1,3 +1,22 @@
+# roctopus 0.2.6
+
+2020-08-18
+
+## Analysis
+
+* Renamed `twomode_netlm()` to `netlm2()`
+* Fixed various printing issues with `netlm2()`
+
+## Package
+
+* Added tests for `netlm2()`
+* Added tests for `create_random()`
+
+## Data
+
+* Added `opensecrets` data
+* Added `powerelite` data
+
 # roctopus 0.2.5
 
 2020-07-21

R/data_opensecrets.R

@@ -0,0 +1,23 @@
+#' Open Secrets
+#'
+#' This data is based on 26 elites who sat on the boards of directors 
+#' for at least two of six economic policy making organizations (Domhoff 2016),
+#' and also made campaign contributions to one or more of six candidates 
+#' running in the primary election contests for the 2008 Presidential nominations 
+#' of the Republican Party (Rudy Giuliani, John McCain, Mitt Romney) 
+#' or the Democratic Party (Hillary Clinton, Christopher Dodd, Barack Obama).
+#'
+#' @docType data
+#' @keywords datasets
+#' @name opensecrets
+#' @usage data(opensecrets)
+#' @format Matrix with 26 rows and 6+6 columns
+#' @source Domhoff, G William. 2016. 
+#' “Who Rules America? Power Elite Database.” http://www2.ucsc.edu/whorulesamerica/power_elite/.
+#' 
+#' The Center for Responsive Politics. 2019. “OpenSecrets.” http://www.opensecrets.org.
+#' 
+#' Knoke, Christopoulos, Diani, and Hollway. 2020. 
+#' \emph{Multimodal Political Networks: The Structural Perspective}. 
+#' Cambridge University Press: Cambridge.
+"opensecrets"

R/data_powerelite.R

@@ -0,0 +1,21 @@
+#' Power Elite
+#'
+#' A 2-mode network of persons serving as directors or trustees of think tanks. 
+#' Think tanks are “public-policy research analysis and engagement organizations 
+#' that generate policy-oriented research, analysis, and advice on domestic and international issues, 
+#' thereby enabling policymakers and the public to make informed decisions about public policy” (McGann 2016: 6). 
+#' The Power Elite Database (Domhoff 2016) includes information on the directors of 33 prominent think tanks in 2012. 
+#' Here we include only 14 directors who held three or more seats among 20 think tanks. 
+#'
+#' @docType data
+#' @keywords datasets
+#' @name powerelite
+#' @usage data(powerelite)
+#' @format Matrix with 14 rows and 20 columns
+#' @source Domhoff, G William. 2016. 
+#' “Who Rules America? Power Elite Database.” http://www2.ucsc.edu/whorulesamerica/power_elite/.
+#' 
+#' Knoke, Christopoulos, Diani, and Hollway. 2020. 
+#' \emph{Multimodal Political Networks: The Structural Perspective}. 
+#' Cambridge University Press: Cambridge.
+"powerelite"

R/mm_qap.R

@@ -9,12 +9,14 @@
 #' @export
 #' @examples
 #' \dontrun{
-#' twomode_netlm(matrix, list(matrix2, matrix3),
-#'               c("Intercept", "Explainer"))
+#' netlm2(matrix, list(matrix2, matrix3),
+#'               c("Explanatory Variable", "Control Variable"))
 #' }
-twomode_netlm <- function(DV, IV, names, rep = 1000){
+netlm2 <- function(DV, IV, names, rep = 1000){
 
-  # if(missing(names)) names <- c("Intercept", lapply(IV, function(x) names(x))
+  if(missing(names)){ 
+    names <- paste0("x", 1:length(IV))
+  }
   # Consider converting to formula
 
   rbperm <- function (m) {
@@ -50,15 +52,17 @@ twomode_netlm <- function(DV, IV, names, rep = 1000){
                                              ifelse(as.numeric(lapply(1:(nIV+1), 
                                                                       function(x) ecdf(permDist[,x])(M.coeff[x])))<0.001, 
                                                     "***", "**"), "*"), ""))
+  rownames(resTable) <- NULL
 print(resTable)
+# Turn this into a print function
 
   cat("\nMultiple R-squared: ", formatC(summary(M.fit)$r.squared),
       ",\tAdjusted R-squared: ", formatC(summary(M.fit)$adj.r.squared),
       "\n", sep="")
 
   obj <- list()
   obj$results <- data.frame(Effect = c("Intercept", names), 
-                            Coefficients = formatC(M.coeff, format="f", digits = 2),
+                            Coefficients = as.numeric(formatC(M.coeff, format="f", digits = 2)),
                             Pvalue = signif(as.numeric(lapply(1:(nIV+1), 
                                                            function(x) ecdf(permDist[,x])(M.coeff[x]))), 
                                          digits=2),
@@ -69,7 +73,8 @@ print(resTable)
                                                 ifelse(as.numeric(lapply(1:(nIV+1), 
                                                                          function(x) ecdf(permDist[,x])(M.coeff[x])))<0.001, 
                                                        "***", "**"), "*"), ""))
+  rownames(obj$results) <- NULL
   obj$r.squared <- formatC(summary(M.fit)$r.squared)
   obj$adj.r.squared <- formatC(summary(M.fit)$adj.r.squared)
-  return(obj)
+  invisible(obj)
 }

R/vis.R

@@ -102,10 +102,6 @@ plot_multilevel <- function(mat,levels=NULL){
        vertex.shape=c(rep("square",ncol(mat)),rep("circle",nrow(mat))),
        layout = f)
 
-  
-  
-  
-  
 }
 
 #' Plotting multilevel networks on a globe

data/opensecrets.rda

@@ -13,3 +13,7 @@ test_that("match creation works", {
 test_that("nest creation works", {
   expect_equal(create_nest(2,4), matrix(c(1,1,0,1,0,0,0,0),2,4))
 })
+
+test_that("random creation works", {
+  expect_false(isTRUE(all.equal(create_random(2,4,.3), create_random(2,4,.3))))
+})

data/powerelite.rda

@@ -0,0 +1,11 @@
+mat1 <- matrix(c(0,1,1,0,0,1,1,1),4,2)
+mat2 <- matrix(c(0,1,0,1,0,1,0,1),4,2)
+mat3 <- matrix(c(0,0,1,1,0,0,1,1),4,2)
+
+test_that("coefficients calculated correctly",{
+  expect_equal(netlm2(mat1, IV = list(mat2, mat3))$results$Coefficients, c(0.37, 0.25, 0.25), tolerance = .011)
+})
+
+test_that("p-values calculated correctly",{
+    expect_equal(netlm2(mat1, IV = list(mat2, mat3))$results$Pvalue, c(0.38, 0.84, 0.79), tolerance = .03)
+})

man/twomode_2x2.Rd

@@ -1,5 +1,3 @@
-devtools::install_bitbucket("jhollway/roctopus", auth_user = "jhollway", password = "VQaKN0TmGD8w")
-
 library(igraph)
 # pdf("~/Desktop/dombycoh.pdf", width=11, height=8)
 par(mfrow = c(2,3))