version 0.1.1

cran · Mar 13, 2017 · ebcc99d · ebcc99d
1 parent 79e62c1
commit ebcc99d
Show file tree

Hide file tree

Showing 7 changed files with 107 additions and 45 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,18 +1,17 @@
 Package: Conigrave
 Type: Package
 Title: Flexible Tools for Multiple Imputation
-Version: 0.1.0
-Date: 2016-06-10
+Version: 0.1.1
+Date: 2017-03-05
 Author: James Conigrave
 Maintainer: James Conigrave <james.conigrave@gmail.com>
 Description: Provides a set of tools that can be used across 'data.frame' and
     'imputationList' objects.
 License: GPL-3
 LazyData: TRUE
-Imports: ggplot2 (>= 2.1.0), mitools (>= 2.3), miceadds (>= 1.8-0),
-        stats (>= 3.3.0)
-RoxygenNote: 5.0.1
+Imports: ggplot2 (>= 2.1.0), mitools (>= 2.3), miceadds (>= 1.8-0)
+RoxygenNote: 6.0.1
 NeedsCompilation: no
-Packaged: 2016-06-16 05:04:12 UTC; James
+Packaged: 2017-03-13 03:40:03 UTC; s00183509
 Repository: CRAN
-Date/Publication: 2016-06-16 12:32:15
+Date/Publication: 2017-03-13 06:52:54
diff --git a/MD5 b/MD5
@@ -1,6 +1,6 @@
-4f2af9497484594cf28e03a687010a32 *DESCRIPTION
-5bc5cfa2d66a18afead16cf2ca3a2f26 *NAMESPACE
-0e2c63f8077a526d9e337ffe9fc9ac09 *R/Interaction.plot.R
-cce1cfe07170c70a92b59e08f09eabd2 *R/correlatrix.R
-b18ed39bbf7ac2e0c536684c7102a040 *man/correlatrix.Rd
-6e276ddf984c22b717c5a7fcbf9d6eac *man/int.plot.Rd
+68310b10856cab72d05d93c396a10555 *DESCRIPTION
+586163350489955f3267bdd031c8be0c *NAMESPACE
+59b24acfef4abd459869b8790e51f859 *R/Interaction.plot.R
+758d6a8c57ad0fe916a2d1a6e1fb857c *R/correlatrix.R
+b207704dea49e64605a1b1a3a8545aa0 *man/correlatrix.Rd
+703a82e2b8b328a852fdab381738ecbc *man/int.plot.Rd
diff --git a/NAMESPACE b/NAMESPACE
@@ -3,6 +3,8 @@
 export(correlatrix)
 export(int.plot)
 import(ggplot2)
-import(stats)
 importFrom(miceadds,micombine.cor)
 importFrom(mitools,MIcombine)
+importFrom(stats,cor.test)
+importFrom(stats,lm)
+importFrom(stats,na.omit)
diff --git a/R/Interaction.plot.R b/R/Interaction.plot.R
@@ -1,6 +1,6 @@
 #' Interaction plot
 #'
-#' Calculates a two way or three way interaction and plots using ggplot2
+#' Calculates a standardized two way or three way interaction and plots using ggplot2
 #' @param data an object of class 'data.frame' or 'imputationList'
 #' @param outcome a string with the name of the outcome variable
 #' @param predictor a string with the name of the predictor variable
@@ -24,6 +24,7 @@
 #' @export
 #' @import ggplot2
 #' @importFrom mitools MIcombine
+#' @importFrom stats cor.test lm na.omit
 #' @return An interaction plot
 
 ################################################################################
@@ -131,8 +132,7 @@ int.plot <- function(data, outcome, predictor, moderator, y.lim = c(-1,1),
                         theme(panel.grid.major=element_blank(),
                               panel.grid.minor=element_blank(),
                               panel.border=element_blank(),
-                              axis.line.x=element_line(),
-                              axis.line.y=element_line())
+                              axis.line=element_line())
 
         ##create dataset for ggplot
         colnames<-c(outcome, predictor, moderator)

diff --git a/R/correlatrix.R b/R/correlatrix.R
@@ -1,35 +1,40 @@
 #' Correlatrix
 #'
-#' Takes in a data.frame or imputationList, a vector of collumn names and produces a correlation matrix
+#' Takes in a data.frame or imputationList, a vector of variable names and produces a correlation matrix
 #' @param data an object of class 'data.frame' or 'imputationList'
-#' @param var.names a vector of collumn names
+#' @param var.names a vector of variable names
+#' @param triangle a string containing one of "lower" "upper" or "both". Indicates if correlations are to be displayed above or below the diagonal. "Both" is selected by default.
 #' @param round a numeral indicating number of decimals
 #' @param method a string containing one of "pearson","spearman" or "kendall"
 #' @param n.matrix logical. If TRUE, matrix of n returned
-#' @param name.max a number indicating the maximum length of variable names
+#' @param abbreviate a number indicating the maximum length of variable names
 #' @examples carsdata<-mtcars
-#' correlatrix(carsdata,names(carsdata),round = 2)
+#' correlatrix(carsdata,names(carsdata)[1:6],round = 2)
 #' correlatrix(carsdata,c("mpg","cyl","disp"))
 #' @export
-#' @import stats
+#' @importFrom stats na.omit cor.test
 #' @importFrom miceadds micombine.cor
 #' @return A correlation matrix
 
-correlatrix <- function(data, var.names, round=3, method = "pearson", n.matrix = F,
-                        name.max = 100){
+correlatrix <- function(data, var.names, triangle = "both", round = 3, method = "pearson", n.matrix = F,
+                        abbreviate = 100){
+##check arguments
+        if(!(triangle %in% c("lower","upper","both"))){
+                stop(paste("Check help file: triangle may not be equal to", triangle))
+        }
+
+
         specify_decimal <- function(x, k) format(round(x, k), nsmall=k)
 
-        result.matrix<-matrix(ncol=length(var.names)+1,nrow=length(var.names)*1)
+        result.matrix<-matrix(ncol=length(var.names),nrow=length(var.names)*1)
         result.matrix<-data.frame(result.matrix)
-        names(result.matrix)<-c("Vars",1:length(var.names))
-        ###create row names
-        for(i in 1:length(var.names)){
-                        result.matrix[i*+1,1]<-substr(var.names[i],1,name.max)
-        }
+
+   ###results
         for (c in 1:length(var.names)){#collumn loop start
                 for (r in 1:length(var.names)){#row loop start{
+                        ###result
                         if(c<r){
-
+                        ##get result
                                 if(class(data) == "data.frame"){
                                 cor.result<-cor.test(as.numeric(data[,var.names[c]]),as.numeric(data[,var.names[r]]),method = method)
                                 result<-cor.result$estimate
@@ -44,7 +49,28 @@ correlatrix <- function(data, var.names, round=3, method = "pearson", n.matrix =
                         }else{
                           result = " "
                           p = 1
-                          }
+                        }
+                        ### place result in data.frame
+                        if(triangle == "upper"){
+                                if(r<c){
+
+                                        if(class(data) == "data.frame"){
+                                                cor.result<-cor.test(as.numeric(data[,var.names[c]]),as.numeric(data[,var.names[r]]),method = method)
+                                                result<-cor.result$estimate
+                                                p<-cor.result$p.value }
+
+                                        if(class(data) == "imputationList"){
+                                                cor.result<-micombine.cor(data,c(var.names[c],var.names[r]), method = method)
+                                                result<-cor.result$r[1]
+                                                p<-cor.result$p[1]}
+
+                                        result<-specify_decimal(result,round)
+                                }else{
+                                        result = " "
+                                        p = 1
+                                }
+                        }
+
                         result.final<-result##add significance stars
 
 
@@ -53,6 +79,8 @@ correlatrix <- function(data, var.names, round=3, method = "pearson", n.matrix =
                                 result.final<-paste(result,"*",sep="")}
                         if(p<0.01){
                                 result.final<-paste(result,"**",sep="")}
+                        if(p<0.001){
+                                result.final<-paste(result,"***",sep="")}
 
                         if(n.matrix == T){
                                         if(class(data) == "data.frame"){
@@ -62,24 +90,57 @@ correlatrix <- function(data, var.names, round=3, method = "pearson", n.matrix =
                                         }
 
                         result.final <- length(na.omit(cor.data[,var.names[c]][is.na(cor.data[,var.names[r]])==F]))
+                        }
+
+                if(triangle == "lower"){
+                        if(c<r){
+                        result.matrix[r,c]<-result.final
+                        }
+                        if(c>r){
+                                result.matrix[r,c]<-" "
+                        }
+                        names(result.matrix)<-1:length(var.names)
+                        for(r in seq_along(var.names)){
+                                row.names(result.matrix)[r] <- paste(r,".",abbreviate(var.names[r],abbreviate), sep = "")
                                 }
 
-                        result.matrix[r,c+1]<-result.final
+                        }
+
+                if(triangle == "upper"){
                         if(c>r){
-                                result.matrix[r,c+1]<-" "
+                                result.matrix[r,c]<-result.final
+                        }
+                        if(c<r){
+                                result.matrix[r,c]<-" "
                         }
+                        names(result.matrix)<-1:length(var.names)
+                        for(r in seq_along(var.names)){
+                                row.names(result.matrix)[r] <- paste(r,".",abbreviate(var.names[r],abbreviate), sep = "")
+                        }
+                }
+
+                if(triangle == "both"){
+                        if(c<r){
+                                result.matrix[r,c]<-result.final
+                                result.matrix[c,r]<-result.final
+                        }
+                        ###collumn and row names
+                        names(result.matrix) <- as.vector(lapply(var.names, function(x) abbreviate(x,abbreviate)))
+                        row.names(result.matrix) <- as.vector(lapply(var.names, function(x) abbreviate(x,abbreviate)))
+                }
+
 
                         #leave diagonal blank
                         for(b in 1:length(var.names)){
-                                result.matrix[b,b+1]<-"-"
+                                result.matrix[b,b]<-"-"
                         }#diagonal loop end
                 }#row loop end
         }#collumn loop end
 
         if(n.matrix == T){
         message("n.matrix == T, therefore matrix of n returned.")
                 }else{
-        message("signif at 0.05*; signif at 0.01**")
+        message("signif at 0.05*; signif at 0.01**; signif at 0.001***")
                 }
         return(result.matrix)
 }

diff --git a/man/correlatrix.Rd b/man/correlatrix.Rd
diff --git a/man/int.plot.Rd b/man/int.plot.Rd