new function and updates

DESCRIPTION

@@ -1,13 +1,13 @@
 Package: daDoctoR
 Type: Package
 Title: FUNCTIONS FOR HEALTH RESEARCH
-Version: 0.1.0.9032
+Version: 0.1.0.9033
 Author: c(person("Andreas", "Gammelgaard Damsbo", email = "agdamsbo@pm.me", role = c("cre", "aut")))
 Maintainer: Andreas Gammelgaard Damsbo <agdamsbo@pm.me>
 Description: I am a Danish medical doctor involved in neuropsychiatric research. 
    Here I have collected functions I use for my data analysis. You are very 
    welcome to get inspired or to use my work.
-Imports: broom, dplyr, epiR, ggplot2, MASS, carData
+Imports: broom, dplyr, epiR, ggplot2, MASS, carData, eulerr
 Suggest: shiny
 License: GPL (>= 2)
 Encoding: UTF-8

NAMESPACE

@@ -9,6 +9,7 @@ export(cpr_check)
 export(cpr_sex)
 export(date_convert)
 export(dob_extract_cpr)
+export(euler_plot)
 export(hwe_allele)
 export(hwe_app)
 export(hwe_geno)

R/calculate_overlap.R

@@ -1,11 +1,11 @@
 #' Calculating overlap from list of identifier numbers
 #'
+#' To use with eulerr package for creating Euler/Venn-diagrams.
 #' Ex for creating euler diagram using the euler() function of the eulerr package.
-#' @param x Date of birth.
+#' Up to five (5) dimensions.
+#' @param x list of variables included. Has to be vectors of identifier numbers.
 #' @keywords overlap
 #' @export
-#' @examples
-#'
 
 calculate_overlap<-function (x)
 {

R/euler_plot.R

@@ -0,0 +1,213 @@
+#' Creates Euler model from list of identifier numbers.
+#'
+#' Calculates overlaps and uses eulerr package to create Euler/Venn-diagrams. Use plot() to create diagram.
+#' Combined with an evolved calculate.overlap() from the VennDiagram library.
+#' Up to five (5) dimensions. Limit set by the complexity of combinations. euler() supports more.
+#' @param x list of variables included. Has to be vectors of identifier numbers.
+#' @param shape same as for euler(). These includes c("circle","ellipse").
+#' @keywords overlap
+#' @export
+
+euler_plot<-function (x,shape)
+{
+  library(eulerr)
+  sh<-shape
+
+  if (1 == length(x)) {
+    overlap <- list("A"=x)
+  }
+  else if (2 == length(x)) {
+    overlap <- list("A" = x[[1]], "B" = x[[2]], "A&B" = intersect(x[[1]],
+                                                             x[[2]]))
+  }
+  else if (3 == length(x)) {
+    A <- x[[1]]
+    B <- x[[2]]
+    C <- x[[3]]
+    nab <- intersect(A, B)
+    nbc <- intersect(B, C)
+    nac <- intersect(A, C)
+    nabc <- intersect(nab, C)
+    a5 = nabc
+    a2 = nab[which(!nab %in% a5)]
+    a4 = nac[which(!nac %in% a5)]
+    a6 = nbc[which(!nbc %in% a5)]
+    a1 = A[which(!A %in% c(a2, a4, a5))]
+    a3 = B[which(!B %in% c(a2, a5, a6))]
+    a7 = C[which(!C %in% c(a4, a5, a6))]
+    overlap <- list("A" = a1,
+                    "B" = a3,
+                    "C" = a7,
+                    "A&B" = a2,
+                    "B&C" = a6,
+                    "A&C" = a4,
+                    "A&B&C" = a5)
+  }
+  else if (4 == length(x)) {
+    A <- x[[1]]
+    B <- x[[2]]
+    C <- x[[3]]
+    D <- x[[4]]
+    n12 <- intersect(A, B)
+    n13 <- intersect(A, C)
+    n14 <- intersect(A, D)
+    n23 <- intersect(B, C)
+    n24 <- intersect(B, D)
+    n34 <- intersect(C, D)
+    n123 <- intersect(n12, C)
+    n124 <- intersect(n12, D)
+    n134 <- intersect(n13, D)
+    n234 <- intersect(n23, D)
+    n1234 <- intersect(n123, D)
+    a6 = n1234
+    a12 = n123[which(!n123 %in% a6)]
+    a11 = n124[which(!n124 %in% a6)]
+    a5 = n134[which(!n134 %in% a6)]
+    a7 = n234[which(!n234 %in% a6)]
+    a15 = n12[which(!n12 %in% c(a6, a11, a12))]
+    a4 = n13[which(!n13 %in% c(a6, a5, a12))]
+    a10 = n14[which(!n14 %in% c(a6, a5, a11))]
+    a13 = n23[which(!n23 %in% c(a6, a7, a12))]
+    a8 = n24[which(!n24 %in% c(a6, a7, a11))]
+    a2 = n34[which(!n34 %in% c(a6, a5, a7))]
+    a9 = A[which(!A %in% c(a4, a5, a6, a10, a11, a12, a15))]
+    a14 = B[which(!B %in% c(a6, a7, a8, a11, a12, a13, a15))]
+    a1 = C[which(!C %in% c(a2, a4, a5, a6, a7, a12, a13))]
+    a3 = D[which(!D %in% c(a2, a5, a6, a7, a8, a10, a11))]
+    overlap <- list("A" = a9,
+                    "B" = a14,
+                    "C" = a1,
+                    "D" = a3,
+                    "A&B" = a15,
+                    "A&C" = a4,
+                    "A&D" = a10,
+                    "B&C" = a13,
+                    "B&D" = a8,
+                    "C&D" = a2,
+                    "A&B&C" = a12,
+                    "A&B&D" = a11,
+                    "A&C&D" = a5,
+                    "B&C&D" = a7,
+                    "A&B&C&D"= a6,
+                    a6 = a6, a12 = a12, a11 = a11, a5 = a5,
+                    a7 = a7, a15 = a15, a4 = a4, a10 = a10, a13 = a13,
+                    a8 = a8, a2 = a2, a9 = a9, a14 = a14, a1 = a1, a3 = a3,A=A,B=B,C=C,D=D)
+  }
+  else if (5 == length(x)) {
+    A <- x[[1]]
+    B <- x[[2]]
+    C <- x[[3]]
+    D <- x[[4]]
+    E <- x[[5]]
+    n12 <- intersect(A, B)
+    n13 <- intersect(A, C)
+    n14 <- intersect(A, D)
+    n15 <- intersect(A, E)
+    n23 <- intersect(B, C)
+    n24 <- intersect(B, D)
+    n25 <- intersect(B, E)
+    n34 <- intersect(C, D)
+    n35 <- intersect(C, E)
+    n45 <- intersect(D, E)
+    n123 <- intersect(n12, C)
+    n124 <- intersect(n12, D)
+    n125 <- intersect(n12, E)
+    n134 <- intersect(n13, D)
+    n135 <- intersect(n13, E)
+    n145 <- intersect(n14, E)
+    n234 <- intersect(n23, D)
+    n235 <- intersect(n23, E)
+    n245 <- intersect(n24, E)
+    n345 <- intersect(n34, E)
+    n1234 <- intersect(n123, D)
+    n1235 <- intersect(n123, E)
+    n1245 <- intersect(n124, E)
+    n1345 <- intersect(n134, E)
+    n2345 <- intersect(n234, E)
+    n12345 <- intersect(n1234, E)
+    a31 = n12345
+    a30 = n1234[which(!n1234 %in% a31)]
+    a29 = n1235[which(!n1235 %in% a31)]
+    a28 = n1245[which(!n1245 %in% a31)]
+    a27 = n1345[which(!n1345 %in% a31)]
+    a26 = n2345[which(!n2345 %in% a31)]
+    a25 = n245[which(!n245 %in% c(a26, a28, a31))]
+    a24 = n234[which(!n234 %in% c(a26, a30, a31))]
+    a23 = n134[which(!n134 %in% c(a27, a30, a31))]
+    a22 = n123[which(!n123 %in% c(a29, a30, a31))]
+    a21 = n235[which(!n235 %in% c(a26, a29, a31))]
+    a20 = n125[which(!n125 %in% c(a28, a29, a31))]
+    a19 = n124[which(!n124 %in% c(a28, a30, a31))]
+    a18 = n145[which(!n145 %in% c(a27, a28, a31))]
+    a17 = n135[which(!n135 %in% c(a27, a29, a31))]
+    a16 = n345[which(!n345 %in% c(a26, a27, a31))]
+    a15 = n45[which(!n45 %in% c(a18, a25, a16, a28, a27,
+                                a26, a31))]
+    a14 = n24[which(!n24 %in% c(a19, a24, a25, a30, a28,
+                                a26, a31))]
+    a13 = n34[which(!n34 %in% c(a16, a23, a24, a26, a27,
+                                a30, a31))]
+    a12 = n13[which(!n13 %in% c(a17, a22, a23, a27, a29,
+                                a30, a31))]
+    a11 = n23[which(!n23 %in% c(a21, a22, a24, a26, a29,
+                                a30, a31))]
+    a10 = n25[which(!n25 %in% c(a20, a21, a25, a26, a28,
+                                a29, a31))]
+    a9 = n12[which(!n12 %in% c(a19, a20, a22, a28, a29,
+                               a30, a31))]
+    a8 = n14[which(!n14 %in% c(a18, a19, a23, a27, a28,
+                               a30, a31))]
+    a7 = n15[which(!n15 %in% c(a17, a18, a20, a27, a28,
+                               a29, a31))]
+    a6 = n35[which(!n35 %in% c(a16, a17, a21, a26, a27,
+                               a29, a31))]
+    a5 = E[which(!E %in% c(a6, a7, a15, a16, a17, a18, a25,
+                           a26, a27, a28, a31, a20, a29, a21, a10))]
+    a4 = D[which(!D %in% c(a13, a14, a15, a16, a23, a24,
+                           a25, a26, a27, a28, a31, a18, a19, a8, a30))]
+    a3 = C[which(!C %in% c(a21, a11, a12, a13, a29, a22,
+                           a23, a24, a30, a31, a26, a27, a16, a6, a17))]
+    a2 = B[which(!B %in% c(a9, a10, a19, a20, a21, a11,
+                           a28, a29, a31, a22, a30, a26, a25, a24, a14))]
+    a1 = A[which(!A %in% c(a7, a8, a18, a17, a19, a9, a27,
+                           a28, a31, a20, a30, a29, a22, a23, a12))]
+    overlap <- list("A" = a1,
+                    "B" = a2,
+                    "C" = a3,
+                    "D" = a4,
+                    "E" = a5,
+                    "A&B" = a9,
+                    "A&C" = a12,
+                    "A&D" = a8,
+                    "A&E" = a7,
+                    "B&C" = a11,
+                    "B&D" = a14,
+                    "B&E" = a10,
+                    "C&D" = a13,
+                    "C&E" = a6,
+                    "D&E" = a15,
+                    "A&B&C" = a22,
+                    "A&B&D" = a19,
+                    "A&B&E" = a20,
+                    "A&C&D" = a23,
+                    "A&C&E" = a17,
+                    "A&D&E" = a18,
+                    "B&C&D" = a24,
+                    "B&C&E" = a21,
+                    "B&D&E" = a25,
+                    "C&D&E" = a16,
+                    "A&B&C&D"= a30,
+                    "A&B&C&E"= a29,
+                    "A&B&D&E"= a28,
+                    "A&C&D&E"= a27,
+                    "B&C&D&E"= a26,
+                    "A&B&C&D&E"= a31)
+  }
+  else {
+    flog.error("Invalid size of input object", name = "VennDiagramLogger")
+    stop("Invalid size of input object")
+  }
+  eul <- euler(unlist(overlap, use.names=T),shape = sh)
+  return(eul)
+}
+

man/calculate_overlap.Rd

@@ -7,12 +7,11 @@
 calculate_overlap(x)
 }
 \arguments{
-\item{x}{Date of birth.}
+\item{x}{list of variables included. Has to be vectors of identifier numbers.}
 }
 \description{
+To use with eulerr package for creating Euler/Venn-diagrams.
 Ex for creating euler diagram using the euler() function of the eulerr package.
-}
+Up to five (5) dimensions.
-\examples{
-
 }
 \keyword{overlap}

man/euler_plot.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/euler_plot.R
+\name{euler_plot}
+\alias{euler_plot}
+\title{Creates Euler model from list of identifier numbers.}
+\usage{
+euler_plot(x, shape)
+}
+\arguments{
+\item{x}{list of variables included. Has to be vectors of identifier numbers.}
+
+\item{shape}{same as for euler(). These includes c("circle","ellipse").}
+}
+\description{
+Calculates overlaps and uses eulerr package to create Euler/Venn-diagrams. Use plot() to create diagram.
+Combined with an evolved calculate.overlap() from the VennDiagram library.
+Up to five (5) dimensions. Limit set by the complexity of combinations. euler() supports more.
+}
+\keyword{overlap}