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new function and updates
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@ -1,13 +1,13 @@
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Package: daDoctoR
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Type: Package
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Title: FUNCTIONS FOR HEALTH RESEARCH
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Version: 0.1.0.9032
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Version: 0.1.0.9033
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Author: c(person("Andreas", "Gammelgaard Damsbo", email = "agdamsbo@pm.me", role = c("cre", "aut")))
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Maintainer: Andreas Gammelgaard Damsbo <agdamsbo@pm.me>
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Description: I am a Danish medical doctor involved in neuropsychiatric research.
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Here I have collected functions I use for my data analysis. You are very
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welcome to get inspired or to use my work.
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Imports: broom, dplyr, epiR, ggplot2, MASS, carData
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Imports: broom, dplyr, epiR, ggplot2, MASS, carData, eulerr
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Suggest: shiny
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License: GPL (>= 2)
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Encoding: UTF-8
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@ -9,6 +9,7 @@ export(cpr_check)
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export(cpr_sex)
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export(date_convert)
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export(dob_extract_cpr)
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export(euler_plot)
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export(hwe_allele)
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export(hwe_app)
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export(hwe_geno)
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@ -1,11 +1,11 @@
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#' Calculating overlap from list of identifier numbers
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#'
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#' To use with eulerr package for creating Euler/Venn-diagrams.
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#' Ex for creating euler diagram using the euler() function of the eulerr package.
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#' @param x Date of birth.
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#' Up to five (5) dimensions.
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#' @param x list of variables included. Has to be vectors of identifier numbers.
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#' @keywords overlap
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#' @export
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#' @examples
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#'
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calculate_overlap<-function (x)
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{
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213
R/euler_plot.R
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213
R/euler_plot.R
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#' Creates Euler model from list of identifier numbers.
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#'
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#' Calculates overlaps and uses eulerr package to create Euler/Venn-diagrams. Use plot() to create diagram.
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#' Combined with an evolved calculate.overlap() from the VennDiagram library.
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#' Up to five (5) dimensions. Limit set by the complexity of combinations. euler() supports more.
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#' @param x list of variables included. Has to be vectors of identifier numbers.
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#' @param shape same as for euler(). These includes c("circle","ellipse").
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#' @keywords overlap
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#' @export
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euler_plot<-function (x,shape)
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{
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library(eulerr)
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sh<-shape
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if (1 == length(x)) {
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overlap <- list("A"=x)
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}
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else if (2 == length(x)) {
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overlap <- list("A" = x[[1]], "B" = x[[2]], "A&B" = intersect(x[[1]],
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x[[2]]))
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}
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else if (3 == length(x)) {
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A <- x[[1]]
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B <- x[[2]]
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C <- x[[3]]
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nab <- intersect(A, B)
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nbc <- intersect(B, C)
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nac <- intersect(A, C)
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nabc <- intersect(nab, C)
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a5 = nabc
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a2 = nab[which(!nab %in% a5)]
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a4 = nac[which(!nac %in% a5)]
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a6 = nbc[which(!nbc %in% a5)]
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a1 = A[which(!A %in% c(a2, a4, a5))]
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a3 = B[which(!B %in% c(a2, a5, a6))]
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a7 = C[which(!C %in% c(a4, a5, a6))]
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overlap <- list("A" = a1,
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"B" = a3,
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"C" = a7,
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"A&B" = a2,
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"B&C" = a6,
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"A&C" = a4,
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"A&B&C" = a5)
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}
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else if (4 == length(x)) {
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A <- x[[1]]
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B <- x[[2]]
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C <- x[[3]]
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D <- x[[4]]
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n12 <- intersect(A, B)
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n13 <- intersect(A, C)
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n14 <- intersect(A, D)
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n23 <- intersect(B, C)
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n24 <- intersect(B, D)
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n34 <- intersect(C, D)
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n123 <- intersect(n12, C)
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n124 <- intersect(n12, D)
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n134 <- intersect(n13, D)
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n234 <- intersect(n23, D)
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n1234 <- intersect(n123, D)
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a6 = n1234
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a12 = n123[which(!n123 %in% a6)]
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a11 = n124[which(!n124 %in% a6)]
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a5 = n134[which(!n134 %in% a6)]
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a7 = n234[which(!n234 %in% a6)]
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a15 = n12[which(!n12 %in% c(a6, a11, a12))]
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a4 = n13[which(!n13 %in% c(a6, a5, a12))]
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a10 = n14[which(!n14 %in% c(a6, a5, a11))]
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a13 = n23[which(!n23 %in% c(a6, a7, a12))]
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a8 = n24[which(!n24 %in% c(a6, a7, a11))]
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a2 = n34[which(!n34 %in% c(a6, a5, a7))]
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a9 = A[which(!A %in% c(a4, a5, a6, a10, a11, a12, a15))]
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a14 = B[which(!B %in% c(a6, a7, a8, a11, a12, a13, a15))]
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a1 = C[which(!C %in% c(a2, a4, a5, a6, a7, a12, a13))]
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a3 = D[which(!D %in% c(a2, a5, a6, a7, a8, a10, a11))]
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overlap <- list("A" = a9,
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"B" = a14,
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"C" = a1,
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"D" = a3,
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"A&B" = a15,
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"A&C" = a4,
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"A&D" = a10,
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"B&C" = a13,
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"B&D" = a8,
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"C&D" = a2,
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"A&B&C" = a12,
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"A&B&D" = a11,
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"A&C&D" = a5,
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"B&C&D" = a7,
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"A&B&C&D"= a6,
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a6 = a6, a12 = a12, a11 = a11, a5 = a5,
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a7 = a7, a15 = a15, a4 = a4, a10 = a10, a13 = a13,
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a8 = a8, a2 = a2, a9 = a9, a14 = a14, a1 = a1, a3 = a3,A=A,B=B,C=C,D=D)
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}
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else if (5 == length(x)) {
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A <- x[[1]]
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B <- x[[2]]
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C <- x[[3]]
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D <- x[[4]]
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E <- x[[5]]
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n12 <- intersect(A, B)
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n13 <- intersect(A, C)
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n14 <- intersect(A, D)
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n15 <- intersect(A, E)
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n23 <- intersect(B, C)
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n24 <- intersect(B, D)
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n25 <- intersect(B, E)
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n34 <- intersect(C, D)
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n35 <- intersect(C, E)
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n45 <- intersect(D, E)
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n123 <- intersect(n12, C)
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n124 <- intersect(n12, D)
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n125 <- intersect(n12, E)
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n134 <- intersect(n13, D)
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n135 <- intersect(n13, E)
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n145 <- intersect(n14, E)
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n234 <- intersect(n23, D)
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n235 <- intersect(n23, E)
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n245 <- intersect(n24, E)
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n345 <- intersect(n34, E)
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n1234 <- intersect(n123, D)
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n1235 <- intersect(n123, E)
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n1245 <- intersect(n124, E)
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n1345 <- intersect(n134, E)
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n2345 <- intersect(n234, E)
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n12345 <- intersect(n1234, E)
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a31 = n12345
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a30 = n1234[which(!n1234 %in% a31)]
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a29 = n1235[which(!n1235 %in% a31)]
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a28 = n1245[which(!n1245 %in% a31)]
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a27 = n1345[which(!n1345 %in% a31)]
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a26 = n2345[which(!n2345 %in% a31)]
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a25 = n245[which(!n245 %in% c(a26, a28, a31))]
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a24 = n234[which(!n234 %in% c(a26, a30, a31))]
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a23 = n134[which(!n134 %in% c(a27, a30, a31))]
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a22 = n123[which(!n123 %in% c(a29, a30, a31))]
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a21 = n235[which(!n235 %in% c(a26, a29, a31))]
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a20 = n125[which(!n125 %in% c(a28, a29, a31))]
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a19 = n124[which(!n124 %in% c(a28, a30, a31))]
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a18 = n145[which(!n145 %in% c(a27, a28, a31))]
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a17 = n135[which(!n135 %in% c(a27, a29, a31))]
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a16 = n345[which(!n345 %in% c(a26, a27, a31))]
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a15 = n45[which(!n45 %in% c(a18, a25, a16, a28, a27,
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a26, a31))]
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a14 = n24[which(!n24 %in% c(a19, a24, a25, a30, a28,
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a26, a31))]
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a13 = n34[which(!n34 %in% c(a16, a23, a24, a26, a27,
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a30, a31))]
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a12 = n13[which(!n13 %in% c(a17, a22, a23, a27, a29,
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a30, a31))]
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a11 = n23[which(!n23 %in% c(a21, a22, a24, a26, a29,
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a30, a31))]
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a10 = n25[which(!n25 %in% c(a20, a21, a25, a26, a28,
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a29, a31))]
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a9 = n12[which(!n12 %in% c(a19, a20, a22, a28, a29,
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a30, a31))]
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a8 = n14[which(!n14 %in% c(a18, a19, a23, a27, a28,
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a30, a31))]
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a7 = n15[which(!n15 %in% c(a17, a18, a20, a27, a28,
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a29, a31))]
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a6 = n35[which(!n35 %in% c(a16, a17, a21, a26, a27,
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a29, a31))]
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a5 = E[which(!E %in% c(a6, a7, a15, a16, a17, a18, a25,
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a26, a27, a28, a31, a20, a29, a21, a10))]
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a4 = D[which(!D %in% c(a13, a14, a15, a16, a23, a24,
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a25, a26, a27, a28, a31, a18, a19, a8, a30))]
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a3 = C[which(!C %in% c(a21, a11, a12, a13, a29, a22,
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a23, a24, a30, a31, a26, a27, a16, a6, a17))]
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a2 = B[which(!B %in% c(a9, a10, a19, a20, a21, a11,
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a28, a29, a31, a22, a30, a26, a25, a24, a14))]
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a1 = A[which(!A %in% c(a7, a8, a18, a17, a19, a9, a27,
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a28, a31, a20, a30, a29, a22, a23, a12))]
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overlap <- list("A" = a1,
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"B" = a2,
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"C" = a3,
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"D" = a4,
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"E" = a5,
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"A&B" = a9,
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"A&C" = a12,
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"A&D" = a8,
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"A&E" = a7,
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"B&C" = a11,
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"B&D" = a14,
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"B&E" = a10,
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"C&D" = a13,
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"C&E" = a6,
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"D&E" = a15,
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"A&B&C" = a22,
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"A&B&D" = a19,
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"A&B&E" = a20,
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"A&C&D" = a23,
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"A&C&E" = a17,
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"A&D&E" = a18,
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"B&C&D" = a24,
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"B&C&E" = a21,
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"B&D&E" = a25,
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"C&D&E" = a16,
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"A&B&C&D"= a30,
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"A&B&C&E"= a29,
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"A&B&D&E"= a28,
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"A&C&D&E"= a27,
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"B&C&D&E"= a26,
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"A&B&C&D&E"= a31)
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}
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else {
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flog.error("Invalid size of input object", name = "VennDiagramLogger")
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stop("Invalid size of input object")
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}
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eul <- euler(unlist(overlap, use.names=T),shape = sh)
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return(eul)
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}
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@ -7,12 +7,11 @@
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calculate_overlap(x)
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}
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\arguments{
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\item{x}{Date of birth.}
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\item{x}{list of variables included. Has to be vectors of identifier numbers.}
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}
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\description{
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To use with eulerr package for creating Euler/Venn-diagrams.
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Ex for creating euler diagram using the euler() function of the eulerr package.
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}
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\examples{
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Up to five (5) dimensions.
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}
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\keyword{overlap}
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19
man/euler_plot.Rd
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19
man/euler_plot.Rd
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@ -0,0 +1,19 @@
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/euler_plot.R
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\name{euler_plot}
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\alias{euler_plot}
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\title{Creates Euler model from list of identifier numbers.}
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\usage{
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euler_plot(x, shape)
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}
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\arguments{
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\item{x}{list of variables included. Has to be vectors of identifier numbers.}
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\item{shape}{same as for euler(). These includes c("circle","ellipse").}
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}
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\description{
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Calculates overlaps and uses eulerr package to create Euler/Venn-diagrams. Use plot() to create diagram.
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Combined with an evolved calculate.overlap() from the VennDiagram library.
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Up to five (5) dimensions. Limit set by the complexity of combinations. euler() supports more.
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}
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\keyword{overlap}
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