initial, not working, placeholder

shinyApp/README.md

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+# shinytw2
+
+Shiny App for TW2 
+https://github.com/alekseyenko/Tw2
+

shinyApp/Tw2copy.R

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+is.dist = function(x) any(class(x)=='dist')
+
+WT.mean = function(dm, f){
+  if(nlevels(f) != 2) return(NULL)
+  lev = levels(f)
+  ns = summary(f)
+  N = sum(ns)
+  dd = as.matrix(dm)
+  dd[upper.tri(dd)]=0 ##
+  SST = sum(dd^2)/N
+  SSW1 = sum(dd[f==lev[1],f==lev[1]]^2)/ns[1] 
+  SSW2 = sum(dd[f==lev[2],f==lev[2]]^2)/ns[2]
+  SSW = SSW1 + SSW2
+
+  (sqrt((ns[1]+ns[2])/(ns[1]*ns[2])))*sqrt(SST-SSW)
+}
+
+
+dist.sigma2 = function(dm){
+  dd = as.matrix(dm)
+  dd[upper.tri(dd)]=0 ##
+  sum(dd^2)/nrow(dm)/(nrow(dm)-1) 
+}
+
+dist.cohen.d = function(dm, f){
+  mean.diff = sqrt(WT.mean(dm, f))
+  lev = levels(f)
+  s1 = dist.sigma2(as.matrix(dm)[f==lev[1], f == lev[1]])
+  s2 = dist.sigma2(as.matrix(dm)[f==lev[1], f == lev[1]])
+  ns=table(f)
+  mean.diff/sqrt(((ns[1]-1)*s1 + (ns[2]-1)*s2)/(sum(ns)-2))
+}
+
+# dist.cohen.d.strata = function(dm, f, strata){
+#   p = unlist(tapply(f,strata,sample))
+#   p2 = unlist(tapply(1:length(f), strata, identity))
+#   # mean.diff = sqrt(WT.mean(dm, f))
+#   mean.diff.strata = sqrt(WT.mean(dm, f[p[p2]]))
+#   lev = levels(f)
+#   s1 = dist.sigma2(as.matrix(dm)[f==lev[1], f == lev[1]])
+#   s2 = dist.sigma2(as.matrix(dm)[f==lev[1], f == lev[1]])
+#   ns=table(f)
+#   mean.diff.strata/sqrt(((ns[1]-1)*s1 + (ns[2]-1)*s2)/(sum(ns)-2))
+# }
+
+WT = function(dm, f){
+  if(nlevels(f) != 2) return(NULL)
+  lev = levels(f)
+  ns = summary(f)
+  N = sum(ns)
+  dd = as.matrix(dm)
+  dd[upper.tri(dd)]=0 ##
+  SST = sum(dd^2)/N
+  SSW1 = sum(dd[f==lev[1],f==lev[1]]^2)/ns[1] 
+  SSW2 = sum(dd[f==lev[2],f==lev[2]]^2)/ns[2]
+  SSW = SSW1 + SSW2
+
+  s1 = SSW1/(ns[1]-1)
+  s2 = SSW2/(ns[2]-1)
+
+  t.stat = (sqrt((ns[1]+ns[2])/(ns[1]*ns[2])))*sqrt(SST-SSW)/sqrt(s1/ns[1] + s2/ns[2])
+  if(is.na(t.stat)){ ## SST - SSW must be negative
+    t.stat = 0
+  }
+  t.stat
+}
+
+# WT.test = function(dm, f, nrep=999){
+#   stats = c(WT(dm, f), replicate(nrep, WT(dm, f[sample(length(f))])))
+#   p.value = sum(stats>=stats[1])/(nrep+1)
+#   t.stat = stats[1]
+#   list(p.value = p.value, t.stat = t.stat, nrep=nrep)  
+# }
+
+strata.permute = function(f, strata){
+  p = unlist(tapply(f,strata,sample)) 
+  p2 = unlist(tapply(1:length(f), strata, identity))
+  f[p[p2]]
+}
+
+WT.test = function(dm, f, strata, nrep=999){
+  stats = c(WT(dm, f), 
+            replicate(nrep,
+                      WT(dm, strata.permute(f, strata))
+                      )
+            )
+  p.value = sum(stats>=stats[1])/(nrep+1)
+  t.stat = stats[1]
+  list(p.value = p.value, t.stat = t.stat, nrep=nrep)  
+}
+
+#Wstar.test=function(dm, f, nrep=999){ 
+  ## This method is not currently implemented. 
+  ## The function is provided as a placeholder.
+#  list(p.value = 1, Wstar = "Unimplemented", nrep=nrep)
+#}

shinyApp/data/sample_data.csv

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+"","id_full","id","TreatmentGroup","trimester3_1","ethnicity_all","ethnicity_HispVSNonhisp","ethnicity_CaucVSAA","ethnicity_CaucVSHisp","bmi_class_all","bmi_normalvsow","bmi_normalvsobese","parity_all","parity_0vs1","parity_0vs2","iom_weight"
+"1","5248-1",5248,"early",0,"Cau","non-Hispanic","Caucasian","Caucasian","underweight/normal","underweight/normal","underweight/normal","1","one previous birth",NA,"inadequate weight gain"
+"2","5248-2",5248,"late",1,"Cau","non-Hispanic","Caucasian","Caucasian","underweight/normal","underweight/normal","underweight/normal","1","one previous birth",NA,"inadequate weight gain"
+"3","5278-1",5278,"early",0,"Cau","non-Hispanic","Caucasian","Caucasian","overweight","overweight",NA,"0","no previous births","no previous births","excessive weight gain"
+"4","5278-2",5278,"late",1,"Cau","non-Hispanic","Caucasian","Caucasian","overweight","overweight",NA,"0","no previous births","no previous births","excessive weight gain"
+"5","5285-1",5285,"early",0,"Cau","non-Hispanic","Caucasian","Caucasian","underweight/normal","underweight/normal","underweight/normal","2+",NA,"two or more previous birth","inadequate weight gain"
+"6","5285-2",5285,"late",1,"Cau","non-Hispanic","Caucasian","Caucasian","underweight/normal","underweight/normal","underweight/normal","2+",NA,"two or more previous birth","inadequate weight gain"
+"9","5294-1",5294,"early",0,"Cau","non-Hispanic","Caucasian","Caucasian","obese",NA,"obese","1","one previous birth",NA,"inadequate weight gain"
+"10","5294-2",5294,"late",1,"Cau","non-Hispanic","Caucasian","Caucasian","obese",NA,"obese","1","one previous birth",NA,"inadequate weight gain"
+"11","5301-1",5301,"early",0,"Hisp","Hispanic",NA,"Hispanic","underweight/normal","underweight/normal","underweight/normal","1","one previous birth",NA,"inadequate weight gain"
+"12","5301-2",5301,"late",1,"Hisp","Hispanic",NA,"Hispanic","underweight/normal","underweight/normal","underweight/normal","1","one previous birth",NA,"inadequate weight gain"

shinyApp/global.R

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+library(phyloseq)
+library(tidyverse)
+library(shiny)
+library(shinydashboard)
+library(shinyjs)
+library(DT)
+
+#source("https://raw.githubusercontent.com/alekseyenko/Tw2/master/code/Tw2.R")
+source("Tw2copy.R")
+
+distance_choices <- phyloseq::distanceMethodList
+

shinyApp/install.R

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+source("https://raw.githubusercontent.com/joey711/phyloseq/master/inst/scripts/installer.R",
+local = TRUE)