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app.R
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app.R
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#STABLE-test
graphics.off()
rm(list = ls())
#check if packages are installed, and if not install them
if (!require("shiny")) install.packages("shiny")
if (!require("shinyWidgets")) install.packages("shinyWidgets")
if (!require("shinyjs")) install.packages("shinyjs")
if (!require("shinyBS")) install.packages("shinyBS")
if (!require("dplyr")) install.packages("dplyr")
if (!require("stringr")) install.packages("stringr")
if (!require("DT")) install.packages("DT")
if (!require("xpose4")) install.packages("xpose4")
if (!require("gsubfn")) install.packages("gsubfn")
if (!require("ggplot2")) install.packages("ggplot2")
if (!require("future")) install.packages("future")
if (!require("pkga")){
if (!require("devtools")) install.packages("devtools")
library(devtools)
install("pkga")
library(pkga)
}
#Set plot theme
theme_set(theme_bw())
# InitiateSCM <- function (path,control=NULL,alltokens=NULL,allmods=NULL){
# results_dir <- "SCM"
# i=1
# if(dir.exists(results_dir)){
# while(dir.exists(results_dir)){
# results_dir<- paste0("SCM(",i,")")
# if(suppressWarnings(dir.create(results_dir))){
# break
# }
# i = i+1
# }
# }else{
# suppressWarnings(dir.create(results_dir))
# }
#
# copyTo<- paste0(results_dir,"/Base")
# dir.create(copyTo)
# CheckThenCreate(path,control,alltokens,allmods)
# CopyModel(path,copyTo,control,alltokens,allmods)
# # homepath <-getwd()
# # relpath <- path
# #
# # RunModel(paste0(homepath,'/',relpath),basename(relpath))
# #
# #
# #
# # write.csv(data.frame(Generation=1,Inidvidual=pop,Dir=popmods), "GAgens.csv",row.names=F)
# }
# UI ----------------------------------------------------------------------
ui <- fluidPage(
useShinyjs(),
div("NMGA", class = "title-bar"),
column(12,
span(icon("plus", "fa-2x"),
id = "newproj",
class = c("nav-bar-el")),
span(icon("save", "fa-2x"),
id = "saveproj",
class = c("nav-bar-el")),
span(icon("folder-open", "fa-2x"),
id = "dir",
class = c("nav-bar-el")),
span("Directory",
id = "proj",
class = c("nav-bar-el")),
span(actionButton("viewmod", "View Models",
class = "nav-bar-button")),
span(actionButton("openGA", "Genetic Algorithm",
class = "nav-bar-button")),
span(actionButton("GAsettings",
icon("gear", "fa-2x"),
class = "nav-bar-button")),
span(actionButton("openSCM",
"SCM",
class = "nav-bar-button")),
span(actionButton("SCMsettings",
icon("gear", "fa-2x"),
class = "nav-bar-button")),
span(actionButton("StopRun", "Stop Run",
icon("stop-circle", "fa-2x"),
class="nav-bar-button",
style = "display: none;")), ## need a way to stop run, need pause as well?
span(actionButton("PauseRun",
"Pause Run",
icon("pause-circle", "fa-2x"),
class="nav-bar-button",
style = "display: none;")), ## need a way to stop run, need pause as well?
span(actionButton("ResumeRun",
"Resume Run",
icon("play-circle", "fa-2x"),
class="nav-bar-button",
style = "display: none;")),
div(id = "new_project_div", style = "display: none;",
span(h2("Control Stream",
class = "nav-bar-button"),
actionButton("select_ctl",
"Select Control Stream",
class = "nav-bar-button"),
class="nav-bar-el"),
span(h2("Control Stream",
class="nav-bar-button"),
actionButton("select_ctl",
"Select Control Stream",
class = "nav-bar-button"),
class = "nav-bar-el")),
class = "nav-bar"),
column(6,
tabsetPanel(id = "tabs", tabPanel("Control Stream",
textAreaInput("ace",
label = NULL,
width = "100%",
cols = NULL,
value = "Select a directory with a single .ctl file")),
tabPanel("Preview",
textAreaInput("previewtext",
label = NULL,
width = "100%",
cols = NULL,
value = "")),
tabPanel("Data",
DT::dataTableOutput("data")))),
column(6,
column(12,
align = "center",
radioGroupButtons("tokentype",
NULL,
choices = c("Covariate",
"ETA",
"EPS",
"Structure",
"Initials",
"Custom"),
selected = NULL)),
column(12,
column(4,
awesomeRadio(inputId = "tokengroupinput",
"Token Group",
choices = c("")),
actionButton("deletetokengroup",
"Delete",
style="background-color: #b71616; color: white;")
),
column(4,
awesomeRadio(inputId = "tokensetinput",
"Token Set",
choices = c("")),
actionButton("preview",
"Preview"),
actionButton("deletetokenset",
"Delete",
style="background-color: #b71616; color: white;")
),
column(4,
awesomeRadio(inputId = "tokeninput",
"Token",
choices = c(""))
),
column(12,
div(id = "tokenedit"
),
div(id = "Covariate",
class = "tokentype",
selectizeInput(
"cov",
"Select Covariate",
NULL,
selected = NULL,
multiple = F,
options = list(maxOptions =
100, create = T)
),
checkboxGroupButtons("covtypes",
"Select Covariate relationships",
choices = c("None",
"Linear",
"Power",
"Exponential",
"Proportional") ),
column(6,
materialSwitch(inputId = "center",
label = "Center Covariate (Median)",
status = "success"),
actionButton("addcovs",
"Add Selected Token Sets")),
column(6,
"Required {Token Group} in:",
HTML("<h4 id='covrequiredpk'>$PK</h4>
<h4 id='covrequiredtheta'>$THETA</h4>"),
class="required-holder")
),
div(id = "ETA",
class = "tokentype",
column(6,
checkboxGroupButtons("etatypes",
"Select IIV relationships",
choices = c("None",
"Normal",
"Logarithmic",
"Normal (Proportional)") ),
actionButton("addetas",
"Add Selected Token Sets")),
column(6,
"Required {Token Group} in:",
HTML("<h4 id='etarequiredpk'>$PK</h4>
<h4 id='etarequiredomega'>$OMEGA</h4>"),
class="required-holder")
),
div(id = "EPS",
class = "tokentype",
checkboxGroupButtons("epstypes",
"Select Residual Error Models",
choices = c("Additive",
"Proportional",
"Additive+Proportional") ),
actionButton("addeps",
"Add Selected Token Sets")
),
div(id = "Initials",
class = "tokentype",
column(6,
numericInput("init_from",
"From",
value = 0 ),
numericInput("init_to",
"To",
value = 100 ),
selectInput("init_num",
"Number of Initial Estimates",
choices = 2:10),
actionButton("addinitial",
"Add Selected Token Sets"))
),
div(id = "Structure",
class = "tokentype",
radioGroupButtons("strtypes",
"Select Structural Component",
choices= c("Compartments",
"Tlag",
"Michaelis-Menten") ),
fluidRow(column(5,
selectizeInput(
"selectcmt",
"Select Compartment",
NULL,
selected = NULL,
multiple = F,
options = list(maxOptions =
100, create = T)
),
radioGroupButtons("ncmt",
"Additional Compartments",
choices= c("1", "2", "3") ),
actionButton("addstr",
"Add Selected Token Sets")))
),
div(id = "Custom",
class = "tokentype",
actionButton("addcustom",
"Add Blank Token Set")
))), class = "token-div-holder"
),
includeScript("www/jquery.highlighttextarea.js"),
includeScript("www/drag.js"),
includeCSS("www/style.css"),
includeCSS("www/jquery.highlighttextarea.min.css"),
# Add tooltips ------------------------------------------------------------
bsTooltip(id = "dir", title = "Load Project"),
bsTooltip(id = "saveproj", title = "Save Project"),
bsTooltip(id = "proj", title = "Open in directory in File Explorer"),
bsTooltip(id = "GAsettings", title = "Genetic Algorithm Settings"),
bsTooltip(id = "SCMsettings", title = "SCM Settings"),
bsTooltip(id = "deletetokengroup", title = "Delete selected token group"),
bsTooltip(id = "preview", title = "Preview control stream with selected token set"),
bsTooltip(id = "deletetokenset", title = "Delete selected token set")
)
# Server ------------------------------------------------------------------
server <- function(input, output,session) {
# Create a new project
onclick("newproj",{
toggle("new_project_div")
})
#these varaibles are used to trigger next generation when no more model tasks are found to be running
invalidate <- reactiveValues(nextGA = 1,
future = 1)
#copy model to new directory when dragged
observe({
if(!is.null(input$draggedfile[1])){
copyTo <- paste0("models/", input$draggedfile[1])
CopyModel(input$draggedfile[2], copyTo, control = input$ace,
alltokens = alltokens, allmods = allmods)
}
}, suspended = F)
# Define globals
status <- reactiveValues(GA_running = F,
GA_paused = T,
SCM_running = F)
alltokens <- data.frame(tokengroup = character(0),
tokenset = character(0),
token = character(0),
stringsAsFactors = FALSE)
GAProgress <- data.frame (Generation = numeric(0),
Fitness = numeric(0))
f <- NULL
summary <- data.frame(Generation = numeric(), meanfit = numeric(), minfit = numeric())
onclick("dir", {
directory <- choose.dir("M:\\Users\\mhismail-shared\\Rprogramming\\genetic algorithm\\")
if (is.na(directory)){
directory <- getwd()
}
setwd(directory)
if(length(list.files(pattern = ".*.ctl"))>0){
updateTextAreaInput(session,
inputId = "ace",
value = paste(readLines(list.files(pattern = ".*.ctl")[1]),
collapse = "\n"))
updateTextAreaInput(session,
inputId = "preview",
value = paste(readLines(list.files(pattern = ".*.ctl")[1]),
collapse = "\n"))
}
if (file.exists("alltokens.csv")){
alltokens <- read.csv("alltokens.csv", as.is = T, stringsAsFactors = F)
}
if (file.exists("Allmodsresults.csv.gz")){
zz <- gzfile('Allmodsresults.csv.gz')
allmods <<- read.csv(zz, stringsAsFactors = F, as.is = T)[-1:-9] #model phenotypes
}
if (file.exists("GA_results.csv")){
summary <- read.csv("GA_results.csv", stringsAsFactors = F, as.is = T)
}
runjs({
paste("$('#proj').text('Current Directory:", basename(directory), "')")
})
})
onclick("proj",{
shell(gsub("/", "\\\\", paste("explorer", getwd())))
}
)
# Saving and loading projects ---------------------------------------------
# Save project on click ---------------------------------------------------
onclick("saveproj",{
write.csv(alltokens, "alltokens.csv", row.names = F)
writeLines(input$ace, list.files(pattern = ".*.ctl")[1])
})
# Hide compartment numbers if Compartments isnt selected ------------------
observe({
if(input$strtypes != "Compartments"){
hide("selectcmt")
hide("ncmt")
}else(show("ncmt"))
})
# END ---------------------------------------------------------
# Parsing control stream --------------------------------------------------
observe({
x <- input$ace
# Parse for tokens inside {} and add to tokengroupinput UI
# choices is tokens found in control stream
# choices2 is tokens found nested in other tokens
choices <- gsub("\\{|:(.*)|\\}", "",
regmatches(x, gregexpr("\\{.*?\\}", x))[[1]])
choices2 <- gsub("\\{|:(.*)|\\}", "",
regmatches(toString(alltokens$token),
gregexpr("\\{.*?\\}",
toString(alltokens$token)))[[1]])
choices <- unique(c(choices, choices2))
if(length(choices) == 0){choices = c("")}
updateAwesomeRadio(session,
inputId = "tokengroupinput",
choices = choices, selected = choices[1])
# Parse control stream, search for "$INPUT", set covariate choices --------
# Choices will be words following $INPUT, filtering out NONMEM reserved ---
a <- strsplit(x, "\n")[[1]]
if(length(strsplit(a[startsWith(a, "$INPUT")], "\\s+")) > 0){
covlist <- strsplit(a[startsWith(a, "$INPUT")], "\\s+")[[1]][-1]
covlist <- covlist[!(covlist %in% c("DATE=DROP", "DATE", "RATE",
"CMT", "ID", "TIME", "AMT",
"SS", "ADDL", "II", "DV",
"MDV", "EVID", "DUR"))]
updateSelectizeInput(session,
"cov",
choices = covlist)
}
# Parse control stream for compartments present
b <- gsub(".*\\$MODEL(.*?)\\$.*", "\\1", x)
c <- regmatches(b, gregexpr("COMP.*\\(.*?\\)", b))[[1]]
d <- gsub(".*\\((.*)\\).*", "\\1", c)
e <- gsub("\\,", "", d)
updateSelectizeInput(session, "selectcmt", choices = e)
}, priority = 100)
# END ---------------------------------------------------------------------
# Parse control stream to see if required tokens are present and --------
# change UI accordingly by adding/removie css class ---------------
observe({
x <- input$ace
#check if required tokens are present
selectedtokengroup <- paste0("\\{", input$tokengroupinput, "\\}")
selectedtokengroupnumbered <- paste0("\\{", input$tokengroupinput, ":[0-9]\\}")
numberedtokengroups <- as.numeric(gsub(paste0("\\{",
selectedtokengroup,
":|\\}"),
"",
regmatches(x,
gregexpr(paste0("\\{",
selectedtokengroup,
":([0-9])\\}"), x))[[1]]))
for (k in numberedtokengroups){
x<- gsub(paste0("\\{", selectedtokengroup, ":", k, "\\}"), tokenlist[k], x)
}
PKblock <- gsub(".*\\$PK(.*?)[(\\$.*)$]", "\\1", x) # Text between $PK and next $
THETAblock <- gsub(".*\\$THETA(.*?)[(\\$.*)$]", "\\1", x) # Text betwen $THETA and $
OMEGAblock <- gsub(".*\\$OMEGA(.*?)[(\\$.*)$]", "\\1", x) # Text betwen $OMEGA and $
if(grepl(selectedtokengroup, PKblock)|grepl(selectedtokengroupnumbered, PKblock)){
removeClass("covrequiredpk", "red")
addClass("covrequiredpk", "green")
}else{
removeClass("covrequiredpk", "green")
addClass("covrequiredpk", "red")}
if(grepl(selectedtokengroup, THETAblock) | grepl(selectedtokengroupnumbered, THETAblock)){
removeClass("covrequiredtheta", "red")
addClass("covrequiredtheta", "green")
}else{
removeClass("covrequiredtheta", "green")
addClass("covrequiredtheta", "red")}
if(grepl(selectedtokengroup, PKblock) | grepl(selectedtokengroupnumbered, PKblock)){
removeClass("etarequiredpk", "red")
addClass("etarequiredpk", "green")
}else{
removeClass("etarequiredpk", "green")
addClass("etarequiredpk", "red")}
if(grepl(selectedtokengroup, OMEGAblock) | grepl(selectedtokengroupnumbered, OMEGAblock)){
removeClass("etarequiredomega", "red")
addClass("etarequiredomega", "green")
}else{
removeClass("etarequiredomega", "green")
addClass("etarequiredomega", "red")}
}, priority = 100)
# END ---------------------------------------------------------------------
# filter tokenset list for selected token group ---------------------------
observe({
if(!is.null(input$tokengroupinput)){
selectedTokenGroup <- input$tokengroupinput
tokensetlist <- filter(alltokens, tokengroup == selectedTokenGroup)$tokenset %>% as.character()
hide("tokeneditdiv", anim = T) #close editing tab on selection of new tokengroup
updateAwesomeRadio(session, inputId = "tokensetinput", choices = unique(tokensetlist), selected = unique(tokensetlist)[1])
}
}, priority = -10)
# END ---------------------------------------------------------------------
# check if cov is in tokengroup and set to selected value if match is found ----------------------
observe({
selectedTokenGroup <- input$tokengroupinput
x <- input$ace
a <- strsplit(x, "\n")[[1]]
if(length(strsplit(a[startsWith(a, "$INPUT")], "\\s+")) > 0){
covlist <- strsplit(a[startsWith(a, "$INPUT")], "\\s+")[[1]][-1]
covlist <- covlist[!(covlist %in% c("DATE=DROP", "DATE", "RATE",
"CMT", "ID", "TIME", "AMT",
"SS", "ADDL", "II", "DV",
"MDV", "EVID", "DUR"))]
bestguess <- covlist[str_detect(selectedTokenGroup, covlist)][which(nchar(covlist[str_detect(selectedTokenGroup, covlist)]) == max(nchar(covlist[str_detect(selectedTokenGroup, covlist)])))]
updateSelectizeInput(session, "cov", selected = bestguess)
}
})
# END ---------------------------------------------------------------------
# filter token list for selected token set ---------------------------
observe({
if(!is.null(input$tokengroupinput) & !is.null(input$tokensetinput)){
selectedTokenGroup <- input$tokengroupinput
selectedTokenSet <- input$tokensetinput
tokenlist <- filter(alltokens,
tokengroup == selectedTokenGroup,
tokenset == selectedTokenSet)$token %>%
as.character()
updateAwesomeRadio(session, inputId = "tokeninput",
choices = tokenlist, selected = unique(tokenlist)[1])
}
}, priority = -11)
# END ---------------------------------------------------------------------
# highlight selected tokengroup -------------------------------------------
# highlight package used: https://github.com/garysieling/jquery-highlighttextarea
onclick("tokengroupinput",
{
updateTabsetPanel(session,"tabs", selected = "Control Stream")
runjs("$('#ace').highlightTextarea('destroy')")
fun<-paste0("$('#ace').highlightTextarea({
words: [{
color: '#FFFF00',
words: ['{", input$tokengroupinput, "}',
'{", input$tokengroupinput, ":[0-9]}']
}
, {
color: '#ff1b0f',
words: []
}]
});")
delay(1, runjs(fun)) #needs delay for tokengroup change to register first
})
# END ---------------------------------------------------------------------
# show how token set appears in control stream ----------------------------
onclick("preview",
{
x <- input$ace
selectedTokenGroup <- input$tokengroupinput
selectedTokenSet <- input$tokensetinput
tokengrouptext <- paste0("\\{", input$tokengroupinput, "\\}")
tokenlist <- filter(alltokens,
tokengroup == selectedTokenGroup,
tokenset == selectedTokenSet)$token %>%
as.character()
tokenlist[tokenlist == "N/A"] <- ""
for (i in 1:length(tokenlist)){
x <- sub(tokengrouptext, tokenlist[i], x)
}
x <- gsub("\\{[^//}]*\\}", "", x)
updateTextAreaInput(session, "previewtext", value = x)
words <- paste0("'", tokenlist, "',", collapse = "")
words <- substr(words, 1, nchar(words) - 1)
updateTabsetPanel(session, "tabs", selected = "Preview")
})
# END ---------------------------------------------------------------------
# display selected token type div (ie covariate, ETA,EPS,etc.) ------------
onclick("tokentype",
{
hide(selector = ".tokentype")
showElement(id = input$tokentype)
})
# END ---------------------------------------------------------------------
# Delete functions -------------------------------------------------------
onclick("deletetokengroup",
{
x <- input$ace
x <- gsub(paste0("\\{", input$tokengroupinput, "\\}"), "", x)
alltokens <- filter(alltokens, tokengroup != input$tokengroupinput)
updateTextAreaInput(session, "ace", value = x)
})
onclick("deletetokenset",
{
alltokens <- filter(alltokens,
!(tokengroup == input$tokengroupinput & tokenset == input$tokensetinput))
tokensetlist <- filter(alltokens,
tokengroup == input$tokengroupinput)$tokenset %>%
as.character()
updateAwesomeRadio(session, inputId = "tokensetinput",
choices = unique(tokensetlist),
selected = unique(tokensetlist)[1])
})
# END ---------------------------------------------------------------------
# Add to existing tokengroup ----------------------------------------------
onclick("addtokensetedit", {
n_tokensets <- length(unique(filter(alltokens,
tokengroup == input$tokengroupinput)$tokenset))
n_tokens <- length(filter(alltokens,
tokengroup == input$tokengroupinput,
tokenset == input$tokensetinput)$token)
tokenToAdd <- data.frame(tokengroup = input$tokengroupinput,
tokenset = paste("Tokenset", n_tokensets + 1),
token = rep("N/A", n_tokens),
stringsAsFactors = F)
# If tokenset exists already, replace it
alltokens <- filter(alltokens,
!(tokengroup %in% tokenToAdd$tokengroup & tokenset %in% tokenToAdd$tokenset))
alltokens <- rbind(alltokens, tokenToAdd, stringsAsFactors = F)
tokensetlist <- filter(alltokens,
tokengroup == input$tokengroupinput)$tokenset %>%
as.character()
updateAwesomeRadio(session, inputId = "tokensetinput",
choices = unique(tokensetlist), selected = unique(tokensetlist)[1])
tokenlist <- filter(alltokens,
tokenset == unique(tokensetlist)[1])$token %>%
as.character()
updateAwesomeRadio(session, inputId = "tokeninput",
choices = as.character(tokenlist), selected = NULL)
selectedtokengroup <- input$tokengroupinput
removeUI(selector = ".tokeneditdiv", immediate = T) #.tokeneditdiv class is tokenset panel div
#only display panel if tokensets exist for selected tokengroup
if (length(alltokens$tokenset[alltokens$tokengroup == input$tokengroupinput]) > 0){
insertUI(selector = "#tokenedit", where = "beforeEnd",
ui = {
column(12, align = "center",
textInput("edittokengroupname",
"Token Group Name",
value = selectedtokengroup,
width = "33%"),
lapply(1:length(unique(alltokens$tokenset[alltokens$tokengroup == input$tokengroupinput])),
function(i) {
column(12,
textInput(paste0("tokenset", i),
"Token Set Name",
value = unique(alltokens$tokenset[alltokens$tokengroup == input$tokengroupinput])[i],
width = "33%"),
lapply(seq_along(alltokens$token[alltokens$tokengroup == input$tokengroupinput &
alltokens$tokenset == unique(alltokens$tokenset[alltokens$tokengroup == input$tokengroupinput])[i]]),
function(j){
column(6,
textAreaInput(paste0("edittoken", i, j),
paste("Token", j),
value = alltokens$token[alltokens$tokengroup == input$tokengroupinput &
alltokens$tokenset == unique(alltokens$tokenset[alltokens$tokengroup == input$tokengroupinput])[i]][j],
resize = "vertical"))}),
class = "tokeneditdiv")}),
column(12,
actionButton("addtokensetedit", "Add Token Set"),
actionButton("addtokenedit", "Add Token"),
actionButton("savetokenedit", label = "Save")), class = "tokeneditdiv", id = "tokeneditdiv")
}, session = session, immediate = T)
}
})
# END---------------------------------------------------------------------
# Add token to existing tokenset ----------------------------------------------
onclick("addtokenedit",{
tokensets <- unique(filter(alltokens,tokengroup == input$tokengroupinput)$tokenset)
tokenToAdd <-data.frame(tokengroup = input$tokengroupinput, tokenset = tokensets, token = "N/A")
alltokens<-rbind(alltokens, tokenToAdd, stringsAsFactors = F)
tokensetlist<- filter(alltokens, tokengroup == input$tokengroupinput)$tokenset %>% as.character()
updateAwesomeRadio(session, inputId = "tokensetinput",
choices = unique(tokensetlist), selected = unique(tokensetlist)[1])
tokenlist <- filter(alltokens, tokenset == unique(tokensetlist)[1])$token %>% as.character()
updateAwesomeRadio(session, inputId = "tokeninput", choices = as.character(tokenlist), selected = NULL)
selectedtokengroup <- input$tokengroupinput
removeUI(selector = ".tokeneditdiv", immediate = T) #.tokeneditdiv class is tokenset panel div
#only display panel if tokensets exist for selected tokengroup
if (length(alltokens$tokenset[alltokens$tokengroup == input$tokengroupinput]) > 0){
insertUI(selector = "#tokenedit", where = "beforeEnd",
ui = {
column(12, align = "center",
textInput("edittokengroupname", "Token Group Name",
value = selectedtokengroup,
width = "33%"),
lapply(1:length(unique(alltokens$tokenset[alltokens$tokengroup == input$tokengroupinput])),
function(i) {
column(12,
textInput(paste0("tokenset", i),
"Token Set Name",
value = unique(alltokens$tokenset[alltokens$tokengroup == input$tokengroupinput])[i] ,
width = "33%"),
lapply(1:length(alltokens$token[alltokens$tokengroup == input$tokengroupinput &
alltokens$tokenset == unique(alltokens$tokenset[alltokens$tokengroup == input$tokengroupinput])[i]]),
function(j){
column(6,
textAreaInput(paste0("edittoken", i, j),
paste("Token", j),
value = alltokens$token[alltokens$tokengroup == input$tokengroupinput &
alltokens$tokenset == unique(alltokens$tokenset[alltokens$tokengroup == input$tokengroupinput])[i]][j],
resize = "vertical"))}),
class = "tokeneditdiv")}),
column(12,
actionButton("addtokensetedit", "Add Token Set"),
actionButton("addtokenedit", "Add Token"),
actionButton("savetokenedit", label = "Save")),
class = "tokeneditdiv", id = "tokeneditdiv")
}, session = session, immediate = T)
}
})
# END---------------------------------------------------------------------
# Create and add covariate tokens ----------------------------------------
onclick("addcovs", {
tokenTypes <- data.frame(tokengroup = input$tokengroupinput,
tokenset = input$covtypes,
stringsAsFactors = FALSE)
x <- input$ace
a <- strsplit(x,"\n")[[1]]
covlist <- strsplit(a[startsWith(a, "$INPUT")], "\\s+")[[1]][-1]
if(any(covlist == input$cov)){
values <- as.numeric(datafile()[which(covlist == input$cov)][[1]])
median <- median(values,na.rm = T) %>% round(2)
if (input$center == T){
lookup <- data.frame(tokenset = rep(c("None",
"Linear",
"Power",
"Exponential",
"Proportional"), each = 2),
token = c("N/A",
"N/A",
paste0("+(", input$cov, "-", median, ")*THETA([1])"),
paste0("(-10,.001,10);", input$tokengroupinput),
paste0("*(",input$cov, "/", median, ")**THETA([1])"),
paste0("(-5,.001,10);", input$tokengroupinput),
paste0("*exp((", input$cov, "-", median, ")*THETA([1]))"),
paste0("(-50,.001,50);", input$tokengroupinput),
paste0("*(1+(", input$cov, "-", median, ")*THETA([1]))"),
paste0("(-100,.001,100);", input$tokengroupinput)),
stringsAsFactors=FALSE)
}
}
if (input$center == F){
lookup <- data.frame(tokenset = rep(c("None",
"Linear",
"Power",
"Exponential",
"Proportional"), each = 2),
token= c("N/A",
"N/A",
paste0("+(", input$cov, ")*THETA([1])"),
paste0("(-100,.001,100);", input$tokengroupinput),
paste0("*", input$cov, "**THETA([1])"),
paste0("(-100,.001,100);", input$tokengroupinput),
paste0("*exp(", input$cov, ")*THETA([1])"),
paste0("(-100,.001,100);", input$tokengroupinput),
paste0("*(1+", input$cov, "*THETA([1]))"),
paste0("(-100,.001,100);", input$tokengroupinput)),
stringsAsFactors = FALSE)
}
tokenToAdd <- merge(tokenTypes, lookup, by = "tokenset") %>%
select(tokengroup, tokenset, token)
# If tokenset exists already, replace it
alltokens <- filter(alltokens,
!(tokengroup %in% tokenToAdd$tokengroup &
tokenset %in% tokenToAdd$tokenset))
alltokens <-rbind(alltokens, tokenToAdd)
tokensetlist <- filter(alltokens,
tokengroup == input$tokengroupinput)$tokenset %>%
as.character()
updateAwesomeRadio(session,
inputId = "tokensetinput",
choices = unique(tokensetlist),
selected = unique(tokensetlist)[1])
tokenlist <- filter(alltokens,
tokenset == unique(tokensetlist)[1])$token %>%
as.character()
updateAwesomeRadio(session,
inputId = "tokeninput",
choices = as.character(tokenlist),
selected = NULL)
hide("Covariate", anim = T)
}
)
# END ---------------------------------------------------------------------
# Create and add eta tokens ----------------------------------------
onclick("addetas",
{
tokenTypes <- data.frame(tokengroup = input$tokengroupinput, tokenset = input$etatypes)
lookup <- data.frame(tokenset = rep(c("None",
"Normal",
"Logarithmic",
"Normal (Proportional)"), each=2),
token= c("N/A",
"N/A",
paste0("+ETA([1])"),
paste0("(0.01);", input$tokengroupinput),
paste0("*exp(ETA([1]))"),
paste0("(0.01);", input$tokengroupinput),
paste0("*(1+ETA([1]))"),
paste0("(0.01);", input$tokengroupinput)),
stringsAsFactors = FALSE)
tokenToAdd <- merge(tokenTypes, lookup, by = "tokenset") %>%
select(tokengroup, tokenset, token)
alltokens <- filter(alltokens,
!(tokengroup %in% tokenToAdd$tokengroup &
tokenset %in% tokenToAdd$tokenset))
alltokens <- rbind(alltokens, tokenToAdd, stringsAsFactors = F)
tokensetlist<- filter(alltokens,
tokengroup == input$tokengroupinput)$tokenset %>%
as.character()
updateAwesomeRadio(session,
inputId = "tokensetinput",
choices = unique(tokensetlist),
selected = unique(tokensetlist)[1])
tokenlist <- filter(alltokens,
tokenset == unique(tokensetlist)[1])$token %>%
as.character()
updateAwesomeRadio(session, inputId = "tokeninput",
choices = as.character(tokenlist),
selected = NULL)
hide("ETA", anim = T)
}
)
# END ---------------------------------------------------------------------
# Create and add eps tokens ----------------------------------------
onclick("addeps",
{
tokenTypes <- data.frame(tokengroup = input$tokengroupinput, tokenset = input$epstypes)
lookup <- data.frame(tokenset = rep(c("Additive",
"Proportional",
"Additive+Proportional"), each=2),
token = c(paste0("Y=F+EPS([1])"),
"(0.01); Additive",
paste0("Y=F*(1+EPS([1]))"),
"(0.01); Proportional",
paste0("Y=F*(1+EPS([1]))+EPS([2])"),
"(0.01); Additive \n (0.01);Proportional"),
stringsAsFactors = FALSE)
tokenToAdd <-merge(tokenTypes, lookup, by = "tokenset") %>%
select(tokengroup, tokenset, token)
alltokens <- filter(alltokens,
!(tokengroup %in% tokenToAdd$tokengroup &
tokenset %in% tokenToAdd$tokenset))
alltokens <- rbind(alltokens, tokenToAdd, stringsAsFactors = F)
tokensetlist <- filter(alltokens,
tokengroup == input$tokengroupinput)$tokenset %>%
as.character()
updateAwesomeRadio(session,
inputId = "tokensetinput",
choices = unique(tokensetlist),
selected = unique(tokensetlist)[1])
tokenlist <- filter(alltokens,
tokenset == unique(tokensetlist)[1])$token %>%
as.character()
updateAwesomeRadio(session,
inputId = "tokeninput",
choices = as.character(tokenlist),
selected = NULL)
hide("EPS", anim = T)
}
)
# END ---------------------------------------------------------------------
# Create and add initial estimates tokens ----------------------------------------
onclick("addinitial",
{
init_from <- input$init_from
init_to <- input$init_to
init_num <- as.numeric(input$init_num)
initials <- round(seq(init_from, init_to, length.out = init_num), 1)
tokenToAdd <- data.frame(tokengroup = input$tokengroupinput,
tokenset = initials,
token = initials)
alltokens <- filter(alltokens,
!(tokengroup %in% tokenToAdd$tokengroup &
tokenset %in% tokenToAdd$tokenset))
alltokens <- rbind(alltokens, tokenToAdd, stringsAsFactors = F)
tokensetlist <- filter(alltokens,
tokengroup == input$tokengroupinput)$tokenset %>%
as.character()
updateAwesomeRadio(session,
inputId = "tokensetinput",
choices = unique(tokensetlist),
selected = unique(tokensetlist)[1])
tokenlist <- filter(alltokens,
tokenset == unique(tokensetlist)[1])$token %>%
as.character()
updateAwesomeRadio(session,
inputId = "tokeninput",
choices = as.character(tokenlist),
selected = NULL)
hide("Initials", anim = T)
}
)
# END ---------------------------------------------------------------------