R/ui_module.R
In omarbenites/fbdesign: Creates a fieldbook
Defines functions
genetic_design_conditional_panels
design_conditional_panels
ui_fieldbook
Documented in
ui_fieldbook
# choices for statistical design input
design_choices <- c(
"Unreplicated Design (UNDR)" = "UNDR",
"Westcott Design (WD)" = "WD",#
"Completely Randomized Design (CRD)" = "CRD",
"Randomized Complete Block Design (RCBD)" = "RCBD",
"Augmented Block Design (ABD)" = "ABD",
"Alpha Design (AD)" = "AD",
"Latin Square Design (LSD)" = "LSD",
"Factorial Two-Way Design in CRD (F2CRD)" = "F2CRD",
"Factorial Two-Way Design in RCBD (F2RCBD)" = "F2RCBD",
#"Split Plot with Plots in CRD (SPCRD)" = "SPCRD",
#"Split Plot with Plots in RCBD (SPRCBD)" = "SPRCBD", #R.Eyzaguirre recommends just one Split Design
"Split Plot with Plots Design" = "SPRCBD", #
#"Split Plot with Plots in LSD (SPLSD)" = "SPLSD",
"Strip Plot Design (STRIP)" = "STRIP"
# "Balanced Incomplete Block Design (BIBD)" = "BIBD",
# "Graeco-Latin Design (GLD)" = "GLD",
# "Youden Design (YD)" = "YD",
# "Cyclic Design (CD)" = "CD",
# "Lattice Design (LD)" = "LD" ,
# #"Augmented Partially Replicated Design (APRD)" = "APRD",
# #"Factorial Design (F2SPPD)" = "F2SPPD",
# "North Carolina Design I" = "NCI"#,
# #"North Carolina Design II" = "NCII",
# #"North Carolina Design III" = "NCIII",
)
#choices for statistical design input
genetic_design_choices <- c(
"North Carolina Design I" = "NCI",
"North Carolina Design II" = "NCII",
"Line by Tester" = "LXT"
)
# Conditional panels for genetic design
genetic_design_conditional_panels <- function(){
list(
shiny::conditionalPanel(
"input.design_geneticFieldbook == 'NCI'|
input.design_geneticFieldbook == 'NCII'",
shiny::selectInput("design_genetic_nc_set", "Set", 2:100, 2),
#shiny::selectInput("design_genetic_nc_r", "Replications", 2:100, 2),
shiny::selectInput("design_genetic_ploidy", "Type of ploidy", choices = c("Diploid","Tetraploid"))
) ,
shiny::conditionalPanel(
"input.design_geneticFieldbook == 'LXT'|
input.design_geneticFieldbook == 'NCI'|
input.design_geneticFieldbook == 'NCII'",
#shiny::selectInput("design_genetic_nc_set", "Set", 2:100, 2),
shiny::selectInput("design_genetic_r", "Replications", 2:100, 2)#,
#shiny::selectInput("design_genetic_ploidy", "Type of ploidy", choices = c("Diploid","Tetraploid"))
) ,
shiny::conditionalPanel(
"input.design_geneticFieldbook == 'LXT'",
#shiny::selectInput("design_genetic_nc_set", "Set", 2:100, 2),
shiny::selectInput("design_genetic_lxt_type", "Type of scheme", list("progenitors and progenie"= 1, "progenie" =2))#
#shiny::selectInput("design_genetic_ploidy", "Type of ploidy", choices = c("Diploid","Tetraploid"))
)
)
}
# Conditional Panels or features according to each statistical design
design_conditional_panels <- function(){
list(
shiny::conditionalPanel(
"input.designFieldbook == 'RCBD' |
input.designFieldbook == 'CRD' |
input.designFieldbook == 'F2CRD' |
input.designFieldbook == 'F2RCBD' |
input.designFieldbook == 'ABD' |
input.designFieldbook == 'DAU' |
input.designFieldbook == 'AD' |
input.designFieldbook == 'SPCRD'|
input.designFieldbook == 'SPRCBD'|
input.designFieldbook == 'SPLSD'|
input.designFieldbook == 'STRIP'",
# TODO: ab - factorial, split
shiny::selectInput("designFieldbook_r", "Replications", 2:100, 2 )
),
# shiny::conditionalPanel(
# "input.designFieldbook == 'UNDR' |
# input.designFieldbook == 'CRD' |
# input.designFieldbook == 'RCBD' |
# input.designFieldbook == 'F2CRD' |
# input.designFieldbook == 'F2RCBD'|
# input.designFieldbook == 'SPRCBD'",
#
# shiny::checkboxInput("designFieldbook_cbrwcol", "Add row and column", value = FALSE)#,
# shiny::conditionalPanel(
# "input.designFieldbook_cbrwcol == true",
# shiny::selectInput("designFieldbook_expdis_colb", "Number of columns", 2:100, 10)
# )
# ),
shiny::conditionalPanel(
"input.designFieldbook == 'SPCRD' |
input.designFieldbook == 'SPRCBD'|
input.designFieldbook == 'F2CRD' |
input.designFieldbook == 'F2RCBD'|
input.designFieldbook == 'SPLSD' |
input.designFieldbook == 'STRIP'
",
#shiny::selectInput("designFieldbook_r", "Replications:", 1:5, 2 ),
textInput(inputId = "factor_name", label = "Enter Additional Factor Name", ""),
br(),
textInput(inputId = "factor_lvl", label = "Type levels of factors (separated by commas ',')", value = "")#,
# textInput(inputId = "factor_lvl1", label = "First Level for Additional Factor",value = ""),
# textInput(inputId = "factor_lvl2", label = "Second Level for Additional Factor",value = ""),
# textInput(inputId = "factor_lvl3", label = "Third Level for Additional Factor",value = "")
),
shiny::conditionalPanel(
"input.designFieldbook == 'SPCRD' |
input.designFieldbook == 'SPRCBD'",
shiny::uiOutput("fbdesign_split_cb")
),
shiny::conditionalPanel(
"input.designFieldbook == 'WD'",
shiny::selectInput("designFieldbook_wd_col", "Number of columns", 50:5000, 100 ),
shiny::selectInput("designFieldbook_wd_colb", "Number of columns between two check columns", 2:100, 10)
),
shiny::conditionalPanel(
"input.designFieldbook == 'ABD'", # TODO: ab - factorial, split
infoBox(title = "IMPORTANT NOTE", subtitle = "Augmented design needs at least 2 checks. Verify if your material have these checks and put an 'x' mark in 'Is_control' column for each check.
Otherwise, Augmented Design does not work.",
icon = icon("bullhorn"), color = "blue", fill = TRUE, width = NULL)
),
shiny::conditionalPanel(
"input.designFieldbook == 'WD'", # TODO: ab - factorial, split
infoBox(title = "IMPORTANT NOTE", subtitle = "Westcott design needs 2 checks and at least 10 genotypes. Verify if your material list has these checks and put an 'x' mark in 'Is_control' column for each check.
Otherwise, Westcott Design does not work.",
icon = icon("bullhorn"), color = "blue", fill = TRUE, width = NULL)
),
shiny::conditionalPanel(
"input.designFieldbook == 'LD'", # TODO: ab - factorial, split
shiny::selectInput("designFieldbook_r", "Replications", 2:100, 2 )
),
shiny::conditionalPanel(
"input.designFieldbook == 'BIBD'",
shiny::selectInput("designFieldbook_maxR", "Repetition maximum (k)", 3:100, 20 )
) ,
shiny::conditionalPanel(
"input.designFieldbook == 'AD' |
input.designFieldbook == 'BIBD'",
# TODO do server side checking of permitted combinations (based on number of treatments)
# trt = k * s
# s = number of blocks
# k = size of block (max is trt)
#
# r = 2: k <= s
# r = 3: s odd; k <= s
# r = 3: s even; k <= (s - 1)
# r = 4: s odd but not multiple of 3; k <= s
#shiny::selectInput("designFieldbook_r", "Replications:", 2:6000, 2 ),
shiny::selectInput("designFieldbook_k", "Block size (k)", 2:100, 4 )
),
shiny::conditionalPanel(
"input.designFieldbook == 'AD'", # TODO: ab - factorial, split
fluidRow(
shiny::wellPanel(
shiny::HTML("<b>ALPHA CONDITION:</b>"),
textOutput("alphaMessage")
)
)
),
# shiny::conditionalPanel(
# "input.designFieldbook == 'CD'",
# # TODO do server side checking of permitted combinations (based on number of treatments)
# # number of treatments 6:30
# shiny::selectInput("designFieldbook_r", "Replications:", 2:10, 2 ),
# shiny::selectInput("designFieldbook_k", "Block size (k):", 2:10,3 )
# ),
### Combine factors in statistical designs ########################
shiny::conditionalPanel(
"input.designFieldbook == 'UNDR' |
input.designFieldbook == 'CRD' |
input.designFieldbook == 'RCBD' |
input.designFieldbook == 'ABD'",
shiny::checkboxInput("designFieldbook_combfactor", "Add experimental conditions",value = FALSE ),
shiny::conditionalPanel(
"input.designFieldbook_combfactor == true",
textInput(inputId = "combfactor_name", label = "Experimental conditions label", ""),
br(),
textInput(inputId = "combfactor_lvl", label = "Type experimental conditions (separated by commas ',')", value = "")#,
)
),
#########################################
###############
shiny::conditionalPanel(
"input.designFieldbook == 'UNDR' |
input.designFieldbook == 'CRD' |
input.designFieldbook == 'RCBD' |
input.designFieldbook == 'ABD'",
shiny::checkboxInput("designFieldbook_cbssample", "Add sub samples", value = FALSE ),
shiny::conditionalPanel(
"input.designFieldbook_cbssample == true",
shiny::numericInput(inputId = "designFieldbook_nsample", label = "Enter samples", value = 10, min = 1, max = 1000)
)
)#,
)
}
#' shiny UI element
#'
#' returns a re-usable user interface element
#'
#' @author Omar Benites
#' @param type type of ui element; default is a tab in a shiny dashboard
#' @param title display title
#' @param name a reference name
#' @export
################## Begin Simple Modules
ui_fieldbook <- function(type="tab",title="Design Fieldbook",name="phenotype_fieldbook_design"){
#############
shinydashboard::tabItem(tabName = name,
h2("Design of Field Experiments"),
shinyjs::useShinyjs(), #to reset panels and UI
tags$head(
tags$style(HTML("
.shiny-output-error-validation {
color: green;
font-size: 120%;
font-family: Arial, Helvetica, sans-serif;
}
"))
),
tabsetPanel( #Begin Master tabSetPanel
tabPanel("Standard Modules",icon = icon("tag", lib = "glyphicon"),
br(),
shiny::wellPanel(
shiny::HTML("<b>Fieldbook ID </b>"),
shiny::textOutput("fbDesign_id")
),
fluidRow(
box(
title = " ", status = "primary", solidHeader = TRUE,
collapsible = TRUE, width = 12,
#shiny::tabsetPanel(# id = "fbDesignNav",
shinydashboard::tabBox(id = "fbDesignNav", height = NULL, width = 12,
shiny::tabPanel("Crop & Location", value = "crop", icon = shiny::icon("leaf"),
br(),
fluidRow(
column(width = 6,
# box(
# title = "Step: 1", status = "warning", solidHeader = TRUE, collapsible = TRUE, width = NULL,height = NULL,
shiny::selectInput("designFieldbook_crop", "Crop", crops()),
#shiny::uiOutput("fbDesign_factor2", inline = TRUE),
#shiny::uiOutput("fbDesign_variables", inline = TRUE),
shiny::dateRangeInput("fbDesign_project_time_line", "Date of experiment", start = Sys.Date() - 2,
end = Sys.Date() + 20, startview = "year",format = "dd/mm/yyyy"),
#shiny::uiOutput("fbDesign_country", inline = TRUE, width = 500),#country
#shiny::selectizeInput("fbDesign_country", inline = TRUE, width = 500),#country
# shiny::selectizeInput("fbDesign_countryTrial", label = "Field country",
# choices = country(), selected = 1, multiple = FALSE),
shiny::uiOutput("fbDesign_country", inline = TRUE, width = 500),
shiny::uiOutput("fbDesign_countrySite", inline = TRUE, width = 500), #,#locality
selectInput('fbDesign_nExp', 'Experiment number', c("-",paste("exp",1:100,sep="")), selectize=TRUE)
)
)
),
shiny::tabPanel("Material List", value = "plants", icon = shiny::icon("list-alt"),
br(),
# fluidRow(
# column(width = 6,
# box(
# title = "Step: 2", status = "warning", solidHeader = TRUE, collapsible = TRUE, width = NULL,
#shiny::uiOutput("designFieldbook_genotypes", inline = TRUE),
# h4("Define Genotypes",style = "font-family: 'Arial', cursive;
# font-weight: 500; line-height: 1.1;
# color: #4d3a7d;"),
br(),
radioButtons("select_import", label = h4("Define Genotypes",style = "font-family: 'Arial', cursive;
font-weight: 500; line-height: 1.1;
color: #4d3a7d;"),
choices = c("Local List", "Template"),
selected = "Local List"),
br(),
#selectInput("fbdesign_gentemp", "Type",c("Clones" = "clones","Parental" = "parental")),
conditionalPanel(
condition = "input.select_import == 'Local List'",
shiny::uiOutput("fbDesign_selmlist"),
shiny::actionButton("fdesign_list_refresh", "Refresh List"),
br()#,
),
shinyWidgets::awesomeCheckbox(inputId = "fbdesign_gentemp",
label = "Load parental study template",
value = FALSE, status = "danger"),
conditionalPanel(
condition = "input.select_import == 'Template'",
conditionalPanel(
condition = "input.fbdesign_gentemp",
downloadButton(outputId = "fbDesign_mlistExportGenTemp", label = "Download parental template")
),
conditionalPanel(
condition = "!input.fbdesign_gentemp",
#downloadButton(outputId = "fbDesign_mlistExportGenTemp", label = "Download Template 2")
downloadButton(outputId = "fbDesign_mlistExport", label = "Download template")
),
fileInput(inputId = 'file_mtlist',label = 'Upload filled template',accept = ".xlsx")#,
),
fluidRow(
#br(),
#shiny::actionLink('exportButton', 'Material List Template'),
infoBoxOutput("approvalBox")#,
)#,
#,
#shinyalert("shinyalert1", FALSE, auto.close.after = 5)
#actionButton("id_success","Save",styleclass="success",icon = "ok")
# )
#)
#)
),
shiny::tabPanel("Fieldbook Traits", value = "traits", icon = shiny::icon("star"),
br(),
#fluidRow(
# column(width = 6,
# box(
# title = "Step: 3", status = "warning", solidHeader = TRUE, collapsible = TRUE, width = NULL,
#shiny::uiOutput("designFieldbook_traits", inline = TRUE)
shinyTree::shinyTree("designFieldbook_traits",search = TRUE,checkbox = TRUE)
# )
# )
# )
),
shiny::tabPanel("Statistical Design", value = "design", icon = shiny::icon("pie-chart"),
conditionalPanel( condition = "output.condition_selmlist==0",
br(),
shiny::selectInput("designFieldbook", "Design", c("Choose one" = "", design_choices), selected = 'RCBD',
multiple = FALSE),
design_conditional_panels()
),
conditionalPanel( condition = "output.condition_selmlist!=0",
br(),
#shiny::selectInput("design_geneticFieldbook", "Genetic design", c("Choose one" = "", genetic_design_choices) ,multiple = FALSE),
shiny::selectInput("design_geneticFieldbook", "Genetic design", c(genetic_design_choices) ,multiple = FALSE),
genetic_design_conditional_panels()
)
),
shiny::tabPanel("Environment", value = 'environment', icon = shiny::icon("recycle"),
br(),
#shiny::checkboxInput("designFieldbook_zigzag", "Zigzag", FALSE),
shiny::radioButtons("designFieldbook_serie", "Label series",
#get_series_labels(), "101, 102, ...", #get_series_labels()[[2]],
1:3, 1,
inline = TRUE)
,
# shiny::conditionalPanel(
# "input.designFieldbook == 'RCBD'",
#shiny::checkboxInput("designFieldbook_cont", "Continuous numbering of plots", FALSE)
#),
shiny::radioButtons("fbDesign_environment_type", "Environment type",choices = list(
"Field" = "Field",
#"Farmers field" = "farmers_field",
"Greenhouse" = "Greenhouse",
"Screenhouse" = "Screenhouse"),selected = "Field" , inline = TRUE),
shiny::checkboxInput("fbDesign_weather_cb", label = "Register weather data"),
shiny::checkboxInput("fbDesign_soil_cb", label = "Register soil data")
# )
#)
#)
),
# shiny::tabPanel("Field", value = "fbDesign_field", icon = shiny::icon("male"),
# shiny::numericInput("fbDesign_field_size (ha)",
# "Field size", 1, 1, 100)
# ),
# shiny::tabPanel("Farmers field", value = "fbDesign_farmers_field"
# ),
# shiny::tabPanel("Greenhouse", value = "fbDesign_greenhouse"
# ),
# shiny::tabPanel("Screenhouse", value = "fbDesign_screenhouse"
# ),
shiny::tabPanel("Plant Installation", value = "fbDesign_planting", icon = shiny::icon("th-large"),
br(),
# fluidRow(
# column(width = 6,
# box(
# title = "Step: 6", status = "warning", solidHeader = TRUE, collapsible = TRUE, width = NULL,
shiny::conditionalPanel(
"input.fbDesign_environment_type == 'Field'",
shiny::numericInput("fbDesign_nplantsrow",
"Number of plants per row", 10, 1, 100),
shiny::numericInput("fbDesign_nrowplot",
"Number of rows per plot", 1, 1, 100),
#shiny::numericInput("fbDesign_psize","Plot size", 30, 1, 100),
shiny::numericInput("fbDesign_distPlants",
"Distance between plants (m)", .3, .1, 1),
shiny::numericInput("fbDesign_distRows",
"Distance between rows (m)", .9, .1, 1),
shiny::uiOutput("fbPlanting_psize", inline=TRUE),
shiny::uiOutput("fbPlanting_pdensity", inline=TRUE),
tags$head(tags$style("#fbDesign_pdensity{color:#191919;
background-color:#ecc464;
#font-size: 20px;
#font-style: italic;
}"
)
),
tags$head(tags$style("#fbDesign_psize{color:#191919;
background-color:#88e3a5;
#font-size: 20px;
#font-style: italic;
}"
)
)
#,
),
shiny::conditionalPanel(
"input.fbDesign_environment_type == 'Field'",
# Deprecated code for number of plant per plot
# shiny::numericInput("fbDesign_nplants",
# "Number of plants per plot/pot", 10 , 1, 100)#,
#It replace the code above.
shiny::uiOutput("fbPlant_plot", inline = TRUE)
#
),
shiny::conditionalPanel(
"input.fbDesign_environment_type == 'Greenhouse'|
input.fbDesign_environment_type == 'Screenhouse'",
shiny::numericInput("fbDesign_nplantxpot",
"Number of plants per pot", 10 , 1, 10000),
shiny::numericInput("fbDesign_npots",
"Number of pots", 1, 1, 10000)#,
)
)#,
)#,
#shinyBS::bsAlert("alert_fb_done")
)
),
#fluidRow( #begin fluidrow
shinyWidgets::prettyRadioButtons(inputId = "fbdesign_book_export",
label = "Choose exportation:", choices = c("HIDAP format","FieldBookApp format"), icon = icon("check"),
bigger = TRUE, status = "info",inline = TRUE,
animation = "jelly"),
#),
shiny::conditionalPanel(
"input.fbdesign_book_export == 'HIDAP format'|
input.fbdesign_book_export == 'FieldBookApp format'",
HTML('<div style="float: right; margin: 0 16px 18px 0px;">'),
shiny::actionButton("fbDesign_draft", "Book Preview", icon("table"), style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
HTML('</div>')#,
),
#HIDAP format
shiny::conditionalPanel(
"input.fbdesign_book_export == 'HIDAP format'",
shinysky::actionButton2("fbDesign_create", label = "Download", icon ="file-excel-o", icon.library = "bootstrap", styleclass= "color: #fff; background-color: #51a351; border-color: #51a351")
),
shiny::conditionalPanel(
"input.fbdesign_book_export == 'FieldBookApp format'",
div(style="display: inline-block;vertical-align:top; width: 150px;", shiny::selectInput("fbdesign_year_fbapp",
"Select year", choices = 2000:3000, selected = 2018)),
# div(style="display: inline-block;vertical-align:top; width: 150px;", shiny::selectInput("fbdesign_cntry_fbapp",
# label="Select Country", choices = value = 0.5)),
div(style="display: inline-block;vertical-align:top; width: 200px;", uiOutput("oufbDesign_country_fbapp")),
div(style="display: inline-block;vertical-align:top; width: 150px;", shiny::textInput('fbdesign_abbruser_fbapp',
label = "Enter trial abbreviation",
value = "", placeholder = "ex.:STO (storage)")),
div(style="display: inline-block;vertical-align:top; width: 200px;", uiOutput("oufbDesign_location_fbapp"),
shiny::downloadButton(outputId = 'fbdesigin_downloadFbAppData', label = 'Download FieldBookApp File')
)
),
br(),
shinysky::shinyalert("alert_fb_done", FALSE, auto.close.after = 4),
shiny::fluidRow(
#box(
#column(width = 12,height=6,
shinydashboard::box(title = "Fieldbook Preview",
status = "primary",
#height = 500,
#width = NULL,
solidHeader = TRUE,
width = 12, collapsible = TRUE,
#shiny::actionButton("butNewFieldbook", "New fieldbook", inline = TRUE)#,
rhandsontable::rHandsontableOutput("fbDesign_table", height = 400)
),
br(),
br(),
br()
#)
#)
),
br(),
br(),
br()
), #end
ui_design_big(type="tab",title="Special Modules",name="phenotype_fieldbook_design")
######
################## End Simple Modules
)# End of Master tabSetPanel
)
}
omarbenites/fbdesign documentation built on May 24, 2019, 12:54 p.m.
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Defines functions genetic_design_conditional_panels design_conditional_panels ui_fieldbook
Documented in ui_fieldbook
# choices for statistical design input
design_choices <- c(
"Unreplicated Design (UNDR)" = "UNDR",
"Westcott Design (WD)" = "WD",#
"Completely Randomized Design (CRD)" = "CRD",
"Randomized Complete Block Design (RCBD)" = "RCBD",
"Augmented Block Design (ABD)" = "ABD",
"Alpha Design (AD)" = "AD",
"Latin Square Design (LSD)" = "LSD",
"Factorial Two-Way Design in CRD (F2CRD)" = "F2CRD",
"Factorial Two-Way Design in RCBD (F2RCBD)" = "F2RCBD",
#"Split Plot with Plots in CRD (SPCRD)" = "SPCRD",
#"Split Plot with Plots in RCBD (SPRCBD)" = "SPRCBD", #R.Eyzaguirre recommends just one Split Design
"Split Plot with Plots Design" = "SPRCBD", #
#"Split Plot with Plots in LSD (SPLSD)" = "SPLSD",
"Strip Plot Design (STRIP)" = "STRIP"
# "Balanced Incomplete Block Design (BIBD)" = "BIBD",
# "Graeco-Latin Design (GLD)" = "GLD",
# "Youden Design (YD)" = "YD",
# "Cyclic Design (CD)" = "CD",
# "Lattice Design (LD)" = "LD" ,
# #"Augmented Partially Replicated Design (APRD)" = "APRD",
# #"Factorial Design (F2SPPD)" = "F2SPPD",
# "North Carolina Design I" = "NCI"#,
# #"North Carolina Design II" = "NCII",
# #"North Carolina Design III" = "NCIII",
)
#choices for statistical design input
genetic_design_choices <- c(
"North Carolina Design I" = "NCI",
"North Carolina Design II" = "NCII",
"Line by Tester" = "LXT"
)
# Conditional panels for genetic design
genetic_design_conditional_panels <- function(){
list(
shiny::conditionalPanel(
"input.design_geneticFieldbook == 'NCI'|
input.design_geneticFieldbook == 'NCII'",
shiny::selectInput("design_genetic_nc_set", "Set", 2:100, 2),
#shiny::selectInput("design_genetic_nc_r", "Replications", 2:100, 2),
shiny::selectInput("design_genetic_ploidy", "Type of ploidy", choices = c("Diploid","Tetraploid"))
) ,
shiny::conditionalPanel(
"input.design_geneticFieldbook == 'LXT'|
input.design_geneticFieldbook == 'NCI'|
input.design_geneticFieldbook == 'NCII'",
#shiny::selectInput("design_genetic_nc_set", "Set", 2:100, 2),
shiny::selectInput("design_genetic_r", "Replications", 2:100, 2)#,
#shiny::selectInput("design_genetic_ploidy", "Type of ploidy", choices = c("Diploid","Tetraploid"))
) ,
shiny::conditionalPanel(
"input.design_geneticFieldbook == 'LXT'",
#shiny::selectInput("design_genetic_nc_set", "Set", 2:100, 2),
shiny::selectInput("design_genetic_lxt_type", "Type of scheme", list("progenitors and progenie"= 1, "progenie" =2))#
#shiny::selectInput("design_genetic_ploidy", "Type of ploidy", choices = c("Diploid","Tetraploid"))
)
)
}
# Conditional Panels or features according to each statistical design
design_conditional_panels <- function(){
list(
shiny::conditionalPanel(
"input.designFieldbook == 'RCBD' |
input.designFieldbook == 'CRD' |
input.designFieldbook == 'F2CRD' |
input.designFieldbook == 'F2RCBD' |
input.designFieldbook == 'ABD' |
input.designFieldbook == 'DAU' |
input.designFieldbook == 'AD' |
input.designFieldbook == 'SPCRD'|
input.designFieldbook == 'SPRCBD'|
input.designFieldbook == 'SPLSD'|
input.designFieldbook == 'STRIP'",
# TODO: ab - factorial, split
shiny::selectInput("designFieldbook_r", "Replications", 2:100, 2 )
),
# shiny::conditionalPanel(
# "input.designFieldbook == 'UNDR' |
# input.designFieldbook == 'CRD' |
# input.designFieldbook == 'RCBD' |
# input.designFieldbook == 'F2CRD' |
# input.designFieldbook == 'F2RCBD'|
# input.designFieldbook == 'SPRCBD'",
#
# shiny::checkboxInput("designFieldbook_cbrwcol", "Add row and column", value = FALSE)#,
# shiny::conditionalPanel(
# "input.designFieldbook_cbrwcol == true",
# shiny::selectInput("designFieldbook_expdis_colb", "Number of columns", 2:100, 10)
# )
# ),
shiny::conditionalPanel(
"input.designFieldbook == 'SPCRD' |
input.designFieldbook == 'SPRCBD'|
input.designFieldbook == 'F2CRD' |
input.designFieldbook == 'F2RCBD'|
input.designFieldbook == 'SPLSD' |
input.designFieldbook == 'STRIP'
",
#shiny::selectInput("designFieldbook_r", "Replications:", 1:5, 2 ),
textInput(inputId = "factor_name", label = "Enter Additional Factor Name", ""),
br(),
textInput(inputId = "factor_lvl", label = "Type levels of factors (separated by commas ',')", value = "")#,
# textInput(inputId = "factor_lvl1", label = "First Level for Additional Factor",value = ""),
# textInput(inputId = "factor_lvl2", label = "Second Level for Additional Factor",value = ""),
# textInput(inputId = "factor_lvl3", label = "Third Level for Additional Factor",value = "")
),
shiny::conditionalPanel(
"input.designFieldbook == 'SPCRD' |
input.designFieldbook == 'SPRCBD'",
shiny::uiOutput("fbdesign_split_cb")
),
shiny::conditionalPanel(
"input.designFieldbook == 'WD'",
shiny::selectInput("designFieldbook_wd_col", "Number of columns", 50:5000, 100 ),
shiny::selectInput("designFieldbook_wd_colb", "Number of columns between two check columns", 2:100, 10)
),
shiny::conditionalPanel(
"input.designFieldbook == 'ABD'", # TODO: ab - factorial, split
infoBox(title = "IMPORTANT NOTE", subtitle = "Augmented design needs at least 2 checks. Verify if your material have these checks and put an 'x' mark in 'Is_control' column for each check.
Otherwise, Augmented Design does not work.",
icon = icon("bullhorn"), color = "blue", fill = TRUE, width = NULL)
),
shiny::conditionalPanel(
"input.designFieldbook == 'WD'", # TODO: ab - factorial, split
infoBox(title = "IMPORTANT NOTE", subtitle = "Westcott design needs 2 checks and at least 10 genotypes. Verify if your material list has these checks and put an 'x' mark in 'Is_control' column for each check.
Otherwise, Westcott Design does not work.",
icon = icon("bullhorn"), color = "blue", fill = TRUE, width = NULL)
),
shiny::conditionalPanel(
"input.designFieldbook == 'LD'", # TODO: ab - factorial, split
shiny::selectInput("designFieldbook_r", "Replications", 2:100, 2 )
),
shiny::conditionalPanel(
"input.designFieldbook == 'BIBD'",
shiny::selectInput("designFieldbook_maxR", "Repetition maximum (k)", 3:100, 20 )
) ,
shiny::conditionalPanel(
"input.designFieldbook == 'AD' |
input.designFieldbook == 'BIBD'",
# TODO do server side checking of permitted combinations (based on number of treatments)
# trt = k * s
# s = number of blocks
# k = size of block (max is trt)
#
# r = 2: k <= s
# r = 3: s odd; k <= s
# r = 3: s even; k <= (s - 1)
# r = 4: s odd but not multiple of 3; k <= s
#shiny::selectInput("designFieldbook_r", "Replications:", 2:6000, 2 ),
shiny::selectInput("designFieldbook_k", "Block size (k)", 2:100, 4 )
),
shiny::conditionalPanel(
"input.designFieldbook == 'AD'", # TODO: ab - factorial, split
fluidRow(
shiny::wellPanel(
shiny::HTML("<b>ALPHA CONDITION:</b>"),
textOutput("alphaMessage")
)
)
),
# shiny::conditionalPanel(
# "input.designFieldbook == 'CD'",
# # TODO do server side checking of permitted combinations (based on number of treatments)
# # number of treatments 6:30
# shiny::selectInput("designFieldbook_r", "Replications:", 2:10, 2 ),
# shiny::selectInput("designFieldbook_k", "Block size (k):", 2:10,3 )
# ),
### Combine factors in statistical designs ########################
shiny::conditionalPanel(
"input.designFieldbook == 'UNDR' |
input.designFieldbook == 'CRD' |
input.designFieldbook == 'RCBD' |
input.designFieldbook == 'ABD'",
shiny::checkboxInput("designFieldbook_combfactor", "Add experimental conditions",value = FALSE ),
shiny::conditionalPanel(
"input.designFieldbook_combfactor == true",
textInput(inputId = "combfactor_name", label = "Experimental conditions label", ""),
br(),
textInput(inputId = "combfactor_lvl", label = "Type experimental conditions (separated by commas ',')", value = "")#,
)
),
#########################################
###############
shiny::conditionalPanel(
"input.designFieldbook == 'UNDR' |
input.designFieldbook == 'CRD' |
input.designFieldbook == 'RCBD' |
input.designFieldbook == 'ABD'",
shiny::checkboxInput("designFieldbook_cbssample", "Add sub samples", value = FALSE ),
shiny::conditionalPanel(
"input.designFieldbook_cbssample == true",
shiny::numericInput(inputId = "designFieldbook_nsample", label = "Enter samples", value = 10, min = 1, max = 1000)
)
)#,
)
}
#' shiny UI element
#'
#' returns a re-usable user interface element
#'
#' @author Omar Benites
#' @param type type of ui element; default is a tab in a shiny dashboard
#' @param title display title
#' @param name a reference name
#' @export
################## Begin Simple Modules
ui_fieldbook <- function(type="tab",title="Design Fieldbook",name="phenotype_fieldbook_design"){
#############
shinydashboard::tabItem(tabName = name,
h2("Design of Field Experiments"),
shinyjs::useShinyjs(), #to reset panels and UI
tags$head(
tags$style(HTML("
.shiny-output-error-validation {
color: green;
font-size: 120%;
font-family: Arial, Helvetica, sans-serif;
}
"))
),
tabsetPanel( #Begin Master tabSetPanel
tabPanel("Standard Modules",icon = icon("tag", lib = "glyphicon"),
br(),
shiny::wellPanel(
shiny::HTML("<b>Fieldbook ID </b>"),
shiny::textOutput("fbDesign_id")
),
fluidRow(
box(
title = " ", status = "primary", solidHeader = TRUE,
collapsible = TRUE, width = 12,
#shiny::tabsetPanel(# id = "fbDesignNav",
shinydashboard::tabBox(id = "fbDesignNav", height = NULL, width = 12,
shiny::tabPanel("Crop & Location", value = "crop", icon = shiny::icon("leaf"),
br(),
fluidRow(
column(width = 6,
# box(
# title = "Step: 1", status = "warning", solidHeader = TRUE, collapsible = TRUE, width = NULL,height = NULL,
shiny::selectInput("designFieldbook_crop", "Crop", crops()),
#shiny::uiOutput("fbDesign_factor2", inline = TRUE),
#shiny::uiOutput("fbDesign_variables", inline = TRUE),
shiny::dateRangeInput("fbDesign_project_time_line", "Date of experiment", start = Sys.Date() - 2,
end = Sys.Date() + 20, startview = "year",format = "dd/mm/yyyy"),
#shiny::uiOutput("fbDesign_country", inline = TRUE, width = 500),#country
#shiny::selectizeInput("fbDesign_country", inline = TRUE, width = 500),#country
# shiny::selectizeInput("fbDesign_countryTrial", label = "Field country",
# choices = country(), selected = 1, multiple = FALSE),
shiny::uiOutput("fbDesign_country", inline = TRUE, width = 500),
shiny::uiOutput("fbDesign_countrySite", inline = TRUE, width = 500), #,#locality
selectInput('fbDesign_nExp', 'Experiment number', c("-",paste("exp",1:100,sep="")), selectize=TRUE)
)
)
),
shiny::tabPanel("Material List", value = "plants", icon = shiny::icon("list-alt"),
br(),
# fluidRow(
# column(width = 6,
# box(
# title = "Step: 2", status = "warning", solidHeader = TRUE, collapsible = TRUE, width = NULL,
#shiny::uiOutput("designFieldbook_genotypes", inline = TRUE),
# h4("Define Genotypes",style = "font-family: 'Arial', cursive;
# font-weight: 500; line-height: 1.1;
# color: #4d3a7d;"),
br(),
radioButtons("select_import", label = h4("Define Genotypes",style = "font-family: 'Arial', cursive;
font-weight: 500; line-height: 1.1;
color: #4d3a7d;"),
choices = c("Local List", "Template"),
selected = "Local List"),
br(),
#selectInput("fbdesign_gentemp", "Type",c("Clones" = "clones","Parental" = "parental")),
conditionalPanel(
condition = "input.select_import == 'Local List'",
shiny::uiOutput("fbDesign_selmlist"),
shiny::actionButton("fdesign_list_refresh", "Refresh List"),
br()#,
),
shinyWidgets::awesomeCheckbox(inputId = "fbdesign_gentemp",
label = "Load parental study template",
value = FALSE, status = "danger"),
conditionalPanel(
condition = "input.select_import == 'Template'",
conditionalPanel(
condition = "input.fbdesign_gentemp",
downloadButton(outputId = "fbDesign_mlistExportGenTemp", label = "Download parental template")
),
conditionalPanel(
condition = "!input.fbdesign_gentemp",
#downloadButton(outputId = "fbDesign_mlistExportGenTemp", label = "Download Template 2")
downloadButton(outputId = "fbDesign_mlistExport", label = "Download template")
),
fileInput(inputId = 'file_mtlist',label = 'Upload filled template',accept = ".xlsx")#,
),
fluidRow(
#br(),
#shiny::actionLink('exportButton', 'Material List Template'),
infoBoxOutput("approvalBox")#,
)#,
#,
#shinyalert("shinyalert1", FALSE, auto.close.after = 5)
#actionButton("id_success","Save",styleclass="success",icon = "ok")
# )
#)
#)
),
shiny::tabPanel("Fieldbook Traits", value = "traits", icon = shiny::icon("star"),
br(),
#fluidRow(
# column(width = 6,
# box(
# title = "Step: 3", status = "warning", solidHeader = TRUE, collapsible = TRUE, width = NULL,
#shiny::uiOutput("designFieldbook_traits", inline = TRUE)
shinyTree::shinyTree("designFieldbook_traits",search = TRUE,checkbox = TRUE)
# )
# )
# )
),
shiny::tabPanel("Statistical Design", value = "design", icon = shiny::icon("pie-chart"),
conditionalPanel( condition = "output.condition_selmlist==0",
br(),
shiny::selectInput("designFieldbook", "Design", c("Choose one" = "", design_choices), selected = 'RCBD',
multiple = FALSE),
design_conditional_panels()
),
conditionalPanel( condition = "output.condition_selmlist!=0",
br(),
#shiny::selectInput("design_geneticFieldbook", "Genetic design", c("Choose one" = "", genetic_design_choices) ,multiple = FALSE),
shiny::selectInput("design_geneticFieldbook", "Genetic design", c(genetic_design_choices) ,multiple = FALSE),
genetic_design_conditional_panels()
)
),
shiny::tabPanel("Environment", value = 'environment', icon = shiny::icon("recycle"),
br(),
#shiny::checkboxInput("designFieldbook_zigzag", "Zigzag", FALSE),
shiny::radioButtons("designFieldbook_serie", "Label series",
#get_series_labels(), "101, 102, ...", #get_series_labels()[[2]],
1:3, 1,
inline = TRUE)
,
# shiny::conditionalPanel(
# "input.designFieldbook == 'RCBD'",
#shiny::checkboxInput("designFieldbook_cont", "Continuous numbering of plots", FALSE)
#),
shiny::radioButtons("fbDesign_environment_type", "Environment type",choices = list(
"Field" = "Field",
#"Farmers field" = "farmers_field",
"Greenhouse" = "Greenhouse",
"Screenhouse" = "Screenhouse"),selected = "Field" , inline = TRUE),
shiny::checkboxInput("fbDesign_weather_cb", label = "Register weather data"),
shiny::checkboxInput("fbDesign_soil_cb", label = "Register soil data")
# )
#)
#)
),
# shiny::tabPanel("Field", value = "fbDesign_field", icon = shiny::icon("male"),
# shiny::numericInput("fbDesign_field_size (ha)",
# "Field size", 1, 1, 100)
# ),
# shiny::tabPanel("Farmers field", value = "fbDesign_farmers_field"
# ),
# shiny::tabPanel("Greenhouse", value = "fbDesign_greenhouse"
# ),
# shiny::tabPanel("Screenhouse", value = "fbDesign_screenhouse"
# ),
shiny::tabPanel("Plant Installation", value = "fbDesign_planting", icon = shiny::icon("th-large"),
br(),
# fluidRow(
# column(width = 6,
# box(
# title = "Step: 6", status = "warning", solidHeader = TRUE, collapsible = TRUE, width = NULL,
shiny::conditionalPanel(
"input.fbDesign_environment_type == 'Field'",
shiny::numericInput("fbDesign_nplantsrow",
"Number of plants per row", 10, 1, 100),
shiny::numericInput("fbDesign_nrowplot",
"Number of rows per plot", 1, 1, 100),
#shiny::numericInput("fbDesign_psize","Plot size", 30, 1, 100),
shiny::numericInput("fbDesign_distPlants",
"Distance between plants (m)", .3, .1, 1),
shiny::numericInput("fbDesign_distRows",
"Distance between rows (m)", .9, .1, 1),
shiny::uiOutput("fbPlanting_psize", inline=TRUE),
shiny::uiOutput("fbPlanting_pdensity", inline=TRUE),
tags$head(tags$style("#fbDesign_pdensity{color:#191919;
background-color:#ecc464;
#font-size: 20px;
#font-style: italic;
}"
)
),
tags$head(tags$style("#fbDesign_psize{color:#191919;
background-color:#88e3a5;
#font-size: 20px;
#font-style: italic;
}"
)
)
#,
),
shiny::conditionalPanel(
"input.fbDesign_environment_type == 'Field'",
# Deprecated code for number of plant per plot
# shiny::numericInput("fbDesign_nplants",
# "Number of plants per plot/pot", 10 , 1, 100)#,
#It replace the code above.
shiny::uiOutput("fbPlant_plot", inline = TRUE)
#
),
shiny::conditionalPanel(
"input.fbDesign_environment_type == 'Greenhouse'|
input.fbDesign_environment_type == 'Screenhouse'",
shiny::numericInput("fbDesign_nplantxpot",
"Number of plants per pot", 10 , 1, 10000),
shiny::numericInput("fbDesign_npots",
"Number of pots", 1, 1, 10000)#,
)
)#,
)#,
#shinyBS::bsAlert("alert_fb_done")
)
),
#fluidRow( #begin fluidrow
shinyWidgets::prettyRadioButtons(inputId = "fbdesign_book_export",
label = "Choose exportation:", choices = c("HIDAP format","FieldBookApp format"), icon = icon("check"),
bigger = TRUE, status = "info",inline = TRUE,
animation = "jelly"),
#),
shiny::conditionalPanel(
"input.fbdesign_book_export == 'HIDAP format'|
input.fbdesign_book_export == 'FieldBookApp format'",
HTML('<div style="float: right; margin: 0 16px 18px 0px;">'),
shiny::actionButton("fbDesign_draft", "Book Preview", icon("table"), style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
HTML('</div>')#,
),
#HIDAP format
shiny::conditionalPanel(
"input.fbdesign_book_export == 'HIDAP format'",
shinysky::actionButton2("fbDesign_create", label = "Download", icon ="file-excel-o", icon.library = "bootstrap", styleclass= "color: #fff; background-color: #51a351; border-color: #51a351")
),
shiny::conditionalPanel(
"input.fbdesign_book_export == 'FieldBookApp format'",
div(style="display: inline-block;vertical-align:top; width: 150px;", shiny::selectInput("fbdesign_year_fbapp",
"Select year", choices = 2000:3000, selected = 2018)),
# div(style="display: inline-block;vertical-align:top; width: 150px;", shiny::selectInput("fbdesign_cntry_fbapp",
# label="Select Country", choices = value = 0.5)),
div(style="display: inline-block;vertical-align:top; width: 200px;", uiOutput("oufbDesign_country_fbapp")),
div(style="display: inline-block;vertical-align:top; width: 150px;", shiny::textInput('fbdesign_abbruser_fbapp',
label = "Enter trial abbreviation",
value = "", placeholder = "ex.:STO (storage)")),
div(style="display: inline-block;vertical-align:top; width: 200px;", uiOutput("oufbDesign_location_fbapp"),
shiny::downloadButton(outputId = 'fbdesigin_downloadFbAppData', label = 'Download FieldBookApp File')
)
),
br(),
shinysky::shinyalert("alert_fb_done", FALSE, auto.close.after = 4),
shiny::fluidRow(
#box(
#column(width = 12,height=6,
shinydashboard::box(title = "Fieldbook Preview",
status = "primary",
#height = 500,
#width = NULL,
solidHeader = TRUE,
width = 12, collapsible = TRUE,
#shiny::actionButton("butNewFieldbook", "New fieldbook", inline = TRUE)#,
rhandsontable::rHandsontableOutput("fbDesign_table", height = 400)
),
br(),
br(),
br()
#)
#)
),
br(),
br(),
br()
), #end
ui_design_big(type="tab",title="Special Modules",name="phenotype_fieldbook_design")
######
################## End Simple Modules
)# End of Master tabSetPanel
)
}
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