inst/Shiny/myapp/ui.R
In p-schaefer/BenthicAnalysis: Benthic Analysis with Test Site Anlysis
shinyUI(
navbarPage(
"Benthic Analysis",
tabPanel("Introduction",
h2("Introduction"),
helpText("A package for the analysis of Benthic Macroinvertebrate (BMI) data
using a Reference Condition Approach. Impairment is determined using the Test Site Analysis (TSA).
This package provides functionallity for:"),
helpText("1) calculation of many commonly used indicator metrics for assessing the status BMI communities;"),
helpText("2) nearest-neighbour site matching using Assessment by Nearest-Neighbour
Analysis (ANNA), the Redundancy Analysis variant of ANNA (RDA-ANNA) or user-defined reference sites;"),
helpText("3) calculation of common Test Site Analysis parameters, including: F-statistic, non-centrality parameter, interval and equivalnce tests,
z-scores for all calculated metrics, mahalanobis distance scores for all sites, partial mahalanobis distance scores
for assessing significance of individual metrics, as well as upper and lower thresholds for impairment ranks;"),
helpText("4) a variety of diagnostic plots and tools for assessing the confidence of the impairment rank. These include a non-paramtetric randomization
test for the impairment rank, jacknife confidence intervals and consistency scores of the selected reference sites and jacknife consistancy of the
entire reference set."),
h2("Instructions"),
h3("Data Input"),
helpText("All input data files must have the same site identification structure.
All input data files must be in .csv format. On rare occasions clicking too many checkboxes in rapid succession
will result in the program getting stuck in an infinite loop and will require closing and reopening it."),
helpText("Minimum requirments are:" ),
helpText("1. Biological data as either raw taxa or summary metrics. Taxa data must follow the format of the example dataset- data('YKBioData')"),
helpText("2. At least one of the following: a table of environmental and habitat features for site
matching and/or a table matching test sites with pre-selected reference sites."),
helpText("3. If only habitat and environmental variables supplied for ANNA/RDA-ANNA site matching the user must specify
which sites are to be treated as reference vs test sites."),
h3("Individual Site Analysis"),
helpText("This section allows for detailed exploration of individual sites"),
h3("Batch Analysis"),
helpText("This section allows for analysis of large numbers of sites.
If the analysis is working correctly a progress bar will appear near the top of the display.
Do not interact with the user interface while the analysis is working, or it may get stuck in an infinte loop.")
),
#########################################################
#DATA INPUT
########################################################
navbarMenu("Data Input",
#########################################################
#Input biological Data
########################################################
tabPanel("Biological Data",
sidebarLayout(
sidebarPanel(
h3("Biological Data"),
helpText("Select file containing raw taxa data for calculating summary metrics, or metrics calculated by the user.",
"Taxa identifiers must to be split into 2 rows."),
fileInput("inbioFile", label = h4("File input - Taxa")),
checkboxInput("metdata",label="Input data are metrics",value=F),
numericInput("taxa.names",
label = h4("Number of rows used for taxa identifiers"),
value = 2),
numericInput("site.names",
label = h4("Number of columns used for site identifiers"),
value = 2),
br(),
"-------------------------------------",
br(),
conditionalPanel("input.metdata==false",actionButton('downloadmetricData', 'Export Metrc Data')),
actionButton('downloadtransmetricData', 'Export Transformed Metrc Data')
),
mainPanel(
tabsetPanel(type="tabs",
tabPanel("Taxa Data", dataTableOutput("bio.data.view")),
tabPanel("Metric Data", dataTableOutput("metric.data.view")),
tabPanel("Metric Summary", verbatimTextOutput("metric.summary.view")),
navbarMenu("Transformations",
tabPanel("Transformations",sidebarLayout(
sidebarPanel(
uiOutput("sel.met.for.trans"),
radioButtons("trans", label = h3("Transformation"),
choices = list("None" = "None", "Log10" = "Log10", "Log10+1" = "Log10+1", "Square Root" = "Square Root", "Inverse" = "Inverse", "Arcsine Sqare Root"= "Arcsine Sqare Root", "Logit" = "Logit", "Delete"="Delete"),
selected = "None"),
actionButton("apply.trans",label="Apply Selection"),
tableOutput("met.trans.table")
),
mainPanel(
plotOutput("met.trans.plot1"),
plotOutput("met.trans.plot2"),
verbatimTextOutput("trans.summary.stats")
)
)),
tabPanel("Transformed Data",dataTableOutput("transformed.data")))
)
)
)),
#########################################################
#Input Environmental Data
########################################################
tabPanel("Site Matching Data",
sidebarLayout(
sidebarPanel(
h3("Habitat and environmental data for ANNA/RDA-ANNA site matching and/or user matched reference sites"),
helpText("At least one of the following two file inputs is required. Site names must match format of biological data."),
br(),
helpText("Select file containing habitat and environmental data for site matching."),
fileInput("inenvFile", label = h4("File input")),
"-------------------------------------",
helpText("User matched test and reference samples."),
fileInput("inrefmatchFile", label = h4("File input")),
br(),
downloadButton('downloadenvData', 'Export Environmental Data')
),
mainPanel(
tabsetPanel(type="tabs",
tabPanel("Environmental Data", dataTableOutput("env.data.view")),
tabPanel("Environmental Data Summary", verbatimTextOutput("env.summary.view")),
tabPanel(title="Reference Site Matches",tableOutput("usersitematch.table"))
)
)
)),
#########################################################
#Identify Reference Sites
########################################################
tabPanel("Select Reference Sites",
sidebarLayout(
sidebarPanel(
h3("Select Reference sites"),
helpText("Select which sites should be treated as Reference sites.
Input file must have same site name structure as biological data file.
Reference sites are identified with a 1, test site with 0.
If user site matching data were provided, reference sites will already be
selected. Modifying the identified reference sites will disallow use of user matched reference sites"),
fileInput("inrefIDFile", label = h4("File input"))
),
mainPanel(
tabsetPanel(type="tabs",
tabPanel(title="Select Reference Sites",conditionalPanel("output.usersitematchwasmodified==0",helpText("User matched reference sites detected. Making changes here will disallow further use of user matched reference sites")),uiOutput("choose_columns")),
tabPanel(title="Selected Reference Sites",verbatimTextOutput("selrefID")),
tabPanel(title="Selected Test Sites",verbatimTextOutput("seltestID"))
)
)
))
),
#########################################################
#INDIVIDUAL SITE ANALYSIS
########################################################
navbarMenu("Individual Site Analysis",
#########################################################
#Test Site Selection
########################################################
tabPanel("Site Selection",
sidebarLayout(
sidebarPanel(
h2("Select Test site"),
helpText("Select which test site should be assessed")
),
mainPanel(tabPanel(title="Select test Site",uiOutput("sel.test.site")))
)),
#########################################################
#Reference Site Matching
########################################################
tabPanel("Reference Site Matching",
sidebarLayout(
sidebarPanel(
h2("Reference Site Matching"),
helpText("Both ANNA and RDA-ANNA "),
br(),
conditionalPanel("output.usersitematchwasmodified==1",
conditionalPanel("output.usersitematchavail==1",h4("User Matched Reference Sites")),
conditionalPanel("output.usersitematchavail==1",checkboxInput("user.ref.sitematch","User matched Reference Sites",value=F))
),
conditionalPanel("output.usersitematchwasmodified==0",helpText("User matched reference sites were modified and can no longer be used")
),
br(),
radioButtons("nn.method", label = h4("Nearest-Neighbour Method"),
choices = list("ANNA" = "ANNA", "RDA-ANNA" = "RDA-ANNA"), selected = "ANNA"),
checkboxInput("adaptive","Adaptive",value=T),
br(),
helpText("Number of reference sites to select. Acts as upper limit if Adaptive selection used."),
numericInput("k.sel", label = h4(""), value = 0)
),
mainPanel(
tabsetPanel(type="tabs",
tabPanel(title="Ordination Plot",
plotOutput("nn.ord",
brush=brushOpts(id = "nnord_brush",resetOnNew = TRUE),
dblclick=dblclickOpts(id="nnord_dclick"),
click=clickOpts(id="nnord_click"),
hover=hoverOpts(id="nnord_hover")),
br(),
wellPanel(h3('Display Axis'),uiOutput("site.match.axis"))),
tabPanel(title="Nearest-Neighbour Distance Plot",
plotOutput("nn.dist",
brush=brushOpts(id = "nndist_brush",resetOnNew = TRUE),
dblclick=dblclickOpts(id="nndist_dclick"),
click=clickOpts(id="ndist_click"),
hover=hoverOpts(id="ndist_hover"))),
tabPanel(title="Model Results",verbatimTextOutput("nn.table")),
tabPanel(title="Selected Reference Sites",verbatimTextOutput("nn.table2"))
)
))),
#########################################################
#Select metrics
########################################################
tabPanel("Select Indicator Metrics",
sidebarLayout(
sidebarPanel(
h2("Select Indicator Metrics"),
helpText("Select which indicator metrics should be used for further analysis.",
"Adaptive metric selection is available if input biological data were raw taxa counts."),
actionButton("selectallmet", label = "Select All"),
actionButton("selectnonemet", label = "Select None"),
br(),
#conditionalPanel("input.metdata==false",
#conditionalPanel("output.nnmethodselected==1",
checkboxInput("mselect","Automatically select indicator metrics for analysis?",value=F)
#)
#)
),
mainPanel(
tabsetPanel(type="tabs",
tabPanel(title="Select Indicator Metrics",uiOutput("choose_columns1")),
tabPanel(title="Indicator Metric Correlations",plotOutput("indicator.pairs.plot"))
)
)
)),
#########################################################
#Test Site Analysis
########################################################
tabPanel("Test Site Anlaysis",
sidebarLayout(
sidebarPanel(
h2("Test Site Analysis"),
helpText("Text describing TSA"),
br(),
br(),
checkboxInput("distance","Use ecological distance to weigh Mahalanobis Distance?",value=F),
checkboxInput("outlier.rem","Remove outlier reference sites?",value=F),
conditionalPanel("input['outlier.rem']==true",sliderInput("outbound.input",label="Boundary for defining outliers",min=0,max=0.8,step=0.05,value=0.15)),
br(),
h4("Selected Reference Sites"),
tableOutput("display.ref.sites"),
br(),
conditionalPanel("input['outlier.rem']==true",h4("Outlier Reference Sites")),
conditionalPanel("input['outlier.rem']==true",tableOutput("display.outlier.ref.sites"))
),
mainPanel(
tabsetPanel(type="tabs",
#tabPanel(title="Testing",
# dataTableOutput("testing")),
tabPanel(title="Mahalanobis Distance Plot",
plotOutput("tsa.distplot")),#,height=600)),
tabPanel(title="Indicator Metric Boxplots",
plotOutput("tsa.boxplot")),#,height=600)),
tabPanel(title="Mahalanobis Distance PCOA",
plotOutput("tsa.pcoa")),#,height=600)),
tabPanel(title="Correspondance Analysis",
plotOutput("tsa.ca")),#,height=600)),
tabPanel(title="Selected Metrics",
conditionalPanel("input.mselect==true",verbatimTextOutput("print.sel.met"))),
tabPanel(title="Tables",
tabsetPanel(type="pills",
tabPanel(title="TSA Results",verbatimTextOutput("tsa.results")),
tabPanel(title="Partial TSA Results",verbatimTextOutput("ptsa.results")),
tabPanel(title="Jacknife Consistency", verbatimTextOutput("tsa.jack"))
))
)
))
)),
#########################################################
#Batch ANALYSIS
########################################################
navbarMenu("Batch Analysis",
#########################################################
#Batch ANNA
########################################################
tabPanel("Configure",
mainPanel(
tabsetPanel(type="tabs",
tabPanel(title="Options",
fluidRow(wellPanel(
uiOutput("batch.nn.method"))
),
conditionalPanel(condition="output.dataavail==1",
fluidRow(
column(7,
conditionalPanel(condition = "input.nnmethod!='User Selected'",
wellPanel(
h4("Site Matching Options"),
helpText("Use an adaptive threshold to determine the number of nearest neighbour reference sites?"),
checkboxInput("ab.adaptive2","Adaptive",value=T),
helpText("Number of reference sites to select. Acts as upper limit if Adaptive selection used."),
numericInput("ab.k.sel2", label = h4(""), value = 0)
)),
wellPanel(
h4("Test Site Analysis Options"),
conditionalPanel(condition = "output.envdataavail1==1",checkboxInput("ab.distance","Use ecological distance to weigh Mahalanobis Distance?",value=F)),
checkboxInput("ab.outlier.rem","Remove outlier reference sites?",value=F)
),
conditionalPanel(condition="output.envdataavail==1",
conditionalPanel(condition="output.ecodistwithuserrefsites==1",fluidRow(wellPanel(h4("Ecological distance Calculation:"),
radioButtons("nnmethod.user",label="For weighted mahalanobis distance calculation only:",choices=c("ANNA","RDA-ANNA"),inline=T),
helpText("Use an adaptive threshold to determine the number of nearest neighbour reference sites?"),
checkboxInput("ab.adaptive1","Adaptive",value=T),
helpText("Number of reference sites to select. Acts as upper limit if Adaptive selection used."),
numericInput("ab.k.sel1", label = h4(""), value = 0)
)))
),
wellPanel(
h4("Ouptput and plotting Options"),
actionButton("ab.dir","Select Directory"),
helpText("Selection window may open minimized, check the task bar."),
textOutput("show.sel.dir"),
"-----------------------------------------",
conditionalPanel("output.envdataavail1==1",checkboxInput("ab.nnscatter.plot","Print Nearest-Neighbour ordination plot?",value=F)),
conditionalPanel("input.nnmethod!='User Selected'",checkboxInput("ab.nndist.plot","Print Nearest-Neighbour distance plot?",value=F)),
checkboxInput("ab.tsadist.plot","Print TSA distance plot?",value=F),
checkboxInput("ab.tsabox.plot","Print TSA boxplot?",value=F),
checkboxInput("ab.tsascatter.plot","Print TSA ordination plot?",value=F),
checkboxInput("ab.cascatter.plot","Print CA ordination plot?",value=F),
checkboxInput("ab.multi.plot","Print multi plot?",value=F),
conditionalPanel("input['ab.multi.plot']==true",
uiOutput("multiplot1"))
),
wellPanel(
conditionalPanel(condition="output.seldir==0",
helpText("Select output directory and at least 3 indicator metrics to begin batch run")
),
conditionalPanel(condition="output.seldir==1",
actionButton("ab.go","Run")
)
)
),
column(5,
wellPanel(
h4("Metric Selection"),
conditionalPanel(condition="input.metdata==false",
conditionalPanel("input.nnmethod!='RDA-ANNA'",checkboxInput("ab.m.select","Automatically select indicator metrics for analysis?",value=F))),
br(),
helpText("Selected Indicator Metrics"),
actionButton("ab.selectallmet", label = "Select All"),
actionButton("ab.selectnonemet", label = "Select None"),
uiOutput("ab.choose_columns1")
))
))),
tabPanel(title="Results",
conditionalPanel(condition = "output.abdone==1",
dataTableOutput("ab.results")))
))))
))
p-schaefer/BenthicAnalysis documentation built on May 3, 2023, 5:49 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
shinyUI(
navbarPage(
"Benthic Analysis",
tabPanel("Introduction",
h2("Introduction"),
helpText("A package for the analysis of Benthic Macroinvertebrate (BMI) data
using a Reference Condition Approach. Impairment is determined using the Test Site Analysis (TSA).
This package provides functionallity for:"),
helpText("1) calculation of many commonly used indicator metrics for assessing the status BMI communities;"),
helpText("2) nearest-neighbour site matching using Assessment by Nearest-Neighbour
Analysis (ANNA), the Redundancy Analysis variant of ANNA (RDA-ANNA) or user-defined reference sites;"),
helpText("3) calculation of common Test Site Analysis parameters, including: F-statistic, non-centrality parameter, interval and equivalnce tests,
z-scores for all calculated metrics, mahalanobis distance scores for all sites, partial mahalanobis distance scores
for assessing significance of individual metrics, as well as upper and lower thresholds for impairment ranks;"),
helpText("4) a variety of diagnostic plots and tools for assessing the confidence of the impairment rank. These include a non-paramtetric randomization
test for the impairment rank, jacknife confidence intervals and consistency scores of the selected reference sites and jacknife consistancy of the
entire reference set."),
h2("Instructions"),
h3("Data Input"),
helpText("All input data files must have the same site identification structure.
All input data files must be in .csv format. On rare occasions clicking too many checkboxes in rapid succession
will result in the program getting stuck in an infinite loop and will require closing and reopening it."),
helpText("Minimum requirments are:" ),
helpText("1. Biological data as either raw taxa or summary metrics. Taxa data must follow the format of the example dataset- data('YKBioData')"),
helpText("2. At least one of the following: a table of environmental and habitat features for site
matching and/or a table matching test sites with pre-selected reference sites."),
helpText("3. If only habitat and environmental variables supplied for ANNA/RDA-ANNA site matching the user must specify
which sites are to be treated as reference vs test sites."),
h3("Individual Site Analysis"),
helpText("This section allows for detailed exploration of individual sites"),
h3("Batch Analysis"),
helpText("This section allows for analysis of large numbers of sites.
If the analysis is working correctly a progress bar will appear near the top of the display.
Do not interact with the user interface while the analysis is working, or it may get stuck in an infinte loop.")
),
#########################################################
#DATA INPUT
########################################################
navbarMenu("Data Input",
#########################################################
#Input biological Data
########################################################
tabPanel("Biological Data",
sidebarLayout(
sidebarPanel(
h3("Biological Data"),
helpText("Select file containing raw taxa data for calculating summary metrics, or metrics calculated by the user.",
"Taxa identifiers must to be split into 2 rows."),
fileInput("inbioFile", label = h4("File input - Taxa")),
checkboxInput("metdata",label="Input data are metrics",value=F),
numericInput("taxa.names",
label = h4("Number of rows used for taxa identifiers"),
value = 2),
numericInput("site.names",
label = h4("Number of columns used for site identifiers"),
value = 2),
br(),
"-------------------------------------",
br(),
conditionalPanel("input.metdata==false",actionButton('downloadmetricData', 'Export Metrc Data')),
actionButton('downloadtransmetricData', 'Export Transformed Metrc Data')
),
mainPanel(
tabsetPanel(type="tabs",
tabPanel("Taxa Data", dataTableOutput("bio.data.view")),
tabPanel("Metric Data", dataTableOutput("metric.data.view")),
tabPanel("Metric Summary", verbatimTextOutput("metric.summary.view")),
navbarMenu("Transformations",
tabPanel("Transformations",sidebarLayout(
sidebarPanel(
uiOutput("sel.met.for.trans"),
radioButtons("trans", label = h3("Transformation"),
choices = list("None" = "None", "Log10" = "Log10", "Log10+1" = "Log10+1", "Square Root" = "Square Root", "Inverse" = "Inverse", "Arcsine Sqare Root"= "Arcsine Sqare Root", "Logit" = "Logit", "Delete"="Delete"),
selected = "None"),
actionButton("apply.trans",label="Apply Selection"),
tableOutput("met.trans.table")
),
mainPanel(
plotOutput("met.trans.plot1"),
plotOutput("met.trans.plot2"),
verbatimTextOutput("trans.summary.stats")
)
)),
tabPanel("Transformed Data",dataTableOutput("transformed.data")))
)
)
)),
#########################################################
#Input Environmental Data
########################################################
tabPanel("Site Matching Data",
sidebarLayout(
sidebarPanel(
h3("Habitat and environmental data for ANNA/RDA-ANNA site matching and/or user matched reference sites"),
helpText("At least one of the following two file inputs is required. Site names must match format of biological data."),
br(),
helpText("Select file containing habitat and environmental data for site matching."),
fileInput("inenvFile", label = h4("File input")),
"-------------------------------------",
helpText("User matched test and reference samples."),
fileInput("inrefmatchFile", label = h4("File input")),
br(),
downloadButton('downloadenvData', 'Export Environmental Data')
),
mainPanel(
tabsetPanel(type="tabs",
tabPanel("Environmental Data", dataTableOutput("env.data.view")),
tabPanel("Environmental Data Summary", verbatimTextOutput("env.summary.view")),
tabPanel(title="Reference Site Matches",tableOutput("usersitematch.table"))
)
)
)),
#########################################################
#Identify Reference Sites
########################################################
tabPanel("Select Reference Sites",
sidebarLayout(
sidebarPanel(
h3("Select Reference sites"),
helpText("Select which sites should be treated as Reference sites.
Input file must have same site name structure as biological data file.
Reference sites are identified with a 1, test site with 0.
If user site matching data were provided, reference sites will already be
selected. Modifying the identified reference sites will disallow use of user matched reference sites"),
fileInput("inrefIDFile", label = h4("File input"))
),
mainPanel(
tabsetPanel(type="tabs",
tabPanel(title="Select Reference Sites",conditionalPanel("output.usersitematchwasmodified==0",helpText("User matched reference sites detected. Making changes here will disallow further use of user matched reference sites")),uiOutput("choose_columns")),
tabPanel(title="Selected Reference Sites",verbatimTextOutput("selrefID")),
tabPanel(title="Selected Test Sites",verbatimTextOutput("seltestID"))
)
)
))
),
#########################################################
#INDIVIDUAL SITE ANALYSIS
########################################################
navbarMenu("Individual Site Analysis",
#########################################################
#Test Site Selection
########################################################
tabPanel("Site Selection",
sidebarLayout(
sidebarPanel(
h2("Select Test site"),
helpText("Select which test site should be assessed")
),
mainPanel(tabPanel(title="Select test Site",uiOutput("sel.test.site")))
)),
#########################################################
#Reference Site Matching
########################################################
tabPanel("Reference Site Matching",
sidebarLayout(
sidebarPanel(
h2("Reference Site Matching"),
helpText("Both ANNA and RDA-ANNA "),
br(),
conditionalPanel("output.usersitematchwasmodified==1",
conditionalPanel("output.usersitematchavail==1",h4("User Matched Reference Sites")),
conditionalPanel("output.usersitematchavail==1",checkboxInput("user.ref.sitematch","User matched Reference Sites",value=F))
),
conditionalPanel("output.usersitematchwasmodified==0",helpText("User matched reference sites were modified and can no longer be used")
),
br(),
radioButtons("nn.method", label = h4("Nearest-Neighbour Method"),
choices = list("ANNA" = "ANNA", "RDA-ANNA" = "RDA-ANNA"), selected = "ANNA"),
checkboxInput("adaptive","Adaptive",value=T),
br(),
helpText("Number of reference sites to select. Acts as upper limit if Adaptive selection used."),
numericInput("k.sel", label = h4(""), value = 0)
),
mainPanel(
tabsetPanel(type="tabs",
tabPanel(title="Ordination Plot",
plotOutput("nn.ord",
brush=brushOpts(id = "nnord_brush",resetOnNew = TRUE),
dblclick=dblclickOpts(id="nnord_dclick"),
click=clickOpts(id="nnord_click"),
hover=hoverOpts(id="nnord_hover")),
br(),
wellPanel(h3('Display Axis'),uiOutput("site.match.axis"))),
tabPanel(title="Nearest-Neighbour Distance Plot",
plotOutput("nn.dist",
brush=brushOpts(id = "nndist_brush",resetOnNew = TRUE),
dblclick=dblclickOpts(id="nndist_dclick"),
click=clickOpts(id="ndist_click"),
hover=hoverOpts(id="ndist_hover"))),
tabPanel(title="Model Results",verbatimTextOutput("nn.table")),
tabPanel(title="Selected Reference Sites",verbatimTextOutput("nn.table2"))
)
))),
#########################################################
#Select metrics
########################################################
tabPanel("Select Indicator Metrics",
sidebarLayout(
sidebarPanel(
h2("Select Indicator Metrics"),
helpText("Select which indicator metrics should be used for further analysis.",
"Adaptive metric selection is available if input biological data were raw taxa counts."),
actionButton("selectallmet", label = "Select All"),
actionButton("selectnonemet", label = "Select None"),
br(),
#conditionalPanel("input.metdata==false",
#conditionalPanel("output.nnmethodselected==1",
checkboxInput("mselect","Automatically select indicator metrics for analysis?",value=F)
#)
#)
),
mainPanel(
tabsetPanel(type="tabs",
tabPanel(title="Select Indicator Metrics",uiOutput("choose_columns1")),
tabPanel(title="Indicator Metric Correlations",plotOutput("indicator.pairs.plot"))
)
)
)),
#########################################################
#Test Site Analysis
########################################################
tabPanel("Test Site Anlaysis",
sidebarLayout(
sidebarPanel(
h2("Test Site Analysis"),
helpText("Text describing TSA"),
br(),
br(),
checkboxInput("distance","Use ecological distance to weigh Mahalanobis Distance?",value=F),
checkboxInput("outlier.rem","Remove outlier reference sites?",value=F),
conditionalPanel("input['outlier.rem']==true",sliderInput("outbound.input",label="Boundary for defining outliers",min=0,max=0.8,step=0.05,value=0.15)),
br(),
h4("Selected Reference Sites"),
tableOutput("display.ref.sites"),
br(),
conditionalPanel("input['outlier.rem']==true",h4("Outlier Reference Sites")),
conditionalPanel("input['outlier.rem']==true",tableOutput("display.outlier.ref.sites"))
),
mainPanel(
tabsetPanel(type="tabs",
#tabPanel(title="Testing",
# dataTableOutput("testing")),
tabPanel(title="Mahalanobis Distance Plot",
plotOutput("tsa.distplot")),#,height=600)),
tabPanel(title="Indicator Metric Boxplots",
plotOutput("tsa.boxplot")),#,height=600)),
tabPanel(title="Mahalanobis Distance PCOA",
plotOutput("tsa.pcoa")),#,height=600)),
tabPanel(title="Correspondance Analysis",
plotOutput("tsa.ca")),#,height=600)),
tabPanel(title="Selected Metrics",
conditionalPanel("input.mselect==true",verbatimTextOutput("print.sel.met"))),
tabPanel(title="Tables",
tabsetPanel(type="pills",
tabPanel(title="TSA Results",verbatimTextOutput("tsa.results")),
tabPanel(title="Partial TSA Results",verbatimTextOutput("ptsa.results")),
tabPanel(title="Jacknife Consistency", verbatimTextOutput("tsa.jack"))
))
)
))
)),
#########################################################
#Batch ANALYSIS
########################################################
navbarMenu("Batch Analysis",
#########################################################
#Batch ANNA
########################################################
tabPanel("Configure",
mainPanel(
tabsetPanel(type="tabs",
tabPanel(title="Options",
fluidRow(wellPanel(
uiOutput("batch.nn.method"))
),
conditionalPanel(condition="output.dataavail==1",
fluidRow(
column(7,
conditionalPanel(condition = "input.nnmethod!='User Selected'",
wellPanel(
h4("Site Matching Options"),
helpText("Use an adaptive threshold to determine the number of nearest neighbour reference sites?"),
checkboxInput("ab.adaptive2","Adaptive",value=T),
helpText("Number of reference sites to select. Acts as upper limit if Adaptive selection used."),
numericInput("ab.k.sel2", label = h4(""), value = 0)
)),
wellPanel(
h4("Test Site Analysis Options"),
conditionalPanel(condition = "output.envdataavail1==1",checkboxInput("ab.distance","Use ecological distance to weigh Mahalanobis Distance?",value=F)),
checkboxInput("ab.outlier.rem","Remove outlier reference sites?",value=F)
),
conditionalPanel(condition="output.envdataavail==1",
conditionalPanel(condition="output.ecodistwithuserrefsites==1",fluidRow(wellPanel(h4("Ecological distance Calculation:"),
radioButtons("nnmethod.user",label="For weighted mahalanobis distance calculation only:",choices=c("ANNA","RDA-ANNA"),inline=T),
helpText("Use an adaptive threshold to determine the number of nearest neighbour reference sites?"),
checkboxInput("ab.adaptive1","Adaptive",value=T),
helpText("Number of reference sites to select. Acts as upper limit if Adaptive selection used."),
numericInput("ab.k.sel1", label = h4(""), value = 0)
)))
),
wellPanel(
h4("Ouptput and plotting Options"),
actionButton("ab.dir","Select Directory"),
helpText("Selection window may open minimized, check the task bar."),
textOutput("show.sel.dir"),
"-----------------------------------------",
conditionalPanel("output.envdataavail1==1",checkboxInput("ab.nnscatter.plot","Print Nearest-Neighbour ordination plot?",value=F)),
conditionalPanel("input.nnmethod!='User Selected'",checkboxInput("ab.nndist.plot","Print Nearest-Neighbour distance plot?",value=F)),
checkboxInput("ab.tsadist.plot","Print TSA distance plot?",value=F),
checkboxInput("ab.tsabox.plot","Print TSA boxplot?",value=F),
checkboxInput("ab.tsascatter.plot","Print TSA ordination plot?",value=F),
checkboxInput("ab.cascatter.plot","Print CA ordination plot?",value=F),
checkboxInput("ab.multi.plot","Print multi plot?",value=F),
conditionalPanel("input['ab.multi.plot']==true",
uiOutput("multiplot1"))
),
wellPanel(
conditionalPanel(condition="output.seldir==0",
helpText("Select output directory and at least 3 indicator metrics to begin batch run")
),
conditionalPanel(condition="output.seldir==1",
actionButton("ab.go","Run")
)
)
),
column(5,
wellPanel(
h4("Metric Selection"),
conditionalPanel(condition="input.metdata==false",
conditionalPanel("input.nnmethod!='RDA-ANNA'",checkboxInput("ab.m.select","Automatically select indicator metrics for analysis?",value=F))),
br(),
helpText("Selected Indicator Metrics"),
actionButton("ab.selectallmet", label = "Select All"),
actionButton("ab.selectnonemet", label = "Select None"),
uiOutput("ab.choose_columns1")
))
))),
tabPanel(title="Results",
conditionalPanel(condition = "output.abdone==1",
dataTableOutput("ab.results")))
))))
))
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