inst/shinyApp/ui_layers/ui_settings.R
In luismurao/ntbox: From Getting Biodiversity Data to Evaluating Species Distribution Models in a Friendly GUI Environment
# App Settings & Materials (tutorials and intro to the app)
osSystem <- Sys.info()["sysname"]
materials <- sidebarLayout(position = "left",
sidebarPanel(
tags$head(
tags$script(src = paste0('http://cdn.mathjax.org/',
'mathjax/latest/MathJax.js',
'?config=TeX-AMS-MML_HTMLorMML'),
type = 'text/javascript'),
includeScript("ui_layers/style/google-analytics.js")
),
titlePanel("NicheToolBox"),
#h3('Welcome to NTB'),
br(),
p(paste0("This application has some tools",
" to analyze and visualize the niche. ",
"In this page you will find the",
" settings of the app.")),
h4("Workflow"),
HTML(paste('Select a folder to save the files and data',
"generated in NicheToolBox. Once you have" ,
"specified the workflow directory, just press the",
strong("Save state"), "button located the top-left",
"corner of the application.")),
br(),br(),
conditionalPanel(paste0("'",osSystem,"' == 'Windows'"),
directoryInput('wf_directory',
label = 'Select workflow directory')),
conditionalPanel(paste0("'",osSystem,"' != 'Windows'"),
shinyFiles::shinyDirButton(id = "wf_directory",
label = "Select workflow directory",
title = "Select a directory from the
directories panel",
icon = icon("folder-open",
lib = "glyphicon"),
buttonType = "info"),
br(),
HTML(paste('<div class="alert alert-info" role="alert">',
verbatimTextOutput("work_directory"),'</div>'))
),
#h3('Settings'),
br(),
h4("Niche layers"),
p(paste0("One ne of the most important ",
"things for your data analysis",
" in NTB is to select the folder",
" with the raster layers that you ",
"will use as niche variables.")),
br(),
p("Please select the folder of raster",
" layers; notice that all of them",
" need to be in the same resolution",
" and extension."),
p("The supported raster formats are: ",".asc",
".bil",",",".tif",",",".nc.",
",",".sdat",",",".img"),
br(),
#directoryInput('ras_layers_directory', label = 'Select a raster layers directory'),
#glyphicon glyphicon-folder-open
conditionalPanel(paste0("'",osSystem,"' == 'Windows'"),
directoryInput('ras_layers_directory',
label = paste('Select a raster',
' layers directory')),
br(),
checkboxInput("load_projLayers_win",
label = "Select projection layers",
value = FALSE),
conditionalPanel("input.load_projLayers_win == true",
h4("Projection layers"),
paste0("These are the layers",
" of environmental change",
" scenario. Please make sure",
" that their names are the",
" same as the niche layers."),
br(),
directoryInput('proj_layers_directory',
label = paste0('Select',
' projection',
' layers',
' directory')))
),
conditionalPanel(paste0("'",osSystem,"' != 'Windows'"),
shinyFiles::shinyDirButton(id = "ras_layers_directory",
label = paste0("Select raster",
" layers directory"),
title = paste0("Select a directory",
" from ",
"the directories panel"),
icon = icon("folder-open",
lib = "glyphicon"),
buttonType = "info"),
br(),
HTML(paste('<div class="alert alert-info" role="alert">',
verbatimTextOutput("layers_directory"),'</div>')),
br(),br(),
checkboxInput("load_projLayers",
label = "Select projection layers",
value = FALSE),
conditionalPanel("input.load_projLayers == true",
h4("Projection layers"),
paste0("This are the layers of",
" environmental change scenario.\n\n",
"NicheToolBox uses them either",
" to project the niche models or",
" the PCAs ",
"computed for your niche layers.\n\n"),
paste0("Please make sure that their",
" names are the same as the",
" niche layers."),
br(),br(),
shinyFiles::shinyDirButton(id = paste0(
"proj_layers_directory"),
label =paste0("Select projection",
" layers directory"),
title = paste0("Select a directory",
" from the directories panel"),
icon = icon("folder-open",
lib = "glyphicon"),
buttonType = "info"),
HTML(paste('<div class="alert alert-info"',
' role="alert">',
verbatimTextOutput("proj_directory"),
'</div>')))),
p(paste0("If you dont have environmental",
" data ntbox provides methods from",
" `raster` package and other sources ("),
HTML('<a href="http://worldclim.org/" target="_blank"> WorldClim</a>,'),
HTML('<a href="http://chelsa-climate.org" target="_blank"> CHELSA</a>,'),
HTML('<a href="http://www.bio-oracle.org" target="_blank"> Bio-Oracle</a>,'),
HTML('<a href="https://envirem.github.io" target="_blank"> ENVIREM</a>'),
") to get environmental data."),
checkboxInput("getEnvData",label = "Get environmental data",value = FALSE),
conditionalPanel("input.getEnvData == true",
selectInput("env_data",label = "Select a source",
choices = c("WorldClim current"="wc",
"CMIP5 future"="wc_future",
"CHELSA current (1 km)" = "ch_pre",
"CHELSA future (1 km)" = "ch_fut",
"ENVIREM current" ="env_pres",
"ENVIREM past" = "env_pass",
"ENVIREM elevation current" ="env_elev_pres",
"ENVIREM elevation past" ="env_elev_pass",
"Bio-Oracle present
(via sdmpredictors)"="bio_pre",
"Bio-Oracle future
(via sdmpredictors)"="bio_fut")),
conditionalPanel("input.env_data=='wc_future'",
selectInput("CMIP5_mod",
"Select a model",
c("ACCESS1-0"= "AC",
"BCC-CSM1-1"="BC",
"CCSM4"="CC",
"CESM1-CAM5-1-FV2"="CE",
"CNRM-CM5"="CN",
"GFDL-CM3"="GF",
"GFDL-ESM2G"="GD",
"GISS-E2-R"="GS",
"HadGEM2-AO"="HD",
"HadGEM2-CC"="HG",
"HadGEM2-ES"="HE",
"INMCM4"="IN",
"IPSL-CM5A-LR"="IP",
"MIROC-ESM-CHEM"="MI",
"MIROC-ESM"="MR",
"MIROC5"="MC",
"MPI-ESM-LR"="MP",
"MRI-CGCM3"="MG",
"NorESM1-M"="NO"),
selected = "CC"),
radioButtons("year_sc","Select a year scenario",
c("2050"=50,"2070"=70)),
radioButtons("rcp","Select a RCP",
c("rcp26"=26,"rcp45"=45,
"rcp60"=60,"rcp85"=85),
selected = 85)),
conditionalPanel("input.env_data=='wc' ||
input.env_data=='wc_future'",
shiny::radioButtons("wc_var",
label = "Select an option",
choices = c("Bioclim"="bio",
"Min temperature
"='tmin',
"Max temperature
"='tmax',
"Precipitation"=
'prec')),
shiny::radioButtons("wc_resol",
label = "Select a resolution",
choices = c("10 minutes"=10,
"5 minutes"=5,
"2.5 minutes"=2.5,
"30 seconds"=0.5))
),
conditionalPanel("input.env_data == 'ch_fut'",
radioButtons("ch_period",
label = "Select a time period",
choices = c("2041-2060",
"2061-2080")),
radioButtons("ch_rcp",
label="Select a RCP",
choices=c("rcp26",
"rcp45",
"rcp85")),
selectInput("ch_model",
label="Select a circulation model",
choices = c('ACCESS1-0',
'bcc-csm1-1',
'BNU-ESM',
'CanESM2',
'CCSM4',
'CESM1-BGC',
'CESM1-CAM5',
'CMCC-CM',
'CMCC-CMS',
'CNRM-CM5',
'CSIRO-Mk3-6-0',
'FGOALS-g2',
'FIO-ESM',
'GFDL-CM3',
'GFDL-ESM2G',
'GFDL-ESM2M',
'GISS-E2-H',
'GISS-E2-H-CC',
'GISS-E2-R',
'GISS-E2-R-CC',
'HadGEM2-AO',
'HadGEM2-CC',
'inmcm4',
'IPSL-CM5A-LR',
'IPSL-CM5A-MR',
'MIROC-ESM',
'MIROC-ESM-CHEM',
'MIROC5',
'MPI-ESM-LR',
'MPI-ESM-MR',
'MRI-CGCM3',
'MRI-ESM1',
'NorESM1-M'))
),
conditionalPanel("input.env_data=='wc' ||
input.env_data=='wc_future'",
radioButtons('env_format',
paste0('Select a format to write',
' your layers. If you have',
' set the workflow','
directory they will be',
' saved on it; otherwise',
' they will be saved in',
' the working directory',
' of your R session.'),
c('.asc','.bil',
'.tif','.nc',
'.sdat','.img'))
),
conditionalPanel("input.env_data=='ch_pre' ||
input.env_data=='ch_fut' ||
input.env_data=='bio_pre' ||
input.env_data=='bio_fut'",
#p(paste0("Get bioclimatic data",
# "from CHELSA")),
checkboxInput("ch_parallel",
"Download in parallel",
value = TRUE)
),
conditionalPanel("input.env_data=='env_pres' ||
input.env_data=='env_pass' ||
input.env_data=='env_elev_pres' ||
input.env_data=='env_elev_pass'",
selectInput("env_reg","Select a region",
choices = c("Africa",
"Australia",
"Eurasia",
"Europe",
"Global"="global",
"NAmerica",
"NewWorld",
"Pacific",
"SAmerica"),
selected = "global"),
conditionalPanel("input.env_data=='env_pass' ||
input.env_data=='env_elev_pass'",
radioButtons("env_period",
"Select time period",
choices = c("Mid-Holocene"=
"holo",
"Last Glacial
Maximum"="lgm")),
conditionalPanel("input.env_data=='env_pass'",
radioButtons("env_gcm",
"Global
circulation
model",
choices = c("ccsm4",
"miroc_esm",
"mpi_esm_p")))
),
radioButtons("env_res",
"Select a resolution",
choices = c("10 arcmin"="10arcmin",
"5 arcmin"="5arcmin",
"2.5 arcmin"="2.5arcmin",
"30 arcsec"="30arcsec")),
radioButtons("env_fmt","Select layers format",
choices = c("geotiff","bil"))
),
conditionalPanel("input.env_data=='bio_fut'",
radioButtons("bio_year",
"Select a year",
choices = c("2050",
"2100",
"2200")),
radioButtons("bio_model",
"Select a model",
choices = c("a")),
radioButtons("bio_scenario",
label = "Select a scenario",
choices = c("a")),
selectInput("bio_type_fut",
label = "Select a variable",
choices = c("a"))
),
conditionalPanel("input.env_data=='bio_pre'",
selectInput("bio_type",
label = "Select a variable",
choices=c('salinity',
'sea_surface_temperature',
'current_velocity',
'sea_water_temperature',
'sea_water_salinity',
'sea_ice_thickness',
'chlorophyll_concentration',
'sea_surface_salinity'))
),
conditionalPanel("input.env_data=='wc' ||
input.env_data=='ch_pre' ||
input.env_data=='env_pres' ||
input.env_data=='env_elev_pres' ||
input.env_data=='bio_pre'",
bsButton("get_now","Get it",
icon = icon("download", lib = "glyphicon"),
style = "primary")
),
conditionalPanel("input.env_data=='wc_future' ||
input.env_data=='ch_fut' ||
input.env_data== 'env_pass' ||
input.env_data== 'env_elev_pass' ||
input.env_data== 'bio_fut'",
bsButton("get_now_future","Get it",
icon = icon("download",
lib = "glyphicon"),
style = "primary")
),
br()
),
bsButton("loadNicheLayers",
"Load niche layers",
icon = icon("upload",
lib = "glyphicon"),
style = "primary"),
busyIndicator("Loading...",wait = 0),
br()
#fileInput(inputId = "worflowPath","Select a folder for your worflow"),
#shinyDirButton('worflowPath', 'Folder select', 'Please select a folder'),
#shinyDirButton("workflowPath",title = "Choose Download Directory",
# label = "Browse Download Directory ", class = "btn-block btn-link"),
#submitButton()
#h4('Tutorials'),
#HTML('In this part you can find some tutorials that show how to use the app.'),
#selectInput(inputId = 'tutorialsm',label = 'Select one of the turtorials',
# choices = c('About'='about1','1. Data'='datose'),
# selected = "about1",multiple = FALSE)
),
mainPanel(
#htmlOutput("page"),
plotOutput("niche_layers"),
conditionalPanel("input.load_projLayers == true ||
input.load_projLayers_win == true",
plotOutput("niche_layers_proj")
)
)
)
luismurao/ntbox documentation built on May 9, 2024, 8:24 p.m.
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# App Settings & Materials (tutorials and intro to the app)
osSystem <- Sys.info()["sysname"]
materials <- sidebarLayout(position = "left",
sidebarPanel(
tags$head(
tags$script(src = paste0('http://cdn.mathjax.org/',
'mathjax/latest/MathJax.js',
'?config=TeX-AMS-MML_HTMLorMML'),
type = 'text/javascript'),
includeScript("ui_layers/style/google-analytics.js")
),
titlePanel("NicheToolBox"),
#h3('Welcome to NTB'),
br(),
p(paste0("This application has some tools",
" to analyze and visualize the niche. ",
"In this page you will find the",
" settings of the app.")),
h4("Workflow"),
HTML(paste('Select a folder to save the files and data',
"generated in NicheToolBox. Once you have" ,
"specified the workflow directory, just press the",
strong("Save state"), "button located the top-left",
"corner of the application.")),
br(),br(),
conditionalPanel(paste0("'",osSystem,"' == 'Windows'"),
directoryInput('wf_directory',
label = 'Select workflow directory')),
conditionalPanel(paste0("'",osSystem,"' != 'Windows'"),
shinyFiles::shinyDirButton(id = "wf_directory",
label = "Select workflow directory",
title = "Select a directory from the
directories panel",
icon = icon("folder-open",
lib = "glyphicon"),
buttonType = "info"),
br(),
HTML(paste('<div class="alert alert-info" role="alert">',
verbatimTextOutput("work_directory"),'</div>'))
),
#h3('Settings'),
br(),
h4("Niche layers"),
p(paste0("One ne of the most important ",
"things for your data analysis",
" in NTB is to select the folder",
" with the raster layers that you ",
"will use as niche variables.")),
br(),
p("Please select the folder of raster",
" layers; notice that all of them",
" need to be in the same resolution",
" and extension."),
p("The supported raster formats are: ",".asc",
".bil",",",".tif",",",".nc.",
",",".sdat",",",".img"),
br(),
#directoryInput('ras_layers_directory', label = 'Select a raster layers directory'),
#glyphicon glyphicon-folder-open
conditionalPanel(paste0("'",osSystem,"' == 'Windows'"),
directoryInput('ras_layers_directory',
label = paste('Select a raster',
' layers directory')),
br(),
checkboxInput("load_projLayers_win",
label = "Select projection layers",
value = FALSE),
conditionalPanel("input.load_projLayers_win == true",
h4("Projection layers"),
paste0("These are the layers",
" of environmental change",
" scenario. Please make sure",
" that their names are the",
" same as the niche layers."),
br(),
directoryInput('proj_layers_directory',
label = paste0('Select',
' projection',
' layers',
' directory')))
),
conditionalPanel(paste0("'",osSystem,"' != 'Windows'"),
shinyFiles::shinyDirButton(id = "ras_layers_directory",
label = paste0("Select raster",
" layers directory"),
title = paste0("Select a directory",
" from ",
"the directories panel"),
icon = icon("folder-open",
lib = "glyphicon"),
buttonType = "info"),
br(),
HTML(paste('<div class="alert alert-info" role="alert">',
verbatimTextOutput("layers_directory"),'</div>')),
br(),br(),
checkboxInput("load_projLayers",
label = "Select projection layers",
value = FALSE),
conditionalPanel("input.load_projLayers == true",
h4("Projection layers"),
paste0("This are the layers of",
" environmental change scenario.\n\n",
"NicheToolBox uses them either",
" to project the niche models or",
" the PCAs ",
"computed for your niche layers.\n\n"),
paste0("Please make sure that their",
" names are the same as the",
" niche layers."),
br(),br(),
shinyFiles::shinyDirButton(id = paste0(
"proj_layers_directory"),
label =paste0("Select projection",
" layers directory"),
title = paste0("Select a directory",
" from the directories panel"),
icon = icon("folder-open",
lib = "glyphicon"),
buttonType = "info"),
HTML(paste('<div class="alert alert-info"',
' role="alert">',
verbatimTextOutput("proj_directory"),
'</div>')))),
p(paste0("If you dont have environmental",
" data ntbox provides methods from",
" `raster` package and other sources ("),
HTML('<a href="http://worldclim.org/" target="_blank"> WorldClim</a>,'),
HTML('<a href="http://chelsa-climate.org" target="_blank"> CHELSA</a>,'),
HTML('<a href="http://www.bio-oracle.org" target="_blank"> Bio-Oracle</a>,'),
HTML('<a href="https://envirem.github.io" target="_blank"> ENVIREM</a>'),
") to get environmental data."),
checkboxInput("getEnvData",label = "Get environmental data",value = FALSE),
conditionalPanel("input.getEnvData == true",
selectInput("env_data",label = "Select a source",
choices = c("WorldClim current"="wc",
"CMIP5 future"="wc_future",
"CHELSA current (1 km)" = "ch_pre",
"CHELSA future (1 km)" = "ch_fut",
"ENVIREM current" ="env_pres",
"ENVIREM past" = "env_pass",
"ENVIREM elevation current" ="env_elev_pres",
"ENVIREM elevation past" ="env_elev_pass",
"Bio-Oracle present
(via sdmpredictors)"="bio_pre",
"Bio-Oracle future
(via sdmpredictors)"="bio_fut")),
conditionalPanel("input.env_data=='wc_future'",
selectInput("CMIP5_mod",
"Select a model",
c("ACCESS1-0"= "AC",
"BCC-CSM1-1"="BC",
"CCSM4"="CC",
"CESM1-CAM5-1-FV2"="CE",
"CNRM-CM5"="CN",
"GFDL-CM3"="GF",
"GFDL-ESM2G"="GD",
"GISS-E2-R"="GS",
"HadGEM2-AO"="HD",
"HadGEM2-CC"="HG",
"HadGEM2-ES"="HE",
"INMCM4"="IN",
"IPSL-CM5A-LR"="IP",
"MIROC-ESM-CHEM"="MI",
"MIROC-ESM"="MR",
"MIROC5"="MC",
"MPI-ESM-LR"="MP",
"MRI-CGCM3"="MG",
"NorESM1-M"="NO"),
selected = "CC"),
radioButtons("year_sc","Select a year scenario",
c("2050"=50,"2070"=70)),
radioButtons("rcp","Select a RCP",
c("rcp26"=26,"rcp45"=45,
"rcp60"=60,"rcp85"=85),
selected = 85)),
conditionalPanel("input.env_data=='wc' ||
input.env_data=='wc_future'",
shiny::radioButtons("wc_var",
label = "Select an option",
choices = c("Bioclim"="bio",
"Min temperature
"='tmin',
"Max temperature
"='tmax',
"Precipitation"=
'prec')),
shiny::radioButtons("wc_resol",
label = "Select a resolution",
choices = c("10 minutes"=10,
"5 minutes"=5,
"2.5 minutes"=2.5,
"30 seconds"=0.5))
),
conditionalPanel("input.env_data == 'ch_fut'",
radioButtons("ch_period",
label = "Select a time period",
choices = c("2041-2060",
"2061-2080")),
radioButtons("ch_rcp",
label="Select a RCP",
choices=c("rcp26",
"rcp45",
"rcp85")),
selectInput("ch_model",
label="Select a circulation model",
choices = c('ACCESS1-0',
'bcc-csm1-1',
'BNU-ESM',
'CanESM2',
'CCSM4',
'CESM1-BGC',
'CESM1-CAM5',
'CMCC-CM',
'CMCC-CMS',
'CNRM-CM5',
'CSIRO-Mk3-6-0',
'FGOALS-g2',
'FIO-ESM',
'GFDL-CM3',
'GFDL-ESM2G',
'GFDL-ESM2M',
'GISS-E2-H',
'GISS-E2-H-CC',
'GISS-E2-R',
'GISS-E2-R-CC',
'HadGEM2-AO',
'HadGEM2-CC',
'inmcm4',
'IPSL-CM5A-LR',
'IPSL-CM5A-MR',
'MIROC-ESM',
'MIROC-ESM-CHEM',
'MIROC5',
'MPI-ESM-LR',
'MPI-ESM-MR',
'MRI-CGCM3',
'MRI-ESM1',
'NorESM1-M'))
),
conditionalPanel("input.env_data=='wc' ||
input.env_data=='wc_future'",
radioButtons('env_format',
paste0('Select a format to write',
' your layers. If you have',
' set the workflow','
directory they will be',
' saved on it; otherwise',
' they will be saved in',
' the working directory',
' of your R session.'),
c('.asc','.bil',
'.tif','.nc',
'.sdat','.img'))
),
conditionalPanel("input.env_data=='ch_pre' ||
input.env_data=='ch_fut' ||
input.env_data=='bio_pre' ||
input.env_data=='bio_fut'",
#p(paste0("Get bioclimatic data",
# "from CHELSA")),
checkboxInput("ch_parallel",
"Download in parallel",
value = TRUE)
),
conditionalPanel("input.env_data=='env_pres' ||
input.env_data=='env_pass' ||
input.env_data=='env_elev_pres' ||
input.env_data=='env_elev_pass'",
selectInput("env_reg","Select a region",
choices = c("Africa",
"Australia",
"Eurasia",
"Europe",
"Global"="global",
"NAmerica",
"NewWorld",
"Pacific",
"SAmerica"),
selected = "global"),
conditionalPanel("input.env_data=='env_pass' ||
input.env_data=='env_elev_pass'",
radioButtons("env_period",
"Select time period",
choices = c("Mid-Holocene"=
"holo",
"Last Glacial
Maximum"="lgm")),
conditionalPanel("input.env_data=='env_pass'",
radioButtons("env_gcm",
"Global
circulation
model",
choices = c("ccsm4",
"miroc_esm",
"mpi_esm_p")))
),
radioButtons("env_res",
"Select a resolution",
choices = c("10 arcmin"="10arcmin",
"5 arcmin"="5arcmin",
"2.5 arcmin"="2.5arcmin",
"30 arcsec"="30arcsec")),
radioButtons("env_fmt","Select layers format",
choices = c("geotiff","bil"))
),
conditionalPanel("input.env_data=='bio_fut'",
radioButtons("bio_year",
"Select a year",
choices = c("2050",
"2100",
"2200")),
radioButtons("bio_model",
"Select a model",
choices = c("a")),
radioButtons("bio_scenario",
label = "Select a scenario",
choices = c("a")),
selectInput("bio_type_fut",
label = "Select a variable",
choices = c("a"))
),
conditionalPanel("input.env_data=='bio_pre'",
selectInput("bio_type",
label = "Select a variable",
choices=c('salinity',
'sea_surface_temperature',
'current_velocity',
'sea_water_temperature',
'sea_water_salinity',
'sea_ice_thickness',
'chlorophyll_concentration',
'sea_surface_salinity'))
),
conditionalPanel("input.env_data=='wc' ||
input.env_data=='ch_pre' ||
input.env_data=='env_pres' ||
input.env_data=='env_elev_pres' ||
input.env_data=='bio_pre'",
bsButton("get_now","Get it",
icon = icon("download", lib = "glyphicon"),
style = "primary")
),
conditionalPanel("input.env_data=='wc_future' ||
input.env_data=='ch_fut' ||
input.env_data== 'env_pass' ||
input.env_data== 'env_elev_pass' ||
input.env_data== 'bio_fut'",
bsButton("get_now_future","Get it",
icon = icon("download",
lib = "glyphicon"),
style = "primary")
),
br()
),
bsButton("loadNicheLayers",
"Load niche layers",
icon = icon("upload",
lib = "glyphicon"),
style = "primary"),
busyIndicator("Loading...",wait = 0),
br()
#fileInput(inputId = "worflowPath","Select a folder for your worflow"),
#shinyDirButton('worflowPath', 'Folder select', 'Please select a folder'),
#shinyDirButton("workflowPath",title = "Choose Download Directory",
# label = "Browse Download Directory ", class = "btn-block btn-link"),
#submitButton()
#h4('Tutorials'),
#HTML('In this part you can find some tutorials that show how to use the app.'),
#selectInput(inputId = 'tutorialsm',label = 'Select one of the turtorials',
# choices = c('About'='about1','1. Data'='datose'),
# selected = "about1",multiple = FALSE)
),
mainPanel(
#htmlOutput("page"),
plotOutput("niche_layers"),
conditionalPanel("input.load_projLayers == true ||
input.load_projLayers_win == true",
plotOutput("niche_layers_proj")
)
)
)
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