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Revert "ajustes"
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This reverts commit d1da2e7.
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Renata de Toledo Capellão committed Jan 25, 2019
1 parent 7d35fb6 commit 771eef5
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Showing 3 changed files with 393 additions and 605 deletions.
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78 changes: 40 additions & 38 deletions Model-R/server.R
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Original file line number Diff line number Diff line change
Expand Up @@ -101,7 +101,7 @@ mk.dirs <- function(dir_path) {
getOccurrences_gbif <- function(species_name) {
key <- rgbif::name_backbone(name = species_name)$speciesKey
if (!is.null(key)) {
gbif_data <- rgbif::occ_search(
gbif_data <-rgbif::occ_search(
hasCoordinate = TRUE,
hasGeospatialIssue = F,
taxonKey = key,
Expand Down Expand Up @@ -168,7 +168,6 @@ MapPreview.ensemble <- function() {
addRectangles(ext11, ext31, ext21, ext41, color = "red", fill = FALSE, dashArray = "5,5", weight = 2)
}
}

setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
options(shiny.maxRequestSize = 100 * 1024^2)
dirColors <- c(`1` = "#595490", `2` = "#527525", `3` = "#A93F35", `4` = "#BA48AA")
Expand Down Expand Up @@ -197,22 +196,21 @@ function(input, output, session) {
}

if (!file.exists(modelsDir)) {

mk.dirs(modelsDir)
showModal(modalDialog(
title = "Project succesfully created!",
paste0("Project directory: ", modelsDir),
easyClose = TRUE
))
modelsDir <<- paste0("./www/results/", input$modelsDir.new)
mk.dirs(modelsDir)
modelsDir <<- modelsDir
}
}

# Load previous project
if (input$select_project == "load_proj") {
modelsDir <- paste0("./www/results/", input$modelsDir.load)

if (dir.exists(modelsDir)) {
if(dir.exists(modelsDir)){
showModal(modalDialog(
title = paste0("Project ", input$modelsDir.load, " succefully loaded!"),
paste0("Output files are dispalyed at the 'Outputs' tab."),
Expand Down Expand Up @@ -287,9 +285,9 @@ function(input, output, session) {
}, options = list(lengthMenu = c(5, 30, 50), pageLength = 5))

observeEvent(input$btn_saveDatasetRaw, {
save_raw <- data.frame("species_name", occurrences)
save_raw <-data.frame("species_name", occurrences)
names(save_raw) <- c("name", "lon", "lat")
write.csv(save_raw, file = paste0(modelsDir, "/occurrences_", input$bio_datasource, "_", species_name, ".csv"), row.names = FALSE)
write.csv(save_raw, file=paste0(modelsDir, "/occurrences_", input$bio_datasource, "_",species_name, ".csv"), row.names = FALSE)
})

# Display map with occurrence records
Expand All @@ -303,7 +301,7 @@ function(input, output, session) {
if (!is.null(occurrences)) {
map <- leaflet(occurrences) %>%
addTiles() %>%
addCircles(color = "red", lat = ~lat, lng = ~lon) %>%
addCircles(color = "red", lat = ~ lat, lng = ~ lon) %>%
setView(lng = -31.5, lat = -13.4, zoom = 3)
map
} else {
Expand Down Expand Up @@ -353,9 +351,9 @@ function(input, output, session) {
}, options = list(searching = FALSE, lengthMenu = c(5, 30, 50), pageLength = 5))

observeEvent(input$btn_saveDatasetClean, {
save_clean <- data.frame("species_name", occurrences)
names(save_clean) <- c("name", "lon", "lat")
write.csv(save_clean, file = paste0(modelsDir, "/occurrences_clean_", species_name, ".csv"), row.names = FALSE)
save_clean<-data.frame("species_name", occurrences)
names(save_clean)<- c("name", "lon", "lat")
write.csv(save_clean, file=paste0(modelsDir, "/occurrences_clean_",species_name, ".csv"), row.names = FALSE)
})

output$mapadistribuicaodatacleaning <- renderLeaflet({
Expand All @@ -370,9 +368,9 @@ function(input, output, session) {
occurrences$id <- 1:nrow(occurrences)
map <- leaflet(occurrences) %>%
addTiles() %>%
addCircles(color = "red", lat = ~lat, lng = ~lon) %>%
addCircles(color = "red", lat = ~ lat, lng = ~ lon) %>%
addMarkers(clusterOptions = markerClusterOptions()) %>%
addMarkers(~lon, ~lat, popup = ~as.character(id))
addMarkers(~ lon, ~ lat, popup = ~ as.character(id))
map
}
} else {
Expand Down Expand Up @@ -401,7 +399,7 @@ function(input, output, session) {
map <- leaflet(occurrences) %>%
addTiles() %>%
addMarkers(clusterOptions = markerClusterOptions()) %>%
addMarkers(~lon, ~lat) %>%
addMarkers(~ lon, ~ lat) %>%
addRectangles(ext11, ext31, ext21, ext41,
color = "red",
fill = TRUE, dashArray = "5,5", weight = 3
Expand All @@ -424,7 +422,7 @@ function(input, output, session) {
map <- leaflet(occurrences) %>%
addTiles() %>%
addMarkers(clusterOptions = markerClusterOptions()) %>%
addMarkers(~lon, ~lat) %>%
addMarkers(~ lon, ~ lat) %>%
addRectangles(ext12, ext32, ext22, ext42,
color = "green", fill = TRUE, dashArray = "5,5",
weight = 3
Expand Down Expand Up @@ -768,16 +766,14 @@ function(input, output, session) {

#### GROUPING ALL MODELING PROCESSES BY CLICKING THE EXECUTE BUTTON ####
observeEvent(input$btnModelar, {
if (any(
input$domain,
if (any(input$domain,
input$maxent,
input$bioclim,
input$mahal,
input$glm,
input$rf,
input$svm.e,
input$svm.k
)
input$svm.k)
) {
if (exists("occurrences") && exists("predictors") && exists("species_name")) {
progress <<- shiny::Progress$new()
Expand Down Expand Up @@ -925,7 +921,7 @@ function(input, output, session) {
observeEvent({
input$btnrefreshprojeto
input$btnModelar
}, {
},{
sp_dirs <<- list.dirs(modelsDir, recursive = F, full.names = F)
updateSelectInput(session, "Select_spdir",
label = paste("Select species"),
Expand All @@ -937,51 +933,51 @@ function(input, output, session) {
input$btnrefreshprojeto
input$btnModelar
input$Select_spdir
}, {
},{
if (length(sp_dirs) == 0) {
modelsDir.sp <<- NULL

} else {
modelsDir.sp <<- paste0(modelsDir, "/", input$Select_spdir)
modelsDir.sp <<- paste0(modelsDir,"/", input$Select_spdir)
}

# metadata
output$metadata_table <- renderDataTable({
metadata <- list.files(path = paste0(modelsDir.sp, "/present"), recursive = T, full.names = T, pattern = "metadata.txt")[1]
metadata <-list.files(path = paste0(modelsDir.sp, "/present"), recursive = T, full.names = T, pattern = "metadata.txt")[1]
metadata <- data.frame(read.delim(metadata, header = TRUE, sep = " ", dec = "."))
metadata$res.x <- format(metadata$res.x, digits = 3, nsmall = 3)
metadata$res.x <- format(metadata$res.x, digits = 3, nsmall = 3)
metadata$res.y <- format(metadata$res.y, digits = 3, nsmall = 3)
metadata
}, options = list(scrollX = TRUE, scrollY = TRUE, searching = FALSE))
}, options = list(scrollX = TRUE, scrollY = TRUE, searching = FALSE)
)

# sdmdata txt table
output$sdmdata_table <- renderDataTable({
sdmdata <- list.files(path = paste0(modelsDir.sp, "/present"), recursive = T, full.names = T, pattern = "sdmdata.txt")[1]
sdmdata <- data.frame(read.delim(sdmdata, header = TRUE, sep = " ", dec = "."))
sdmdata$lon <- format(sdmdata$lon, digits = 3, nsmall = 3)
sdmdata$lat <- format(sdmdata$lat, digits = 3, nsmall = 3)
sdmdata$lon <-format(sdmdata$lon, digits = 3, nsmall = 3)
sdmdata$lat <-format(sdmdata$lat, digits = 3, nsmall = 3)
sdmdata
}, options = list(scrollX = TRUE, searching = FALSE))
},options = list(scrollX = TRUE, searching = FALSE))

# sdmdata png map
output$sdmdata_png <- renderImage({
list(
src = list.files(path = paste0(modelsDir.sp, "/present"), recursive = T, full.names = T, pattern = "sdmdata_.*png$")[1],
list(src = list.files(path = paste0(modelsDir.sp, "/present"), recursive = T, full.names = T, pattern = "sdmdata_.*png$")[1],
contentType = "image/png",
alt = "This is alternate text"
)
alt = "This is alternate text")
})

# stats
output$stats <- renderDataTable({
stats.file <- list.files(path = paste0(modelsDir.sp, "/present/final_models"), recursive = T, full.names = T, pattern = "final_statistics.csv")[1]
stats.file <- read.csv(stats.file, row.names = 1)
for (i in c(1:ncol(stats.file))) {
if (is.numeric(stats.file[, i])) {
stats.file[, i] <- format(stats.file[, i], digits = 3, nsmall = 4)
for(i in c(1:ncol(stats.file))){
if(is.numeric(stats.file[,i])){
stats.file[,i] <- format(stats.file[,i], digits = 3, nsmall = 4)
}
}
stats.file
}, options = list(lengthMenu = c(5, 30, 50), pageLength = 10, scrollX = TRUE, searching = FALSE))
}, options = list(lengthMenu = c(5, 30, 50), pageLength = 10))

# #### Binary and Continuous models ####

Expand Down Expand Up @@ -1022,5 +1018,11 @@ function(input, output, session) {
))
})
})
}, ignoreNULL = T, ignoreInit = T)

}, ignoreNULL = T,ignoreInit = T)
}





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