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Merge branch 'master' of github.com:noaa-nwfsc/FishSET into 175-add-p…
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…rompt-to-save-table-when-switching-tabs

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@Paul-Carvalho
Paul-Carvalho committed Jan 3, 2025
2 parents 3cf287e + 5abeeab commit ab1a6fa
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Showing 2 changed files with 34 additions and 40 deletions.
38 changes: 19 additions & 19 deletions R/spatial_qaqc.R
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Original file line number Diff line number Diff line change
Expand Up @@ -231,7 +231,7 @@ spatial_qaqc <- function(dat, project, spat, lon.dat, lat.dat, lon.spat = NULL,
}

# points on land ----

sf_use_s2(FALSE) # by default 'sf' package enables 's2' but this sometimes generates errors with st_intersects
land_pts <- sf::st_intersects(dat_sf, base_map)

obs_on_land <- lengths(land_pts) > 0
Expand Down Expand Up @@ -263,7 +263,6 @@ spatial_qaqc <- function(dat, project, spat, lon.dat, lat.dat, lon.spat = NULL,
}

# points outside zone ----

pts_int <- sf::st_intersects(dat_sf, spatdat)

obs_outside <- lengths(pts_int) == 0
Expand Down Expand Up @@ -355,24 +354,25 @@ spatial_qaqc <- function(dat, project, spat, lon.dat, lat.dat, lon.spat = NULL,
fishset_theme()

# Spatial summary table ----

if (any(!is.null(out_col), !is.null(land_col), !is.null(bound_col))) {

spat_tab <- agg_helper(dataset, value = c(expected_col, out_col, land_col, bound_col),
group = c("YEAR", group), fun = sum)

year_tab <- agg_helper(dataset, value = "YEAR", group = group, count = TRUE, fun = "percent")

spat_tab <- dplyr::left_join(spat_tab, year_tab, by = "YEAR")

last_cols <- names(spat_tab)[!names(spat_tab) %in% c("YEAR", "n", group)]

spat_tab <- spat_tab[order(spat_tab$YEAR),
c("YEAR", "n", group, last_cols)]
}
spat_tab <- agg_helper(dataset, value = c(expected_col, out_col, land_col, bound_col),
group = c("YEAR", group), fun = sum)

year_tab <- agg_helper(dataset, value = "YEAR", group = group, count = TRUE, fun = "percent")

spat_tab <- dplyr::left_join(spat_tab, year_tab, by = "YEAR")

last_cols <- names(spat_tab)[!names(spat_tab) %in% c("YEAR", "n", group)]

spat_tab <- spat_tab[order(spat_tab$YEAR),
c("YEAR", "n", group, last_cols)]

# distance from nearest zone (meters) ----
if (sum(obs_outside) > 0) {
if(p_expected < 50) {
showNotification("Over 50% of the observations are outside of the study location and/or on land. Check for erros in latitude and longitude values in the primary data table.",
type = "error",
duration = 60)

} else if(sum(obs_outside) > 0) {

nearest <- sf::st_nearest_feature(dat_sf[obs_outside, ], spatdat)
dist.rec <- sf::st_distance(dat_sf[obs_outside, ], spatdat[nearest, ],
Expand Down Expand Up @@ -427,7 +427,7 @@ spatial_qaqc <- function(dat, project, spat, lon.dat, lat.dat, lon.spat = NULL,

if (sum(obs_on_bound, obs_outside) == 0) {

cat(c("All observations occur on land and within regulatory zones.",
cat(c("All observations occur within regulatory zones.",
"No observations fall on zone boundaries."), file = tmp)
}

Expand Down
36 changes: 15 additions & 21 deletions inst/ShinyFiles/MainApp/server.R
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Original file line number Diff line number Diff line change
Expand Up @@ -3343,8 +3343,8 @@ server = function(input, output, session) {

if (!is_value_empty(out)) {

flag_nms <- c("ON_LAND", "OUTSIDE_ZONE", "ON_ZONE_BOUNDARY")
spat_qaqc_r$flag <- vapply(flag_nms, function(x) x %in% names(out$dataset), logical(1))
flag_nms <- c("ON_LAND", "OUTSIDE_ZONE", "ON_ZONE_BOUNDARY", "EXPECTED_LOC")
spat_qaqc_r$flag <- flag_nms %in% names(out$dataset)

spat_qaqc$out_df <- subset(out$dataset, select=-c(YEAR)) # remove 'YEAR' from table
out$dataset <- NULL
Expand Down Expand Up @@ -3522,20 +3522,21 @@ server = function(input, output, session) {

if (input$select_spat_tab == "out_zone") {

if (sum(dist_filter()) > 0) spat_qaqc$out_df[dist_filter(), c(input$spat_qaqc_ID, input$spat_qaqc_date, input$spat_qaqc_lat,
input$spat_qaqc_lon, "ON_LAND", "ON_ZONE_BOUNDARY", "EXPECTED_LOC")]
} else { # "all"
if (sum(dist_filter()) > 0){
spat_qaqc$out_df[dist_filter(), c(input$spat_qaqc_ID, input$spat_qaqc_date, input$spat_qaqc_lat,
input$spat_qaqc_lon, "ON_LAND", "OUTSIDE_ZONE", "ON_ZONE_BOUNDARY", "EXPECTED_LOC")]
}

new_cols <- c("ON_LAND", "ON_ZONE_BOUNDARY", "EXPECTED_LOC")
} else { # "all"
new_cols <- c("ON_LAND", "OUTSIDE_ZONE", "ON_ZONE_BOUNDARY", "EXPECTED_LOC")
new_cols <- new_cols[which(spat_qaqc_r$flag)]

spat_qaqc$out_df[,c(input$spat_qaqc_ID, input$spat_qaqc_lat,
input$spat_qaqc_lon, new_cols)]
input$spat_qaqc_lon, new_cols)]
}
}
})


observe({
spat_qaqc_r$c_tab <- c_tab()
})
Expand Down Expand Up @@ -3586,7 +3587,6 @@ server = function(input, output, session) {
observeEvent(input$dist_remove_bttn, {

# add pop-up confirming removal

showModal(
modalDialog(title = paste("Remove", sum(dist_filter()), "rows?"),

Expand Down Expand Up @@ -3662,19 +3662,13 @@ server = function(input, output, session) {

q_test <- quietly_test(degree)

if (input$select_spat_tab == "out_zone") {

values$dataset[dist_filter(), ] <-
q_test(c_tab(), project = project$name, lat = input$spat_qaqc_lat,
lon = input$spat_qaqc_lon, latsign = input$spat_filter_lat,
lonsign = input$spat_filter_lon, replace = TRUE)
} else {
values$dataset <-
q_test(values$dataset, project = project$name, lat = input$spat_qaqc_lat,
lon = input$spat_qaqc_lon, latsign = input$spat_filter_lat,
lonsign = input$spat_filter_lon, replace = TRUE)

values$dataset <-
q_test(c_tab(), project = project$name, lat = input$spat_qaqc_lat,
lon = input$spat_qaqc_lon, latsign = input$spat_filter_lat,
lonsign = input$spat_filter_lon, replace = TRUE)
}
# Reassign reactive to update table
spat_qaqc$out_df[,c(input$spat_qaqc_lat,lon = input$spat_qaqc_lon)] <- values$dataset[,c(input$spat_qaqc_lat,lon = input$spat_qaqc_lon)]

showNotification("Spatial corrections completed", type = "message", duration = 60)
})
Expand Down

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