I'm hoping someone can help me to figure out the issue with my code. I'm trying to figure out the issue with my code for like 5 hours and checked these links 
This is my code for reading my data and wrangle data
#Read and wrangle data
dvc_read <- st_read("/Users/Desktop/shap/accident_data.shp", # shapefile stored in repo
stringsAsFactors = FALSE # read factor columns as character columns
)
dvc_wrangle <- dvc_read %>%
st_transform(crs = 4326) %>% # transform coords to latlong
# decapitalise everything for easy handling
rename_all(tolower) %>%
mutate_if(is.character, tolower) %>% # simplify strings
# deal with dates
mutate(
Date = ymd(Date), # the issue is with line
Month = case_when( # and this line
Month == 1 ~ "Jan", Month == 2 ~ "Feb",
Month == 3 ~ "Mar", Month == 4 ~ "Apr",
Month == 5 ~ "May", Month == 6 ~ "Jun",
Month == 7 ~ "Jul", Month == 8 ~ "Aug",
Month == 9 ~ "Sep", Month == 10 ~ "Oct",
Month == 11 ~ "Nov", Month == 12 ~ "Dec",
TRUE ~ "Unknown"
),
# clean up strings (not perfect)
Severity = if_else(Severity %in% c("1", "2", "3"), "unknown", Severity),
Accident.Description = if_else(Accident.Description == "Road closed", "Road_closed", Accident.Description),
City = if_else(str_detect(City, "x") == TRUE, "unknown", City),
City = if_else(
City %in% c(
"Brooklyn", "Jamaica", "Merrick", "Roosevelt", "unclassified",
), "unknown", City
),
# final name tidy-up
Accident.Description = str_replace_all(Accident.Description, "_", " ")
) %>%
# title case for these columns
mutate_at(vars(Severity, Accident.Description, City), tools::toTitleCase) # To Title Case
###
# extract latlong cols from sf geometry and bind back to df
dvc_xy <- as.data.frame(st_coordinates(dvc_wrangle))
dvc <- bind_cols(dvc_wrangle, dvc_xy) %>% rename(latitude = X, longitude = Y)
saveRDS(dvc,"/Users/Desktop/shap/dvc.RDS")
dvc <- readRDS("data/dvc.RDS")
# Month order for dropdown input
mo_order <- c("Jan", "Feb", "Mar", "Apr", "May", "Jun",
"Jul", "Aug", "Sep", "Oct", "Nov", "Dec")
I'll add the Ui code and the server code just for a better understanding
The UI code:
ui <- dashboardPage(
dashboardHeader(
title = "Title",
titleWidth = 450
), # end dashboardHeader()
dashboardSidebar(
HTML("<br>"),
box(
title = "Filters",
width = 12,
background = "blue",
collapsible = TRUE, collapsed = FALSE,
selectInput(
inputId = "input_year",
label = "Year",
choices = sort(unique(dvc$Year)),
multiple = TRUE,
selected = sample(unique(dvc$Year), 1)
),
selectInput(
inputId = "input_month",
label = "Month",
choices = unique(dvc$Month[order(match(dvc$Month, mo_order))]),
multiple = TRUE,
selected = sample(unique(dvc$Month), 3)
),
selectInput(
inputId = "input_la",
label = "Accident.Description",
choices = sort(unique(dvc$Accident.Description)),
multiple = TRUE,
selected = sample(unique(dvc$Accident.Description), 3)
)
) # end box()
), # end dashboardSidebar()
dashboardBody(
fluidRow(
valueBoxOutput("output_valueselection"),
valueBoxOutput("output_valueyearla"),
valueBoxOutput("output_valueyear"),
tabBox(
id = "tabset1",
width = 12,
tabPanel("Map", leafletOutput("output_map", height = "600px")),
tabPanel("Table", dataTableOutput("output_table"))
)
) # end fluidRow()
) # end dashboardBody()
) # end of ui dashboardPage()
The server code:
server <- function(input, output) {
# Value box - year
output$output_valueyear <- renderValueBox({
shinydashboard::valueBox(
value = dvc %>% st_drop_geometry() %>% filter(Year %in% input$input_year) %>% count() %>% pull(),
subtitle = "Collisions in selected year(s)",
icon = icon("calendar", lib = "font-awesome"),
color = "blue",
width = 4
)
}) # end of renderValueBox
# Value box - year by la
output$output_valueyearla <- renderValueBox({
shinydashboard::valueBox(
value = dvc %>% st_drop_geometry() %>% filter(Year %in% input$input_year, Accident.Description %in% input$input_la) %>% count() %>% pull(),
subtitle = "Collisions in selected LA(s) and year(s)",
icon = icon("map-o", lib = "font-awesome"),
color = "blue",
width = 4
)
}) # end of renderValueBox
# Value box - total in your selection
output$output_valueselection <- renderValueBox({
shinydashboard::valueBox(
value = dvc %>% st_drop_geometry() %>% filter(Year %in% input$input_year, Month %in% input$input_month, Accident.Description %in% input$input_la) %>% count() %>% pull(),
subtitle = "Collisions in selection",
icon = icon("car", lib = "font-awesome"),
color = "blue",
width = 4
)
}) # end of renderValueBox
# Interactive map with Leaflet
output$output_map <- renderLeaflet({
dvc %>%
filter(
Year %in% input$input_year,
Month %in% input$input_month,
Accident.Description %in% input$input_la
) %>%
leaflet() %>%
addProviderTiles(providers$OpenStreetMap) %>%
addAwesomeMarkers(
icon = awesomeIcons(
icon = "exclamation-circle",
iconColor = "#FFFFFF",
library = "fa",
markerColor = "darkblue"
),
popup = ~paste0(
"<style>
td, th {
text-align: left;
padding: 3px;
}
</style>",
"<table>",
"<tr>","<td>", "Date", "</td>", "<td>", Date, "</td>", "<tr>",
"<tr>","<td>", "LA", "</td>", "<td>", Accident.Description, "</td>", "<tr>",
"<tr>","<td>", "City", "</td>", "<td>", City, "</td>", "<tr>",
"<tr>","<td>", "Species", "</td>", "<td>", Severity, "</td>", "<tr>",
"</table>"
)
)
}) # end of renderLeaflet
# Interactive table with DT
output$output_table <- renderDataTable({
dvc %>%
st_drop_geometry() %>%
filter(
Year %in% input$input_year,
Month %in% input$input_month,
Accident.Description %in% input$input_la
) %>%
select(
Date = Date,
Year = Year,
Month = Month,
`Accident.Description` = Accident.Description,
City = City,
`Severity` = Severity
) %>%
datatable(
filter = "top",
extensions = c("Scroller", "Buttons"), # scroll instead of paginate
rownames = FALSE, # remove row names
style = "bootstrap", # style
width = "100%", # full width
height = "800px",
options = list(
deferRender = TRUE,
# scroll
scrollY = 300,
scroller = TRUE,
# button
autoWidth = TRUE, # column width consistent when making selections
dom = "Blrtip",
buttons =
list(
list(
extend = "collection",
buttons = c("csv", "excel"), # download extension options
text = "Download" # text to display
)
)
) # end of options = list()
) # end of datatable()
}) # end of renderDataTable()
} # end of server function
I really appreciate your help with this issue and fixing the bug I have in my code.
Update:
Here's my data using dput():
structure(list(lat = c(40.61955, 40.61955, 40.61955, 40.61955,
40.61955, 40.61955), long = c(-74.02346, -74.02346, -74.02346,
-74.02346, -74.02346, -74.02346), Year = c("2020", "2020", "2019",
"2020", "2020", "2019"), Month = c("2", "11", "10", "9", "1",
"9"), Day = c("6", "21", "26", "20", "11", "15"), Date = c("2020-02-06",
"2020-11-21", "2019-10-26", "2020-09-20", "2020-01-11", "2019-09-15"
), Accident.Description = c("Right lane blocked", "Two lanes blocked",
"Two lanes blocked", "Right lane blocked", "Right lane blocked",
"One lane blocked"), Severity = c("3", "3", "3", "3", "3", "3"
), geometry = structure(list(structure(c(-74.02346, 40.61955), class = c("XY",
"POINT", "sfg")), structure(c(-74.02346, 40.61955), class = c("XY",
"POINT", "sfg")), structure(c(-74.02346, 40.61955), class = c("XY",
"POINT", "sfg")), structure(c(-74.02346, 40.61955), class = c("XY",
"POINT", "sfg")), structure(c(-74.02346, 40.61955), class = c("XY",
"POINT", "sfg")), structure(c(-74.02346, 40.61955), class = c("XY",
"POINT", "sfg"))), class = c("sfc_POINT", "sfc"), precision = 0, bbox = structure(c(xmin = -74.02346,
ymin = 40.61955, xmax = -74.02346, ymax = 40.61955), class = "bbox"), crs = structure(list(
input = "NAD83", wkt = "GEOGCRS[\"NAD83\",\n DATUM[\"North American Datum 1983\",\n ELLIPSOID[\"GRS 1980\",6378137,298.257222101,\n LENGTHUNIT[\"metre\",1]]],\n PRIMEM[\"Greenwich\",0,\n ANGLEUNIT[\"degree\",0.0174532925199433]],\n CS[ellipsoidal,2],\n AXIS[\"latitude\",north,\n ORDER[1],\n ANGLEUNIT[\"degree\",0.0174532925199433]],\n AXIS[\"longitude\",east,\n ORDER[2],\n ANGLEUNIT[\"degree\",0.0174532925199433]],\n ID[\"EPSG\",4269]]"), class = "crs"), n_empty = 0L)), row.names = c(NA,
6L), class = c("sf", "data.frame"), sf_column = "geometry", agr = structure(c(lat = NA_integer_,
long = NA_integer_, Year = NA_integer_, Month = NA_integer_,
Day = NA_integer_, Date = NA_integer_, Accident.Description = NA_integer_, Severity = NA_integer_), .Label = c("constant", "aggregate",
"identity"), class = "factor"))
Update II:
Thank you all for helping! I really appreciate all the answers you gave me!! I fixed the issues with the code but I'm still facing issues with one column which is the "accident.description" column. Although I changed the name to be "accident" where I thought the dot caused the issue but couldn't figure it out. The error message for this column below:
Error: Problem with `mutate()` column `accident.description`.
ℹ `accident.description = if_else(...)`.
x object 'accident.description' not found
This is my updated code:
dvc_wrangle <- dvc_read %>%
st_transform(crs = 4326) %>% # transform coords to latlong
# decapitalise everything for easy handling
rename_all(tolower) %>%
mutate_if(is.character, tolower) %>% # simplify strings
# deal with dates
mutate(
Date = ymd(date),
Month = case_when(
month == 1 ~ "Jan", month == 2 ~ "Feb",
month == 3 ~ "Mar", month == 4 ~ "Apr",
month == 5 ~ "May", month == 6 ~ "Jun",
month == 7 ~ "Jul", month == 8 ~ "Aug",
month == 9 ~ "Sep", month == 10 ~ "Oct",
month == 11 ~ "Nov", month == 12 ~ "Dec",
TRUE ~ "Unknown"
),
# clean up strings (not perfect)
Severity = if_else(severity %in% c("1", "2", "3"), "unknown", severity),
accident.description = if_else(accident.description == "Road closed", "Road_closed", accident.description),
City = if_else(str_detect(city, "x") == TRUE, "unknown", city),
City = if_else(
city %in% c(
"Brooklyn", "Jamaica", "Merrick", "Roosevelt", "unclassified",
), "unknown", city
),
# final name tidy-up
Accident.Description = str_replace_all(Accident.Description, "_", " ")
) %>%
# title case for these columns
mutate_at(vars(Severity, Accident.Description, City), tools::toTitleCase) # To Title Case
I changed the Road closed to be "road closed" and the name of the column to be "accident" like this but still getting the same error message:
Accident = if_else(accident %in% c("Road closed", "Two lanes blocked", "One lane blocked"), "unknown", accident),
CodePudding user response：
You put every column name to lowercase with rename_all(tolower). Therefore, column Date doesn't exist but column date does. Replacing Date by date works.
You have to fix that for all other column names in mutate(). Also, you modify the variable City but it is not in the data you provide (perhaps you just forgot to include it).
I didn't run the app but this should fix your dplyr error.
CodePudding user response：
Diagnosis
Your issue is fairly simple. Once the Date column is renamed as date
# decapitalise everything for easy handling rename_all(tolower) %>%
then that problematic line
# deal with dates mutate( Date = ymd(Date), # the issue is with line
contains an expression ymd(Date) that refers to a nonexistent column Date.
So R searches outside the data mask for something named Date...and the first thing it finds is the function lubridate::Date(), which has (presumably) been loaded into your workspace as Date, via library(lubridate). Note that functions are also known as "closures" in R.
In that problematic expression
ymd(Date)
you are thus supplying a closure as input to ymd(), which expects a character vector. Hence the error:
x cannot coerce type 'closure' to vector of type 'character'
Solution
Simply alter your code to reference the date column, which is now lowercase.
# deal with dates
mutate(
Date = ymd(date),
# ^^^^
Warning
As observed here by @bretauv, there are further errors later in your code. Some you can fix by making the same correction to other column names.