Error in geom_sf(data = world, show.legend = F) : object '...' not found

rachel · April 11, 2019, 3:13pm

Mara, I'm having exactly the same error pattern as stote did, but unfortunately no amount of re-installing, re-loading, or re-starting the session altogether is resolving it. My code was working beautifully yesterday, and then when I went to re-run today, I get the errors. So it must be an order or packages issue? SO grateful if you can help.

centroids <- read_delim("C:/Users/ch111111/Dropbox /Folder/centroids.csv", delim = "\t")%>%
mutate(country.code = countrycode(SHORT_NAME, "country.name","iso3c", warn = T))%>%
select(lat = "LAT", long = "LONG", country.code)

centroids[, c("lat", "long")] <- project(xy = as.matrix(centroids[, c("long", "lat")]), proj = "+proj=robin")

absolute_GDP <- read_excel(path, sheet = "Cumulative GDP lost (13)") %>%
rename(country = Country, cum_GDP = Cumulative GDP Lost ) %>%
mutate(iso = countrycode(country, "country.name", "iso3c")) %>%
mutate(cum_GDP = cum_GDP / 10^9)

centroids <- left_join(centroids, absolute_GDP, by = c("country.code" = "iso")) %>%
filter(!is.na(cum_GDP))

ggplot() +
geom_sf(data = world, show.legend = F) +
geom_point(data = centroids, aes(x = lat, y = long, size = cum_GDP)) +
scale_size_area(max_size = 25, breaks = c(0.1, 1, 50, floor(max(centroids$cum_GDP)))) +
theme_bw()

mara · April 11, 2019, 3:26pm

Could you please turn this into a self-contained reprex (short for reproducible example)? It will help us help you if we can be sure we're all working with/looking at the same stuff.

install.packages("reprex")

If you've never heard of a reprex before, you might want to start by reading the tidyverse.org help page. The reprex dos and don'ts are also useful.

There's also a nice FAQ on how to do a minimal reprex for beginners, below:

FAQ: How to do a minimal reproducible example ( reprex ) for beginners Guides & FAQs

A minimal reproducible example consists of the following items: A minimal dataset, necessary to reproduce the issue The minimal runnable code necessary to reproduce the issue, which can be run on the given dataset, and including the necessary information on the used packages. Let's quickly go over each one of these with examples: Minimal Dataset (Sample Data) You need to provide a data frame that is small enough to be (reasonably) pasted on a post, but big enough to reproduce your issue. Let's say, as an example, that you are working with the iris data frame head(iris) #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.…

What to do if you run into clipboard problems

If you run into problems with access to your clipboard, you can specify an outfile for the reprex, and then copy and paste the contents into the forum.

reprex::reprex(input = "fruits_stringdist.R", outfile = "fruits_stringdist.md")

For pointers specific to the community site, check out the reprex FAQ.

rachel · April 11, 2019, 5:14pm

Mara, thanks for this! Here is my reprex:

library(datapasta)
library(ggplot2)
#datapasta:: df_paste(head(centroids, 5))

df <- data.frame(stringsAsFactors=FALSE,
                                                    lat = c(12396114.3738155, 1111619.42307639, 325672.675245503,
                                                            -7235015.91810587,
                                                            -6432333.51408773),
                                                   long = c(-2670804.78590195, 5043993.78855193, 5406895.92108048,
                                                            6328945.06430578,
                                                            -3204964.2454797),
                                           country.code = c("AUS", "AUT", "BEL", "CAN", "CHL"),
                                                country = c("Australia", "Austria", "Belgium", "Canada", "Chile"),
                                                cum_GDP = c(0.998576308865479, 0.74325557414624, 0.362645540999268,
                                                            3.80026640072534,
                                                            1.40930621014813)
                                        )
ggplot() + 
  geom_sf(data = world, show.legend = F) + 
  geom_point(data = centroids, aes(x = lat, y = long, size = cum_GDP), alpha = 0.5) + 
  scale_size_area(max_size = 25, breaks = c(0.1, 1, 50, floor(max(centroids$cum_GDP)))) +
  theme_bw()

Error in geom_sf(data = world, show.legend = F) :
object 'world' not found

andresrcs · April 11, 2019, 5:19pm

You are not showing from where are you getting the world object, this should contain the "simple features" required to render the map.

rachel · April 11, 2019, 5:21pm

Thanks @andresrcs. I had loaded sf - have now included that in my reprex. Same error, unfortunately.

library(datapasta)
library(ggplot2)
library(sf)
#datapasta:: df_paste(head(centroids, 5))

df <- data.frame(stringsAsFactors=FALSE,
                                                    lat = c(12396114.3738155, 1111619.42307639, 325672.675245503,
                                                            -7235015.91810587,
                                                            -6432333.51408773),
                                                   long = c(-2670804.78590195, 5043993.78855193, 5406895.92108048,
                                                            6328945.06430578,
                                                            -3204964.2454797),
                                           country.code = c("AUS", "AUT", "BEL", "CAN", "CHL"),
                                                country = c("Australia", "Austria", "Belgium", "Canada", "Chile"),
                                                cum_GDP = c(0.998576308865479, 0.74325557414624, 0.362645540999268,
                                                            3.80026640072534,
                                                            1.40930621014813)
                                        )
ggplot() + 
  geom_sf(data = world, show.legend = F) + 
  geom_point(data = centroids, aes(x = lat, y = long, size = cum_GDP), alpha = 0.5) + 
  scale_size_area(max_size = 25, breaks = c(0.1, 1, 50, floor(max(centroids$cum_GDP)))) +
  theme_bw()

Error in geom_sf(data = world, show.legend = F) :
object 'world' not found

andresrcs · April 11, 2019, 6:01pm

world is not part of sf that is why you are getting that message, check again the instructions you are following, they should be getting this object from another package like this for example

library("rnaturalearth")
library("rnaturalearthdata")

world <- ne_countries(scale = "medium", returnclass = "sf")

rachel · April 11, 2019, 6:33pm

Thanks for your help, @andresrcs. I'm not following instructions - I actually got all of this code to work before without these additional lines. I followed your suggestion and am no longer getting an error, but am getting a figure that doesn't have a map in the background (see image).

 library(datapasta)
library(ggplot2)
library(sf)
library(rnaturalearth)
library(rnaturalearthdata)
#datapasta:: df_paste(head(centroids, 5))

df <- data.frame(stringsAsFactors=FALSE,
                                                    lat = c(12396114.3738155, 1111619.42307639, 325672.675245503,
                                                            -7235015.91810587,
                                                            -6432333.51408773),
                                                   long = c(-2670804.78590195, 5043993.78855193, 5406895.92108048,
                                                            6328945.06430578,
                                                            -3204964.2454797),
                                           country.code = c("AUS", "AUT", "BEL", "CAN", "CHL"),
                                                country = c("Australia", "Austria", "Belgium", "Canada", "Chile"),
                                                cum_GDP = c(0.998576308865479, 0.74325557414624, 0.362645540999268,
                                                            3.80026640072534,
                                                            1.40930621014813)
                                        )

world <- ne_countries(returnclass = "sf")

ggplot() + 
  geom_sf(data = world, show.legend = F) + 
  geom_point(data = centroids, aes(x = lat, y = long, size = cum_GDP), alpha = 0.5) + 
  scale_size_area(max_size = 25, breaks = c(0.1, 1, 50, floor(max(centroids$cum_GDP)))) +
  theme_bw()

andresrcs · April 11, 2019, 7:09pm

This is do to the format of your coordinates the map uses longitude-latitude coordinates and I think your dots are UTM coordinates.

I don't know the right projection (this is why the dots are not in the right place) but it should be something similar to this

library(ggplot2)
library(sf)
library(rnaturalearth)
library(rnaturalearthdata)
library(rgdal)

df <- data.frame(stringsAsFactors=FALSE,
                 lat = c(12396114.3738155, 1111619.42307639, 325672.675245503,
                         -7235015.91810587,
                         -6432333.51408773),
                 long = c(-2670804.78590195, 5043993.78855193, 5406895.92108048,
                          6328945.06430578,
                          -3204964.2454797),
                 country.code = c("AUS", "AUT", "BEL", "CAN", "CHL"),
                 country = c("Australia", "Austria", "Belgium", "Canada", "Chile"),
                 cum_GDP = c(0.998576308865479, 0.74325557414624, 0.362645540999268,
                             3.80026640072534,
                             1.40930621014813)
)

df <- spTransform(SpatialPoints(cbind(df$lat,df$long), proj4string=CRS("+proj=utm +zone=30")),CRS("+proj=longlat")) %>% 
    as.data.frame() %>%
    cbind(df)

world <- ne_countries(returnclass = "sf")

ggplot() + 
    geom_sf(data = world, show.legend = F) + 
    geom_point(data = df, aes(x = coords.x2, y = coords.x1, size = cum_GDP), alpha = 0.5) + 
    theme_bw()

system · May 2, 2019, 7:09pm

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