CODEWITHSUNDEEP
r
Jose Montoya
Jose Montoya

Reputation: 167

Problems with shape files

I want to make a map with the coronavirus infected people by state in US . So the idea is to visualize a map with all states of US and see a range of infected people( i.e 500-2000 , etc) in all the map. This should be represented by different shades of one color. The dark shades would be the states with more cases of coronavirus(states).

So this is my code:

install.packages("sp")
library(sp)

install.packages("sf")
library(sf)

install.packages("maptools")
library(maptools)

install.packages("spdep")
library(spdep)
install.packages("rgdal")
     library(rgdal)
install.packages("RColorBrewer")
library(RColorBrewer)
install.packages("readxl")
library(readxl)




# 
shp_usa <- readOGR("USA_States.shp")
names(shp_usa)                              
shp_usa@data 

# 
infected <- read_excel("C:/Users/josem/OneDrive/Escritorio/infectedUS/CasesUS.xlsx") 
names(infected)      


usa_infected <- shp_usa
usa_infected <- merge(x= shp_usa@data,y= infected,by.x= "STATE_NAME",by.y="State",all.x = TRUE,sort  = FALSE)
summary(usa_infected)



# Map Cases by state USA

    spplot(usa_infected[usa_infected@Cases > 0, ],"Cases.x", at = quantile(usa_infected$Cases.x, p = c(0, .25, .5, .75, 1), na.rm = TRUE), col.regions = brewer.pal(5, "Reds"), main = expression("Cases by State"))

But I have two problems: 1. I don't know what exactly write in this part of the code : by.x=? by.y=? in order to do the task.

usa_infected <- merge(shp_usa@data,infected,by.x= "STATE_NAME",by.y="State",all.x = TRUE,sort  = FALSE)
  1. To visualize the map I have this code 
    spplot(usa_infected[usa_infected@Cases > 0, ],"Cases.y", at = quantile(usa_infected$Cases.y, p = c(0, .25, .5, .75, 1), na.rm = TRUE), col.regions = brewer.pal(5, "Reds"), main = expression("Cases by State"))

But after run the code I got this message:

Error in `[.data.frame`(usa_infected, usa_infected@Cases > 0, ) : 


 trying to get slot "Cases" from an object (class "data.frame") that is not an S4 object

I have these 2 data sets: 1- This is from a shp file from USA.

 structure(list(STATE_NAME = structure(c(48L, 42L, 51L, 50L, 46L, 
    24L, 38L, 30L, 16L, 22L, 28L, 33L, 39L, 7L, 40L, 31L, 15L, 29L, 
    45L, 5L, 36L, 14L, 9L, 21L, 6L, 18L, 17L, 47L, 26L, 3L, 37L, 
    34L, 43L, 44L, 25L, 11L, 41L, 4L, 19L, 10L, 23L, 12L, 1L, 27L, 
    20L, 35L, 8L, 13L, 2L, 49L, 32L), .Label = c("Alabama", "Alaska", 
    "Arizona", "Arkansas", "California", "Colorado", "Connecticut", 
    "Delaware", "District of Columbia", "Florida", "Georgia", "Hawaii", 
    "Idaho", "Illinois", "Indiana", "Iowa", "Kansas", "Kentucky", 
    "Louisiana", "Maine", "Maryland", "Massachusetts", "Michigan", 
    "Minnesota", "Mississippi", "Missouri", "Montana", "Nebraska", 
    "Nevada", "New Hampshire", "New Jersey", "New Mexico", "New York", 
    "North Carolina", "North Dakota", "Ohio", "Oklahoma", "Oregon", 
    "Pennsylvania", "Rhode Island", "South Carolina", "South Dakota", 
    "Tennessee", "Texas", "Utah", "Vermont", "Virginia", "Washington", 
    "West Virginia", "Wisconsin", "Wyoming"), class = "factor"), 
        STATE_FIPS = structure(c(48L, 42L, 51L, 50L, 46L, 24L, 38L, 
        30L, 16L, 22L, 28L, 33L, 39L, 7L, 40L, 31L, 15L, 29L, 45L, 
        5L, 36L, 14L, 9L, 21L, 6L, 18L, 17L, 47L, 26L, 3L, 37L, 34L, 
        43L, 44L, 25L, 11L, 41L, 4L, 19L, 10L, 23L, 12L, 1L, 27L, 
        20L, 35L, 8L, 13L, 2L, 49L, 32L), .Label = c("01", "02", 
        "04", "05", "06", "08", "09", "10", "11", "12", "13", "15", 
        "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", 
        "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", 
        "36", "37", "38", "39", "40", "41", "42", "44", "45", "46", 
        "47", "48", "49", "50", "51", "53", "54", "55", "56"), class = "factor"), 
        STATE_ABBR = structure(c(48L, 42L, 51L, 49L, 47L, 24L, 38L, 
        31L, 13L, 20L, 30L, 35L, 39L, 7L, 40L, 32L, 16L, 34L, 45L, 
        5L, 36L, 15L, 8L, 21L, 6L, 18L, 17L, 46L, 25L, 4L, 37L, 28L, 
        43L, 44L, 26L, 11L, 41L, 3L, 19L, 10L, 23L, 12L, 2L, 27L, 
        22L, 29L, 9L, 14L, 1L, 50L, 33L), .Label = c("AK", "AL", 
        "AR", "AZ", "CA", "CO", "CT", "DC", "DE", "FL", "GA", "HI", 
        "IA", "ID", "IL", "IN", "KS", "KY", "LA", "MA", "MD", "ME", 
        "MI", "MN", "MO", "MS", "MT", "NC", "ND", "NE", "NH", "NJ", 
        "NM", "NV", "NY", "OH", "OK", "OR", "PA", "RI", "SC", "SD", 
        "TN", "TX", "UT", "VA", "VT", "WA", "WI", "WV", "WY"), class = "factor"), 
        Cases = c(364, 8, 1, 6, 1, 5, 21, 5, 13, 95, 10, 216, 16, 
        3, 5, 15, 6, 7, 2, 157, 4, 19, 10, 9, 33, 8, 1, 9, 1, 6, 
        2, 7, 9, 21, 1, 22, 9, 1, 13, 26, 2, 2, NA, NA, NA, NA, NA, 
        NA, NA, NA, NA)), class = "data.frame", row.names = c(NA, 
    -51L))

2- And this is database for infected :

structure(list(State = c("Arizona", "Wyoming", "Arkansas", "California", 
"Colorado", "Connecticut", "District of Columbia", "Florida", 
"Georgia", "Hawaii", "Illinois", "Indiana", "Iowa", "Kansas", 
"Kentucky", "Louisiana", "Maryland", "Massachusetts", "Michigan", 
"Minnesota", "Mississippi", "Missouri", "Nebraska", "Nevada", 
"New Hampshire", "New Jersey", "New York", "North Carolina", 
"Ohio", "Oklahoma", "Oregon", "Pennsylvania", "Rhode Island", 
"South Carolina", "South Dakota", "Tennessee", "Texas", "Utah", 
"Vermont", "Virginia", "Washington", "Wisconsin"), Cases = c(6, 
1, 1, 157, 33, 3, 10, 26, 22, 2, 19, 6, 13, 1, 8, 13, 9, 95, strong text
2, 5, 1, 1, 10, 7, 5, 15, 216, 7, 4, 2, 21, 16, 5, 9, 8, 9, 21, 
2, 1, 9, 364, 6)), row.names = c(NA, -42L), class = c("tbl_df", 
"tbl", "data.frame"))

Upvotes: 0

Views: 389

Answers (1)

Kempie
Kempie

Reputation: 293

So first of all, readShapeSpatial is deprecated and should rather use rgdal::readOGR or sf::st_read.

to answer your questions:

1: Your merge is correct if you want to assign new cases to each state in the exel file. (There are already cases in the shape). I prefer assigning the dataframes to the by clause name to show more clearly what is happening) such as: 

 merge(x= shp_usa@data,y =infected,by.x= "STATE_NAME",by.y="State",all.x = TRUE,sort  = FALSE)

Note. Duplicate column names will change with a suffix of the link name i.e Cases.x and Cases.y

2: As the warning states "unable to find an inherited method for function ‘spplot’ for signature ‘"data.frame"’)" it means it is trying to plot from the shapefile's data frame and not the spatial file. This is becuase you call the data frame with the @data call (usa_infected@data), try and change this to:

spplot(usa_infected[usa_infected$Cases.y > 0, ],"Cases.y", at = quantile(usa_infected$Cases.y, p = c(0, .25, .5, .75, 1), na.rm = TRUE), col.regions = brewer.pal(5, "Reds"), main = expression("Cases by State"))

Upvotes: 1

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