KarimSamiha_R_Week_7_Assignment

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R Spatial Lab Assignment # 1 - Week 7

Don’t use a single chunk for the entire assignment. Break it into multiple chunks.

task 1: Set up a R project for the R-Spatial section.

# setting up R project for R-Spatial section

dir.create("~/Documents/R-Spatial", recursive = TRUE)

## Warning in dir.create("~/Documents/R-Spatial", recursive = TRUE):
## '/Users/samikarim/Documents/R-Spatial' already exists

setwd("~/Documents/R-Spatial")

task 2: Read the NYC postal areas in Shapefiles into sf objects. As NYC DOH publishes COVID-19 data by zip code, we will utilize the postal area data later.

# read shapefile into sf object

nyc_zip_sf <- st_read("data/ZIP_CODE_040114/ZIP_CODE_040114.shp")

## Reading layer `ZIP_CODE_040114' from data source 
##   `/Users/samikarim/Documents/R-spatial/data/ZIP_CODE_040114/ZIP_CODE_040114.shp' 
##   using driver `ESRI Shapefile'
## Simple feature collection with 263 features and 12 fields
## Geometry type: POLYGON
## Dimension:     XY
## Bounding box:  xmin: 913129 ymin: 120020.9 xmax: 1067494 ymax: 272710.9
## Projected CRS: NAD83 / New York Long Island (ftUS)

str(nyc_zip_sf)

## Classes 'sf' and 'data.frame':   263 obs. of  13 variables:
##  $ ZIPCODE   : chr  "11436" "11213" "11212" "11225" ...
##  $ BLDGZIP   : chr  "0" "0" "0" "0" ...
##  $ PO_NAME   : chr  "Jamaica" "Brooklyn" "Brooklyn" "Brooklyn" ...
##  $ POPULATION: num  18681 62426 83866 56527 72280 ...
##  $ AREA      : num  22699295 29631004 41972104 23698630 36868799 ...
##  $ STATE     : chr  "NY" "NY" "NY" "NY" ...
##  $ COUNTY    : chr  "Queens" "Kings" "Kings" "Kings" ...
##  $ ST_FIPS   : chr  "36" "36" "36" "36" ...
##  $ CTY_FIPS  : chr  "081" "047" "047" "047" ...
##  $ URL       : chr  "http://www.usps.com/" "http://www.usps.com/" "http://www.usps.com/" "http://www.usps.com/" ...
##  $ SHAPE_AREA: num  0 0 0 0 0 0 0 0 0 0 ...
##  $ SHAPE_LEN : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ geometry  :sfc_POLYGON of length 263; first list element: List of 1
##   ..$ : num [1:159, 1:2] 1038098 1038142 1038171 1038280 1038521 ...
##   ..- attr(*, "class")= chr [1:3] "XY" "POLYGON" "sfg"
##  - attr(*, "sf_column")= chr "geometry"
##  - attr(*, "agr")= Factor w/ 3 levels "constant","aggregate",..: NA NA NA NA NA NA NA NA NA NA ...
##   ..- attr(*, "names")= chr [1:12] "ZIPCODE" "BLDGZIP" "PO_NAME" "POPULATION" ...

task 3: Read and process the NYS health facilities spreadsheet data. Create sf objects from geographic coordinates.

Quarto markdown is different from R markdown in terms of chunk options. See chunk options at Quarto website.

# read csv into df 

nyshealth_df <- read_csv("data/NYS_Health_Facility.csv", 
                               show_col_types = FALSE, 
                               lazy = FALSE)
str(nyshealth_df)

## spc_tbl_ [3,990 × 36] (S3: spec_tbl_df/tbl_df/tbl/data.frame)
##  $ Facility ID                 : num [1:3990] 204 620 654 1156 2589 ...
##  $ Facility Name               : chr [1:3990] "Hospice at Lourdes" "Charles T Sitrin Health Care Center Inc" "Central Park Rehabilitation and Nursing Center" "East Side Nursing Home" ...
##  $ Short Description           : chr [1:3990] "HSPC" "NH" "NH" "NH" ...
##  $ Description                 : chr [1:3990] "Hospice" "Residential Health Care Facility - SNF" "Residential Health Care Facility - SNF" "Residential Health Care Facility - SNF" ...
##  $ Facility Open Date          : chr [1:3990] "06/01/1985" "02/01/1989" "02/01/1989" "08/01/1979" ...
##  $ Facility Address 1          : chr [1:3990] "4102 Old Vestal Road" "2050 Tilden Avenue" "116 Martin Luther King East" "62 Prospect St" ...
##  $ Facility Address 2          : chr [1:3990] NA NA NA NA ...
##  $ Facility City               : chr [1:3990] "Vestal" "New Hartford" "Syracuse" "Warsaw" ...
##  $ Facility State              : chr [1:3990] "New York" "New York" "New York" "New York" ...
##  $ Facility Zip Code           : chr [1:3990] "13850" "13413" "13205" "14569" ...
##  $ Facility Phone Number       : num [1:3990] 6.08e+09 3.16e+09 3.15e+09 5.86e+09 5.86e+09 ...
##  $ Facility Fax Number         : num [1:3990] NA NA NA NA NA ...
##  $ Facility Website            : chr [1:3990] NA NA NA NA ...
##  $ Facility County Code        : num [1:3990] 3 32 33 60 2 ...
##  $ Facility County             : chr [1:3990] "Broome" "Oneida" "Onondaga" "Wyoming" ...
##  $ Regional Office ID          : num [1:3990] 3 3 3 1 1 1 7 1 7 5 ...
##  $ Regional Office             : chr [1:3990] "Central New York Regional Office" "Central New York Regional Office" "Central New York Regional Office" "Western Regional Office - Buffalo" ...
##  $ Main Site Name              : chr [1:3990] NA NA NA NA ...
##  $ Main Site Facility ID       : num [1:3990] NA NA NA NA NA ...
##  $ Operating Certificate Number: chr [1:3990] "0301501F" "3227304N" "3301326N" "6027303N" ...
##  $ Operator Name               : chr [1:3990] "Our Lady of Lourdes Memorial Hospital Inc" "Charles T Sitrin Health Care Center, Inc" "CPRNC, LLC" "East Side Nursing Home Inc" ...
##  $ Operator Address 1          : chr [1:3990] "169 Riverside Drive" "Box 1000 Tilden Avenue" "116 Martin Luther King East" "62 Prospect Street" ...
##  $ Operator Address 2          : chr [1:3990] NA NA NA NA ...
##  $ Operator City               : chr [1:3990] "Binghamton" "New Hartford" "Syracuse" "Warsaw" ...
##  $ Operator State              : chr [1:3990] "New York" "New York" "New York" "New York" ...
##  $ Operator Zip Code           : chr [1:3990] "13905" "13413" "13205" "14569" ...
##  $ Cooperator Name             : chr [1:3990] NA NA NA NA ...
##  $ Cooperator Address          : chr [1:3990] NA NA NA NA ...
##  $ Cooperator Address 2        : chr [1:3990] NA NA NA NA ...
##  $ Cooperator City             : chr [1:3990] NA NA NA NA ...
##  $ Cooperator State            : chr [1:3990] "New York" "New York" "New York" "New York" ...
##  $ Cooperator Zip Code         : chr [1:3990] NA NA NA NA ...
##  $ Ownership Type              : chr [1:3990] "Not for Profit Corporation" "Not for Profit Corporation" "LLC" "Business Corporation" ...
##  $ Facility Latitude           : num [1:3990] 42.1 43.1 NA 42.7 42.1 ...
##  $ Facility Longitude          : num [1:3990] -76 -75.2 NA -78.1 -78 ...
##  $ Facility Location           : chr [1:3990] "(42.097095, -75.975243)" "(43.05497, -75.228828)" NA "(42.738979, -78.12867)" ...
##  - attr(*, "spec")=
##   .. cols(
##   ..   `Facility ID` = col_double(),
##   ..   `Facility Name` = col_character(),
##   ..   `Short Description` = col_character(),
##   ..   Description = col_character(),
##   ..   `Facility Open Date` = col_character(),
##   ..   `Facility Address 1` = col_character(),
##   ..   `Facility Address 2` = col_character(),
##   ..   `Facility City` = col_character(),
##   ..   `Facility State` = col_character(),
##   ..   `Facility Zip Code` = col_character(),
##   ..   `Facility Phone Number` = col_double(),
##   ..   `Facility Fax Number` = col_double(),
##   ..   `Facility Website` = col_character(),
##   ..   `Facility County Code` = col_double(),
##   ..   `Facility County` = col_character(),
##   ..   `Regional Office ID` = col_double(),
##   ..   `Regional Office` = col_character(),
##   ..   `Main Site Name` = col_character(),
##   ..   `Main Site Facility ID` = col_double(),
##   ..   `Operating Certificate Number` = col_character(),
##   ..   `Operator Name` = col_character(),
##   ..   `Operator Address 1` = col_character(),
##   ..   `Operator Address 2` = col_character(),
##   ..   `Operator City` = col_character(),
##   ..   `Operator State` = col_character(),
##   ..   `Operator Zip Code` = col_character(),
##   ..   `Cooperator Name` = col_character(),
##   ..   `Cooperator Address` = col_character(),
##   ..   `Cooperator Address 2` = col_character(),
##   ..   `Cooperator City` = col_character(),
##   ..   `Cooperator State` = col_character(),
##   ..   `Cooperator Zip Code` = col_character(),
##   ..   `Ownership Type` = col_character(),
##   ..   `Facility Latitude` = col_double(),
##   ..   `Facility Longitude` = col_double(),
##   ..   `Facility Location` = col_character()
##   .. )
##  - attr(*, "problems")=<externalptr>

# filter out NA from dataframe 

sum(is.na(nyshealth_df$`Facility Longitude`))

## [1] 142

sum(is.na(nyshealth_df$`Facility Latitude`))

## [1] 142

nyshealth_df_ <- nyshealth_df %>%
  dplyr::filter(
    !is.na(`Facility Longitude`),
    !is.na(`Facility Latitude`)
  )

# create sf object with geographic coordinates 

nyshealth_sf <- st_as_sf(nyshealth_df_, 
                               coords = c("Facility Longitude", "Facility Latitude"))
str(nyshealth_sf)

## sf [3,848 × 35] (S3: sf/tbl_df/tbl/data.frame)
##  $ Facility ID                 : num [1:3848] 204 620 1156 2589 3455 ...
##  $ Facility Name               : chr [1:3848] "Hospice at Lourdes" "Charles T Sitrin Health Care Center Inc" "East Side Nursing Home" "Wellsville Manor Care Center" ...
##  $ Short Description           : chr [1:3848] "HSPC" "NH" "NH" "NH" ...
##  $ Description                 : chr [1:3848] "Hospice" "Residential Health Care Facility - SNF" "Residential Health Care Facility - SNF" "Residential Health Care Facility - SNF" ...
##  $ Facility Open Date          : chr [1:3848] "06/01/1985" "02/01/1989" "08/01/1979" "02/01/1989" ...
##  $ Facility Address 1          : chr [1:3848] "4102 Old Vestal Road" "2050 Tilden Avenue" "62 Prospect St" "4192A Bolivar Road" ...
##  $ Facility Address 2          : chr [1:3848] NA NA NA NA ...
##  $ Facility City               : chr [1:3848] "Vestal" "New Hartford" "Warsaw" "Wellsville" ...
##  $ Facility State              : chr [1:3848] "New York" "New York" "New York" "New York" ...
##  $ Facility Zip Code           : chr [1:3848] "13850" "13413" "14569" "14895" ...
##  $ Facility Phone Number       : num [1:3848] 6.08e+09 3.16e+09 5.86e+09 5.86e+09 7.17e+09 ...
##  $ Facility Fax Number         : num [1:3848] NA NA NA NA NA ...
##  $ Facility Website            : chr [1:3848] NA NA NA NA ...
##  $ Facility County Code        : num [1:3848] 3 32 60 2 14 ...
##  $ Facility County             : chr [1:3848] "Broome" "Oneida" "Wyoming" "Allegany" ...
##  $ Regional Office ID          : num [1:3848] 3 3 1 1 1 7 1 7 5 7 ...
##  $ Regional Office             : chr [1:3848] "Central New York Regional Office" "Central New York Regional Office" "Western Regional Office - Buffalo" "Western Regional Office - Buffalo" ...
##  $ Main Site Name              : chr [1:3848] NA NA NA NA ...
##  $ Main Site Facility ID       : num [1:3848] NA NA NA NA NA ...
##  $ Operating Certificate Number: chr [1:3848] "0301501F" "3227304N" "6027303N" "0228305N" ...
##  $ Operator Name               : chr [1:3848] "Our Lady of Lourdes Memorial Hospital Inc" "Charles T Sitrin Health Care Center, Inc" "East Side Nursing Home Inc" "Wellsville Manor LLC" ...
##  $ Operator Address 1          : chr [1:3848] "169 Riverside Drive" "Box 1000 Tilden Avenue" "62 Prospect Street" "4192a Bolivar Road" ...
##  $ Operator Address 2          : chr [1:3848] NA NA NA NA ...
##  $ Operator City               : chr [1:3848] "Binghamton" "New Hartford" "Warsaw" "Wellsville" ...
##  $ Operator State              : chr [1:3848] "New York" "New York" "New York" "New York" ...
##  $ Operator Zip Code           : chr [1:3848] "13905" "13413" "14569" "14897" ...
##  $ Cooperator Name             : chr [1:3848] NA NA NA NA ...
##  $ Cooperator Address          : chr [1:3848] NA NA NA NA ...
##  $ Cooperator Address 2        : chr [1:3848] NA NA NA NA ...
##  $ Cooperator City             : chr [1:3848] NA NA NA NA ...
##  $ Cooperator State            : chr [1:3848] "New York" "New York" "New York" "New York" ...
##  $ Cooperator Zip Code         : chr [1:3848] NA NA NA NA ...
##  $ Ownership Type              : chr [1:3848] "Not for Profit Corporation" "Not for Profit Corporation" "Business Corporation" "LLC" ...
##  $ Facility Location           : chr [1:3848] "(42.097095, -75.975243)" "(43.05497, -75.228828)" "(42.738979, -78.12867)" "(42.126461, -77.967834)" ...
##  $ geometry                    :sfc_POINT of length 3848; first list element:  'XY' num [1:2] -76 42.1
##  - attr(*, "sf_column")= chr "geometry"
##  - attr(*, "agr")= Factor w/ 3 levels "constant","aggregate",..: NA NA NA NA NA NA NA NA NA NA ...
##   ..- attr(*, "names")= chr [1:34] "Facility ID" "Facility Name" "Short Description" "Description" ...

# set coordinate reference system

st_crs(nyshealth_sf) <- 4326
st_crs(nyshealth_sf)

## Coordinate Reference System:
##   User input: EPSG:4326 
##   wkt:
## GEOGCRS["WGS 84",
##     ENSEMBLE["World Geodetic System 1984 ensemble",
##         MEMBER["World Geodetic System 1984 (Transit)"],
##         MEMBER["World Geodetic System 1984 (G730)"],
##         MEMBER["World Geodetic System 1984 (G873)"],
##         MEMBER["World Geodetic System 1984 (G1150)"],
##         MEMBER["World Geodetic System 1984 (G1674)"],
##         MEMBER["World Geodetic System 1984 (G1762)"],
##         MEMBER["World Geodetic System 1984 (G2139)"],
##         MEMBER["World Geodetic System 1984 (G2296)"],
##         ELLIPSOID["WGS 84",6378137,298.257223563,
##             LENGTHUNIT["metre",1]],
##         ENSEMBLEACCURACY[2.0]],
##     PRIMEM["Greenwich",0,
##         ANGLEUNIT["degree",0.0174532925199433]],
##     CS[ellipsoidal,2],
##         AXIS["geodetic latitude (Lat)",north,
##             ORDER[1],
##             ANGLEUNIT["degree",0.0174532925199433]],
##         AXIS["geodetic longitude (Lon)",east,
##             ORDER[2],
##             ANGLEUNIT["degree",0.0174532925199433]],
##     USAGE[
##         SCOPE["Horizontal component of 3D system."],
##         AREA["World."],
##         BBOX[-90,-180,90,180]],
##     ID["EPSG",4326]]

nyshealth_sf

## Simple feature collection with 3848 features and 34 fields
## Geometry type: POINT
## Dimension:     XY
## Bounding box:  xmin: -79.6299 ymin: -75.45935 xmax: 43.21162 ymax: 44.97849
## Geodetic CRS:  WGS 84
## # A tibble: 3,848 × 35
##    `Facility ID` `Facility Name`                 `Short Description` Description
##  *         <dbl> <chr>                           <chr>               <chr>      
##  1           204 Hospice at Lourdes              HSPC                Hospice    
##  2           620 Charles T Sitrin Health Care C… NH                  Residentia…
##  3          1156 East Side Nursing Home          NH                  Residentia…
##  4          2589 Wellsville Manor Care Center    NH                  Residentia…
##  5          3455 Harris Hill Nursing Facility, … NH                  Residentia…
##  6          3853 Garden City Surgi Center        DTC                 Diagnostic…
##  7          4249 Willcare                        CHHA                Certified …
##  8          4473 Good Shepherd Hospice           HSPC                Hospice    
##  9          6230 NYU Langone Rutherford          HOSP-EC             Hospital E…
## 10          6482 Endoscopy Center of Long Islan… DTC                 Diagnostic…
## # ℹ 3,838 more rows
## # ℹ 31 more variables: `Facility Open Date` <chr>, `Facility Address 1` <chr>,
## #   `Facility Address 2` <chr>, `Facility City` <chr>, `Facility State` <chr>,
## #   `Facility Zip Code` <chr>, `Facility Phone Number` <dbl>,
## #   `Facility Fax Number` <dbl>, `Facility Website` <chr>,
## #   `Facility County Code` <dbl>, `Facility County` <chr>,
## #   `Regional Office ID` <dbl>, `Regional Office` <chr>, …

task 4: Read and process the NYS retail food stores data. Create sf objects from geographic coordinates for NYC.

# read csv into df 

nysretailfood_df <- read_csv("data/NYS_Retail_Food_Stores.csv", 
                               show_col_types = FALSE, 
                               lazy = FALSE)
str(nysretailfood_df)

## spc_tbl_ [29,389 × 15] (S3: spec_tbl_df/tbl_df/tbl/data.frame)
##  $ County            : chr [1:29389] "Albany" "Albany" "Albany" "Albany" ...
##  $ License Number    : chr [1:29389] "733149" "704590" "727909" "720557" ...
##  $ Operation Type    : chr [1:29389] "Store" "Store" "Store" "Store" ...
##  $ Establishment Type: chr [1:29389] "A" "JAC" "JAC" "JAC" ...
##  $ Entity Name       : chr [1:29389] "SPEEDWAY LLC" "1250 SELKIRK INC" "RED-KAP SALES INC" "SAEED SADIQ, SAIKA NOREEN" ...
##  $ DBA Name          : chr [1:29389] "12110" "1250 SELKIRK" "1667 GENERAL STORE" "19 STREET QUICK STOP" ...
##  $ Street Number     : chr [1:29389] "719" "1250" "1667" "315" ...
##  $ Street Name       : chr [1:29389] "NEW LOUDON RD" "RTE 9W & 396" "WESTERN AVENUE" "19TH STREET" ...
##  $ Address Line 2    : logi [1:29389] NA NA NA NA NA NA ...
##  $ Address Line 3    : logi [1:29389] NA NA NA NA NA NA ...
##  $ City              : chr [1:29389] "LATHAM" "SELKIRK" "ALBANY" "WATERVLIET" ...
##  $ State             : chr [1:29389] "NY" "NY" "NY" "NY" ...
##  $ Zip Code          : num [1:29389] 12110 12158 12203 12189 12210 ...
##  $ Square Footage    : num [1:29389] 300 3000 2000 1200 1800 0 0 200 0 2000 ...
##  $ Location          : chr [1:29389] "719 NEW LOUDON RD\nLATHAM, NY 12110\n(42.739618, -73.761949)" "1250 RTE 9 W\nSELKIRK, NY 12158\n(42.547591, -73.8073)" "1667 WESTERN AVENUE\nALBANY, NY 12203\n(42.686553, -73.854665)" "315 19TH STREET\nWATERVLIET, NY 12189\n(42.73063, -73.703443)" ...
##  - attr(*, "spec")=
##   .. cols(
##   ..   County = col_character(),
##   ..   `License Number` = col_character(),
##   ..   `Operation Type` = col_character(),
##   ..   `Establishment Type` = col_character(),
##   ..   `Entity Name` = col_character(),
##   ..   `DBA Name` = col_character(),
##   ..   `Street Number` = col_character(),
##   ..   `Street Name` = col_character(),
##   ..   `Address Line 2` = col_logical(),
##   ..   `Address Line 3` = col_logical(),
##   ..   City = col_character(),
##   ..   State = col_character(),
##   ..   `Zip Code` = col_double(),
##   ..   `Square Footage` = col_number(),
##   ..   Location = col_character()
##   .. )
##  - attr(*, "problems")=<externalptr>

# has no coordinates, read xy csv into df 

nysretailfood_xy_df <- read.csv("data/nys_retail_food_store_xy.csv",fileEncoding='latin1', check.names=F)

str(nysretailfood_xy_df)

## 'data.frame':    29389 obs. of  18 variables:
##  $ ï..County         : chr  "Albany" "Albany" "Albany" "Albany" ...
##  $ License.Number    : int  733149 704590 727909 720557 15890 735254 708848 716318 713889 715759 ...
##  $ Operation.Type    : chr  "Store" "Store" "Store" "Store" ...
##  $ Establishment.Type: chr  "A     " "JAC   " "JAC   " "JAC   " ...
##  $ Entity.Name       : chr  "SPEEDWAY LLC                     " "1250 SELKIRK INC                 " "RED-KAP SALES INC                " "SAEED SADIQ, SAIKA NOREEN        " ...
##  $ DBA.Name          : chr  "12110                  " "1250 SELKIRK           " "1667 GENERAL STORE     " "19 STREET QUICK STOP   " ...
##  $ Street.Number     : chr  "719" "1250" "1667" "315" ...
##  $ Street.Name       : chr  "NEW LOUDON RD                " "RTE 9W & 396                " "WESTERN AVENUE              " "19TH STREET                  " ...
##  $ Address.Line.2    : logi  NA NA NA NA NA NA ...
##  $ Address.Line.3    : logi  NA NA NA NA NA NA ...
##  $ City              : chr  "LATHAM            " "SELKIRK           " "ALBANY            " "WATERVLIET        " ...
##  $ State             : chr  "NY" "NY" "NY" "NY" ...
##  $ Zip.Code          : int  12110 12158 12203 12189 12210 12209 12110 12084 12077 12159 ...
##  $ Square.Footage    : chr  "300" "3,000" "2,000" "1,200" ...
##  $ Location          : chr  "719 NEW LOUDON RD\nLATHAM, NY 12110\n(42.739618, -73.761949)" "1250 RTE 9 W\nSELKIRK, NY 12158\n(42.547591, -73.8073)" "1667 WESTERN AVENUE\nALBANY, NY 12203\n(42.686553, -73.854665)" "315 19TH STREET\nWATERVLIET, NY 12189\n(42.73063, -73.703443)" ...
##  $ Coords            : chr  "42.739618, -73.761949" "42.547591, -73.8073" "42.686553, -73.854665" "42.73063, -73.703443" ...
##  $ Y                 : num  42.7 42.5 42.7 42.7 42.7 ...
##  $ X                 : num  -73.8 -73.8 -73.9 -73.7 -73.8 ...

# filter out NA from dataframe  

sum(is.na(nysretailfood_xy_df$`X`))

## [1] 5417

sum(is.na(nysretailfood_xy_df$`Y`))

## [1] 5417

nysretailfood_xy_df_ <- nysretailfood_xy_df %>%
  dplyr::filter(
    !is.na(`X`),
    !is.na(`Y`)
  )

# create sf object with geographic coordinates 

nysretailfood_sf <- st_as_sf(nysretailfood_xy_df_, 
                               coords = c("X", "Y"))
str(nysretailfood_sf)

## Classes 'sf' and 'data.frame':   23972 obs. of  17 variables:
##  $ ï..County         : chr  "Albany" "Albany" "Albany" "Albany" ...
##  $ License.Number    : int  733149 704590 727909 720557 15890 735254 708848 713889 715759 723927 ...
##  $ Operation.Type    : chr  "Store" "Store" "Store" "Store" ...
##  $ Establishment.Type: chr  "A     " "JAC   " "JAC   " "JAC   " ...
##  $ Entity.Name       : chr  "SPEEDWAY LLC                     " "1250 SELKIRK INC                 " "RED-KAP SALES INC                " "SAEED SADIQ, SAIKA NOREEN        " ...
##  $ DBA.Name          : chr  "12110                  " "1250 SELKIRK           " "1667 GENERAL STORE     " "19 STREET QUICK STOP   " ...
##  $ Street.Number     : chr  "719" "1250" "1667" "315" ...
##  $ Street.Name       : chr  "NEW LOUDON RD                " "RTE 9W & 396                " "WESTERN AVENUE              " "19TH STREET                  " ...
##  $ Address.Line.2    : logi  NA NA NA NA NA NA ...
##  $ Address.Line.3    : logi  NA NA NA NA NA NA ...
##  $ City              : chr  "LATHAM            " "SELKIRK           " "ALBANY            " "WATERVLIET        " ...
##  $ State             : chr  "NY" "NY" "NY" "NY" ...
##  $ Zip.Code          : int  12110 12158 12203 12189 12210 12209 12110 12077 12159 12084 ...
##  $ Square.Footage    : chr  "300" "3,000" "2,000" "1,200" ...
##  $ Location          : chr  "719 NEW LOUDON RD\nLATHAM, NY 12110\n(42.739618, -73.761949)" "1250 RTE 9 W\nSELKIRK, NY 12158\n(42.547591, -73.8073)" "1667 WESTERN AVENUE\nALBANY, NY 12203\n(42.686553, -73.854665)" "315 19TH STREET\nWATERVLIET, NY 12189\n(42.73063, -73.703443)" ...
##  $ Coords            : chr  "42.739618, -73.761949" "42.547591, -73.8073" "42.686553, -73.854665" "42.73063, -73.703443" ...
##  $ geometry          :sfc_POINT of length 23972; first list element:  'XY' num  -73.8 42.7
##  - attr(*, "sf_column")= chr "geometry"
##  - attr(*, "agr")= Factor w/ 3 levels "constant","aggregate",..: NA NA NA NA NA NA NA NA NA NA ...
##   ..- attr(*, "names")= chr [1:16] "ï..County" "License.Number" "Operation.Type" "Establishment.Type" ...

# set coordinate reference system to wgs 

st_crs(nysretailfood_sf) <- 4326
st_crs(nysretailfood_sf)

## Coordinate Reference System:
##   User input: EPSG:4326 
##   wkt:
## GEOGCRS["WGS 84",
##     ENSEMBLE["World Geodetic System 1984 ensemble",
##         MEMBER["World Geodetic System 1984 (Transit)"],
##         MEMBER["World Geodetic System 1984 (G730)"],
##         MEMBER["World Geodetic System 1984 (G873)"],
##         MEMBER["World Geodetic System 1984 (G1150)"],
##         MEMBER["World Geodetic System 1984 (G1674)"],
##         MEMBER["World Geodetic System 1984 (G1762)"],
##         MEMBER["World Geodetic System 1984 (G2139)"],
##         MEMBER["World Geodetic System 1984 (G2296)"],
##         ELLIPSOID["WGS 84",6378137,298.257223563,
##             LENGTHUNIT["metre",1]],
##         ENSEMBLEACCURACY[2.0]],
##     PRIMEM["Greenwich",0,
##         ANGLEUNIT["degree",0.0174532925199433]],
##     CS[ellipsoidal,2],
##         AXIS["geodetic latitude (Lat)",north,
##             ORDER[1],
##             ANGLEUNIT["degree",0.0174532925199433]],
##         AXIS["geodetic longitude (Lon)",east,
##             ORDER[2],
##             ANGLEUNIT["degree",0.0174532925199433]],
##     USAGE[
##         SCOPE["Horizontal component of 3D system."],
##         AREA["World."],
##         BBOX[-90,-180,90,180]],
##     ID["EPSG",4326]]

nysretailfood_sf

## Simple feature collection with 23972 features and 16 fields
## Geometry type: POINT
## Dimension:     XY
## Bounding box:  xmin: -79.75953 ymin: 40.50782 xmax: -71.93873 ymax: 44.99484
## Geodetic CRS:  WGS 84
## First 10 features:
##    ï..County License.Number Operation.Type Establishment.Type
## 1     Albany         733149          Store             A     
## 2     Albany         704590          Store             JAC   
## 3     Albany         727909          Store             JAC   
## 4     Albany         720557          Store             JAC   
## 5     Albany          15890          Store             A     
## 6     Albany         735254          Store             JAC   
## 7     Albany         708848          Store             JAC   
## 8     Albany         713889          Store             JAC   
## 9     Albany         715759          Store             JAC   
## 10    Albany         723927          Store             JAC   
##                          Entity.Name                DBA.Name Street.Number
## 1  SPEEDWAY LLC                      12110                             719
## 2  1250 SELKIRK INC                  1250 SELKIRK                     1250
## 3  RED-KAP SALES INC                 1667 GENERAL STORE               1667
## 4  SAEED SADIQ, SAIKA NOREEN         19 STREET QUICK STOP              315
## 5  AZIZ MOHAMMAD S                   24 HR ALBANY NEWS                   8
## 6  7-ELEVEN INC                      7-ELEVEN                          477
## 7  ADVANCED FRESH CONCEPTS FRANCHISE AFC SUSHI @ PRICE CHOPP           873
## 8  ADVANCED FRESH CONCEPTS FRANCHISE AFC SUSHI @ PRICE CHOPP           329
## 9  ADVANCED FRESH CONCEPTS FRANCHISE AFC SUSHI @PRICE CHOPPE          1395
## 10 ADVANCED FRESH CONCEPTS FRAN CORP AFC SUSHI@ PRICE CHOPPE          2080
##                        Street.Name Address.Line.2 Address.Line.3
## 1    NEW LOUDON RD                             NA             NA
## 2     RTE 9W & 396                             NA             NA
## 3     WESTERN AVENUE                           NA             NA
## 4    19TH STREET                               NA             NA
## 5  CENTRAL AVE                                 NA             NA
## 6    DELAWARE AVE                              NA             NA
## 7          NEW LOUDON RD                       NA             NA
## 8        GLENMONT RD                           NA             NA
## 9         NEW SCOTLAND RD                      NA             NA
## 10    WESTERN AVE                              NA             NA
##                  City State Zip.Code Square.Footage
## 1  LATHAM                NY    12110            300
## 2  SELKIRK               NY    12158          3,000
## 3  ALBANY                NY    12203          2,000
## 4  WATERVLIET            NY    12189          1,200
## 5  ALBANY                NY    12210          1,800
## 6  ALBANY                NY    12209              0
## 7  LATHAM                NY    12110              0
## 8  GLENMONT              NY    12077              0
## 9  SLINGERLANDS          NY    12159          2,000
## 10 GUILDERLAND           NY    12084            400
##                                                                 Location
## 1           719 NEW LOUDON RD\nLATHAM, NY 12110\n(42.739618, -73.761949)
## 2                 1250 RTE 9 W\nSELKIRK, NY 12158\n(42.547591, -73.8073)
## 3         1667 WESTERN AVENUE\nALBANY, NY 12203\n(42.686553, -73.854665)
## 4          315 19TH STREET\nWATERVLIET, NY 12189\n(42.73063, -73.703443)
## 5               8 CENTRAL AVE\nALBANY, NY 12210\n(42.657136, -73.763712)
## 6            477 DELAWARE AVE\nALBANY, NY 12209\n(42.639931, -73.784962)
## 7            873 NEW LOUDON RD\nLATHAM, NY 12110\n(42.75459, -73.758714)
## 8           329 GLENMONT RD\nGLENMONT, NY 12077\n(42.601045, -73.790364)
## 9  1395 NEW SCOTLAND RD\nSLINGERLANDS, NY 12159\n(42.636568, -73.856367)
## 10       2080 WESTERN AVE\nGUILDERLAND, NY 12084\n(42.698502, -73.89159)
##                   Coords                   geometry
## 1  42.739618, -73.761949 POINT (-73.76195 42.73962)
## 2    42.547591, -73.8073  POINT (-73.8073 42.54759)
## 3  42.686553, -73.854665 POINT (-73.85466 42.68655)
## 4   42.73063, -73.703443 POINT (-73.70344 42.73063)
## 5  42.657136, -73.763712 POINT (-73.76371 42.65714)
## 6  42.639931, -73.784962 POINT (-73.78496 42.63993)
## 7   42.75459, -73.758714 POINT (-73.75871 42.75459)
## 8  42.601045, -73.790364 POINT (-73.79036 42.60104)
## 9  42.636568, -73.856367 POINT (-73.85637 42.63657)
## 10  42.698502, -73.89159  POINT (-73.89159 42.6985)

# set coordinate reference system to nys long island 

nysretailfood_sf_ <- st_transform(nysretailfood_sf, 2263)

st_crs(nysretailfood_sf_)

## Coordinate Reference System:
##   User input: EPSG:2263 
##   wkt:
## PROJCRS["NAD83 / New York Long Island (ftUS)",
##     BASEGEOGCRS["NAD83",
##         DATUM["North American Datum 1983",
##             ELLIPSOID["GRS 1980",6378137,298.257222101,
##                 LENGTHUNIT["metre",1]]],
##         PRIMEM["Greenwich",0,
##             ANGLEUNIT["degree",0.0174532925199433]],
##         ID["EPSG",4269]],
##     CONVERSION["SPCS83 New York Long Island zone (US survey foot)",
##         METHOD["Lambert Conic Conformal (2SP)",
##             ID["EPSG",9802]],
##         PARAMETER["Latitude of false origin",40.1666666666667,
##             ANGLEUNIT["degree",0.0174532925199433],
##             ID["EPSG",8821]],
##         PARAMETER["Longitude of false origin",-74,
##             ANGLEUNIT["degree",0.0174532925199433],
##             ID["EPSG",8822]],
##         PARAMETER["Latitude of 1st standard parallel",41.0333333333333,
##             ANGLEUNIT["degree",0.0174532925199433],
##             ID["EPSG",8823]],
##         PARAMETER["Latitude of 2nd standard parallel",40.6666666666667,
##             ANGLEUNIT["degree",0.0174532925199433],
##             ID["EPSG",8824]],
##         PARAMETER["Easting at false origin",984250,
##             LENGTHUNIT["US survey foot",0.304800609601219],
##             ID["EPSG",8826]],
##         PARAMETER["Northing at false origin",0,
##             LENGTHUNIT["US survey foot",0.304800609601219],
##             ID["EPSG",8827]]],
##     CS[Cartesian,2],
##         AXIS["easting (X)",east,
##             ORDER[1],
##             LENGTHUNIT["US survey foot",0.304800609601219]],
##         AXIS["northing (Y)",north,
##             ORDER[2],
##             LENGTHUNIT["US survey foot",0.304800609601219]],
##     USAGE[
##         SCOPE["Engineering survey, topographic mapping."],
##         AREA["United States (USA) - New York - counties of Bronx; Kings; Nassau; New York; Queens; Richmond; Suffolk."],
##         BBOX[40.47,-74.26,41.3,-71.8]],
##     ID["EPSG",2263]]

# check differences between coordinates

st_crs(nysretailfood_sf)$proj4string

## [1] "+proj=longlat +datum=WGS84 +no_defs"

st_crs(nysretailfood_sf_)$proj4string

## [1] "+proj=lcc +lat_0=40.1666666666667 +lon_0=-74 +lat_1=41.0333333333333 +lat_2=40.6666666666667 +x_0=300000 +y_0=0 +datum=NAD83 +units=us-ft +no_defs"

sf::st_bbox(nysretailfood_sf)

##      xmin      ymin      xmax      ymax 
## -79.75953  40.50782 -71.93873  44.99484

st_bbox(nysretailfood_sf_)

##      xmin      ymin      xmax      ymax 
## -574632.2  124371.4 1552535.4 1761473.6

# filter to nyc only using zip codes 

nysretailfood_sf_$Zip.Code <- as.character(nysretailfood_sf_$Zip.Code)
nyc_zip_sf$ZIPCODE <- as.character(nyc_zip_sf$ZIPCODE)

nysretailfood_nyc_sf <- nysretailfood_sf_ %>%
  filter(Zip.Code %in% nyc_zip_sf$ZIPCODE)

task 5: Use simple mapping method such as mapview with a basemap to verify the above datasets in terms of their geographic locations.

# mapview for all three sf objects 

mapview(nyc_zip_sf, layer.name='Zip Codes')

mapview(nyshealth_sf, layer.name='NYS Health Facilities')

mapview(nysretailfood_nyc_sf, layer.name='NYC Retail Food Stores')

task 6: Save the three sf objects in a RData file or in a single GeoPackage file/database.

# save all three sf objects into an RData file

save(nyc_zip_sf, nyshealth_sf, nysretailfood_nyc_sf,
     file = './data/nys_nyc_zipcodes_health_retailfood.RData')

# save all three sf objects into a single GeoPackage file/database

st_write(nyc_zip_sf, 
         dsn = './data/ny_zhr_data.gpkg', 
         layer='nyc_zip_codes',
         delete_layer = TRUE)

## Deleting layer `nyc_zip_codes' using driver `GPKG'
## Writing layer `nyc_zip_codes' to data source 
##   `./data/ny_zhr_data.gpkg' using driver `GPKG'
## Writing 263 features with 12 fields and geometry type Polygon.

st_write(nyshealth_sf,          
         dsn = './data/ny_zhr_data.gpkg', 
         layer='nys_health_facilities',
         delete_layer = TRUE)

## Deleting layer `nys_health_facilities' using driver `GPKG'
## Writing layer `nys_health_facilities' to data source 
##   `./data/ny_zhr_data.gpkg' using driver `GPKG'
## Writing 3848 features with 34 fields and geometry type Point.

st_write(nysretailfood_nyc_sf,          
         dsn = './data/ny_zhr_data.gpkg', 
         layer='nyc_retail_food_stores',
         delete_layer = TRUE)

## Deleting layer `nyc_retail_food_stores' using driver `GPKG'
## Writing layer `nyc_retail_food_stores' to data source 
##   `./data/ny_zhr_data.gpkg' using driver `GPKG'
## Writing 11372 features with 16 fields and geometry type Point.