#loading required packages
require(sp)
require(rgdal)
require(maptools)
require(rgeos)

#load example data, set "dsn=" to your working directory or specify the path
example <- readOGR(dsn=".",layer="ReproducibleExample")

#Attempting a UnionSpatialPolygons based on the COUNTY field
example.df <- as(example, "data.frame")
countycol <- example.df$COUNTY
example.diss <- unionSpatialPolygons(example, countycol)

slot(example, "polygons") <- lapply(slot(example, "polygons"), checkPolygonsHoles)

fix <- slot(example, "polygons")
fixa <- lapply(fix, checkPolygonsHoles)

require(devtools)
install_github("eblondel/cleangeo")
require(cleangeo)

#get a report of geometry validity & issues for a sp spatial object
report <- clgeo_CollectionReport(sp)
summary <- clgeo_SummaryReport(report)
issues <- report[report$valid == FALSE,]

#get suspicious features (indexes)
nv <- clgeo_SuspiciousFeatures(report)
mysp <- sp[nv[-14],]

#try to clean data
mysp.clean <- clgeo_Clean(mysp, print.log = TRUE)

#check if they are still errors
report.clean <- clgeo_CollectionReport(mysp.clean)
summary.clean <- clgeo_SummaryReport(report.clean)

#try to clean data
mysp <- sp[-9002,]
mysp.clean <- clgeo_Clean(mysp, print.log = TRUE)

#check if they are still errors
report.clean <- clgeo_CollectionReport(mysp.clean)
summary.clean <- clgeo_SummaryReport(report.clean)

#Attempting a UnionSpatialPolygons based on the COUNTY field
mysp.df <- as(mysp, "data.frame")
countycol <- mysp.df$COUNTY
mysp.diss <- unionSpatialPolygons(mysp.clean, countycol)

require(maptools)
mysp <- readShapePoly("ReproducibleExample.shp")

#plot the result
plot(mysp, border= "lightgray")
plot(mysp.diss, border="red", add = TRUE)