I'm trying to scrape an irregular table from Wikipedia using rvest. The table has cells that span multiple rows. The documentation for html_table clearly states that this is a limitation. I'm just wondering if there's a workaround.
The table looks like this:
My code:
library(rvest)
url <- "https://en.wikipedia.org/wiki/Arizona_League"
parks <- url %>%
read_html() %>%
html_nodes(xpath='/html/body/div[3]/div[3]/div[4]/div/table[2]') %>%
html_table(fill=TRUE) %>% # fill=FALSE yields the same results
.[[1]]
Returns this:
Where there are several errors, for example: row 4 under "City" should be "Mesa", NOT "Chicago Cubs". I'd be happy with blank cells as I could "fill down" as needed, but the wrong data is a problem. Help is much appreciated.
I have a way to code it.
It is not perfect, a bit long but it does the trick:
library(rvest)
url <- "https://en.wikipedia.org/wiki/Arizona_League"
# get the lines of the table
lines <- url %>%
read_html() %>%
html_nodes(xpath="//table[starts-with(#class, 'wikitable')]") %>%
html_nodes(xpath = 'tbody/tr')
#define the empty table
ncol <- lines %>%
.[[1]] %>%
html_children()%>%
length()
nrow <- length(lines)
table <- as.data.frame(matrix(nrow = nrow,ncol = ncol))
# fill the table
for(i in 1:nrow){
# get content of the line
linecontent <- lines[[i]]%>%
html_children()%>%
html_text()%>%
gsub("\n","",.)
# attribute the content to free columns
colselect <- is.na(table[i,])
table[i,colselect] <- linecontent
# get the line repetition of each columns
repetition <- lines[[i]]%>%
html_children()%>%
html_attr("rowspan")%>%
ifelse(is.na(.),1,.) %>% # if no rowspan, then it is a normal row, not a multiple one
as.numeric
# repeat the cells of the multiple rows down
for(j in 1:length(repetition)){
span <- repetition[j]
if(span > 1){
table[(i+1):(i+span-1),colselect][,j] <- rep(linecontent[j],span-1)
}
}
}
The idea is to have the html lines of the table in the lines variable by getting the /tr nodes. I then create an empty table: number of columns is the length of the children of the first row (because it contains the titles), number of line the length of lines. I fill it by hand in a for loop (didn't amanger a nicer way here).
The difficulty is that the amount of column text given in a row changes when there is already a multiple row column spanning on the current row. For example :
lines[[3]]%>%
html_children()%>%
html_text()%>%
gsub("\n","",.)
gives only 5 values :
[1] "Arizona League Athletics Gold" "Oakland Athletics" "Mesa" "Fitch Park"
[5] "10,000"
instead of the 6 columns, because the first column is East on 8 rows. This East value appears only on the first rows it spans on.
The trick is to repeat the cells down in the table when they have a rowspan attribute (meaning they span on several rows). It allows to select on the next row only the NA columns, so that the amount of text given by the html line match the amount of free columns in the table we fill.
This is done with the colselect variable, which is a bolean giving the free rows before repeting the cells of the given row.
The result :
V1 V2 V3 V4 V5 V6
1 Division Team MLB Affiliation City Stadium Capacity
2 East Arizona League Angels Los Angeles Angels Tempe Tempe Diablo Stadium 9,785
3 East Arizona League Athletics Gold Oakland Athletics Mesa Fitch Park 10,000
4 East Arizona League Athletics Green Oakland Athletics Mesa Fitch Park 10,000
5 East Arizona League Cubs 1 Chicago Cubs Mesa Sloan Park 15,000
6 East Arizona League Cubs 2 Chicago Cubs Mesa Sloan Park 15,000
7 East Arizona League Diamondbacks Arizona Diamondbacks Scottsdale Salt River Fields at Talking Stick 11,000
8 East Arizona League Giants Black San Francisco Giants Scottsdale Scottsdale Stadium 12,000
9 East Arizona League Giants Orange San Francisco Giants Scottsdale Scottsdale Stadium 12,000
10 Central Arizona League Brewers Gold Milwaukee Brewers Phoenix American Family Fields of Phoenix 8,000
11 Central Arizona League Dodgers Lasorda Los Angeles Dodgers Phoenix Camelback Ranch 12,000
12 Central Arizona League Indians Blue Cleveland Indians Goodyear Goodyear Ballpark 10,000
13 Central Arizona League Padres 2 San Diego Padres Peoria Peoria Sports Complex 12,882
14 Central Arizona League Reds Cincinnati Reds Goodyear Goodyear Ballpark 10,000
15 Central Arizona League White Sox Chicago White Sox Phoenix Camelback Ranch 12,000
16 West Arizona League Brewers Blue Milwaukee Brewers Phoenix American Family Fields of Phoenix 8,000
17 West Arizona League Dodgers Mota Los Angeles Dodgers Phoenix Camelback Ranch 12,000
18 West Arizona League Indians Red Cleveland Indians Goodyear Goodyear Ballpark 10,000
19 West Arizona League Mariners Seattle Mariners Peoria Peoria Sports Complex 12,882
20 West Arizona League Padres 1 San Diego Padres Peoria Peoria Sports Complex 12,882
21 West Arizona League Rangers Texas Rangers Surprise Surprise Stadium 10,500
22 West Arizona League Royals Kansas City Royals Surprise Surprise Stadium 10,500
Edit
I made a shorter version of the function, with more explanation here
Related
So I'm trying to make a bar chart that displays the most popular airports that flew to Chicago. For some reason, I'm finding it to be extremely difficult to have my bars be labeled by the airport names specifically.
I have a data frame called ty
> ty
Name
1 Atlanta, GA: Hartsfield-Jackson Atlanta International
2 New York, NY: LaGuardia
3 Minneapolis, MN: Minneapolis-St Paul International
4 Los Angeles, CA: Los Angeles International
5 Denver, CO: Denver International
6 Washington, DC: Ronald Reagan Washington National
7 Orlando, FL: Orlando International
8 Phoenix, AZ: Phoenix Sky Harbor International
9 Detroit, MI: Detroit Metro Wayne County
10 Las Vegas, NV: McCarran International
11 San Francisco, CA: San Francisco International
12 Dallas/Fort Worth, TX: Dallas/Fort Worth International
13 Boston, MA: Logan International
14 Philadelphia, PA: Philadelphia International
15 Newark, NJ: Newark Liberty International
I also have a data frame called df
id numArrivals
1 10397 964
2 12953 962
3 13487 883
4 12892 823
5 11292 776
6 11278 771
7 13204 725
8 14107 700
9 11433 672
10 12889 647
11 14771 611
12 11298 580
13 10721 569
14 14100 567
15 11618 488
The id corresponds to the airport name 10397 is Atlanta, GA: Hartsfield-Jackson Atlanta International and they continue in that order.
However, when I run:
plotly::plot_ly(df,x=ty["Name"],y=df$numArrivals,type="bar",color=I("rgba(0,92,124,1)"))
I am given this chart.
How can I make the labels of my bars into the names of the airport rather than just numbers?
Feel free to use ggplotly() to create your plot. I used the code below to create a small example.
example <- data.frame(airport = c("Atlanta, GA: Hartsfield-Jackson Atlanta International","New York, NY: LaGuardia","Minneapolis, MN: Minneapolis-St Paul International"),
id = c(10397,12953,13487),
numArrivals = c(964,962,883),stringsAsFactors = F)
library(ggplot2)
library(plotly)
a <- ggplot(example,aes(x=airport,y=numArrivals,fill=id)) + geom_bar(stat = "identity") + coord_flip()
ggplotly(a)
The final result looks like this.
I run into problems assigning a county to some city places. When querying via the acs package
> geo.lookup(state = "NY", place = "New York")
state state.name county.name place place.name
1 36 New York <NA> NA <NA>
2 36 New York Bronx County, Kings County, New York County, Queens County, Richmond County 51000 New York city
3 36 New York Oneida County 51011 New York Mills village
, you can see that "New York", for instance, has a bunch of counties. So do Los Angeles, Portland, Oklahoma, Columbus etc. How can such data be assigned to a "county"?
Following code is currently used to match "county.name" with the corresponding county FIPS code. Unfortunately, it only works for cases of only one county name output in the query.
Script
dat <- c("New York, NY","Boston, MA","Los Angeles, CA","Dallas, TX","Palo Alto, CA")
dat <- strsplit(dat, ",")
dat
library(tigris)
library(acs)
data(fips_codes) # FIPS codes with state, code, county information
GeoLookup <- lapply(dat,function(x) {
geo.lookup(state = trimws(x[2]), place = trimws(x[1]))[2,]
})
df <- bind_rows(GeoLookup)
#Rename cols to match
colnames(fips_codes) = c("state.abb", "statefips", "state.name", "countyfips", "county.name")
# Here is a problem, because it works with one item in "county.name" but not more than one (see output below).
df <- df %>% left_join(fips_codes, by = c("state.name", "county.name"))
df
Returns:
state state.name county.name place place.name state.abb statefips countyfips
1 36 New York Bronx County, Kings County, New York County, Queens County, Richmond County 51000 New York city <NA> <NA> <NA>
2 25 Massachusetts Suffolk County 7000 Boston city MA 25 025
3 6 California Los Angeles County 20802 East Los Angeles CDP CA 06 037
4 48 Texas Collin County, Dallas County, Denton County, Kaufman County, Rockwall County 19000 Dallas city <NA> <NA> <NA>
5 6 California San Mateo County 20956 East Palo Alto city CA 06 081
In order to retain data, the left_join might better be matched as "look for county.name that contains place.name (without the appending xy city in the name), or choose the first item by default. It would be great to see how this could be done.
In general: I assume, there's no better way than this approach?
Thanks for your help!
What about something like the code below to create a "long" data frame for joining. We use the tidyverse pipe operator to chain operations. strsplit returns a list, which we unnest to stack the list values (the county names that go with each combination of state.name and place.name) into a long data frame where each county.name now gets its own row.
library(tigris)
library(acs)
library(tidyverse)
dat = geo.lookup(state = "NY", place = "New York")
state state.name county.name place place.name
1 36 New York <NA> NA <NA>
2 36 New York Bronx County, Kings County, New York County, Queens County, Richmond County 51000 New York city
3 36 New York Oneida County 51011 New York Mills village
dat = dat %>%
group_by(state.name, place.name) %>%
mutate(county.name = strsplit(county.name, ", ")) %>%
unnest
state state.name place place.name county.name
<chr> <chr> <int> <chr> <chr>
1 36 New York NA <NA> <NA>
2 36 New York 51000 New York city Bronx County
3 36 New York 51000 New York city Kings County
4 36 New York 51000 New York city New York County
5 36 New York 51000 New York city Queens County
6 36 New York 51000 New York city Richmond County
7 36 New York 51011 New York Mills village Oneida County
UPDATE: Regarding the second question in your comment, assuming you have the vector of metro areas already, how about this:
dat <- c("New York, NY","Boston, MA","Los Angeles, CA","Dallas, TX","Palo Alto, CA")
df <- map_df(strsplit(dat, ", "), function(x) {
geo.lookup(state = x[2], place = x[1])[-1, ] %>%
group_by(state.name, place.name) %>%
mutate(county.name = strsplit(county.name, ", ")) %>%
unnest
})
df
state state.name place place.name county.name
1 36 New York 51000 New York city Bronx County
2 36 New York 51000 New York city Kings County
3 36 New York 51000 New York city New York County
4 36 New York 51000 New York city Queens County
5 36 New York 51000 New York city Richmond County
6 36 New York 51011 New York Mills village Oneida County
7 25 Massachusetts 7000 Boston city Suffolk County
8 25 Massachusetts 7000 Boston city Suffolk County
9 6 California 20802 East Los Angeles CDP Los Angeles County
10 6 California 39612 Lake Los Angeles CDP Los Angeles County
11 6 California 44000 Los Angeles city Los Angeles County
12 48 Texas 19000 Dallas city Collin County
13 48 Texas 19000 Dallas city Dallas County
14 48 Texas 19000 Dallas city Denton County
15 48 Texas 19000 Dallas city Kaufman County
16 48 Texas 19000 Dallas city Rockwall County
17 48 Texas 40516 Lake Dallas city Denton County
18 6 California 20956 East Palo Alto city San Mateo County
19 6 California 55282 Palo Alto city Santa Clara County
UPDATE 2: If I understand your comments, for cities (actually place names in the example) with more than one county, we want only the county that includes the same name as the city (for example, New York County in the case of New York city), or the first county in the list otherwise. The following code selects a county with the same name as the city or, if there isn't one, the first county for that city. You might have to tweak it a bit to make it work for the entire U.S. For example, for it to work for Louisiana, you might need gsub(" County| Parish"... instead of gsub(" County"....
map_df(strsplit(dat, ", "), function(x) {
geo.lookup(state = x[2], place = x[1])[-1, ] %>%
group_by(state.name, place.name) %>%
mutate(county.name = strsplit(county.name, ", ")) %>%
unnest %>%
slice(max(1, which(grepl(sub(" [A-Za-z]*$","", place.name), gsub(" County", "", county.name))), na.rm=TRUE))
})
state state.name place place.name county.name
<chr> <chr> <int> <chr> <chr>
1 36 New York 51000 New York city New York County
2 36 New York 51011 New York Mills village Oneida County
3 25 Massachusetts 7000 Boston city Suffolk County
4 6 California 20802 East Los Angeles CDP Los Angeles County
5 6 California 39612 Lake Los Angeles CDP Los Angeles County
6 6 California 44000 Los Angeles city Los Angeles County
7 48 Texas 19000 Dallas city Dallas County
8 48 Texas 40516 Lake Dallas city Denton County
9 6 California 20956 East Palo Alto city San Mateo County
10 6 California 55282 Palo Alto city Santa Clara County
Could you prep the data by using something like the below code?
new_york_data <- geo.lookup(state = "NY", place = "New York")
prep_data <- function(full_data){
output <- data.frame()
for(row in 1:nrow(full_data)){
new_rows <- replicateCounty(full_data[row, ])
output <- plyr::rbind.fill(output, new_rows)
}
return(output)
}
replicateCounty <- function(row){
counties <- str_trim(unlist(str_split(row$county.name, ",")))
output <- data.frame(state = row$state,
state.name = row$state.name,
county.name = counties,
place = row$place,
place.name = row$place.name)
return(output)
}
prep_data(new_york_data)
It's a little messy and you'll need the plyr and stringr packages. Once you prep the data, you should be able to join on it
I'm writing an R script that parses out the a state abbreviation from a column in a data.frame. It then uses the which() function to determine the index of the found state abbreviation in a look up data frame that contains state abbreviations and their corresponding full state names. I then use the found index to access the the full state name and append it to a vector called completeList. I then add the vector completeList which should contain the full state names to my original data frame under a newly created column STATE_NAME.
However, for some reason completeList only contains the indexes that were found earlier and not the full state names that I expected. What did I do wrong?
#read in csv weather data file
file <- read.csv(header = TRUE, file = "C:\\Users\\michael.guarino1\\Desktop\\Work\\weather\\nov_2_1976\\734677_cleaned.csv")
#read in csv state Abbreviation file
abbreviationsFile<-read.csv(header=TRUE, file="C:\\Users\\michael.guarino1\\Desktop\\Work\\weather\\stateAbbreviationMatches.csv")
#iterate through STATION_NAME and store abreviations
completeList<-c()
for(stateAbvr in file$STATION_NAME){
addTo<-(substring(stateAbvr,(nchar(stateAbvr)-4),(nchar(stateAbvr)-3)))
index<-which(abbreviationsFile$Abbreviation==addTo)
addCompleteStateName<-(abbreviationsFile[index,1])
completeList<-append(completeList, addCompleteStateName)
}
file["STATE_NAME"]<-completeList
>completeList
[1] 27 17 17 29 42 50 20 53 45 19 22 52 9 29 26 37 8 58 35
Here is the csv file where the abbreviation of the station is found
STATION STATION_NAME ELEVATION
GHCND:USC00202381 EAST JORDAN MI US 180.1
GHCND:USC00111290 CARLYLE RESERVOIR IL US 153
GHCND:USC00116661 PAW PAW 2 S IL US 274.9
GHCND:USC00228556 SUMRALL MS US 88.1
GHCND:USC00340292 ARDMORE OK US 267.9
GHCND:USC00408522 SPARTA WASTEWATER PLANT TN US 289.9
GHCND:USC00148341 VALLEY FALLS KS US 283.5
GHCND:USW00014742 BURLINGTON INTERNATIONAL AIRPORT VT US 101.2
GHCND:USC00367782 SALINA 3 W PA US 338
GHCND:USC00134142 IOWA FALLS IA US 356.9
GHCND:USC00161565 CARVILLE 2 SW LA US 9.1
GHCND:USC00421446 CITY CRK WATER PLANT UT US 1628.9
GHCND:USW00013781 WILMINGTON NEW CASTLE CO AIRPORT DE US 22.6
GHCND:USC00229400 WATER VALLEY MS US 116.1
GHCND:USC00190562 BELCHERTOWN MA US 171
GHCND:USW00094728 NEW YORK CENTRAL PARK OBS BELVEDERE TOWER NY US 40.2
GHCND:USC00060973 BURLINGTON CT US 155.4
GHCND:USC00475516 MINOCQUA WI US 484.9
GHCND:USC00286055 NEW BRUNSWICK 3 SE NJ US 38.1
Here is the csv file where we look up abbreviations and find the corresponding full state name
State/Possession Abbreviation
Alabama AL
Alaska AK
American Samoa AS
Arizona AZ
Arkansas AR
California CA
Colorado CO
Connecticut CT
Delaware DE
District of Columbia DC
Federated States of Micronesia FM
Florida FL
Georgia GA
Guam GU
Hawaii HI
Idaho ID
Illinois IL
Indiana IN
Iowa IA
Kansas KS
Kentucky KY
Louisiana LA
Maine ME
Marshall Islands MH
Maryland MD
Massachusetts MA
Michigan MI
Minnesota MN
Mississippi MS
Missouri MO
Montana MT
Nebraska NE
Nevada NV
New Hampshire NH
New Jersey NJ
New Mexico NM
New York NY
North Carolina NC
North Dakota ND
Northern Mariana Islands MP
Ohio OH
Oklahoma OK
Oregon OR
Palau PW
Pennsylvania PA
Puerto Rico PR
Rhode Island RI
South Carolina SC
South Dakota SD
Tennessee TN
Texas TX
Utah UT
Vermont VT
Virgin Islands VI
Virginia VA
Washington WA
West Virginia WV
Wisconsin WI
Wyoming WY
Why am I not getting the full state name?
figured it out 😎
#read in csv weather data file
file <- read.csv(header = TRUE, file = "C:\\Users\\michael.guarino1\\Desktop\\Work\\weather\\nov_2_1976\\734677_cleaned.csv")
#read in csv state Abbreviation file
abbreviationsFile<-read.csv(header=TRUE, file="C:\\Users\\michael.guarino1\\Desktop\\Work\\weather\\stateAbbreviationMatches.csv")
#iterate through STATION_NAME and store abreviations
completeList<-c()
for(stateAbvr in file$STATION_NAME){
addTo<-(substring(stateAbvr,(nchar(stateAbvr)-4),(nchar(stateAbvr)-3)))
index<-which(abbreviationsFile$Abbreviation==addTo)
addCompleteStateName<-(abbreviationsFile[index,1])
completeList<-append(completeList, toString(addCompleteStateName))
}
file["STATE_NAME"]<-completeList
the type was being forced to an integer
The variable addCompleteStateName is a factor. You can convert it to a character to append the labels.
#iterate through STATION_NAME and store abreviations
completeList<-c()
for(stateAbvr in file$STATION_NAME){
addTo<-(substring(stateAbvr,(nchar(stateAbvr)-4),(nchar(stateAbvr)-3)))
index<-which(abbreviationsFile$Abbreviation==addTo)
addCompleteStateName<-(abbreviationsFile[index,1])
# modified to convert addCompleteStateName to character
completeList<-append(completeList, as.character(addCompleteStateName))
}
file["STATE_NAME"]<-completeList
I have a one column like this:
x <- c('WV West Virginia','FL Florida','CA California','SC South Carolina')
# [1] WV West Virginia FL Florida
# [3] CA California SC South Carolina
How can I separate the abbreviation from the whole state name. And I want to give the two new columns two different headers. I think I can only solve this by separating the all upper letter words away.
With tidyr we can use separate to expand the column into two while specifying the new names. The argument extra=merge limits the output to the given columns. The separator will default to non-alpha-numerics:
library(tidyr)
separate(df, x, c("Abb", "State"), extra="merge")
# Abb State
#1 WV West Virginia
#2 FL Florida
#3 CA California
#4 SC South Carolina
Data
x = c('WV West Virginia', 'FL Florida','CA California', 'SC South Carolina')
Two approaches without external packages:
Approach 1: you could use substring in combination with nchar.
dat <-data.frame(raw=c("WV West Virginia","FL Florida", "CA California","SC South Carolina"),
stringsAsFactors=F)
dat$code <- substr(dat$raw,1,2)
dat$state <- substr(dat$raw, 4, nchar(dat$raw))
> dat
raw code state
1 WV West Virginia WV West Virginia
2 FL Florida FL Florida
3 CA California CA California
4 SC South Carolina SC South Carolina
Approach two: you could use regular expressions to replace parts of your strings:
##approach two: regex
dat$code <- sub(" .+","",dat$raw)
dat$state <- sub("[A-Z]{2} ","",dat$raw)
Use the state.* constants that come with the base datasets package
DF = data.frame(raw=c("WV West Virginia","FL Florida","CA California","SC South Carolina"))
DF$state.abbr <- substr(DF$raw, 1, 2)
DF$state.name <- state.name[ match(DF$state.abbr, state.abb) ]
# raw state.abbr state.name
# 1 WV West Virginia WV West Virginia
# 2 FL Florida FL Florida
# 3 CA California CA California
# 4 SC South Carolina SC South Carolina
This way, you can afford to have typos or other oddities in the state names.
Use the reshape2 package.
library(reshape2)
x <- rbind('WV West Virginia','FL Florida','CA California','SC South Carolina')
colsplit(x," ",c("Code","State"))
Output:
Code State
1 WV West Virginia
2 FL Florida
3 CA California
4 SC South Carolina
Based on #rawr's comment, we could split 'x' at white space that follows the first two characters, i.e. showed by the regex lookaround ((?<=^.{2})). The output will be a list, which we rbind, convert to data.frame and then cbind with the original vector 'x'.
cbind(x, as.data.frame(do.call(rbind,strsplit(x, '(?<=^.{2})\\s+', perl=TRUE)),
stringsAsFactors=FALSE))
# x V1 V2
#1 WV West Virginia WV West Virginia
#2 FL Florida FL Florida
#3 CA California CA California
#4 SC South Carolina SC South Carolina
Or instead of the regex lookaround, we could use stri_split with n=2 and split at whitespace.
library(stringi)
cbind(x,as.data.frame(do.call(rbind,stri_split(x, regex='\\s+', n=2))))
Here's a data.table/ gsub approach:
x <- c('WV West Virginia','FL Florida','CA California','SC South Carolina')
data.table::data.table(x)[,
abb := gsub("(^[A-Z]{2})( .+)", "\\1", x)][,
state := gsub("(^[A-Z]{2})( .+)", "\\2", x)][]
## x abb state
## 1: WV West Virginia WV West Virginia
## 2: FL Florida FL Florida
## 3: CA California CA California
## 4: SC South Carolina SC South Carolina
Hopefully title is not too badly worded. I have a tree that I used cutree to obtain groups from, but it is clear that the groups are not numbered left-to-right or right-to-left (I know the orientation within a branch doesn't matter so much, was hoping the grouping would be the same as the ordering in the hclust object). Is it possible to extract groups from a tree (using the height option of cutree) and know which of those groups are more related to one another? I walk through an example using USArrests below.
hc <- hclust(dist(USArrests), "ave")
plot(hc)
cutree(hc,h=60)
Alabama Alaska Arizona Arkansas California
1 1 1 2 1
Colorado Connecticut Delaware Florida Georgia
2 3 1 4 2
Hawaii Idaho Illinois Indiana Iowa
3 3 1 3 3
Kansas Kentucky Louisiana Maine Maryland
3 3 1 3 1
Massachusetts Michigan Minnesota Mississippi Missouri
2 1 3 1 2
Montana Nebraska Nevada New Hampshire New Jersey
3 3 1 3 2
New Mexico New York North Carolina North Dakota Ohio
1 1 4 3 3
Oklahoma Oregon Pennsylvania Rhode Island South Carolina
2 2 3 2 1
South Dakota Tennessee Texas Utah Vermont
3 2 2 3 3
Virginia Washington West Virginia Wisconsin Wyoming
2 2 3 3 2
If you plot the tree it is clear that groups 1 and 4 are more related then groups 2 and 3 are more related. However when I just print the contents of each group there is no way to know what that relationship is. Is there a function or standard process I am missing? The real data I'm working with I split 36k values into 10 groups, so it would be tough to visually validate the relationships as I do with the example data, and want to code it as a script for future analyses. Thanks ahead of time.
I think you want to use
hc <- hclust(dist(USArrests), "ave")
cuthc <- cut(as.dendrogram(hc), h=60)
This will return a list with an $upper showing the tree above the cut, and a $lower element which is a list of each of the subtrees made from the cut. We can plot them with
layout(matrix(1:4, ncol=2))
sapply(1:4, function(i) plot(cuthc$lower[[i]]))
Then, if you want to extract the names and groups in the order they appear in the dendrograms, you can do
stack(setNames(Map(labels, cuthc$lower),seq_along(cuthc$lower)))
Here I use stack() and setNames() just to assign a unique ID to each element in the $lower list. stack() doesn't like it when the list isn't named