Hi R listers,
I am trying to group distances of nests to the vegetation into classes that
are define by (0-5m, 6-10m, 11-15m, 16-20m, 21-25m, 26-30m, 31-35m, 36-40m,
41-45m, 46-50m, 51-55m, 56-60m). Each row is a nest and all the distances to
the vegetation is in a column.
In plyr, I have tried - below script but I think I am going about this the
wrong way and am not successful.
#Veg index star = resp
Veg.index <- function(values, weights=c(0, 5, 10, 15, 20, 25, 30, 35, 40,
45, 50, 55, 60, 65, 70)) {
star <- values*weights
return(apply(star, 1, sum) / apply(values, 1, sum))
}
data.to.analyze$VegIndex <- Veg.index(data.to.analyze[,c("0", "5", "10",
"15", "20", "25", "30", "35", "40", "45", "50", "55", "60", "65", "70")])
write.csv(data.to.analyze, "3turtlehatch.csv", row.names=FALSE)
Please advise, Jean
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Creating vegetation distance groups from one column
11 messages · Jean V Adams, Jhope, arun +1 more
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Hello, Without sample data it's difficult to give an answer but see ?cut. To give a data example, the best way is to use ?dput(). dput( head(mydata, 30) ) # Paste the output of this in a post Hope this helps, Rui Barradas Em 04-10-2012 08:27, Jhope escreveu:
Hi R listers,
I am trying to group distances of nests to the vegetation into classes that
are define by (0-5m, 6-10m, 11-15m, 16-20m, 21-25m, 26-30m, 31-35m, 36-40m,
41-45m, 46-50m, 51-55m, 56-60m). Each row is a nest and all the distances to
the vegetation is in a column.
In plyr, I have tried - below script but I think I am going about this the
wrong way and am not successful.
#Veg index star = resp
Veg.index <- function(values, weights=c(0, 5, 10, 15, 20, 25, 30, 35, 40,
45, 50, 55, 60, 65, 70)) {
star <- values*weights
return(apply(star, 1, sum) / apply(values, 1, sum))
}
data.to.analyze$VegIndex <- Veg.index(data.to.analyze[,c("0", "5", "10",
"15", "20", "25", "30", "35", "40", "45", "50", "55", "60", "65", "70")])
write.csv(data.to.analyze, "3turtlehatch.csv", row.names=FALSE)
Please advise, Jean
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Hi, Allow me to recap my question. In plyr I am trying to group distances of nests to the vegetation into classes that are defined by (0-5m, 6-10m, 11-15m, 16-20m, 21-25m, 26-30m, 31-35m). Each row is a nest and all the distances to the vegetation is in a column. As well I would like to create classes from the HTL starting at (-5-0m, 1-5m, 6-10m, 11-15m, 16-20m, 21-25m, 26m-30m). I have included a sample of the data through dput() - see below. If that is too tiresome, I've also included head(data.to.analyze) below that. Best, Jean
dput(head(data.to.analyze, 30))
structure(list(QuadratEvent = c("8.1A", "10.1A", "14.1A", "19.1A",
"23.1A", "24.1A", "25.1A", "29.1A", "30.1A", "31.1A", "32.1A",
"33.1A", "38.1A", "39.1A", "41.1A", "47.1A", "48.1A", "50.1A",
"52.1A", "53.1A", "58.1A", "63.1A", "68.1A", "73.1A", "75.1A",
"79.1A", "29BA", "90.1B", "90.2B", "82.1B"), ExDate = c("Nov. 26, 2010",
"Nov. 26, 2010", "Nov. 18, 2010", "Nov. 22, 2010", "Nov. 20, 2010",
"Nov. 28, 2010", "Nov. 28, 2010", "Nov. 27, 2010", "Nov. 20, 2010",
"Nov. 20, 2010", "Nov. 26, 2010", "Nov. 26, 2010", "Nov. 20, 2010",
"Nov. 26, 2010", "Nov. 27, 2010", "Nov. 27, 2010", "Nov. 26, 2010",
"Nov. 27, 2010", "Nov. 27, 2010", "Nov. 27, 2010", "Nov. 27, 2010",
"Nov. 26, 2010", "Nov. 26, 2010", "Nov. 28, 2010", "Nov. 28, 2010",
"Nov. 26, 2010", "Nov. 28, 2010", "Jan. 1, 2011", "Jan. 1, 2011",
"Dec. 23, 2010"), Sector = c("14", "13", "20", "79", "34", "34",
"34", "36", "67", "66", "67", "67", "67", "66", "70", "70", "68",
"57", "55", "56", "40", "27", "26", "27", "28", "19", "36", "70",
"70", "47"), Quadrat = c("8", "10", "14", "19", "23", "24", "25",
"29", "30", "31", "32", "33", "38", "39", "41", "47", "48", "50",
"52", "53", "58", "63", "68", "73", "75", "79", "29B", "90",
"90", "82"), Aeventexhumed = c("A", "A", "A", "A", "A", "A",
"A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A",
"A", "A", "A", "A", "A", "A", "A", "A", "B", "B", "B"), ST0 = c(6L,
4L, 6L, 0L, 135L, 660L, 321L, 608L, 50L, 5L, 88L, 48L, 7L, 60L,
0L, 69L, 195L, 68L, 162L, 47L, 595L, 144L, 111L, 478L, 636L,
136L, 515L, 213L, 0L, 175L), ST1 = c(0L, 0L, 0L, 0L, 23L, 0L,
0L, 0L, 4L, 0L, 0L, 0L, 0L, 0L, 1L, 2L, 0L, 39L, 2L, 1L, 4L,
9L, 1L, 5L, 25L, 4L, 139L, 0L, 0L, 0L), ST2 = c(1L, 0L, 2L, 0L,
1L, 2L, 2L, 0L, 153L, 0L, 0L, 0L, 117L, 93L, 3L, 2L, 0L, 0L,
6L, 2L, 0L, 17L, 1L, 11L, 67L, 0L, 31L, 68L, 0L, 0L), ST3 = c(98L,
109L, 26L, 0L, 6L, 0L, 0L, 0L, 1L, 3L, 11L, 88L, 3L, 342L, 9L,
3L, 4L, 72L, 7L, 81L, 0L, 33L, 103L, 0L, 0L, 218L, 162L, 0L,
74L, 0L), ST4 = c(1L, 1L, 11L, 0L, 0L, 0L, 0L, 0L, 27L, 1L, 0L,
0L, 7L, 0L, 8L, 6L, 0L, 0L, 5L, 4L, 0L, 38L, 150L, 0L, 0L, 19L,
5L, 0L, 0L, 0L), Shells = c(72L, 74L, 106L, 102L, 125L, 4L, 15L,
0L, 31L, 111L, 0L, 0L, 86L, 48L, 21L, 35L, 0L, 0L, 12L, 13L,
0L, 23L, 20L, 3L, 4L, 115L, 5L, 2L, 0L, 0L), Hatchlings = c(3L,
4L, 1L, 1L, 48L, 0L, 0L, 0L, 45L, 99L, 0L, 0L, 93L, 9L, 0L, 0L,
0L, 6L, 2L, 6L, 0L, 9L, 13L, 0L, 0L, 9L, 0L, 0L, 0L, 0L), MaxHatch = c(72L,
74L, 106L, 102L, 125L, 4L, 15L, 0L, 45L, 111L, 0L, 0L, 93L, 48L,
21L, 35L, 0L, 6L, 12L, 13L, 0L, 23L, 20L, 3L, 4L, 118L, 5L, 2L,
0L, 0L), DeadHatch = c(2L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 4L, 0L,
0L, 0L, 1L, 5L, 0L, 0L, 0L, 0L, 0L, 2L, 0L, 0L, 0L, 0L, 0L, 6L,
0L, 0L, 0L, 0L), Oldeggs = c(0L, 21L, 165L, 0L, 0L, 36L, 0L,
0L, 96L, 45L, 5L, 142L, 10L, 81L, 103L, 92L, 0L, 0L, 0L, 0L,
108L, 0L, 0L, 0L, 93L, 0L, 0L, 0L, 0L, 0L), TotalEggs = c(178L,
188L, 151L, 102L, 290L, 666L, 338L, 608L, 280L, 120L, 99L, 136L,
227L, 543L, 42L, 117L, 199L, 185L, 194L, 148L, 599L, 264L, 386L,
497L, 732L, 495L, 857L, 283L, 74L, 175L), QuadratID = structure(c(107L,
4L, 22L, 38L, 43L, 44L, 46L, 54L, 57L, 58L, 60L, 61L, 67L, 69L,
72L, 79L, 80L, 81L, 83L, 85L, 91L, 94L, 97L, 103L, 105L, 106L,
56L, 109L, NA, 108L), .Label = c("", "1.1", "1.2", "10.1", "10.2",
"100.1", "100.2", "108.1", "108.2", "110.1", "110.2", "114.1",
"114.2", "121.1", "121.2", "127.1", "127.2", "128.1", "128.2",
"135.1", "135.2", "14.1", "15.1", "15.2", "151.1", "151.2", "152.1",
"152.2", "153.1", "153.2", "154.1", "154.2", "155.1", "155.2",
"16.1", "16.2", "18.1", "19.1", "21.1", "21.2", "22.1", "22.2",
"23.1", "24.1", "24.2", "25.1", "25.2", "26.1", "26.2", "27.1",
"27.2", "28.1", "28.2", "29.1", "29.2", "29B", "30.1", "31.1",
"31.2", "32.1", "33.1", "33.2", "35.1", "35.2", "37.1", "37.2",
"38.1", "38.2", "39.1", "40.1", "40.2", "41.1", "42.1", "42.2",
"43.1", "43.2", "46.1", "46.2", "47.1", "48.1", "50.1", "50.2",
"52.1", "52.2", "53.1", "53.2", "54.1", "54.2", "56.1", "56.2",
"58.1", "62.1", "62.2", "63.1", "65.1", "65.2", "68.1", "68.2",
"68.3", "68.4", "69.1", "70.1", "73.1", "74.1", "75.1", "79.1",
"8.1", "82.1", "90.1", "94.1", "94.2"), class = "factor"), Sector = c(14L,
13L, 20L, 79L, 34L, 34L, 34L, 36L, 67L, 66L, 67L, 67L, 67L, 66L,
70L, 70L, 68L, 57L, 55L, 56L, 40L, 27L, 26L, 27L, 28L, 19L, 36L,
70L, NA, 47L), Aeventexhumed = structure(c(2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 3L, NA, 3L), .Label = c("", "A", "B",
"C"), class = "factor"), Veg = c(9.75, 16.34, 3.15, 5.7, 12.2,
4.82, 3.3, 1.85, 17.75, 27.13, 0.84, 8.45, 16.42, 20.4, 22.4,
25, 25.4, 15.1, 13.7, 17.1, NA, 17.3, 24.3, 9.35, 5.4, 15.5,
1.85, 11, NA, 3), Berm = c(NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, 10, NA, 11), HTL = c(4.66, -2.47, 16, NA, 2.35, 22.85,
24, 15.7, 9.55, 4.2, 9.65, 19.8, 13.85, 8.7, 7.4, 2.9, 2.9, 4.26,
1.2, 1.05, NA, 3.2, 3.8, 2.55, 6.55, 2, 15.7, 20, NA, 20), Estuary = c(NA,
NA, NA, 11.8, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, 3.5, NA, NA, NA, 8.05, NA, NA, NA, NA, NA), Rayos =
c("Rayos.1",
"Rayos.1", "Rayos.2", "Rayos.2", "Rayos.3", "Rayos.3", "Rayos.3",
"Rayos.3", "Rayos.5", "Rayos.5", "Rayos.5", "Rayos.5", "Rayos.5",
"Rayos.5", "Rayos.5", "Rayos.5", "Rayos.5", "Rayos.4", "Rayos.4",
"Rayos.4", "Rayos.3", "Rayos.2", "Rayos.2", "Rayos.2", "Rayos.2",
"Rayos.2", "Rayos.3", "Rayos.5", "Rayos.NA", "Rayos.4"), NotHatched =
c(106L,
114L, 45L, 0L, 165L, 662L, 323L, 608L, 249L, 9L, 99L, 136L, 141L,
495L, 21L, 82L, 199L, 185L, 182L, 135L, 599L, 241L, 366L, 494L,
728L, 380L, 852L, 281L, 74L, 175L), DevelopIndex = c(3.86516853932584,
4.92021276595745, 5.62251655629139, 1, 3.40689655172414, 5.98198198198198,
1.13313609467456, 2, 3.53571428571429, 1.15, 4.66666666666667,
4.05882352941176, 2.26872246696035, 4.15469613259669, 5.21428571428571,
2.97435897435897, 4.93969849246231, 4.1027027027027, 1.32474226804124,
3.92567567567568, 3.02003338898164, 3.26136363636364, 4.03626943005181,
5.95171026156942, 1.11885245901639, 4.06060606060606, 4.07117852975496,
3.97879858657244, 2, 6)), .Names = c("QuadratEvent", "ExDate",
"Sector", "Quadrat", "Aeventexhumed", "ST0", "ST1", "ST2", "ST3",
"ST4", "Shells", "Hatchlings", "MaxHatch", "DeadHatch", "Oldeggs",
"TotalEggs", "QuadratID", "Sector", "Aeventexhumed", "Veg", "Berm",
"HTL", "Estuary", "Rayos", "NotHatched", "DevelopIndex"), row.names = c(NA,
30L), class = "data.frame")
----------------------------------------
head(data.to.analyze)
QuadratEvent ExDate Sector Quadrat Aeventexhumed ST0 ST1 ST2 ST3
ST4 Shells
1 8.1A Nov. 26, 2010 14 8 A 6 0 1 98
1 72
2 10.1A Nov. 26, 2010 13 10 A 4 0 0 109
1 74
3 14.1A Nov. 18, 2010 20 14 A 6 0 2 26
11 106
4 19.1A Nov. 22, 2010 79 19 A 0 0 0 0
0 102
5 23.1A Nov. 20, 2010 34 23 A 135 23 1 6
0 125
6 24.1A Nov. 28, 2010 34 24 A 660 0 2 0
0 4
Hatchlings MaxHatch DeadHatch Oldeggs TotalEggs QuadratID Sector
Aeventexhumed Veg Berm
1 3 72 2 0 178 8.1 14
A 9.75 NA
2 4 74 0 21 188 10.1 13
A 16.34 NA
3 1 106 1 165 151 14.1 20
A 3.15 NA
4 1 102 0 0 102 19.1 79
A 5.70 NA
5 48 125 0 0 290 23.1 34
A 12.20 NA
6 0 4 0 36 666 24.1 34
A 4.82 NA
HTL Estuary Rayos NotHatched DevelopIndex
1 4.66 NA Rayos.1 106 3.865169
2 -2.47 NA Rayos.1 114 4.920213
3 16.00 NA Rayos.2 45 5.622517
4 NA 11.8 Rayos.2 0 1.000000
5 2.35 NA Rayos.3 165 3.406897
6 22.85 NA Rayos.3 662 5.981982
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Thank you! That has worked for me when creating graphs. In plyr I used the
script:
# Veg Index
data.to.analyze$VegIndex <- cut(data.to.analyze$Veg,
breaks=seq(0, 35, 5), include.lowest=TRUE)
VegIndex <- data.to.analyze$VegIndex
plot(VegIndex)
But the vegetation distances on the x-axis in the graph are showing up as:
[-5,0] (0,5] (5,10] (10,15] (15,20] (20,25] (25,30]
I am concerned these vegetation classes are not grouped probably and there
is overlap between the classes. It should read, preferably without brackets
or only one kind ():
(-5-0) (1-5) (6-10) (11-15) (16-20) (21-25) (26-30)
How do I fix this?
Please advise, Jean
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Hi,
Try this:
data.to.analyze<-read.table(text="
Area Veg
456?????? 0
3400????? 10
79????????? 25
56?????????? 18
467???????? 4
67????????? 7
839??????? 30
1120????? 16
3482????? 32
",sep="",header=TRUE)
data.to.analyze$VegIndex=cut(data.to.analyze
? $Veg,breaks=c(-5,0,5,10,15,20,25,30,35),
??? labels=c("(-5-0)", "(1-5)", "(6-10)", "(11-15)", "(16-20)","(21-25)","(26-30)","(31-35)"))
VegIndex <- data.to.analyze$VegIndex
plot(VegIndex)
A.K.
----- Original Message -----
From: Jhope <jeanwaijang at gmail.com>
To: r-help at r-project.org
Cc:
Sent: Friday, October 5, 2012 3:38 AM
Subject: Re: [R] Creating vegetation distance groups from one column
Thank you! That has worked for me when creating graphs. In plyr I used the
script:
# Veg Index
data.to.analyze$VegIndex <- cut(data.to.analyze$Veg,
? ? ? breaks=seq(0, 35, 5), include.lowest=TRUE)
VegIndex <- data.to.analyze$VegIndex
plot(VegIndex)
But the vegetation distances on the x-axis in the graph are showing up as:
[-5,0] (0,5] (5,10] (10,15] (15,20] (20,25] (25,30]
I am concerned these vegetation classes are not grouped probably and there
is overlap between the classes. It should read, preferably without brackets
or only one kind ():
(-5-0) (1-5) (6-10) (11-15) (16-20) (21-25) (26-30)
How do I fix this?
Please advise, Jean
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R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Hello,
That now seems to be a presentation problem. See this example:
x <- 0:30 + runif(124)
y <- cut(x, breaks = seq(0, 35, 5))
l <- levels(y)
l1 <- sub("\\]", ")", l[1])
l2 <- as.numeric(sub("\\(([[:digit:]]+),.*", "\\1", l[-1])) + 1
l3 <- sub(".*,([[:digit:]]+).*", "\\1", l[-1])
l.new <- c(l1, paste0("(", l2, ",", l3, ")"))
levels(y) <- l.new
str(y)
barplot(table(y))
Instead of 'y' use data.to.analyze$VegIndex and it should give what you
want.
Hope this helps,
Rui Barradas
Em 05-10-2012 08:38, Jhope escreveu:
Thank you! That has worked for me when creating graphs. In plyr I used the
script:
# Veg Index
data.to.analyze$VegIndex <- cut(data.to.analyze$Veg,
breaks=seq(0, 35, 5), include.lowest=TRUE)
VegIndex <- data.to.analyze$VegIndex
plot(VegIndex)
But the vegetation distances on the x-axis in the graph are showing up as:
[-5,0] (0,5] (5,10] (10,15] (15,20] (20,25] (25,30]
I am concerned these vegetation classes are not grouped probably and there
is overlap between the classes. It should read, preferably without brackets
or only one kind ():
(-5-0) (1-5) (6-10) (11-15) (16-20) (21-25) (26-30)
How do I fix this?
Please advise, Jean
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Hi, I have tried the script posted but received the following errors. I hope I copied it correctly. I'm sorry but I don't know how to alter the script myself. Please advise, Jean
x <- 0:30 + runif(124) data.to.analyze$VegIndex <- cut(x, breaks = seq(0, 35, 5))
Error in `$<-.data.frame`(`*tmp*`, "VegIndex", value = c(1L, 1L, 1L, 1L, : replacement has 124 rows, data has 123
l <- levels(data.to.analyze$VegIndex)
l1 <- sub("\\]", ")", l[1])
l2 <- as.numeric(sub("\\(([[:digit:]]+),.*", "\\1", l[-1])) + 1
l3 <- sub(".*,([[:digit:]]+).*", "\\1", l[-1])
l.new <- c(l1, paste0("(",l2,",",l3, ")"))
Error: could not find function "paste0"
levels(data.to.analyze$VegIndex) <- l.new
Error: object 'l.new' not found
str(data.to.analyze$VegIndex)
NULL
barplot(table(data.to.analyze$VegIndex))
Error in plot.window(xlim, ylim, log = log, ...) : need finite 'xlim' values In addition: Warning messages: 1: In min(w.l) : no non-missing arguments to min; returning Inf 2: In max(w.r) : no non-missing arguments to max; returning -Inf 3: In min(x) : no non-missing arguments to min; returning Inf 4: In max(x) : no non-missing arguments to max; returning -Inf -- View this message in context: http://r.789695.n4.nabble.com/Creating-vegetation-distance-groups-from-one-column-tp4644970p4645230.html Sent from the R help mailing list archive at Nabble.com.
Hi Thanks to all for posting!
In plyr I did try something similar, a combination of what I learned from
all who replied. It seemed to work. If anyone knows of any criticism about
the grouping structure please let me know. I need this to be accurate.
Grouping defined by (0-5m) (6-10m) (11-15m) (16-20m) (21-25m) (26-30m)
(31-35m) without overlap of measurements. See script below:
data.to.analyze$VegIndex = cut
(data.to.analyze$Veg,breaks=c(0,5,10,15,20,25,30,35),
labels=c("(0-5)", "(6-10)", "(11-15)",
"(16-20)", "(21-25)", "(26-30)", "(31-35)"))
VegIndex <- data.to.analyze$VegIndex
plot(VegIndex)
Saludos, Jean
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Hello, My example with 'x' was just that, an example. Inline. Em 06-10-2012 00:03, Jhope escreveu:
Hi, I have tried the script posted but received the following errors. I hope I copied it correctly. I'm sorry but I don't know how to alter the script myself. Please advise, Jean
x <- 0:30 + runif(124) data.to.analyze$VegIndex <- cut(x, breaks = seq(0, 35, 5))
Error in `$<-.data.frame`(`*tmp*`, "VegIndex", value = c(1L, 1L, 1L, 1L, : replacement has 124 rows, data has 123
Use cut(data.to.analize$VegIndex, breaks = seq(0, 35, 5))
l <- levels(data.to.analyze$VegIndex)
l1 <- sub("\\]", ")", l[1])
l2 <- as.numeric(sub("\\(([[:digit:]]+),.*", "\\1", l[-1])) + 1
l3 <- sub(".*,([[:digit:]]+).*", "\\1", l[-1])
l.new <- c(l1, paste0("(",l2,",",l3, ")"))
Error: could not find function "paste0"
paste0 was introduced with R 2.15.0, update your version of R and in the mean time use paste(...etc..., sep = "") Rui Barradas
levels(data.to.analyze$VegIndex) <- l.new
Error: object 'l.new' not found
str(data.to.analyze$VegIndex)
NULL
barplot(table(data.to.analyze$VegIndex))
Error in plot.window(xlim, ylim, log = log, ...) : need finite 'xlim' values In addition: Warning messages: 1: In min(w.l) : no non-missing arguments to min; returning Inf 2: In max(w.r) : no non-missing arguments to max; returning -Inf 3: In min(x) : no non-missing arguments to min; returning Inf 4: In max(x) : no non-missing arguments to max; returning -Inf -- View this message in context: http://r.789695.n4.nabble.com/Creating-vegetation-distance-groups-from-one-column-tp4644970p4645230.html Sent from the R help mailing list archive at Nabble.com.
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