[R] row sum with all absence in a presence-absence matrix
Dear list I have a matrix composed of islandID as rows and speciesID as columns. IslandID: Island A, B, C .O (15 islands in total) SpeciesID: D0001, D0002, D0003 .D0100 (100 species in total) The cell of the matrix describes presence (1) or absence (0) of the species in an island. Now I would like to search how many species are found in (1, presence) for Island A, Island D, and Island L respectively. Please kindly advise the R code for the search purpose. Thank you. [[alternative HTML version deleted]] __ R-help@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.
[R] Compare species presence and absence between sites
Dear List, I want to compare the presence and absence of bird species based on the sites in a matrix. The matrix has 5 rows for Island A, B, C, D, and E. It has 100 columns for bird species D001-D100. In each cell of the matrix, the presence-absence of bird species will be recorded as 1 or 0. (For example, if species D001 is found on Island D, the matrix cell of species D001 and Island D will be 1.) Now I want to know the different bird species between Island B and E. In other words, I would like to find out bird species present (1) on Island B but absent (0)on island E, and vice versa (absent (0) on Island B but present (1)on island E). Please kindly advise how to code the purpose above. Thank you in advance. Elaine [[alternative HTML version deleted]] __ R-help@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.
Re: [R] Compare species presence and absence between sites
Thanks Rui and Arun.
Both worked well.
One more question, what shall I add for Rui's code if only the comparison
of TRUE (no FALSE) to be shown in the result?
Elaine
code
different - function(x, y) x == 1 y == 0
set.seed(7054)
mat - matrix(sample(0:1, 500, TRUE), nrow = 5)
rownames(mat) - LETTERS[1:5]
colnames(mat) - sprintf(D%03d, 1:100)
different(mat[B,], mat[E,])
On Fri, Sep 27, 2013 at 9:31 PM, arun smartpink...@yahoo.com wrote:
Just to add:
If you wanted the difference of every combination of rows:
set.seed(248)
mat1-
matrix(sample(0:1,5*100,replace=TRUE),ncol=100,dimnames=list(LETTERS[1:5],paste0(D,sprintf(%03d,1:100)))
)
dat-expand.grid(LETTERS[1:5],LETTERS[1:5],stringsAsFactors=FALSE)
dat1-dat[!paste0(dat[,1],dat[,2]) %in% paste0(LETTERS[1:5],LETTERS[1:5]),]
lst1- lapply(seq_len(nrow(dat1)),function(i)
{x-mat1[unlist(dat1[i,]),]; which(different(x[1,],x[2,]))}) #using Rui's
function
names(lst1)- paste(dat1[,1],dat1[,2],sep=_)
A.K.
- Original Message -
From: Rui Barradas ruipbarra...@sapo.pt
To: Elaine Kuo elaine.kuo...@gmail.com
Cc: r-help@r-project.org r-help@r-project.org
Sent: Friday, September 27, 2013 7:39 AM
Subject: Re: [R] Compare species presence and absence between sites
Hello,
Something like this?
different - function(x, y) x == 1 y == 0
set.seed(7054)
mat - matrix(sample(0:1, 500, TRUE), nrow = 5)
rownames(mat) - LETTERS[1:5]
colnames(mat) - sprintf(D%03d, 1:100)
different(mat[B,], mat[E,])
Hope this helps,
Rui Barradas
Em 27-09-2013 11:48, Elaine Kuo escreveu:
Dear List,
I want to compare the presence and absence of bird species based on the
sites in a matrix.
The matrix has 5 rows for Island A, B, C, D, and E.
It has 100 columns for bird species D001-D100.
In each cell of the matrix,
the presence-absence of bird species will be recorded as 1 or 0.
(For example, if species D001 is found on Island D,
the matrix cell of species D001 and Island D will be 1.)
Now I want to know the different bird species between Island B and E.
In other words, I would like to find out bird species present (1) on
Island
B but absent (0)on island E, and vice versa (absent (0) on Island B but
present (1)on island E).
Please kindly advise how to code the purpose above.
Thank you in advance.
Elaine
[[alternative HTML version deleted]]
__
R-help@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.
__
R-help@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.
[[alternative HTML version deleted]]
__
R-help@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.
[R] search species with all absence in a presence-absence matrix
Dear list I have a matrix composed of islandID as rows and speciesID as columns. IslandID: Island A, B, C .O (15 islands in total) SpeciesID: D0001, D0002, D0003 .D0100 (100 species in total) The cell of the matrix describes presence (1) or absence (0) of the species in an island. Now I would like to search the species with absence (0) in all the islands (Island A to Island O.) Please kindly advise the R code for the search purpose. Thank you. Elaine [[alternative HTML version deleted]] __ R-help@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.
[R] to retrieve specific data from a matrix
Dear list, I want to retrieve a specific data from a matrix with 3000 columns. The matrix has island ID as its rows and species ID as its columns. There are 20 rows and 3000 columns in the matrix. (Island ID: Species 1- Species 20/ species ID: Species 1- Species 3000) The contents of the matrix grids is 1 or 0, for presence and absence. Now I would like to check in Island 1 which species is 1. (Island 1 as row 2) Please kindly advise how to code the command and thank you in advance. Elaine [[alternative HTML version deleted]] __ R-help@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.
Re: [R] merge matrix row data
Hello arun
Thanks for the answers.
I understand the answer to question 2.
However, about question 1, sorry I did not clarify the question.
1. If the row names are 1, 2, and 4 etc (numbers) instead of GID 1, GID 2,
and GID 3,
is there any modification in need for the code ?
The original data looks like below.
Original matrix
GID D0989 D9820 D5629 D4327 D2134
1 100 1 0
2 011 0 0
4 001 0 0
5 110 0 0
7 010 0 1
Resulting matrix
D0989 D9820 D5629 D4327 D2134
Island A 11 0 1 0
Island B 01 1 0 1
Elaine
On Thu, Aug 1, 2013 at 7:15 AM, arun smartpink...@yahoo.com wrote:
Hi Elaine,
In that case:
Do you have GID in the IslandA and IslandBs?
IslandA-c(GID 1, GID 5)
IslandB- c(GID 2, GID 4, GID 7)
If there is no change in the two Islands, then using the same dataset:
mat1- as.matrix(read.table(text=
D0989 D9820 D5629 D4327 D2134
GID_1100 1 0
GID_2011 0 0
GID_4001 0 0
GID_5110 0 0
GID_7010 0 1
,sep=,header=TRUE))
row.names(mat1)- gsub(.*\\_,,row.names(mat1)) #to replace the GID_
from the row.names()
mat1
# D0989 D9820 D5629 D4327 D2134
#1 1 0 0 1 0
#2 0 1 1 0 0
#4 0 0 1 0 0
#5 1 1 0 0 0
#7 0 1 0 0 1
IslandA-c(GID 1, GID 5)
IslandB- c(GID 2, GID 4, GID 7)
res-t(sapply(c(IslandA,IslandB),function(x) {x1-
mat1[match(gsub(.*\\s+,,get(x)),row.names(mat1)),];(!!colSums(x1))*1}))
res
# D0989 D9820 D5629 D4327 D2134
#IslandA 1 1 0 1 0
#IslandB 0 1 1 0 1
Regarding the use of !!colSums()
You can check these:
t(sapply(c(IslandA,IslandB),function(x) {x1-
mat1[match(gsub(.*\\s+,,get(x)),row.names(mat1)),];!colSums(x1)}))
#D0989 D9820 D5629 D4327 D2134
#IslandA FALSE FALSE TRUE FALSE TRUE
#IslandB TRUE FALSE FALSE TRUE FALSE
t(sapply(c(IslandA,IslandB),function(x) {x1-
mat1[match(gsub(.*\\s+,,get(x)),row.names(mat1)),];!!colSums(x1)}))
#D0989 D9820 D5629 D4327 D2134
#IslandA TRUE TRUE FALSE TRUE FALSE
#IslandB FALSE TRUE TRUE FALSE TRUE
# *1 will replace TRUE with 1 and FALSE with 0.
A.K.
From: Elaine Kuo elaine.kuo...@gmail.com
To: arun smartpink...@yahoo.com
Sent: Wednesday, July 31, 2013 6:58 PM
Subject: Re: [R] merge matrix row data
Dear Arun,
Thank you for the clear explanation.
The row.names question is a mistyping, for I do not have enough sleep last
night.
Two more questions
1. If the row names are 1, 2, and 4 etc (numbers) instead of GID 1, GID 2,
and GID 3,
is there any modification in need for the code ?
2. Please kindly explain the code
(!!colSums(x1))*1}
It is the critical part to merge the row data.
Thanks again.
Elaine
On Thu, Aug 1, 2013 at 6:45 AM, arun smartpink...@yahoo.com wrote:
Dear Elaine,
I used that line only because you didn't provide the data using dput().
So, I need to either use delimiter , or just leave a space by first
joining the GID and the numbers using _. I chose the latter as I
didn't had that much time to spent by putting , between each entries.
After that, I removed _ using the ?gsub(). As Bert pointed out, there
are many online resources for understanding regular expression.
In this particular case, what I did was to single out the _ in the
first pair of quotes, and replace with space in the second pair of quotes
. Therefore, GID_1, would become GID 1, which is what your original
dataset looks like.
If you type row.names(mat1) on the R console and enter, you will be able
to get the output.
Hope it helps.
Arun
From: Elaine Kuo elaine.kuo...@gmail.com
To: arun smartpink...@yahoo.com
Cc: R help r-help@r-project.org
Sent: Wednesday, July 31, 2013 5:07 PM
Subject: Re: [R] merge matrix row data
Dear Arun
Thank you for the very useful help.
However, please kindly explain the code below.
row.names(mat1)- gsub([_], ,row.names(mat1))
1. what does [_] mean?
2. what doesmean?
3. what does row.names(mat1) mean?
I checked ?gsub but still did not get the idea.
Thank you again
Elaine
On Wed, Jul 31, 2013 at 9:35 PM, arun smartpink...@yahoo.com wrote:
HI,
Please use ?dput()
mat1- as.matrix(read.table(text=
D0989 D9820 D5629 D4327 D2134
GID_1100 1 0
GID_2011 0 0
GID_4001 0 0
GID_5110 0
Re: [R] merge matrix row data
Hello Arun
Thank for comments.
You are right. GID is the first column in the matrix this time.
In the second row of the first column, it used to be GID 1 in the first
e-mail.
But you are also right. You answered it already, and this time In the
second row of the first column is 1.
Below is part of dput()(too many columns)
.. .Names = c(GID,
D5291, D5293, D7414, D7415, D7416, D7417, D7418,
D7419, D7420, D7421, D7422, D7423, D7424, D7425,
D7426, D7427, D7428, D7429, D7430, D7431, D7432,
D7433, D7434, D7435, D7436, D7437, D7438, D7439,
D7440, D7441, D7442, D7443, D7444, D7445, D7446,
Elaine
On Thu, Aug 1, 2013 at 12:35 PM, arun smartpink...@yahoo.com wrote:
Hi Elaine,
I am not sure how your original matrix keeps on changing from the
original post. Here, your statement about rownames are 1, 2, 4 (the answer
I already provided in the last post) and the matrix you showed looks
different. It seems like GID is the first column in the matrix. I
requested you to dput() the data to reduce these confusions.
mat1-as.matrix(read.table(text=
GID D0989 D9820 D5629 D4327 D2134
1 100 1 0
2 011 0 0
4 001 0 0
5 110 0 0
7 010 0 1
,sep=,header=TRUE))
IslandA-c(GID 1, GID 5)
IslandB- c(GID 2, GID 4, GID
7)t(sapply(c(IslandA,IslandB),function(x) {x1-
mat1[match(gsub(.*\\s+,,get(x)),mat1[,1]),-1];(!!colSums(x1))*1}))
#D0989 D9820 D5629 D4327 D2134
#IslandA 1 1 0 1 0
#IslandB 0 1 1 0 1
A.K.
From: Elaine Kuo elaine.kuo...@gmail.com
To: arun smartpink...@yahoo.com
Cc: R help r-help@r-project.org
Sent: Thursday, August 1, 2013 12:00 AM
Subject: Re: [R] merge matrix row data
Hello arun
Thanks for the answers.
I understand the answer to question 2.
However, about question 1, sorry I did not clarify the question.
1. If the row names are 1, 2, and 4 etc (numbers) instead of GID 1, GID 2,
and GID 3,
is there any modification in need for the code ?
The original data looks like below.
Original matrix
GID D0989 D9820 D5629 D4327 D2134
1 100 1 0
2 011 0 0
4 001 0 0
5 110 0 0
7 010 0 1
Resulting matrix
D0989 D9820 D5629 D4327 D2134
Island A 11 0 1 0
Island B 01 1 0 1
Elaine
On Thu, Aug 1, 2013 at 7:15 AM, arun smartpink...@yahoo.com wrote:
Hi Elaine,
In that case:
Do you have GID in the IslandA and IslandBs?
IslandA-c(GID 1, GID 5)
IslandB- c(GID 2, GID 4, GID 7)
If there is no change in the two Islands, then using the same dataset:
mat1- as.matrix(read.table(text=
D0989 D9820 D5629 D4327 D2134
GID_1100 1 0
GID_2011 0 0
GID_4001 0 0
GID_5110 0 0
GID_7010 0 1
,sep=,header=TRUE))
row.names(mat1)- gsub(.*\\_,,row.names(mat1)) #to replace the GID_
from the row.names()
mat1
# D0989 D9820 D5629 D4327 D2134
#1 1 0 0 1 0
#2 0 1 1 0 0
#4 0 0 1 0 0
#5 1 1 0 0 0
#7 0 1 0 0 1
IslandA-c(GID 1, GID 5)
IslandB- c(GID 2, GID 4, GID 7)
res-t(sapply(c(IslandA,IslandB),function(x) {x1-
mat1[match(gsub(.*\\s+,,get(x)),row.names(mat1)),];(!!colSums(x1))*1}))
res
# D0989 D9820 D5629 D4327 D2134
#IslandA 1 1 0 1 0
#IslandB 0 1 1 0 1
Regarding the use of !!colSums()
You can check these:
t(sapply(c(IslandA,IslandB),function(x) {x1-
mat1[match(gsub(.*\\s+,,get(x)),row.names(mat1)),];!colSums(x1)}))
#D0989 D9820 D5629 D4327 D2134
#IslandA FALSE FALSE TRUE FALSE TRUE
#IslandB TRUE FALSE FALSE TRUE FALSE
t(sapply(c(IslandA,IslandB),function(x) {x1-
mat1[match(gsub(.*\\s+,,get(x)),row.names(mat1)),];!!colSums(x1)}))
#D0989 D9820 D5629 D4327 D2134
#IslandA TRUE TRUE FALSE TRUE FALSE
#IslandB FALSE TRUE TRUE FALSE TRUE
# *1 will replace TRUE with 1 and FALSE with 0.
A.K.
From: Elaine Kuo elaine.kuo...@gmail.com
To: arun smartpink...@yahoo.com
Sent: Wednesday, July 31, 2013 6:58 PM
Subject: Re: [R] merge matrix row data
Dear Arun,
Thank you for the clear explanation.
The row.names question is a mistyping, for I do not have enough sleep
last night.
Two more questions
1. If the row names are 1, 2, and 4 etc (numbers) instead
Re: [R] merge matrix row data
Hello arun
I modified your code a little bit but failed to retrieve the row.names.
The response is NULL.
Please kindly help and thanks.
Elaine
Code
load(h:/b_W_line/R_workspace/dataset_Residence_2748.RData)
dim(dataR)
str(dataR)
dataR.m- as.matrix(dataR, header=TRUE)
dataR.m[,1]
row.names(dataR.m)
dput(dataR.m)
.skipped...0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L), .Dim = c(4873L, 14L), .Dimnames = list(NULL,
c(GID, D0407, D0409, D0410, D0462, D0463, D0473,
D0475, D0488, D0489, D0492, D0493, D0504, D0536
)))
On Thu, Aug 1, 2013 at 1:24 PM, Elaine Kuo elaine.kuo...@gmail.com wrote:
Hello Arun
Thank for comments.
You are right. GID is the first column in the matrix this time.
In the second row of the first column, it used to be GID 1 in the first
e-mail.
But you are also right. You answered it already, and this time In the
second row of the first column is 1.
Below is part of dput()(too many columns)
.. .Names = c(GID,
D5291, D5293, D7414, D7415, D7416, D7417, D7418,
D7419, D7420, D7421, D7422, D7423, D7424, D7425,
D7426, D7427, D7428, D7429, D7430, D7431, D7432,
D7433, D7434, D7435, D7436, D7437, D7438, D7439,
D7440, D7441, D7442, D7443, D7444, D7445, D7446,
Elaine
On Thu, Aug 1, 2013 at 12:35 PM, arun smartpink...@yahoo.com wrote:
Hi Elaine,
I am not sure how your original matrix keeps on changing from the
original post. Here, your statement about rownames are 1, 2, 4 (the answer
I already provided in the last post) and the matrix you showed looks
different. It seems like GID is the first column in the matrix. I
requested you to dput() the data to reduce these confusions.
mat1-as.matrix(read.table(text=
GID D0989 D9820 D5629 D4327 D2134
1 100 1 0
2 011 0 0
4 001 0 0
5 110 0 0
7 010 0 1
,sep=,header=TRUE))
IslandA-c(GID 1, GID 5)
IslandB- c(GID 2, GID 4, GID
7)t(sapply(c(IslandA,IslandB),function(x) {x1-
mat1[match(gsub(.*\\s+,,get(x)),mat1[,1]),-1];(!!colSums(x1))*1}))
#D0989 D9820 D5629 D4327 D2134
#IslandA 1 1 0 1 0
#IslandB 0 1 1 0 1
A.K.
From: Elaine Kuo elaine.kuo...@gmail.com
To: arun smartpink...@yahoo.com
Cc: R help r-help@r-project.org
Sent: Thursday, August 1, 2013 12:00 AM
Subject: Re: [R] merge matrix row data
Hello arun
Thanks for the answers.
I understand the answer to question 2.
However, about question 1, sorry I did not clarify the question.
1. If the row names are 1, 2, and 4 etc (numbers) instead of GID 1, GID
2, and GID 3,
is there any modification in need for the code ?
The original data looks like below.
Original matrix
GID D0989 D9820 D5629 D4327 D2134
1 100 1 0
2 011 0 0
4 001 0 0
5 110 0 0
7 010 0 1
Resulting matrix
D0989 D9820 D5629 D4327 D2134
Island A 11 0 1 0
Island B 01 1 0 1
Elaine
On Thu, Aug 1, 2013 at 7:15 AM, arun smartpink...@yahoo.com wrote:
Hi Elaine,
In that case:
Do you have GID in the IslandA and IslandBs?
IslandA-c(GID 1, GID 5)
IslandB- c(GID 2, GID 4, GID 7)
If there is no change in the two Islands, then using the same dataset:
mat1- as.matrix(read.table(text=
D0989 D9820 D5629 D4327 D2134
GID_1100 1 0
GID_2011 0 0
GID_4001 0 0
GID_5110 0 0
GID_7010 0 1
,sep=,header=TRUE))
row.names(mat1)- gsub(.*\\_,,row.names(mat1)) #to replace the
GID_ from the row.names()
mat1
# D0989 D9820 D5629 D4327 D2134
#1 1 0 0 1 0
#2 0 1 1 0 0
#4 0 0 1 0 0
#5 1 1 0 0 0
#7 0 1 0 0 1
IslandA-c(GID 1, GID 5)
IslandB- c(GID 2, GID 4, GID 7)
res-t(sapply(c(IslandA,IslandB),function(x) {x1-
mat1[match(gsub(.*\\s+,,get(x)),row.names(mat1)),];(!!colSums(x1))*1}))
res
# D0989 D9820 D5629 D4327 D2134
#IslandA 1 1 0 1 0
#IslandB 0 1 1 0 1
Regarding the use of !!colSums()
You can check these:
t(sapply(c(IslandA,IslandB),function(x) {x1-
mat1[match(gsub(.*\\s+,,get(x)),row.names(mat1)),];!colSums(x1)}))
#D0989 D9820 D5629 D4327 D2134
#IslandA FALSE FALSE TRUE FALSE TRUE
#IslandB TRUE FALSE FALSE TRUE FALSE
t(sapply(c(IslandA,IslandB),function(x) {x1-
mat1[match
[R] merge matrix row data
Dear list, I have a matrix showing the species presence-absence on a map. Its rows are map locations, represented by GridCellID, such as GID1 and GID 5. Its columns are species ID, such as D0989, D9820, and D5629. The matrix is as followed. Now I want to merge the GridCellID according to the map location of each island. For instance, Island A consist of GID 1 and 5. Island B consist of GID 2, 4, and 7. In GID 1 and 5, species D0989 are both 1. Then I want to merge GID 1 and 5 into Island A, with species D0989 as 1. The original matrix and the resulting matrix are listed below. Please kindly advise how to code the calculation in R. Please do not hesitate to ask if anything is unclear. Thank you in advance. Elaine Original matrix D0989 D9820 D5629 D4327 D2134 GID 1100 1 0 GID 2011 0 0 GID 4001 0 0 GID 5110 0 0 GID 7010 0 1 Resulting matrix D0989 D9820 D5629 D4327 D2134 Island A 11 0 1 0 Island B 01 1 0 1 [[alternative HTML version deleted]] __ R-help@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.
Re: [R] merge matrix row data
Dear Arun
Thank you for the very useful help.
However, please kindly explain the code below.
row.names(mat1)- gsub([_], ,row.names(mat1))
1. what does [_] mean?
2. what doesmean?
3. what does row.names(mat1) mean?
I checked ?gsub but still did not get the idea.
Thank you again
Elaine
On Wed, Jul 31, 2013 at 9:35 PM, arun smartpink...@yahoo.com wrote:
HI,
Please use ?dput()
mat1- as.matrix(read.table(text=
D0989 D9820 D5629 D4327 D2134
GID_1100 1 0
GID_2011 0 0
GID_4001 0 0
GID_5110 0 0
GID_7010 0 1
,sep=,header=TRUE))
row.names(mat1)- gsub([_], ,row.names(mat1))
IslandA-c(GID 1, GID 5)
IslandB- c(GID 2, GID 4, GID 7)
res- t(sapply(c(IslandA,IslandB),function(x)
{x1-mat1[match(get(x),row.names(mat1)),];(!!colSums(x1))*1} ))
res
#D0989 D9820 D5629 D4327 D2134
#IslandA 1 1 0 1 0
#IslandB 0 1 1 0 1
A.K.
- Original Message -
From: Elaine Kuo elaine.kuo...@gmail.com
To: r-h...@stat.math.ethz.ch r-h...@stat.math.ethz.ch
Cc:
Sent: Wednesday, July 31, 2013 9:03 AM
Subject: [R] merge matrix row data
Dear list,
I have a matrix showing the species presence-absence on a map.
Its rows are map locations, represented by GridCellID, such as GID1 and GID
5.
Its columns are species ID, such as D0989, D9820, and D5629.
The matrix is as followed.
Now I want to merge the GridCellID according to the map location of each
island.
For instance, Island A consist of GID 1 and 5. Island B consist of GID 2,
4, and 7.
In GID 1 and 5, species D0989 are both 1.
Then I want to merge GID 1 and 5 into Island A, with species D0989 as 1.
The original matrix and the resulting matrix are listed below.
Please kindly advise how to code the calculation in R.
Please do not hesitate to ask if anything is unclear.
Thank you in advance.
Elaine
Original matrix
D0989 D9820 D5629 D4327 D2134
GID 1100 1 0
GID 2011 0 0
GID 4001 0 0
GID 5110 0 0
GID 7010 0 1
Resulting matrix
D0989 D9820 D5629 D4327 D2134
Island A 11 0 1 0
Island B 01 1 0 1
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Re: [R] [R-sig-eco] extract beta.sim from dist type data (package betapart)
Hello Sarah, Thank you for the help very much. Please kindly advise manuals dealing with the object list (or dist). In addition, I would like to show the beta diversity index in a map. Please kindly advise any other R package in need. Elaine On Wed, Jul 17, 2013 at 10:20 PM, Sarah Goslee sarah.gos...@gmail.comwrote: Replied to on the R-sig-ecology list, with a request not to cross-post. Briefly, the output is a list with named components, so can be extracted as usual. Sarah On Wed, Jul 17, 2013 at 5:50 AM, Elaine Kuo elaine.kuo...@gmail.com wrote: Dear List, This is Elaine. I am using beta.part to calculate the beta diversity index. The function of beta.part can generate three kinds of beta diversity indice at one time. However, it is Simpson index that I want. The calculation result is composed of three rows and N/A columns (dist class). I do not know how to extract one of the indice in the form of dist class. No relevant example is found the manual. (I tried as.vector as below but failed.) Please kindly help and thank you in advance. Elaine Code library(betapart) dist.sim-beta.pair(dataR, index.family=sor) # Unfold distance matrices into vectors data.sim-data.frame(as.vector(dist.sim)) -- Sarah Goslee http://www.functionaldiversity.org __ R-help@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. [[alternative HTML version deleted]] __ R-help@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.
[R] how to calculate the average values of each row in a matrix
Hello, I have a matrix (class matrix) composed of GridCell (row and column). The matrix value is the beta diversity index value between two grids. Now I would like to get the average value of each GridCell. Please kindly advise how to make the calculation. Thank you. Elaine The matrix looks like (cited from Michael Friendly) I would like to get the average value of each color. Obs stim RPur Red Yel Gy1 Gy2 Green Blue BlP Pur1 Pur2 1 RPur . . . . . . . . . . 2 Red11.5. . . . . . . . . 3 Yel13.1 6.0. . . . . . . . 4 Gy112.6 7.9 6.2. . . . . . . 5 Gy210.6 8.4 8.4 5.2. . . . . . 6 Green 10.6 9.4 9.9 6.5 4.1 . . . . . 7 Blue 10.8 10.2 10.3 8.8 7.06.4. . . . 8 BlP 7.3 11.3 12.7 11.2 10.49.9 4.2 . . . 9 Pur15.4 11.5 12.9 11.7 10.89.4 8.4 4.5. . 10 Pur25.0 11.5 10.7 10.2 10.6 10.1 8.1 6.43 . [[alternative HTML version deleted]] __ R-help@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.
[R] extract beta.sim from dist type data (package betapart)
Dear List, This is Elaine. I am using beta.part to calculate the beta diversity index. The function of beta.part can generate three kinds of beta diversity indice at one time. However, it is Simpson index that I want. The calculation result is composed of three rows and N/A columns (dist class). I do not know how to extract one of the indice in the form of dist class. No relevant example is found the manual. (I tried as.vector as below but failed.) Please kindly help and thank you in advance. Elaine Code library(betapart) dist.sim-beta.pair(dataR, index.family=sor) # Unfold distance matrices into vectors data.sim-data.frame(as.vector(dist.sim)) [[alternative HTML version deleted]] __ R-help@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.
Re: [R] error of betadiver in vegan
Hello, Thanks for Jari's comment. It worked well after correction. However, an error jumped out for the code below. Error: cannot allocate vector of size 90.6 Mb Please kindly advise how to modify it. Thank you. Elaine Code # Non-Passerine table dataNP_1 -read.dbf(H:/temp_D/stage_4_R_2748/NP_1-10.dbf, as.is = FALSE) dataNP_2 -read.dbf(H:/temp_D/stage_4_R_2748/NP_11-19.dbf, as.is = FALSE) dataNP-merge(dataNP_1,dataNP_2,by=c(GID),all=T) .. skip... # Non-Passerine and Passerine table (2748 species) dataR-merge(dataP,dataNP,by=c(GID),all=T) dim(dataR) str(dataR) library(vegan) ## The beta sim index (Lennon 2001) d - betadiver(dataR, sim) On Fri, Jul 12, 2013 at 2:13 PM, Jari Oksanen jari.oksa...@oulu.fi wrote: Elaine Kuo elaine.kuo.tw at gmail.com writes: Hello, I am using betadiver (vegan) to calculate beta diversity. However, an error message shows Error in ifelse(x 0, 1, 0) : (list) object cannot be coerced to type 'double' ...snip... ## Raw data R - betadiver(dataR) ## The indices betadiver(help=TRUE) ## The beta sim index (Lennon 2001) d - betadiver(R, sim) Elaine, Look carefully what you do here: betadiver needs data as input -- not beta diversities. Your last command is equal to this oneliner: d - betadiver(betadiver(dataR), sim) This is guaranteed to fail. Use instead d - betadiver(dataR, sim) Cheers, Jari Oksanen __ R-help@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. [[alternative HTML version deleted]] __ R-help@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.
[R] memory problem of betadiver of vegan
Hello List, This is Elaine. I am running betadiver for a dataset of 4873 rows and 2749 columns. (4873 rows = 4873 gridcell of the study region and 2749 columns for the bird species) The dataset was produced by combing 5 dbf. When running the code o, an error message jumped out, saying Error: cannot allocate vector of size 90.6 Mb I posted the issue in r-help and checked the previous mails about R memory problems. gc() and save .Rdata were tried but did not work. Also, I tried to transformed the dataset into a matrix, using the code m below. However, an error also appeared, saying Error in ifelse(x 0, 1, 0) : (list) object cannot be coerced to type 'double'. Please kindly advise how to alleviate the memory problem, particularly in modifying the code of betadiver of vegan. Thank you. Elaine code m matrixR-matrix(data = dataR, nrow = 4873, ncol = 2749) d - betadiver(matrixR, sim) code o # Non-Passerine table dataNP_1 -read.dbf(H:/temp_D/stage_4_R_2748/NP_1-10.dbf, as.is = FALSE) dataNP_2 -read.dbf(H:/temp_D/stage_4_R_2748/NP_11-19.dbf, as.is = FALSE) dataNP-merge(dataNP_1,dataNP_2,by=c(GID),all=T) .. skip... # Non-Passerine and Passerine table (2748 species) dataR-merge(dataP,dataNP,by=c(GID),all=T) dim(dataR) str(dataR) library(vegan) ## The beta sim index (Lennon 2001) d - betadiver(dataR, sim) [[alternative HTML version deleted]] __ R-help@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.
Re: [R] memory problem of betadiver of vegan
Hello List, I solved the problem by using the code with 31 votes http://stackoverflow.com/questions/1358003/tricks-to-manage-the-available-memory-in-an-r-session On Sat, Jul 13, 2013 at 6:15 AM, Elaine Kuo elaine.kuo...@gmail.com wrote: Hello List, This is Elaine. I am running betadiver for a dataset of 4873 rows and 2749 columns. (4873 rows = 4873 gridcell of the study region and 2749 columns for the bird species) The dataset was produced by combing 5 dbf. When running the code o, an error message jumped out, saying Error: cannot allocate vector of size 90.6 Mb I posted the issue in r-help and checked the previous mails about R memory problems. gc() and save .Rdata were tried but did not work. Also, I tried to transformed the dataset into a matrix, using the code m below. However, an error also appeared, saying Error in ifelse(x 0, 1, 0) : (list) object cannot be coerced to type 'double'. Please kindly advise how to alleviate the memory problem, particularly in modifying the code of betadiver of vegan. Thank you. Elaine code m matrixR-matrix(data = dataR, nrow = 4873, ncol = 2749) d - betadiver(matrixR, sim) code o # Non-Passerine table dataNP_1 -read.dbf(H:/temp_D/stage_4_R_2748/NP_1-10.dbf, as.is = FALSE) dataNP_2 -read.dbf(H:/temp_D/stage_4_R_2748/NP_11-19.dbf, as.is = FALSE) dataNP-merge(dataNP_1,dataNP_2,by=c(GID),all=T) .. skip... # Non-Passerine and Passerine table (2748 species) dataR-merge(dataP,dataNP,by=c(GID),all=T) dim(dataR) str(dataR) library(vegan) ## The beta sim index (Lennon 2001) d - betadiver(dataR, sim) [[alternative HTML version deleted]] __ R-help@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.
[R] error of betadiver in vegan
Hello, I am using betadiver (vegan) to calculate beta diversity. However, an error message shows Error in ifelse(x 0, 1, 0) : (list) object cannot be coerced to type 'double' R version: 3.0.0 Please kindly advise how to solve the issue. Also, please kindly tell if any more information is in need. Thank you. Elaine code # Non-Passerine table dataNP_1 -read.dbf(H:/temp_D/stage_4_R_2748/NP_1-10.dbf, as.is = FALSE) dataNP_2 -read.dbf(H:/temp_D/stage_4_R_2748/NP_11-19.dbf, as.is = FALSE) dataNP-merge(dataNP_1,dataNP_2,by=c(GID),all=T) .. skip... # Non-Passerine and Passerine table (2748 species) dataR-merge(dataP,dataNP,by=c(GID),all=T) dim(dataR) str(dataR) library(vegan) ## Raw data R - betadiver(dataR) ## The indices betadiver(help=TRUE) ## The beta sim index (Lennon 2001) d - betadiver(R, sim) [[alternative HTML version deleted]] __ R-help@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.
[R] pearson correlation significant level
Hello I am using package Hmisc to calculate the pearson correlation and the significant level for the matrix of t_i and t_r. (temperature minimum and temperature range) However, I have difficulty interpreting the result, even after checking the manual. Please kindly help to indicate if the p-value is zero. Thank you in advance. Elaine The code library(Hmisc) rcorr(as.matrix(datat), type=pearson) # type can be pearson or spearman The result is t_i t_r t_i 1.00 -0.89 t_r -0.89 1.00 n= 4873 P t_i t_r t_i 0 t_r 0 [[alternative HTML version deleted]] __ R-help@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.
Re: [R] R package for bootstrapping (comparing two quadratic regression models)
Thanks Jean. Y1 = observed value Y2= estimated value Elaine On Mon, May 6, 2013 at 9:22 PM, Adams, Jean jvad...@usgs.gov wrote: Elaine, I suggest that you consult with a statistician to see if it even makes sense to compare the two models you describe. The first model makes sense to me, the second one does not. Isn't y2 in the second equation equal to the estimated y1 from the first equation? You need to talk with someone about what you have, where it came from, and what questions you are trying to answer. Jean On Fri, May 3, 2013 at 6:08 PM, Elaine Kuo elaine.kuo...@gmail.comwrote: Hello , I want to compare two quadratic regression models with non-parametric bootstrap. However, I do not know which R package can serve the purpose, such as boot, rms, or bootstrap, DeltaR. Please kindly advise and thank you. Elaine The two quadratic regression models are y1=a1x^2+b1x+c1 y1= observed migration distance of butterflies() y2=a2x^2+b2x+c2 y2= predicted migration distance of butterflies (based on body mass) x= body mass of butterflies null hypothesis: a1=a2 and b1=b2 and c1=c2 bootstrap to test if the coeffients (a, b, c) of the y1 and the y2 model differ [[alternative HTML version deleted]] __ R-help@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. [[alternative HTML version deleted]] __ R-help@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.
[R] slope coefficient of a quadratic regression bootstrap
Hello,
I want to know if two quadratic regressions are significantly different.
I was advised to make the test using
step 1 bootstrapping both quadratic regressions and get their slope
coefficients.
(Let's call the slope coefficient *â*^1 and *â*^2)
step 2 use the slope difference *â*^1-*â*^2 and bootstrap the slope
coefficent
step 3 find out the sampling distribution above and calculate the % =0
step 4 multiple the % by 2
However, I am new to the package boot.
I wrote a code for step 1 and got a error message.
Please kindly advise how to modify it and thank you.
Elaine
code
require(boot)
function.fit2 - function(data){
#data - data[indices,] # select obs. in bootstrap sample
fit2 -lm(logDIS~logBMN+I(logBMN^2))
coefficients(fit2) # return coefficient vector
}
boot.fit2 - boot(dataN, function.fit2, 1000)
error
fit2.boot - boot(dataN, fun.fit2, 1000)
Error in statistic(data, original, ...) : unused argument (original)
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Re: [R] slope coefficient of a quadratic regression bootstrap
Hello all,
I found the following code worked.
code
require(boot)
function.fit2 - function(data,i){
d - data[i,] # select obs. in bootstrap sample
fit2 -lm(logDIS~logBMN+I(logBMN^2), data=dataN)
coefficients(fit2) # return coefficient vector
}
boot.fit2 - boot(dataN, function.fit2, 1000)
On Mon, May 6, 2013 at 7:36 AM, Elaine Kuo elaine.kuo...@gmail.com wrote:
Hello,
I want to know if two quadratic regressions are significantly different.
I was advised to make the test using
step 1 bootstrapping both quadratic regressions and get their slope
coefficients.
(Let's call the slope coefficient *â*^1 and *â*^2)
step 2 use the slope difference *â*^1-*â*^2 and bootstrap the slope
coefficent
step 3 find out the sampling distribution above and calculate the % =0
step 4 multiple the % by 2
However, I am new to the package boot.
I wrote a code for step 1 and got a error message.
Please kindly advise how to modify it and thank you.
Elaine
code
require(boot)
function.fit2 - function(data){
#data - data[indices,] # select obs. in bootstrap
sample
fit2 -lm(logDIS~logBMN+I(logBMN^2))
coefficients(fit2) # return coefficient vector
}
boot.fit2 - boot(dataN, function.fit2, 1000)
error
fit2.boot - boot(dataN, fun.fit2, 1000)
Error in statistic(data, original, ...) : unused argument (original)
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and provide commented, minimal, self-contained, reproducible code.
[R] compare two quadratic regression using bootstrap
Hello,
I want to know if two quadratic regressions are significantly different.
I was advised to make the test using
step 1 bootstrapping both quadratic regressions and get their slope
coefficients.
(Let's call the slope coefficient *â*^1 and *â*^2)
step 2 use the slope difference *â*^1-*â*^2 and bootstrap the slope
coefficent
step 3 find out the sampling distribution above and calculate the % =0
step 4 multiple the % by 2
However, I am new to the package boot.
I finished writing code for step 1 as below.
Please kindly advise how to code step 2 and 3.
Thank you.
Elaine
code
require(boot)
function.fit2 - function(data,i){
d - data[i,] # select obs. in bootstrap sample
fit2 -lm(logDIS~logBMN+I(logBMN^2), data=dataN)
coefficients(fit2) # return coefficient vector
}
boot.fit2 - boot(dataN, function.fit2, 1000)
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Re: [R] significantly different from one (not zero) using lm
Hello, Thanks. But the parameter offset is new to me. Please kindly explain why setting offset to x will give a significant test of whether the slope coefficient is different from one. (I checked the ?lm but still do not understand it well) Thanks again Elaine On Wed, May 1, 2013 at 11:12 AM, Thomas Lumley tlum...@uw.edu wrote: Or use an offset lm( y ~ x+offset(x), data = dat) The offset gives x a coefficient of 1, so the coefficient of x in this model is the difference between the coefficient of x in the model without an offset and 1 -- the thing you want. -thomas On Wed, May 1, 2013 at 2:54 PM, Paul Johnson pauljoh...@gmail.com wrote: It is easy to construct your own test. I test against null of 0 first so I can be sure I match the right result from summary.lm. ## get the standard error seofb - sqrt(diag(vcov(lm1))) ## calculate t. Replace 0 by your null myt - (coef(lm1) - 0)/seofb mypval - 2*pt(abs(myt), lower.tail = FALSE, df = lm1$df.residual) ## Note you can pass a vector of different nulls for the coefficients myt - (coef(lm1) - c(0,1))/seofb We could write this into a function if we wanted to get busy. Not a bad little homework exercise, I think. dat - data.frame(x = rnorm(100), y = rnorm(100)) lm1 - lm(y ~ x, data = dat) summary(lm1) Call: lm(formula = y ~ x, data = dat) Residuals: Min 1Q Median 3Q Max -3.0696 -0.5833 0.1351 0.7162 2.3229 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) -0.001499 0.104865 -0.0140.989 x -0.039324 0.113486 -0.3470.730 Residual standard error: 1.024 on 98 degrees of freedom Multiple R-squared: 0.001224,Adjusted R-squared: -0.008968 F-statistic: 0.1201 on 1 and 98 DF, p-value: 0.7297 seofb - sqrt(diag(vcov(lm1))) myt - (coef(lm1) - 0)/seofb mypval - 2*pt(abs(myt), lower.tail = FALSE, df = lm1$df.residual) myt (Intercept) x -0.01429604 -0.34650900 mypval (Intercept) x 0.9886229 0.7297031 myt - (coef(lm1) - 1)/seofb mypval - 2*pt(abs(myt), lower.tail = FALSE, df = lm1$df.residual) myt (Intercept) x -9.550359 -9.158166 mypval (Intercept)x 1.145542e-15 8.126553e-15 On Tue, Apr 30, 2013 at 9:07 PM, Elaine Kuo elaine.kuo...@gmail.com wrote: Hello, I am work with a linear regression model: y=ax+b with the function of lm. y= observed migration distance of butterflies x= predicted migration distance of butterflies Usually the result will show if the linear term a is significantly different from zero based on the p-value. Now I would like to test if the linear term is significantly different from one. (because I want to know if the regression line (y=ax+b) is significantly from the line with the linear term =1 and the intercept =0) Please kindly advise if it is possible to adjust some default parameters in the function to achieve the goal. Thank you. Elaine [[alternative HTML version deleted]] __ R-help@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. -- Paul E. Johnson Professor, Political Science Assoc. Director 1541 Lilac Lane, Room 504 Center for Research Methods University of Kansas University of Kansas http://pj.freefaculty.org http://quant.ku.edu [[alternative HTML version deleted]] __ R-help@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. -- Thomas Lumley Professor of Biostatistics University of Auckland [[alternative HTML version deleted]] __ R-help@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.
[R] significant test of two quadratic regression models (lm)
Hello, I am work with two quadratic regression models y=ax^2+bx+c with the function of lm. y1= observed migration distance of butterflies(y1=a1x^2+b1x+c1) y2= predicted migration distance of butterflies (based on body mass) (y2=a2x^2+b2x+c2) x= body mass of butterflies Now I would like to check the two regression model differ by testing if the coeffients (a, b, c) of the y1 and the y2 model differ (null hypothesis: a1=a2 and b1=b2 and c1=c2) Please kindly advise any significant test in R for the purpose. Also, please kindly advise how to apply Bonferroni procedure in the test if necessary. Thank you in advance. Elaine [[alternative HTML version deleted]] __ R-help@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.
[R] R package for bootstrapping (comparing two quadratic regression models)
Hello , I want to compare two quadratic regression models with non-parametric bootstrap. However, I do not know which R package can serve the purpose, such as boot, rms, or bootstrap, DeltaR. Please kindly advise and thank you. Elaine The two quadratic regression models are y1=a1x^2+b1x+c1 y1= observed migration distance of butterflies() y2=a2x^2+b2x+c2 y2= predicted migration distance of butterflies (based on body mass) x= body mass of butterflies null hypothesis: a1=a2 and b1=b2 and c1=c2 bootstrap to test if the coeffients (a, b, c) of the y1 and the y2 model differ [[alternative HTML version deleted]] __ R-help@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.
[R] significantly different from one (not zero) using lm
Hello, I am work with a linear regression model: y=ax+b with the function of lm. y= observed migration distance of butterflies x= predicted migration distance of butterflies Usually the result will show if the linear term a is significantly different from zero based on the p-value. Now I would like to test if the linear term is significantly different from one. (because I want to know if the regression line (y=ax+b) is significantly from the line with the linear term =1 and the intercept =0) Please kindly advise if it is possible to adjust some default parameters in the function to achieve the goal. Thank you. Elaine [[alternative HTML version deleted]] __ R-help@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.
[R] MOS-test using package vegan
Dear all, I am using MOStest in vegan to examine the hump-shaped of a quadratic regression model. In the manual of vegan, it mentions that the value of MOStest include isHump. My result showed the quadratic regression is hump-shaped according to the p-value (nearly 0). However, the value isHump did not show up. Please kindly help where to find isHump. Further, I do not understand the result of the function plot for the MOStested regression model, after reading the manual of vegan. (There are three graphs in the result, y-x plot, residuals and fitted regression model, and cook's distance) Please kindly share any references to interpret the graphs. Thank you. Elaine code library(vegan) mos_test - MOStest(BMN, DIS, family=gaussian) plot(mos_test) [[alternative HTML version deleted]] __ R-help@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.
[R] failed to download vegan
Hello, This is Elaine. I am using R 3.0 to download package vegan but failed. The warning message is package vegan successfully unpacked and MD5 sums checked Warning: unable to move temporary installation C:\Users\elaine\Documents\R\win-library\3.0\file16c82da53b1b\vegan to C:\Users\elaine\Documents\R\win-library\3.0\vegan I cannot find the folder \file16c82da53b1b\ below C:\Users\elaine\Documents\R\win-library\3.0 Please kindly help how to download or move the vegan to the folder it should be in. Thank you very much Elaine [[alternative HTML version deleted]] __ R-help@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.
Re: [R] failed to download vegan
Hello All, I manually moved the vegan.zip to C:\Users\elaine\Documents\R\ win-library\3.0\vegan. Then unzipping the file. It worked to require vegan Elaine On Wed, Apr 17, 2013 at 8:56 AM, Elaine Kuo elaine.kuo...@gmail.com wrote: Hello, This is Elaine. I am using R 3.0 to download package vegan but failed. The warning message is package vegan successfully unpacked and MD5 sums checked Warning: unable to move temporary installation C:\Users\elaine\Documents\R\win-library\3.0\file16c82da53b1b\vegan to C:\Users\elaine\Documents\R\win-library\3.0\vegan I cannot find the folder \file16c82da53b1b\ below C:\Users\elaine\Documents\R\win-library\3.0 Please kindly help how to download or move the vegan to the folder it should be in. Thank you very much Elaine [[alternative HTML version deleted]] __ R-help@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.
[R] put strip below the panel (dotplot)
Hello I am using lattice dotplot and I would like to put the strip under the panel. I found the code strip is for the strip above the panel, and strip.left for the strip left to the panel. Please kindly advise how to write the code for the strip under the panel Thank you Elaine [[alternative HTML version deleted]] __ R-help@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.
[R] resizing panels but some strip letters disappeared (dotplot)
Hello, I am using library(latticeExtra) resizePanels to have better visual display in dotplot (lattice). However, some panels became smaller and the strip letters of those panels were partially missing. Please kindly advise how to keep all strip letters remaining when resizing panels. Thank you. Elaine [[alternative HTML version deleted]] __ R-help@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.
Re: [R] locating boxplot in bwplot (lattice)
Hello, I used group in dotplot to classify diet by colors. Elaine On Mon, Feb 25, 2013 at 6:27 AM, Elaine Kuo elaine.kuo...@gmail.com wrote: Hello sorry that I did not make the letter clearly stated. Now I have 21 boxplots (No. 1, No. 2No. 21 from the left to the right)(lattice). I want the first two (No. 1 and 2) to become red and the rest (No. 3 to No. 21) to become blue. (rep will make No. 1 and 2, No. 9 and 10, No. 17 and 18, No. become red.) Please kindly advise R-code that can specify the red color for No. 1 and 2, the blue color for the rest. Thanks again. Elaine On Mon, Feb 25, 2013 at 4:17 AM, Peter Ehlers ehl...@ucalgary.ca wrote: On 2013-02-24 03:50, Elaine Kuo wrote: Hello Thank you for the advice on vector. I found a previous mail on this issue and pasted it below. Now here comes a different scenario. I have more than 20 boxplots and just wanted the first two from the left to be red and the rest to be blue. Please kindly advise how to code the color without writing the color names 18 times. Thanks again. Elaine [...snip...] I haven't followed this thread, but is there some reason why you can't just use rep()? Example (from the help page for bwplot): mycol - rep( c(red, blue), c(2, 6) ) bwplot(voice.part ~ height, data = singer, fill = mycol) Peter Ehlers [[alternative HTML version deleted]] __ R-help@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.
Re: [R] locating boxplot in bwplot (lattice)
Hello
Thank you for the advice on vector.
I found a previous mail on this issue and pasted it below.
Now here comes a different scenario.
I have more than 20 boxplots and just wanted the first two from the left to
be red and the rest to be blue.
Please kindly advise how to code the color without writing the color names
18 times.
Thanks again.
Elaine
code for color using vector
dataset - data.frame ( time = rep(1:5,times=9),
genotype = factor(rep(rep
(c(A,B,C),each=5),times=3 )),
location= factor(rep (paste(LOC,1:3),each=15)),
color = rep (rep
(c(red,green,blue),each=5),times=3
),
result = rnorm (45))
library(lattice)
# The black, red, green behaviour you were seeing is because
# dataset$color is a factor
dataset$color
# which is coded 1, 2, 3 levels = (red, green, blue).
# This is being interpreted as the first three colours of the palette
pallete()
# coerce the vector to a character vector
as.character(dataset$color)
# gives you
xyplot( result ~ time | location, data=dataset,groups=genotype,
fill.color = as.character(dataset$color),
panel = function(x, y,fill.color,...,subscripts) {
fill = fill.color [subscripts]
panel.xyplot(x, y,pch=19, col=fill, type =b)}
)
# Lines only take a single value so only the first value of the vector,
# red, is passed to line colour.
# these are simple alternatives
xyplot( result ~ time | location, data=dataset, groups=genotype,
pch=c(1,2,3), type=b,
col=c(red,blue,green))
xyplot( result ~ time | location, data=dataset, groups=genotype,
pch=c(1,2,3), type=b,
col=dataset$color)
# or use
par.settings - list(superpose.symbol = list(col = c(red, green,
blue), fill = c(red, green, blue)), superpose.line = list(col =
c(red, green, blue)) )
xyplot( result ~ time | location, data=dataset,groups=genotype,pch=19,
type = b, par.settings = par.settings)
On Sun, Feb 24, 2013 at 6:29 PM, Andrés Aragón Martínez armand...@gmail.com
wrote:
Hi Elaine,
In your dataset create a vector with the order in which you want appear
the levels, then use that vector in the argument reorder.
Andrés AM
El 24/02/2013, a las 00:59, Elaine Kuo elaine.kuo...@gmail.com escribió:
Hello,
I tried to manipulate the order of boxplots using the reorder below and
worked.
However, please kindly advise how to specify the colors of each boxplot
(bird group),
like red, green, and blue, from the left to the right.
Thanks again.
code
bwplot(GE_distance~OF, data=dataN,
index.cond = function(x, y) mean(y),
xlab=list(Taxonomy group, cex = 1.6),
prepanel = function(x, y) {
list(xlim = levels(reorder(x, y)))
},
panel = function(x, y, ...) {
panel.bwplot(reorder(x, y),y, ...)
})
data
migration distance (km)bird group
10987 Charadriiformes
9867Charadriiformes
8702Charadriiformes
9432Charadriiformes
9054Charadriiformes
5087 Falconiiformes
5783 Falconiiformes
5298Falconiiformes
5687 Falconiiformes
3987Gruiformes
3298Gruiformes
3567Gruiformes
3409Gruiformes
3321Gruiformes
3598Gruiformes
On Sat, Feb 23, 2013 at 6:29 AM, Ben Bolker bbol...@gmail.com wrote:
Elaine Kuo elaine.kuo.tw at gmail.com writes:
Hello
I am using lattice bwplot to draw migration distance of three groups of
birds.
The boxplots from the left to right is displayed
in alphabetic order of the boxplot names, as the default setting.
However, I would like the boxplots from the left to right to be
displayed
according to the migration distance from the short values to the long
ones.
In the data below, from the left to the right should be Gruiformes,
Falconiiformes, and Charadriiformes.
Please kindly advise how to modify the code below.
Define the order of the levels of your factor
accordingly. Take a look at
http://stackoverflow.com/questions/15033107/
specifing-order-of-lattice-plot-panels
(broken URL to meet gmane line length limits)
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R
Re: [R] locating boxplot in bwplot (lattice)
Hello sorry that I did not make the letter clearly stated. Now I have 21 boxplots (No. 1, No. 2No. 21 from the left to the right)(lattice). I want the first two (No. 1 and 2) to become red and the rest (No. 3 to No. 21) to become blue. (rep will make No. 1 and 2, No. 9 and 10, No. 17 and 18, No. become red.) Please kindly advise R-code that can specify the red color for No. 1 and 2, the blue color for the rest. Thanks again. Elaine On Mon, Feb 25, 2013 at 4:17 AM, Peter Ehlers ehl...@ucalgary.ca wrote: On 2013-02-24 03:50, Elaine Kuo wrote: Hello Thank you for the advice on vector. I found a previous mail on this issue and pasted it below. Now here comes a different scenario. I have more than 20 boxplots and just wanted the first two from the left to be red and the rest to be blue. Please kindly advise how to code the color without writing the color names 18 times. Thanks again. Elaine [...snip...] I haven't followed this thread, but is there some reason why you can't just use rep()? Example (from the help page for bwplot): mycol - rep( c(red, blue), c(2, 6) ) bwplot(voice.part ~ height, data = singer, fill = mycol) Peter Ehlers [[alternative HTML version deleted]] __ R-help@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.
Re: [R] locating boxplot in bwplot (lattice)
Hello,
I tried to manipulate the order of boxplots using the reorder below and
worked.
However, please kindly advise how to specify the colors of each boxplot
(bird group),
like red, green, and blue, from the left to the right.
Thanks again.
code
bwplot(GE_distance~OF, data=dataN,
index.cond = function(x, y) mean(y),
xlab=list(Taxonomy group, cex = 1.6),
prepanel = function(x, y) {
list(xlim = levels(reorder(x, y)))
},
panel = function(x, y, ...) {
panel.bwplot(reorder(x, y),y, ...)
})
data
migration distance (km)bird group
10987 Charadriiformes
9867Charadriiformes
8702Charadriiformes
9432Charadriiformes
9054Charadriiformes
5087 Falconiiformes
5783 Falconiiformes
5298Falconiiformes
5687 Falconiiformes
3987Gruiformes
3298Gruiformes
3567Gruiformes
3409Gruiformes
3321Gruiformes
3598Gruiformes
On Sat, Feb 23, 2013 at 6:29 AM, Ben Bolker bbol...@gmail.com wrote:
Elaine Kuo elaine.kuo.tw at gmail.com writes:
Hello
I am using lattice bwplot to draw migration distance of three groups of
birds.
The boxplots from the left to right is displayed
in alphabetic order of the boxplot names, as the default setting.
However, I would like the boxplots from the left to right to be displayed
according to the migration distance from the short values to the long
ones.
In the data below, from the left to the right should be Gruiformes,
Falconiiformes, and Charadriiformes.
Please kindly advise how to modify the code below.
Define the order of the levels of your factor
accordingly. Take a look at
http://stackoverflow.com/questions/15033107/
specifing-order-of-lattice-plot-panels
(broken URL to meet gmane line length limits)
__
R-help@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.
[[alternative HTML version deleted]]
__
R-help@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.
[R] locating boxplot in bwplot (lattice)
Hello I am using lattice bwplot to draw migration distance of three groups of birds. The boxplots from the left to right is displayed in alphabetic order of the boxplot names, as the default setting. However, I would like the boxplots from the left to right to be displayed according to the migration distance from the short values to the long ones. In the data below, from the left to the right should be Gruiformes, Falconiiformes, and Charadriiformes. Please kindly advise how to modify the code below. The data is as below. Thank you. Elaine Code Library(lattice) bwplot(migration_distance~bird) data migration distance (km)bird group 10987 Charadriiformes 9867Charadriiformes 8702Charadriiformes 9432Charadriiformes 9054Charadriiformes 5087 Falconiiformes 5783 Falconiiformes 5298Falconiiformes 5687 Falconiiformes 3987Gruiformes 3298Gruiformes 3567Gruiformes 3409Gruiformes 3321Gruiformes 3598Gruiformes [[alternative HTML version deleted]] __ R-help@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.
[R] how to make a median line thicker in bwplot (lattice)
Hello, I am drawing a boxplot using bwplot in lattice. I would like to learn how to draw a thicker median line instead of the default setting. Thank you. Code bwplot(, pch=rep(|,2)) Elaine [[alternative HTML version deleted]] __ R-help@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.
[R] how to change whisker width in bwplot (lattice)
Hello, I am using lattice to draw boxplots. I would like to make the whisker look shorter than the box width. Please kindly advise how to modify the code. Thank you. Elaine code bwplot(x,y, pch=rep(|,2), box.umbrella = list(col = black, lty = 1)) [[alternative HTML version deleted]] __ R-help@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.
[R] how to draw confidence interval lines of a fitted curve of polynominal regression
Hello, I drew a plot of weight and height of people and fitted it with a polynominal regression x^2. (using curve()) Now I would like to draw the confidence interval line for the fitted curve. Please kindly advise the code for the purpose. Thank you. Elaine [[alternative HTML version deleted]] __ R-help@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.
[R] customize color in xyplot
Hello I want to draw a plot and classify the dot by different color, according to the habitats. I am using xyplot in lattice but do not know how to assign specific colors to the habitats. Please kindly advise how to modify the code. Thank you. Elaine code dataN -read.csv(H:/Mig_bird_586_20130109.csv,header=T, row.names=1) dataN$Habitat -factor(dataN$Habitat) dim(dataN) dataN[1,] habitat.code - c(Water, Land) habitat.colors - c(darkblue,forestgreen) levels(dataN$Habitat) - habitat.code # graph par(mai=c(1.03,1.03,0.4,0.4)) par(new=T) xyplot(GE_distance~Habitat, data=dataN, xlab=list(Habitat, cex = 1.4), ylab=list(Migration Distance (km),cex = 1.4), cex=1.5) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] add categorical labels in plot
Hello I want to draw a plot using the code below. Further, I want to add labels (White, Yellow, Red) to x-axis. Please kindly advise how to add the categorical labels, by modifying the code. Thank you. Elaine Code dataN -read.csv(H:/skin_color.csv,header=T, row.names=1) dim(dataN) dataN[1,] str(dataN) obs.group-dataN$skin_color levels(dataN$skin_color) - skin.code skin.code - c(White, Yellow, Red) # graph par(mai=c(1.03,1.03,0.4,0.4)) par(new=T) plot(dataN$skin_color, dataN$body_length, xlab=Skin Color, ylab=Body Lenght, xaxt=n, type=p, pch=1,lwd=2.0, cex.lab=1.4, cex.axis=1.2, font.axis=2, cex=1.5, las=1, bty=l, col=c(gray38,orange,red2)[obs.group]) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] two-group comparison in boxplot
Hello I have a data composing three columns: body weight, body length, and sex. I want to draw a box plot, X-axis for body weight, Y-axis for body length. In the boxplot, I want to compare the body length between two sexes of three groups of body weight: 50, 51-100, 101 kg. (For instance, from left to right, the first boxplot: sex =1, body weight 50 the second boxplot: sex =2, body weight 50 the third boxplot: sex =1, body weight 51-100 the fourth boxplot: sex =2, body weight51-100 the fifth boxplot: sex =1, body weight 101 the sixth boxplot: sex =2, body weight 101) Please kindly advise how to modify the code below for the above purpose. Thank you. Elaine Code library(HH) # data input 1 (all data) dataN-read.csv(H:/body_status.csv,header=T, row.names=1) dataN$sex -factor(dataN$sex) dim(dataN) dataN[1,] str(dataN) sex.colors - c(darkblue,red2) sex.code - c(Boy, Girl) levels(dataN$sex) - sex.code # graph par(mai=c(1,1.03,0.4,0.4)) par(new=T) bwplot(body_length~body_weight, data=dataN, xlab=list(Body weight, cex = 1.4), ylab=list(Body length,cex = 1.4), xaxt=n, yaxt=n,type=p, lwd=1.5, cex.lab=1.4, cex.axis=1.2, font.axis=2, cex=1.5, las=1, bty=l, panel=panel.bwplot.intermediate.hh, col=Diet.colors, pch=rep(|,3), scales=list(x=list(rot=90)), par.settings=list(box.umbrella=list(lty=1))) data No body_weight body_length Sex 1 87 154 1 2 76 189 2 3 54 176 2 4 87 162 2 5 67 190 2 6 89 143 1 7 73 167 2 8 86 189 2 9 90 196 1 10 94 154 1 11 61 167 2 12 102 180 2 13 106 193 1 14 110 206 2 15 114 219 2 16 118 156 2 17 122 198 2 18 87 187 1 19 67 174 1 20 46 179 2 21 54 164 1 22 98 167 1 23 93 198 1 24 62 201 1 25 60 173 1 26 78 165 1 27 75 169 2 28 66 178 1 29 42 174 1 30 90 178 2 31 105 172 2 32 118 180 1 33 94 187 2 34 85 176 1 35 72 145 2 36 66 165 2 37 56 162 2 38 89 159 2 39 73 167 1 40 52 190 1 41 51 154 1 42 98 176 2 43 74 172 2 44 78 171 2 45 97 173 1 46 45 167 2 47 46 163 2 48 107 164 1 49 93 160 2 [[alternative HTML version deleted]] __ R-help@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.
[R] how to change font size of axis label (not axis title)
Hello, I am using lattice to produce xyplot. I want to change the font size of axis-X label. Please kindly advise how to write the code. Thank you. For changing the font size of axis-X title it would be xlab=list(Diet of Breeding Ground, cex = 1.4) Elaine [[alternative HTML version deleted]] __ R-help@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.
[R] panel failure in xyplot
Hello I ran the code below but it said: no object 'panel.xyplot.intermediate.hh' Please kindly advise how to modify the code. thank you. (It works with panel.bwplot.intermediate.hh) Elaine code library(HH) # data input dataN -read.csv(H:/R_data/Mig_bird_586.csv,header=T, row.names=1) dim(dataN) dataN[1,] str(dataN) diet.code - c(Herbivore, Omnivore, Carnivore) Diet.colors - c(forestgreen, darkblue,red2) levels(dataN$Diet) - diet.code # graph par(mai=c(1.03,1.03,0.4,0.4)) par(new=T) xyplot(GE_distance~Diet, data=dataN, xlab=list(Diet of Breeding Ground, cex = 1.4), ylab=list(Migration Distance,cex = 1.4), xaxt=n, yaxt=n,type=p, lwd=1.5, cex.lab=1.4, cex.axis=1.2, font.axis=2, cex=1.5, las=1, bty=l, panel=panel.xyplot.intermediate.hh, col=Diet.colors, pch=rep(|,3), scales=list(x=list(rot=0)), par.settings=list(box.umbrella=list(lty=1))) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] color in xyplot
Hello I want to draw a xyplot. Its dots will have three colors: red for meat, green for vegetable, and blue for both. I used the code below but could not make the dot in the same group show the same color. Please kindly advise how to modify it. Thank you. code library (lattice) diet.code - c(Herbivore, Omnivore, Carnivore) Diet.colors - c(forestgreen, darkblue,red2) levels(dataN$Diet) - diet.code # graph par(mai=c(1.03,1.03,0.4,0.4)) par(new=T) xyplot(GE_distance~Diet, data=dataN, xlab=list(Diet of Breeding Ground, cex = 1.4), ylab=list(Migration Distance,cex = 1.4), xaxt=n, yaxt=n,type=p, lwd=1.5, cex.lab=1.4, cex.axis=1.2, font.axis=2, cex=1.5, las=1, bty=l, col=rep(Diet.colors)) [[alternative HTML version deleted]] __ R-help@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.
[R] plot xaxp issue
Hello, I have data of Body length and Body weight of 8 boys and 7 girls. I want to draw the plot of Body length (for X) and Body weight (for Y) based on sex. Then the two plots want to be overlapped for comparison. I used the code below but found the unit length of X axis of boy and girl plot are not the same. For instance, the length between 0 and 1 of boy plot is larger than that in girl plot. The same thing happened to Y axis as well. (In other words, though axap and yaxp were set to be the same, the display were not the same.) Please kindly advise correction of the code. Thank you. Elaine # plot code boy-read.csv(H:/boy_data.csv,header=T) girl-read.csv(H:/girl_data.csv,header=T) par(mai=c(1.03,1.03,0.4,0.4)) plot(boy$body_length, boy$body_weight, xlab= body_length (cm), ylab= body_weight ( kg ), xaxp=c(0,200,4), yaxp=c(0,100,4), type=p, pch=1,lwd=1.0, cex.lab=1.4, cex.axis=1.2, font.axis=2, cex=1.5, las=1, bty=l,col=firebrick3) boyline-lm(body_weight ~ body_length, boy) summary(boyline) abline(boyline,col=firebrick3,lwd=2) #~~~ # graph par(mai=c(1.03,1.03,0.4,0.4)) par(new=T) plot(girl$body_length, girl$body_weight, xlab= body_length (cm), ylab= body_weight ( kg ), xaxp=c(0,200,4), yaxp=c(0,100,4), type=p, pch=1,lwd=1.0, cex.lab=1.4, cex.axis=1.2, font.axis=2, cex=1.5, las=1, bty=l,col=saddlebrown) girlline-lm(body_weight~ body_length, girl) summary(girlline) abline(girlline,col=saddlebrown,lwd=2) __ R-help@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.
Re: [R] plot xaxp issue
Thanks a lot. Please kindly indicate the meaning of the c(8,7). together - rbind(boy, girl) together$sex - factor(rep(c(boy, girl), c(8,7))) Elaine On Mon, Jan 7, 2013 at 4:55 PM, PIKAL Petr petr.pi...@precheza.cz wrote: Hi Instead of two plots with par(new = TRUE) try to put boys and girls together (quite natural thing, they will be pleased 8-) together - rbind(boy, girl) together$sex - factor(rep(c(boy, girl), c(8,7))) plot(together$body_length, together$body_weight, , col=c(firebrick3,saddlebrown)[as.numeric(together$sex)], ) Regards Petr -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Elaine Kuo Sent: Monday, January 07, 2013 9:27 AM To: r-help@r-project.org Subject: [R] plot xaxp issue Hello, I have data of Body length and Body weight of 8 boys and 7 girls. I want to draw the plot of Body length (for X) and Body weight (for Y) based on sex. Then the two plots want to be overlapped for comparison. I used the code below but found the unit length of X axis of boy and girl plot are not the same. For instance, the length between 0 and 1 of boy plot is larger than that in girl plot. The same thing happened to Y axis as well. (In other words, though axap and yaxp were set to be the same, the display were not the same.) Please kindly advise correction of the code. Thank you. Elaine # plot code boy-read.csv(H:/boy_data.csv,header=T) girl-read.csv(H:/girl_data.csv,header=T) par(mai=c(1.03,1.03,0.4,0.4)) plot(boy$body_length, boy$body_weight, xlab= body_length (cm), ylab= body_weight ( kg ), xaxp=c(0,200,4), yaxp=c(0,100,4), type=p, pch=1,lwd=1.0, cex.lab=1.4, cex.axis=1.2, font.axis=2, cex=1.5, las=1, bty=l,col=firebrick3) boyline-lm(body_weight ~ body_length, boy) summary(boyline) abline(boyline,col=firebrick3,lwd=2) #~~~ # graph par(mai=c(1.03,1.03,0.4,0.4)) par(new=T) plot(girl$body_length, girl$body_weight, xlab= body_length (cm), ylab= body_weight ( kg ), xaxp=c(0,200,4), yaxp=c(0,100,4), type=p, pch=1,lwd=1.0, cex.lab=1.4, cex.axis=1.2, font.axis=2, cex=1.5, las=1, bty=l,col=saddlebrown) girlline-lm(body_weight~ body_length, girl) summary(girlline) abline(girlline,col=saddlebrown,lwd=2) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot xaxp issue
Thank you Petr, the code is wonderful. One more question, you used [as.numeric(together$sex)] to drawing plots many times (Par(new)). Please kindly advise if there is a similar method to replace drawing ablines many times. If not, I am afraid that the ablines will not follow the same Y and X-axis places. Elaine On Mon, Jan 7, 2013 at 8:11 PM, Elaine Kuo elaine.kuo...@gmail.com wrote: Thanks a lot. Please kindly indicate the meaning of the c(8,7). together - rbind(boy, girl) together$sex - factor(rep(c(boy, girl), c(8,7))) Elaine On Mon, Jan 7, 2013 at 4:55 PM, PIKAL Petr petr.pi...@precheza.cz wrote: Hi Instead of two plots with par(new = TRUE) try to put boys and girls together (quite natural thing, they will be pleased 8-) together - rbind(boy, girl) together$sex - factor(rep(c(boy, girl), c(8,7))) plot(together$body_length, together$body_weight, , col=c(firebrick3,saddlebrown)[as.numeric(together$sex)], ) Regards Petr -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Elaine Kuo Sent: Monday, January 07, 2013 9:27 AM To: r-help@r-project.org Subject: [R] plot xaxp issue Hello, I have data of Body length and Body weight of 8 boys and 7 girls. I want to draw the plot of Body length (for X) and Body weight (for Y) based on sex. Then the two plots want to be overlapped for comparison. I used the code below but found the unit length of X axis of boy and girl plot are not the same. For instance, the length between 0 and 1 of boy plot is larger than that in girl plot. The same thing happened to Y axis as well. (In other words, though axap and yaxp were set to be the same, the display were not the same.) Please kindly advise correction of the code. Thank you. Elaine # plot code boy-read.csv(H:/boy_data.csv,header=T) girl-read.csv(H:/girl_data.csv,header=T) par(mai=c(1.03,1.03,0.4,0.4)) plot(boy$body_length, boy$body_weight, xlab= body_length (cm), ylab= body_weight ( kg ), xaxp=c(0,200,4), yaxp=c(0,100,4), type=p, pch=1,lwd=1.0, cex.lab=1.4, cex.axis=1.2, font.axis=2, cex=1.5, las=1, bty=l,col=firebrick3) boyline-lm(body_weight ~ body_length, boy) summary(boyline) abline(boyline,col=firebrick3,lwd=2) #~~~ # graph par(mai=c(1.03,1.03,0.4,0.4)) par(new=T) plot(girl$body_length, girl$body_weight, xlab= body_length (cm), ylab= body_weight ( kg ), xaxp=c(0,200,4), yaxp=c(0,100,4), type=p, pch=1,lwd=1.0, cex.lab=1.4, cex.axis=1.2, font.axis=2, cex=1.5, las=1, bty=l,col=saddlebrown) girlline-lm(body_weight~ body_length, girl) summary(girlline) abline(girlline,col=saddlebrown,lwd=2) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot xaxp issue
Hello,
Thanks again.
But something wrong with the subset after lm
It is not about drawing plot many times but coding points or graphic objects
by some factor. In your case sex.
Instead of
boyline-lm(body_weight ~ body_length, boy)
use collective data frame together and subset only one sex.
boy-read.csv(H:/boy_data.csv,header=T)
girl-read.csv(H:/girl_data.csv,header=T)
together - rbind(boy, girl)
together$sex - factor(rep(c(boy, girl), c(8,7)))
plot(together$body_length, together$body_weight, ,
col=c(firebrick3,saddlebrown)[as.numeric(together$sex)], )
boyline-lm(body_weight ~ body_length, data=together, subset(sex==boy))
abline(boyline,col=firebrick3,lwd=2)
I updated it aas
boyline-lm(body_weight ~ body_length, data=together,
subset(together,sex==boy))
But an error showed, saying:
error in xj[i] : useless type of 'list'
Please kindly help and thanks again.
BTW, the code below might need update as well.
Elaine
In case of more than two sexes (some SF authors mentioned it is possible) you
can use simple loop.
for (i in 1:2)) {
subs - together$sex==levels(together$sex)[i]
line-lm(body_weight ~ body_length, data=together, subset=subs)
abline(line, col=c(firebrick3,saddlebrown)[i],lwd=2)
}
The original code with advice by Petr
#~~
boy-read.csv(H:/boy_data.csv,header=T)
girl-read.csv(H:/girl_data.csv,header=T)
together - rbind(boy, girl)
together$sex - factor(rep(c(boy, girl), c(8,7)))
plot(together$body_length, together$body_weight, ,
col=c(firebrick3,saddlebrown)[as.numeric(together$sex)], )
boyline-lm(body_weight ~ body_length, data=together, subset(sex==boy))
abline(boyline,col=firebrick3,lwd=2)
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot xaxp issue
Hello, I figured out that the code should be boyline-lm(body_weight ~ body_length, data=subset (together,,sex==boy)) However, the could be omitted if the field name happened to be numeric, such as 1, 2, or 3. Please kindly explain why the could be omitted for numbers. Thanks again. Elaine On Tue, Jan 8, 2013 at 8:40 AM, Elaine Kuo elaine.kuo...@gmail.com wrote: boyline-lm(body_weight ~ body_length, data=together, subset(together,sex==boy)) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] error in a abline loop
Hello
I have data of body length and body weight of people of different skin colors.
I tried to write a code to plot body length and body weight according
to the skin colors.
(Thanks for Petr's advice so far.)
A loop is used but an error shows up in the following code.
It says:
unexpected '}' in
red3,red3,saddlebrown,coral4,chocolate4,darkblue,navy,grey38)[i],lwd=2)
}
Please kindly advise how to modify the code.
Thank you.
The code
data -read.csv(H:/skincolor.csv,header=T)
# graph
par(mai=c(1.03,1.03,0.4,0.4))
plot(data$body_weight, data$body_length,
xaxp=c(0,200,4),
yaxp=c(0,200,4),
type=p,
pch=1,lwd=1.0,
cex.lab=1.4, cex.axis=1.2,
font.axis=2,
cex=1.5,
las=1,
bty=l,col=c(yellow,chocolate1,darkorange2,
red3,saddlebrown,coral4,grey38)[as.numeric(data$skin_color)])
#~~~
##
for (i in 1:7) {
subs - data$skin_color==levels(data$skin_color)[i]
line-lm(body_weight~body_length, data=subset(data, subset=subs),
abline(line,col=c(yellow,chocolate1,darkorange2,
red3,saddlebrown,coral4,grey38)[i],lwd=2)
}
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] error in a abline loop
Hello
Thanks.
It is right a ) is missing for lm.
With the modification, I ran the code but the command seems not
closed, with + instead of .
Please kindly help.
The code modified
for (i in 1:7) {
subs - data$skin_color==levels(data$skin_color)[i]
line-lm(body_weight~body_length, data=subset(data, subset=subs))
abline(line,col=c(yellow,chocolate1,darkorange2,
red3,saddlebrown,coral4,grey38)[i],lwd=2) )
}
Elaine
On Tue, Jan 8, 2013 at 10:03 AM, arun smartpink...@yahoo.com wrote:
HI,
A possible guess ( with no data):
for (i in 1:7) {
subs - data$skin_color==levels(data$skin_color)[i]
line-lm(body_weight~body_length, data=subset(data, subset=subs))
#closing parentheses
abline(line,col=c(yellow,chocolate1,darkorange2,
red3,saddlebrown,coral4,grey38)[i],lwd=2)
}
A.K.
- Original Message -
From: Elaine Kuo elaine.kuo...@gmail.com
To: r-help@r-project.org
Cc:
Sent: Monday, January 7, 2013 8:23 PM
Subject: [R] error in a abline loop
Hello
I have data of body length and body weight of people of different skin colors.
I tried to write a code to plot body length and body weight according
to the skin colors.
(Thanks for Petr's advice so far.)
A loop is used but an error shows up in the following code.
It says:
unexpected '}' in
red3,red3,saddlebrown,coral4,chocolate4,darkblue,navy,grey38)[i],lwd=2)
}
Please kindly advise how to modify the code.
Thank you.
The code
data -read.csv(H:/skincolor.csv,header=T)
# graph
par(mai=c(1.03,1.03,0.4,0.4))
plot(data$body_weight, data$body_length,
xaxp=c(0,200,4),
yaxp=c(0,200,4),
type=p,
pch=1,lwd=1.0,
cex.lab=1.4, cex.axis=1.2,
font.axis=2,
cex=1.5,
las=1,
bty=l,col=c(yellow,chocolate1,darkorange2,
red3,saddlebrown,coral4,grey38)[as.numeric(data$skin_color)])
#~~~
##
for (i in 1:7) {
subs - data$skin_color==levels(data$skin_color)[i]
line-lm(body_weight~body_length, data=subset(data, subset=subs),
abline(line,col=c(yellow,chocolate1,darkorange2,
red3,saddlebrown,coral4,grey38)[i],lwd=2)
}
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] averaging X of specific Y (latitude)
Hello,
Thank you again, David.
I tried with the first step of the command deput as followed
datam -read.csv ('H:/Butterfly_RS_20121217.csv',header=T, row.names=1)
dput(datam, Migrant_RS_L_txt)
However, there is a error message that
the object Migrant_RS_L_txt is not found.
I read the example but still unsure which file (or object) should be input
behind datam.
Please kindly help and thank you again
Elaine
On Mon, Dec 17, 2012 at 9:28 AM, David L Carlson dcarl...@tamu.edu wrote:
It is not necessary to rearrange the order. The aggregate function will do
that. To get the mean Range for a latitude combining species within a
latitude just remove Species:
aggregate(Range~floor(Latitude), dta, mean)
floor(Latitude) Range
1 9 616.440
2 10 714.360
3 12 851.550
4 16 690.770
5 18 766.155
---
David
From: Elaine Kuo [mailto:elaine.kuo...@gmail.com]
Sent: Sunday, December 16, 2012 5:17 PM
To: dcarl...@tamu.edu; r-help@r-project.org; r-sig-...@stat.math.ethz.ch
Subject: Re: [R] averaging X of specific Y (latitude)
Thank you, David.
Your answer reminded me of rearranging the order according to the latitude
before running the calculation.
One more question,
please kindly help with the code to calculate the mean of the ranges of the
same latitude?
Or should any re-arrangement be noticed before the mean calculation?
Thank you.
Elaine
- Original Message -
From: David L Carlson dcarl...@tamu.edu
To: 'Elaine Kuo' elaine.kuo...@gmail.com; r-help@r-project.org;
'r-sig-geo' r-sig-...@stat.math.ethz.ch
Cc:
Sent: Sunday, December 16, 2012 11:32 AM
Subject: Re: [R] averaging X of specific Y (latitude)
It is better to use dput() in R to create a text version of your data for
us
to work with. The aggregate command below gives you the mean ranges by
butterfly species and latititude and saves the result as Bfly. The
colnames() command simply renames the columns:
dta - structure(list(Species = structure(1:11, .Label = c(Butterfly
A1,
+ Butterfly A2, Butterfly A3, Butterfly A4, Butterfly B1,
+ Butterfly B2, Butterfly B3, Butterfly B4, Butterfly B5,
+ Butterfly C1, Butterfly C2), class = factor), Range = c(130.5,
+ 450.68, 1102.38, 893.34, 820.2, 872.2, 488.2, 620.11, 982.78,
+ 720.32, 912.2), Latitude = c(9.45, 10.2, 9.3, 16.4, 10.54, 10.87,
+ 16.79, 18.3, 12.98, 12.67, 18.07)), .Names = c(Species, Range,
+ Latitude), class = data.frame, row.names = c(NA, -11L))
Bfly - aggregate(Range~Species+floor(Latitude), dta, mean)
colnames(Bfly) - c(Species, Latitude, Mean)
Bfly
Species LatitudeMean
1 Butterfly A19 130.50
2 Butterfly A39 1102.38
3 Butterfly A2 10 450.68
4 Butterfly B1 10 820.20
5 Butterfly B2 10 872.20
6 Butterfly B5 12 982.78
7 Butterfly C1 12 720.32
8 Butterfly A4 16 893.34
9 Butterfly B3 16 488.20
10 Butterfly B4 18 620.11
11 Butterfly C2 18 912.20
--
David L Carlson
Associate Professor of Anthropology
Texas AM University
College Station, TX 77843-4352
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of Elaine Kuo
Sent: Saturday, December 15, 2012 10:15 PM
To: r-help@r-project.org; r-sig-geo
Subject: [R] averaging X of specific Y (latitude)
Hello
I have a table describing butterfly range traits.
It is composed of three columns as below
Species name range size (X)latitude of range midpoint (Y)
There are 11 kinds of butterflies.
Each has its range size, and the latitude of each range midpoint ranges
from 9 to 19.
I would like to have the average range size of every degree of
latitude.
For example, the average range size of latitude degree 10 (10.0-10.99:
Butterfly A2, B1, B2)
Please kindly help with R code to calculate the average values.
Thank you.
Elaine
The details are as followed.
Butterfly A1 130.5 9.45
Butterfly A2 450.68 10.2
Butterfly A3 1102.389.3
Butterfly A4893.34 16.4
Butterfly B1 820.2 10.54
Butterfly B2872.2 10.87
Butterfly B3488.2 16.79
Butterfly B4620.11 18.3
Butterfly B5982.78 12.98
Butterfly C1 720.32 12.67
Butterfly C2912.2 18.07
[[alternative HTML version deleted]]
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Re: [R] averaging X of specific Y (latitude)
Thank you, Berend.
I tried
1. dput (datam, datam)
2. dput (datam)
both worked
Elaine
On Mon, Dec 17, 2012 at 7:30 PM, Berend Hasselman b...@xs4all.nl wrote:
On 17-12-2012, at 12:06, Elaine Kuo wrote:
Hello,
Thank you again, David.
I tried with the first step of the command deput as followed
It's dput not deput.
datam -read.csv ('H:/Butterfly_RS_20121217.csv',header=T, row.names=1)
dput(datam, Migrant_RS_L_txt)
However, there is a error message that
the object Migrant_RS_L_txt is not found.
I read the example but still unsure which file (or object) should be
input
behind datam.
Please kindly help and thank you again
Variable (object) if used like that should contain the name of a file to
which you want the output of dput to be written to.
You can also use
dput(datam)
which implies file= (default) and output going to the console.
Berend
Elaine
On Mon, Dec 17, 2012 at 9:28 AM, David L Carlson dcarl...@tamu.edu
wrote:
It is not necessary to rearrange the order. The aggregate function will
do
that. To get the mean Range for a latitude combining species within a
latitude just remove Species:
aggregate(Range~floor(Latitude), dta, mean)
floor(Latitude) Range
1 9 616.440
2 10 714.360
3 12 851.550
4 16 690.770
5 18 766.155
---
David
From: Elaine Kuo [mailto:elaine.kuo...@gmail.com]
Sent: Sunday, December 16, 2012 5:17 PM
To: dcarl...@tamu.edu; r-help@r-project.org;
r-sig-...@stat.math.ethz.ch
Subject: Re: [R] averaging X of specific Y (latitude)
Thank you, David.
Your answer reminded me of rearranging the order according to the
latitude
before running the calculation.
One more question,
please kindly help with the code to calculate the mean of the ranges of
the
same latitude?
Or should any re-arrangement be noticed before the mean calculation?
Thank you.
Elaine
- Original Message -
From: David L Carlson dcarl...@tamu.edu
To: 'Elaine Kuo' elaine.kuo...@gmail.com; r-help@r-project.org;
'r-sig-geo' r-sig-...@stat.math.ethz.ch
Cc:
Sent: Sunday, December 16, 2012 11:32 AM
Subject: Re: [R] averaging X of specific Y (latitude)
It is better to use dput() in R to create a text version of your data
for
us
to work with. The aggregate command below gives you the mean ranges by
butterfly species and latititude and saves the result as Bfly. The
colnames() command simply renames the columns:
dta - structure(list(Species = structure(1:11, .Label = c(Butterfly
A1,
+ Butterfly A2, Butterfly A3, Butterfly A4, Butterfly B1,
+ Butterfly B2, Butterfly B3, Butterfly B4, Butterfly B5,
+ Butterfly C1, Butterfly C2), class = factor), Range = c(130.5,
+ 450.68, 1102.38, 893.34, 820.2, 872.2, 488.2, 620.11, 982.78,
+ 720.32, 912.2), Latitude = c(9.45, 10.2, 9.3, 16.4, 10.54, 10.87,
+ 16.79, 18.3, 12.98, 12.67, 18.07)), .Names = c(Species, Range,
+ Latitude), class = data.frame, row.names = c(NA, -11L))
Bfly - aggregate(Range~Species+floor(Latitude), dta, mean)
colnames(Bfly) - c(Species, Latitude, Mean)
Bfly
Species LatitudeMean
1 Butterfly A19 130.50
2 Butterfly A39 1102.38
3 Butterfly A2 10 450.68
4 Butterfly B1 10 820.20
5 Butterfly B2 10 872.20
6 Butterfly B5 12 982.78
7 Butterfly C1 12 720.32
8 Butterfly A4 16 893.34
9 Butterfly B3 16 488.20
10 Butterfly B4 18 620.11
11 Butterfly C2 18 912.20
--
David L Carlson
Associate Professor of Anthropology
Texas AM University
College Station, TX 77843-4352
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of Elaine Kuo
Sent: Saturday, December 15, 2012 10:15 PM
To: r-help@r-project.org; r-sig-geo
Subject: [R] averaging X of specific Y (latitude)
Hello
I have a table describing butterfly range traits.
It is composed of three columns as below
Species name range size (X)latitude of range midpoint (Y)
There are 11 kinds of butterflies.
Each has its range size, and the latitude of each range midpoint ranges
from 9 to 19.
I would like to have the average range size of every degree of
latitude.
For example, the average range size of latitude degree 10 (10.0-10.99:
Butterfly A2, B1, B2)
Please kindly help with R code to calculate the average values.
Thank you.
Elaine
The details are as followed.
Butterfly A1 130.5 9.45
Butterfly A2 450.68 10.2
Butterfly A3 1102.389.3
Butterfly A4893.34 16.4
Butterfly B1 820.2 10.54
Re: [R] averaging X of specific Y (latitude)
One more question: Please kindly explain why it is written as row.names = c(NA, -11L)). (in the code below) I am unsure why it is negative 11. Thank you . Elaine code dta - structure(list(Species = structure(1:11, .Label = c(Butterfly A1, + Butterfly A2, Butterfly A3, Butterfly A4, Butterfly B1, + Butterfly B2, Butterfly B3, Butterfly B4, Butterfly B5, + Butterfly C1, Butterfly C2), class = factor), Range = c(130.5, + 450.68, 1102.38, 893.34, 820.2, 872.2, 488.2, 620.11, 982.78, + 720.32, 912.2), Latitude = c(9.45, 10.2, 9.3, 16.4, 10.54, 10.87, + 16.79, 18.3, 12.98, 12.67, 18.07)), .Names = c(Species, Range, + Latitude), class = data.frame, row.names = c(NA, -11L))) - Original Message - From: David L Carlson dcarl...@tamu.edu To: 'Elaine Kuo' elaine.kuo...@gmail.com; r-help@r-project.org; 'r-sig-geo' r-sig-...@stat.math.ethz.ch Cc: Sent: Sunday, December 16, 2012 11:32 AM Subject: Re: [R] averaging X of specific Y (latitude) It is better to use dput() in R to create a text version of your data for us to work with. The aggregate command below gives you the mean ranges by butterfly species and latititude and saves the result as Bfly. The colnames() command simply renames the columns: dta - structure(list(Species = structure(1:11, .Label = c(Butterfly A1, + Butterfly A2, Butterfly A3, Butterfly A4, Butterfly B1, + Butterfly B2, Butterfly B3, Butterfly B4, Butterfly B5, + Butterfly C1, Butterfly C2), class = factor), Range = c(130.5, + 450.68, 1102.38, 893.34, 820.2, 872.2, 488.2, 620.11, 982.78, + 720.32, 912.2), Latitude = c(9.45, 10.2, 9.3, 16.4, 10.54, 10.87, + 16.79, 18.3, 12.98, 12.67, 18.07)), .Names = c(Species, Range, + Latitude), class = data.frame, row.names = c(NA, -11L)) Bfly - aggregate(Range~Species+floor(Latitude), dta, mean) colnames(Bfly) - c(Species, Latitude, Mean) Bfly Species LatitudeMean 1 Butterfly A19 130.50 2 Butterfly A39 1102.38 3 Butterfly A2 10 450.68 4 Butterfly B1 10 820.20 5 Butterfly B2 10 872.20 6 Butterfly B5 12 982.78 7 Butterfly C1 12 720.32 8 Butterfly A4 16 893.34 9 Butterfly B3 16 488.20 10 Butterfly B4 18 620.11 11 Butterfly C2 18 912.20 -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Elaine Kuo Sent: Saturday, December 15, 2012 10:15 PM To: r-help@r-project.org; r-sig-geo Subject: [R] averaging X of specific Y (latitude) Hello I have a table describing butterfly range traits. It is composed of three columns as below Species name range size (X)latitude of range midpoint (Y) There are 11 kinds of butterflies. Each has its range size, and the latitude of each range midpoint ranges from 9 to 19. I would like to have the average range size of every degree of latitude. For example, the average range size of latitude degree 10 (10.0-10.99: Butterfly A2, B1, B2) Please kindly help with R code to calculate the average values. Thank you. Elaine The details are as followed. Butterfly A1 130.5 9.45 Butterfly A2 450.68 10.2 Butterfly A3 1102.389.3 Butterfly A4893.34 16.4 Butterfly B1 820.2 10.54 Butterfly B2872.2 10.87 Butterfly B3488.2 16.79 Butterfly B4620.11 18.3 Butterfly B5982.78 12.98 Butterfly C1 720.32 12.67 Butterfly C2912.2 18.07 [[alternative HTML version deleted]] __ R-help@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. __ R-help@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. [[alternative HTML version deleted]] __ R-help@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
Re: [R] averaging X of specific Y (latitude)
Another question (I am sure it is the last one tentatively): After creating a text.file using dput (let's name the created file datam), please kindly advise how to use the text file in writing the code using structure like below. Thank you. code dta - structure(list(Species = structure(1:11, .Label = c(Butterfly A1, + Butterfly A2, Butterfly A3, Butterfly A4, Butterfly B1, + Butterfly B2, Butterfly B3, Butterfly B4, Butterfly B5, + Butterfly C1, Butterfly C2), class = factor), Range = c(130.5, + 450.68, 1102.38, 893.34, 820.2, 872.2, 488.2, 620.11, 982.78, + 720.32, 912.2), Latitude = c(9.45, 10.2, 9.3, 16.4, 10.54, 10.87, + 16.79, 18.3, 12.98, 12.67, 18.07)), .Names = c(Species, Range, + Latitude), class = data.frame, row.names = c(NA, -11L))) Elaine On Mon, Dec 17, 2012 at 7:40 PM, Elaine Kuo elaine.kuo...@gmail.com wrote: One more question: Please kindly explain why it is written as row.names = c(NA, -11L)). (in the code below) I am unsure why it is negative 11. Thank you . Elaine code dta - structure(list(Species = structure(1:11, .Label = c(Butterfly A1, + Butterfly A2, Butterfly A3, Butterfly A4, Butterfly B1, + Butterfly B2, Butterfly B3, Butterfly B4, Butterfly B5, + Butterfly C1, Butterfly C2), class = factor), Range = c(130.5, + 450.68, 1102.38, 893.34, 820.2, 872.2, 488.2, 620.11, 982.78, + 720.32, 912.2), Latitude = c(9.45, 10.2, 9.3, 16.4, 10.54, 10.87, + 16.79, 18.3, 12.98, 12.67, 18.07)), .Names = c(Species, Range, + Latitude), class = data.frame, row.names = c(NA, -11L))) - Original Message - From: David L Carlson dcarl...@tamu.edu To: 'Elaine Kuo' elaine.kuo...@gmail.com; r-help@r-project.org; 'r-sig-geo' r-sig-...@stat.math.ethz.ch Cc: Sent: Sunday, December 16, 2012 11:32 AM Subject: Re: [R] averaging X of specific Y (latitude) It is better to use dput() in R to create a text version of your data for us to work with. The aggregate command below gives you the mean ranges by butterfly species and latititude and saves the result as Bfly. The colnames() command simply renames the columns: dta - structure(list(Species = structure(1:11, .Label = c(Butterfly A1, + Butterfly A2, Butterfly A3, Butterfly A4, Butterfly B1, + Butterfly B2, Butterfly B3, Butterfly B4, Butterfly B5, + Butterfly C1, Butterfly C2), class = factor), Range = c(130.5, + 450.68, 1102.38, 893.34, 820.2, 872.2, 488.2, 620.11, 982.78, + 720.32, 912.2), Latitude = c(9.45, 10.2, 9.3, 16.4, 10.54, 10.87, + 16.79, 18.3, 12.98, 12.67, 18.07)), .Names = c(Species, Range, + Latitude), class = data.frame, row.names = c(NA, -11L)) Bfly - aggregate(Range~Species+floor(Latitude), dta, mean) colnames(Bfly) - c(Species, Latitude, Mean) Bfly Species LatitudeMean 1 Butterfly A19 130.50 2 Butterfly A39 1102.38 3 Butterfly A2 10 450.68 4 Butterfly B1 10 820.20 5 Butterfly B2 10 872.20 6 Butterfly B5 12 982.78 7 Butterfly C1 12 720.32 8 Butterfly A4 16 893.34 9 Butterfly B3 16 488.20 10 Butterfly B4 18 620.11 11 Butterfly C2 18 912.20 -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Elaine Kuo Sent: Saturday, December 15, 2012 10:15 PM To: r-help@r-project.org; r-sig-geo Subject: [R] averaging X of specific Y (latitude) Hello I have a table describing butterfly range traits. It is composed of three columns as below Species name range size (X)latitude of range midpoint (Y) There are 11 kinds of butterflies. Each has its range size, and the latitude of each range midpoint ranges from 9 to 19. I would like to have the average range size of every degree of latitude. For example, the average range size of latitude degree 10 (10.0-10.99: Butterfly A2, B1, B2) Please kindly help with R code to calculate the average values. Thank you. Elaine The details are as followed. Butterfly A1 130.5 9.45 Butterfly A2 450.68 10.2 Butterfly A3 1102.389.3 Butterfly A4893.34 16.4 Butterfly B1 820.2 10.54 Butterfly B2872.2 10.87 Butterfly B3488.2 16.79 Butterfly B4620.11 18.3 Butterfly B5982.78 12.98 Butterfly C1 720.32 12.67 Butterfly C2912.2 18.07 [[alternative HTML version deleted
Re: [R] averaging X of specific Y (latitude)
Thank you, David. Now I know how to use dput. Two more questions conjured up when running the code: 1. If there are about 500 species of butterflies, please kindly advise if it is possible to input the butterfly names (for .Label) using code, instead of keying in them one by one. 2. Aggregrate command Last time we produced the mean of range sizes. Please kindly advise if it is possible to produce barplot showing the value range, instead of mean. Thank you Elaine code dta - structure(list(Species = structure(1:11, .Label = c(Butterfly A1, + Butterfly A2, Butterfly A3, Butterfly A4, Butterfly B1, + Butterfly B2, Butterfly B3, Butterfly B4, Butterfly B5, + Butterfly C1, Butterfly C2), class = factor), Range = c(130.5, + 450.68, 1102.38, 893.34, 820.2, 872.2, 488.2, 620.11, 982.78, + 720.32, 912.2), Latitude = c(9.45, 10.2, 9.3, 16.4, 10.54, 10.87, + 16.79, 18.3, 12.98, 12.67, 18.07)), .Names = c(Species, Range, + Latitude), class = data.frame, row.names = c(NA, -11L)) Bfly - aggregate(Range~Species+floor(Latitude), dta, mean) colnames(Bfly) - c(Species, Latitude, Mean) Bfly Species LatitudeMean 1 Butterfly A19 130.50 2 Butterfly A39 1102.38 3 Butterfly A2 10 450.68 4 Butterfly B1 10 820.20 5 Butterfly B2 10 872.20 6 Butterfly B5 12 982.78 7 Butterfly C1 12 720.32 8 Butterfly A4 16 893.34 9 Butterfly B3 16 488.20 10 Butterfly B4 18 620.11 11 Butterfly C2 18 912.20 On Tue, Dec 18, 2012 at 12:27 AM, David L Carlson dcarl...@tamu.edu wrote: You are only using dput to create a version of your data that you can post in your email along with your question. You do not use it in your analysis. You originally posted a table of your data that requires extra steps for us to convert into a useable form so I suggested you use dput in the future to create a version of the data that is easy for r-help subscribers to use in order to recreate your data. That makes it easier to answer your question. ** ** -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 ** ** *From:* Elaine Kuo [mailto:elaine.kuo...@gmail.com] *Sent:* Monday, December 17, 2012 5:56 AM *To:* dcarl...@tamu.edu; r-help@r-project.org *Subject:* Re: [R] averaging X of specific Y (latitude) ** ** Another question (I am sure it is the last one tentatively): ** ** After creating a text.file using dput (let's name the created file datam), please kindly advise how to use the text file in writing the code using structure like below. ** ** Thank you. ** ** code dta - structure(list(Species = structure(1:11, .Label = c(Butterfly A1, + Butterfly A2, Butterfly A3, Butterfly A4, Butterfly B1, + Butterfly B2, Butterfly B3, Butterfly B4, Butterfly B5, + Butterfly C1, Butterfly C2), class = factor), Range = c(130.5, + 450.68, 1102.38, 893.34, 820.2, 872.2, 488.2, 620.11, 982.78, + 720.32, 912.2), Latitude = c(9.45, 10.2, 9.3, 16.4, 10.54, 10.87, + 16.79, 18.3, 12.98, 12.67, 18.07)), .Names = c(Species, Range, + Latitude), class = data.frame, row.names = c(NA, -11L))) ** ** Elaine ** ** ** ** On Mon, Dec 17, 2012 at 7:40 PM, Elaine Kuo elaine.kuo...@gmail.com wrote: One more question: ** ** Please kindly explain why it is written as row.names = c(NA, -11L)). (in the code below) ** ** I am unsure why it is negative 11. Thank you . ** ** Elaine ** ** code ** ** dta - structure(list(Species = structure(1:11, .Label = c(Butterfly A1, + Butterfly A2, Butterfly A3, Butterfly A4, Butterfly B1, + Butterfly B2, Butterfly B3, Butterfly B4, Butterfly B5, + Butterfly C1, Butterfly C2), class = factor), Range = c(130.5, + 450.68, 1102.38, 893.34, 820.2, 872.2, 488.2, 620.11, 982.78, + 720.32, 912.2), Latitude = c(9.45, 10.2, 9.3, 16.4, 10.54, 10.87, + 16.79, 18.3, 12.98, 12.67, 18.07)), .Names = c(Species, Range, + Latitude), class = data.frame, row.names = c(NA, -11L))) ** ** - Original Message - From: David L Carlson dcarl...@tamu.edu To: 'Elaine Kuo' elaine.kuo...@gmail.com; r-help@r-project.org; 'r-sig-geo' r-sig-...@stat.math.ethz.ch Cc: Sent: Sunday, December 16, 2012 11:32 AM Subject: Re: [R] averaging X of specific Y (latitude) It is better to use dput() in R to create a text version of your data for us to work with. The aggregate command below gives you the mean ranges by butterfly species and latititude and saves the result as Bfly. The colnames() command simply renames the columns: dta - structure(list(Species = structure(1:11, .Label = c(Butterfly A1, + Butterfly A2, Butterfly A3, Butterfly A4, Butterfly B1, + Butterfly B2, Butterfly B3, Butterfly B4, Butterfly B5
Re: [R] averaging X of specific Y (latitude)
Hello David, Thank you for the response. I changed the e-mail format to text via gmail setting. 1. the butterfly names You are right that the butterfly names are stored in the original data. However, in your code, it is necessary to input the names for the command structure. The method I used to input is 1. display them in the original excel file, as one column with 11 rows. 2. add commas in a column, right to the name column. 3. copy the columns of butterfly names and commas, then pasting them in the wordpad. 4. copy the wordpad text with butterfly names and commas into your code Since the method sounds tedious, particularly when the number of butterfly names increases over 11, I would like to ask for less time-consuming method to elicit butterfly names as factor. (Maybe using some R command I do not know) 2. Latitude degree Thank you for helping generate the mean of range size per latitudinal degree, using the code:\ Bfly - aggregate(Range~floor(Latitude), dta, mean) Please kindly advise if it is possible to calculate the mean of range size per 5 latitudinal degrees, such as 6-10, 11-15, or 16-20 latitudinal degrees. Thank you again. Elaine dta - structure(list(Species = structure(1:11, .Label = c(Butterfly A1, + Butterfly A2, Butterfly A3, Butterfly A4, Butterfly B1, + Butterfly B2, Butterfly B3, Butterfly B4, Butterfly B5, + Butterfly C1, Butterfly C2), class = factor), Range = c(130.5, + 450.68, 1102.38, 893.34, 820.2, 872.2, 488.2, 620.11, 982.78, + 720.32, 912.2), Latitude = c(9.45, 10.2, 9.3, 16.4, 10.54, 10.87, + 16.79, 18.3, 12.98, 12.67, 18.07)), .Names = c(Species, Range, + Latitude), class = data.frame, row.names = c(NA, -11L)) Bfly - aggregate(Range~Species+floor(Latitude), dta, mean) colnames(Bfly) - c(Species, Latitude, Mean) Bfly Species LatitudeMean 1 Butterfly A19 130.50 2 Butterfly A39 1102.38 3 Butterfly A2 10 450.68 4 Butterfly B1 10 820.20 5 Butterfly B2 10 872.20 6 Butterfly B5 12 982.78 7 Butterfly C1 12 720.32 8 Butterfly A4 16 893.34 9 Butterfly B3 16 488.20 10 Butterfly B4 18 620.11 11 Butterfly C2 18 912.20 -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 On Tue, Dec 18, 2012 at 11:07 AM, David L Carlson dcarl...@tamu.edu wrote: You should change your email format to text (you keep sending messages in html format). Where are the butterfly names? Are they not in your original data? Create your data.frame from the original data (which presumably has the butterfly names in it already). Then use dput() if you need to email the data to r-help. You cannot compute statistics or graphics from the result of the dput() function. Yes you can produce a barplot. Type ?barplot to get the instructions. -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 From: Elaine Kuo [mailto:elaine.kuo...@gmail.com] Sent: Monday, December 17, 2012 6:37 PM To: dcarl...@tamu.edu Cc: r-help@r-project.org Subject: Re: [R] averaging X of specific Y (latitude) Thank you, David. Now I know how to use dput. Two more questions conjured up when running the code: 1. If there are about 500 species of butterflies, please kindly advise if it is possible to input the butterfly names (for .Label) using code, instead of keying in them one by one. 2. Aggregrate command Last time we produced the mean of range sizes. Please kindly advise if it is possible to produce barplot showing the value range, instead of mean. Thank you Elaine code dta - structure(list(Species = structure(1:11, .Label = c(Butterfly A1, + Butterfly A2, Butterfly A3, Butterfly A4, Butterfly B1, + Butterfly B2, Butterfly B3, Butterfly B4, Butterfly B5, + Butterfly C1, Butterfly C2), class = factor), Range = c(130.5, + 450.68, 1102.38, 893.34, 820.2, 872.2, 488.2, 620.11, 982.78, + 720.32, 912.2), Latitude = c(9.45, 10.2, 9.3, 16.4, 10.54, 10.87, + 16.79, 18.3, 12.98, 12.67, 18.07)), .Names = c(Species, Range, + Latitude), class = data.frame, row.names = c(NA, -11L)) Bfly - aggregate(Range~Species+floor(Latitude), dta, mean) colnames(Bfly) - c(Species, Latitude, Mean) Bfly Species LatitudeMean 1 Butterfly A19 130.50 2 Butterfly A39 1102.38 3 Butterfly A2 10 450.68 4 Butterfly B1 10 820.20 5 Butterfly B2 10 872.20 6 Butterfly B5 12 982.78 7 Butterfly C1 12 720.32 8 Butterfly A4 16 893.34 9 Butterfly B3 16 488.20 10 Butterfly B4 18 620.11 11 Butterfly C2 18 912.20 On Tue, Dec 18, 2012 at 12:27 AM, David L Carlson dcarl...@tamu.edu wrote: You are only using dput to create a version of your data that you can post in your email along
Re: [R] averaging X of specific Y (latitude)
Thank you, David. Your answer reminded me of rearranging the order according to the latitude before running the calculation. One more question, please kindly help with the code to calculate the mean of the ranges of the same latitude? Or should any re-arrangement be noticed before the mean calculation? Thank you. Elaine - Original Message - From: David L Carlson dcarl...@tamu.edu To: 'Elaine Kuo' elaine.kuo...@gmail.com; r-help@r-project.org; 'r-sig-geo' r-sig-...@stat.math.ethz.ch Cc: Sent: Sunday, December 16, 2012 11:32 AM Subject: Re: [R] averaging X of specific Y (latitude) It is better to use dput() in R to create a text version of your data for us to work with. The aggregate command below gives you the mean ranges by butterfly species and latititude and saves the result as Bfly. The colnames() command simply renames the columns: dta - structure(list(Species = structure(1:11, .Label = c(Butterfly A1, + Butterfly A2, Butterfly A3, Butterfly A4, Butterfly B1, + Butterfly B2, Butterfly B3, Butterfly B4, Butterfly B5, + Butterfly C1, Butterfly C2), class = factor), Range = c(130.5, + 450.68, 1102.38, 893.34, 820.2, 872.2, 488.2, 620.11, 982.78, + 720.32, 912.2), Latitude = c(9.45, 10.2, 9.3, 16.4, 10.54, 10.87, + 16.79, 18.3, 12.98, 12.67, 18.07)), .Names = c(Species, Range, + Latitude), class = data.frame, row.names = c(NA, -11L)) Bfly - aggregate(Range~Species+floor(Latitude), dta, mean) colnames(Bfly) - c(Species, Latitude, Mean) Bfly Species LatitudeMean 1 Butterfly A19 130.50 2 Butterfly A39 1102.38 3 Butterfly A2 10 450.68 4 Butterfly B1 10 820.20 5 Butterfly B2 10 872.20 6 Butterfly B5 12 982.78 7 Butterfly C1 12 720.32 8 Butterfly A4 16 893.34 9 Butterfly B3 16 488.20 10 Butterfly B4 18 620.11 11 Butterfly C2 18 912.20 -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Elaine Kuo Sent: Saturday, December 15, 2012 10:15 PM To: r-help@r-project.org; r-sig-geo Subject: [R] averaging X of specific Y (latitude) Hello I have a table describing butterfly range traits. It is composed of three columns as below Species name range size (X)latitude of range midpoint (Y) There are 11 kinds of butterflies. Each has its range size, and the latitude of each range midpoint ranges from 9 to 19. I would like to have the average range size of every degree of latitude. For example, the average range size of latitude degree 10 (10.0-10.99: Butterfly A2, B1, B2) Please kindly help with R code to calculate the average values. Thank you. Elaine The details are as followed. Butterfly A1 130.5 9.45 Butterfly A2 450.68 10.2 Butterfly A3 1102.389.3 Butterfly A4893.34 16.4 Butterfly B1 820.2 10.54 Butterfly B2872.2 10.87 Butterfly B3488.2 16.79 Butterfly B4620.11 18.3 Butterfly B5982.78 12.98 Butterfly C1 720.32 12.67 Butterfly C2912.2 18.07 [[alternative HTML version deleted]] __ R-help@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. __ R-help@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. [[alternative HTML version deleted]] __ R-help@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.
[R] average X value of specific Y
Hello I have a table describing butterfly range traits. It is composed of three columns as below Species name range size (X)latitude of range midpoint (Y) There are 11 kinds of butterflies. Each has its range size, and the latitude of each range midpoint ranges from 9 to 19. I would like to have the average range size of every degree of latitude. For example, the average range size of latitude degree 10 (10.0-10.99: Butterfly A2, B1, B2) Please kindly help with python code to calculate the average values. Thank you. Elaine The details are as followed. Butterfly A1 130.5 9.45 Butterfly A2 450.68 10.2 Butterfly A3 1102.389.3 Butterfly A4893.34 16.4 Butterfly B1 820.2 10.54 Butterfly B2872.2 10.87 Butterfly B3488.2 16.79 Butterfly B4620.11 18.3 Butterfly B5982.78 12.98 Butterfly C1 720.32 12.67 Butterfly C2912.2 18.07 [[alternative HTML version deleted]] __ R-help@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.
[R] averaging X of specific Y (latitude)
Hello I have a table describing butterfly range traits. It is composed of three columns as below Species name range size (X)latitude of range midpoint (Y) There are 11 kinds of butterflies. Each has its range size, and the latitude of each range midpoint ranges from 9 to 19. I would like to have the average range size of every degree of latitude. For example, the average range size of latitude degree 10 (10.0-10.99: Butterfly A2, B1, B2) Please kindly help with R code to calculate the average values. Thank you. Elaine The details are as followed. Butterfly A1 130.5 9.45 Butterfly A2 450.68 10.2 Butterfly A3 1102.389.3 Butterfly A4893.34 16.4 Butterfly B1 820.2 10.54 Butterfly B2872.2 10.87 Butterfly B3488.2 16.79 Butterfly B4620.11 18.3 Butterfly B5982.78 12.98 Butterfly C1 720.32 12.67 Butterfly C2912.2 18.07 [[alternative HTML version deleted]] __ R-help@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.
Re: [R] [R-sig-Geo] averaging X of specific Y (latitude)
Hello, Yes, it is a data frame. This is the first time to hear table function or cut function. Please kindly point out how to use them. By the way, if the dataset (data frame) includes more than 2000 kinds of butterfly range sizes and the latitude of range midpoints, please kindly help with any suggestion to perform the task. Thank you Elaine On Sun, Dec 16, 2012 at 12:20 PM, Hodgess, Erin hodge...@uhd.edu wrote: Hi! Is it a data frame, please? Have you tried the table function or cut function? Sincerely, Erin From: r-sig-geo-boun...@r-project.org [r-sig-geo-boun...@r-project.org] on behalf of Elaine Kuo [elaine.kuo...@gmail.com] Sent: Saturday, December 15, 2012 10:15 PM To: r-help@r-project.org; r-sig-geo Subject: [R-sig-Geo] averaging X of specific Y (latitude) Hello I have a table describing butterfly range traits. It is composed of three columns as below Species name range size (X)latitude of range midpoint (Y) There are 11 kinds of butterflies. Each has its range size, and the latitude of each range midpoint ranges from 9 to 19. I would like to have the average range size of every degree of latitude. For example, the average range size of latitude degree 10 (10.0-10.99: Butterfly A2, B1, B2) Please kindly help with R code to calculate the average values. Thank you. Elaine The details are as followed. Butterfly A1 130.5 9.45 Butterfly A2 450.68 10.2 Butterfly A3 1102.389.3 Butterfly A4893.34 16.4 Butterfly B1 820.2 10.54 Butterfly B2872.2 10.87 Butterfly B3488.2 16.79 Butterfly B4620.11 18.3 Butterfly B5982.78 12.98 Butterfly C1 720.32 12.67 Butterfly C2912.2 18.07 [[alternative HTML version deleted]] ___ R-sig-Geo mailing list r-sig-...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo [[alternative HTML version deleted]] __ R-help@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.
Re: [R] change lm log(x) to glm poisson
Hello, Thanks for the book list. Some are added. - Faraway. 2006. Extending the Linear Model With R: Generalized Linear, Mixed Effects and Nonparametric Regression Models (Texts in Statistical Science). - Venables and Ripley. 2002. Modern Applied Statistics with S (4th ed.). (Chapter 7) - Crawley. 2005. Statistics: An Introduction using R. (Chapter 13) On Mon, Oct 29, 2012 at 11:35 AM, Mark Leeds marklee...@gmail.com wrote: Hi Josh and Elaine: John Fox's CAR book ( the companion to his applied regression text ) is really great for implementing GLMs in R. It also has a brief but quality discussion of the theory behind them. His text goes into more detail. Dobson's Introduction to generalized linear models is also decent. So is Faraway's text but I don't remember the title. Mark On Sun, Oct 28, 20 12 at 11:25 PM, Joshua Wiley jwiley.ps...@gmail.com wrote: Hi Elaine, If you want identical models, you need to use the same family and then the formula is the same. Here is an example with a built in dataset: ## these two are identical coef(lm(mpg ~ hp + log(wt), data = mtcars)) (Intercept) hp log(wt) 38.86095585 -0.02808968 -13.06001270 coef(glm(mpg ~ hp + log(wt), data = mtcars, family = gaussian)) (Intercept) hp log(wt) 38.86095585 -0.02808968 -13.06001270 ## not identical coef(glm(mpg ~ hp + wt, data = mtcars, family = gaussian(link = log))) (Intercept) hp wt 3.88335638 -0.00173717 -0.20851238 I show the log link because the poisson family default to a log link, but that is equivalent to: log(E(y)) = Xb where X is your design matrix (intercept, A, B, log(C), log(D) for you). In short the link function operates on the outcome, not the predictors so even though the poisson family includes a log link, it will not yield the same results as a log transformation of two of your predictors. I do not have any online references off the top of my head, but it seems like you may be well served by reading some about generalized linear models and the concept of link functions. Cheers, Josh On Sun, Oct 28, 2012 at 8:01 PM, Elaine Kuo elaine.kuo...@gmail.com wrote: Hello list, I am running a regression using lm(Y~A+B+log(C)+log(D)) Now, I would like to test if glm can produce similar results. So the code was revised as glm(Y~A+B+C+D, family=poisson) (code 1) However, I found some example using glm for lm. It suggests that the code should be revised like glm(Y~A+B+log(C)+log(D), family=poisson) (code 2) Please kindly advise which code is correct. Thank you. Elaine [[alternative HTML version deleted]] __ R-help@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. -- Joshua Wiley Ph.D. Student, Health Psychology Programmer Analyst II, Statistical Consulting Group University of California, Los Angeles https://joshuawiley.com/ __ R-help@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. [[alternative HTML version deleted]] __ R-help@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.
[R] change lm log(x) to glm poisson
Hello list, I am running a regression using lm(Y~A+B+log(C)+log(D)) Now, I would like to test if glm can produce similar results. So the code was revised as glm(Y~A+B+C+D, family=poisson) (code 1) However, I found some example using glm for lm. It suggests that the code should be revised like glm(Y~A+B+log(C)+log(D), family=poisson) (code 2) Please kindly advise which code is correct. Thank you. Elaine [[alternative HTML version deleted]] __ R-help@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.
[R] lm and glm
Dear list, I am making a linear regression of the following format. lm(Y~X1+X2+log(X3)+log(X4)) Now I would like to check the linear regression above using generalized linear model. Please kindly if the following format is correct and thank you. (If it is wrong, please indicate why.) glm(Y~X1+X2+log(X3)+log(X4), family=poisson(link=log)) Also, please kindly suggest any references comparing the codes of lm and glm. Elaine [[alternative HTML version deleted]] __ R-help@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.
[R] two indirect effects of path analysis
Hello, This is Elaine. I am trying a path analysis using lavaan Package. There are three explanatory variables: X, Z, and M. The response variable is Y. A, b, and c have direct effects on Y. On the other hand, X and Z also have direct effects on M. In other words, X and Z have indirect effects on Y. I found the code example of lavaan package describes only one indirect effect as below. Please kindly advise how to modify it as two indirect effects. Thank you. Elaine set.seed(1234) X - rnorm(100) M - 0.5*X + rnorm(100) Y - 0.7*M + rnorm(100) Data - data.frame(X = X, Y = Y, M = M) model - ' # direct effect + Y ~ c*X + # mediator + M ~ a*X + Y ~ b*M + # indirect effect (a*b) + ab := a*b + # total effect + total := c + (a*b) + ' fit - sem(model, data=Data) summary(fit) [[alternative HTML version deleted]] __ R-help@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.
Re: [R] changing outlier shapes of boxplots using lattice
Hello Ilai, Thank you for the response. It did help a lot. However, a beginner to lattice has three questions. Q1 Please kindly explain why in this case OP is using it with no at argument, so it is possible to display the median and the outliers with different pch? Q2. what is the relationship between package HH and graphic-drawing? I checked ??HH and found little explanation on its function of graphic-drawing. Q3 Please kindly advise how to make outliers empty circle (pch=2) in this case as the code below. Thank you. code Diet.colors - c(forestgreen,darkgreen,chocolate1,darkorange2,sienna2, red2,firebrick3,saddlebrown,coral4,chocolate4,darkblue,navy,grey38) levels(dataN$Diet_B) - diet.code bwplot(MS_midpoint_lat~Diet_B, data=dataN, xlab=list(Diet of Breeding Ground, cex = 1.4), ylab = list(Latitudinal Midpoint Breeding Ground ,cex = 1.4), lwd=1.5, cex.lab=1.4, cex.axis=1.2, font.axis=2, cex=1.5, las=1, panel=panel.bwplot.intermediate.hh, bty=l, col=Diet.colors, pch=rep(l,13), scales=list(x=list(rot=90)), par.settings=list(plot.symbol = list(pch = 2, cex = 2),box.umbrella=list(lty=1))) Elaine On Sat, Sep 29, 2012 at 2:44 AM, ilai ke...@math.montana.edu wrote: On Fri, Sep 28, 2012 at 6:57 AM, Richard M. Heiberger r...@temple.eduwrote: Elaine, For panel.bwplot you see that the central dot and the outlier dots are controlled by the same pch argument. ??? I don't think so... bwplot(rgamma(20,.1,1)~gl(2,10), pch=rep(17,2), panel = lattice::panel.bwplot) I think you mean panel.bwplot.intermidiate.hh ? BTW thank you for the useful HH package but in this case OP is using it with no at argument, so why not Diet.colors - c(forestgreen, darkgreen,chocolate1,darkorange2, sienna2,red2,firebrick3,saddlebrown,coral4,chocolate4,darkblue,navy,grey38) bwplot(rgamma(20*13,1,.1)~gl(13,20), fill = Diet.colors, pch = |, par.settings = list(box.umbrella=list(lty=1))) cheers I initially set the pch=| to match your first example with the horizontal indicator for the median. I would be inclined to use the default circle for the outliers and therefore also for the median. Rich On Fri, Sep 28, 2012 at 7:13 AM, Sarah Goslee sarah.gos...@gmail.com wrote: I would guess that if you find the bit that says pch=| and change it to pch=1 it will solve your question, and that reading ?par will tell you why. Sarah On Thursday, September 27, 2012, Elaine Kuo wrote: Hello This is Elaine. I am using package lattice to generate boxplots. Using Richard's code, the display was almost perfect except the outlier shape. Based on the following code, the outliers are vertical lines. However, I want the outliers to be empty circles. Please kindly help how to modify the code to change the outlier shapes. Thank you. code package (lattice) dataN - data.frame(GE_distance=rnorm(260), Diet_B=factor(rep(1:13, each=20))) Diet.colors - c(forestgreen, darkgreen,chocolate1,darkorange2, sienna2,red2,firebrick3,saddlebrown,coral4, chocolate4,darkblue,navy,grey38) levels(dataN$Diet_B) - Diet.colors bwplot(GE_distance ~ Diet_B, data=dataN, xlab=list(Diet of Breeding Ground, cex = 1.4), ylab = list( Distance between Centers of B and NB Range (1000 km), cex = 1.4), panel=panel.bwplot.intermediate.hh, col=Diet.colors, pch=rep(|,13), scales=list(x=list(rot=90)), par.settings=list(box.umbrella=list(lty=1))) [[alternative HTML version deleted]] __ R-help@r-project.org javascript:; mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Sarah Goslee http://www.stringpage.com http://www.sarahgoslee.com http://www.functionaldiversity.org [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman
[R] changing outlier shapes of boxplots using lattice
Hello This is Elaine. I am using package lattice to generate boxplots. Using Richard's code, the display was almost perfect except the outlier shape. Based on the following code, the outliers are vertical lines. However, I want the outliers to be empty circles. Please kindly help how to modify the code to change the outlier shapes. Thank you. code package (lattice) dataN - data.frame(GE_distance=rnorm(260), Diet_B=factor(rep(1:13, each=20))) Diet.colors - c(forestgreen, darkgreen,chocolate1,darkorange2, sienna2,red2,firebrick3,saddlebrown,coral4, chocolate4,darkblue,navy,grey38) levels(dataN$Diet_B) - Diet.colors bwplot(GE_distance ~ Diet_B, data=dataN, xlab=list(Diet of Breeding Ground, cex = 1.4), ylab = list( Distance between Centers of B and NB Range (1000 km), cex = 1.4), panel=panel.bwplot.intermediate.hh, col=Diet.colors, pch=rep(|,13), scales=list(x=list(rot=90)), par.settings=list(box.umbrella=list(lty=1))) [[alternative HTML version deleted]] __ R-help@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.
Re: [R] boxplot of different colors
hello Richard, Thank a lot. The plot is breathtaking. I would like to make three modifications. Please kindly help and thanks. 1. making outliers from dash to empty circle (pch=2) I tried plot.symbol as the code below but failed. 2. making font size of axis (levels) larger to 1.2 unsure where to adjust in the code 3. making levels along x-axis horizontal instead of vertical unsure where to adjust in the code. Elaine Code dataN - data.frame(GE_distance=rnorm(260), Diet_B=factor(rep(1:13, each=20))) Diet.colors - c(forestgreen, darkgreen,chocolate1,darkorange2, sienna2,red2,firebrick3,saddlebrown,coral4, chocolate4,darkblue,navy,grey38) levels(dataN$Diet_B) - Diet.colors diet = list(lty=1,pch=1) bwplot(GE_distance ~ Diet_B, data=dataN, xlab=list(Diet of Breeding Ground, cex = 1.4), ylab = list( Distance between Centers of B and NB Range (1000 km), cex = 1.4), panel=panel.bwplot.intermediate.hh, col=Diet.colors, pch=rep(|,13), scales=list(x=list(rot=90)), par.settings=list(box.umbrella=diet,plot.symbol = diet)) On Tue, Sep 25, 2012 at 11:48 AM, Richard M. Heiberger r...@temple.eduwrote: See ?panel.bwplot for pch=|. That explains that pch=| puts horizontal lines instead of dots at the median(and also at the outliers). The rep makes it into a vector to be indexed by panel.bwplot.intermediate.hh in each of its calls to panel.bwplot The names under each plot are the levels of the factor, in this example levels(Diet_B). You called them 1:13 in your example. If you want to give them names do so as a factor. For example Control the staples with box.umbrella, again see ?panel.bwplot and ?trellis.par.get The revised example here does all three of your requests. dataN - data.frame(GE_distance=rnorm(260), Diet_B=factor(rep(1:13, each=20))) Diet.colors - c(forestgreen, darkgreen,chocolate1,darkorange2, sienna2,red2,firebrick3,saddlebrown,coral4, chocolate4,darkblue,navy,grey38) levels(dataN$Diet_B) - Diet.colors bwplot(GE_distance ~ Diet_B, data=dataN, xlab=list(Diet of Breeding Ground, cex = 1.4), ylab = list( Distance between Centers of B and NB Range (1000 km), cex = 1.4), panel=panel.bwplot.intermediate.hh, col=Diet.colors, pch=rep(|,13), scales=list(x=list(rot=90)), par.settings=list(box.umbrella=list(lty=1))) On Mon, Sep 24, 2012 at 11:13 PM, Elaine Kuo elaine.kuo...@gmail.comwrote: Hello Richard, Your answer is a great help to my problem. The boxplot of 13 colors is very beautiful :) By the way, I have three subsequent questions of your code 1. the meaning of pch=rep(|,13) I read the R manual but could not interpret the part. pch means the point type in plot, but here not sure. 2. how to write names under each box In boxplot, names can explain each box, but here names does not work. 3. how to make staple from dash to solid line Thanks again Elaine On Tue, Sep 25, 2012 at 7:00 AM, Richard M. Heiberger r...@temple.eduwrote: ## I would do this in lattice using the panel.bwplot.intermediate.hh ## function from the HH package. ## install.packages(HH) ## if necessary library(HH) dataN - data.frame(GE_distance=rnorm(260), Diet_B=factor(rep(1:13, each=20))) Diet.colors - c(forestgreen, darkgreen,chocolate1,darkorange2, sienna2,red2,firebrick3,saddlebrown,coral4, chocolate4,darkblue,navy,grey38) bwplot(GE_distance ~ Diet_B, data=dataN, xlab=list(Diet of Breeding Ground, cex = 1.4), ylab = list( Distance between Centers of B and NB Range (1000 km), cex = 1.4), panel=panel.bwplot.intermediate.hh, col=Diet.colors, pch=rep(|,13)) On Mon, Sep 24, 2012 at 6:23 PM, Elaine Kuo elaine.kuo...@gmail.comwrote: Hello, I am making a boxplot of 13 boxes. I tried to color the box using 13 colors but failed. Only red and brown were displayed. Green, blue, and grey disappeared. Please kindly advise modification after checking the code below. Thank you in advance. Elaine R code # data input dataN -read.csv(H:/a_mig_distance_B_NB/R_data/Mig_bird_586_20120925.csv,header=T, row.names=1) dim(dataN) dataN[1,] str(dataN) # graph par(mai=c(1,1.03,0.4,0.4)) obs.group-dataN$Diet_B par(new=T) boxplot(GE_distance~Diet_B, data=dataN,xlab=Diet of Breeding Ground,ylab=, yaxt=n,type=p, pch=1,lwd=0.95, cex.lab=1.4, cex.axis=1.2, font.axis=2, cex=1.5, las=1, bty=l, col=c(forestgreen, darkgreen,chocolate1,darkorange2,sienna2, red2,firebrick3, saddlebrown,coral4,chocolate4,darkblue,navy,grey38)[obs.group])) op = par(mar = c(5,5,4,2) + 0.1) title(ylab = Distance between Centers
[R] boxplot of different colors
Hello, I am making a boxplot of 13 boxes. I tried to color the box using 13 colors but failed. Only red and brown were displayed. Green, blue, and grey disappeared. Please kindly advise modification after checking the code below. Thank you in advance. Elaine R code # data input dataN -read.csv(H:/a_mig_distance_B_NB/R_data/Mig_bird_586_20120925.csv,header=T, row.names=1) dim(dataN) dataN[1,] str(dataN) # graph par(mai=c(1,1.03,0.4,0.4)) obs.group-dataN$Diet_B par(new=T) boxplot(GE_distance~Diet_B, data=dataN,xlab=Diet of Breeding Ground,ylab=, yaxt=n,type=p, pch=1,lwd=0.95, cex.lab=1.4, cex.axis=1.2, font.axis=2, cex=1.5, las=1, bty=l, col=c(forestgreen, darkgreen,chocolate1,darkorange2,sienna2, red2,firebrick3, saddlebrown,coral4,chocolate4,darkblue,navy,grey38)[obs.group])) op = par(mar = c(5,5,4,2) + 0.1) title(ylab = Distance between Centers of B and NB Range (1000 km), cex.lab = 1.4,line = 3) axis(side=2,yaxp=c(0,2,4),cex.lab=1.4, cex.axis=1.2,font.axis=2, las=1) [[alternative HTML version deleted]] __ R-help@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.
Re: [R] boxplot of different colors
Hello Richard, Your answer is a great help to my problem. The boxplot of 13 colors is very beautiful :) By the way, I have three subsequent questions of your code 1. the meaning of pch=rep(|,13) I read the R manual but could not interpret the part. pch means the point type in plot, but here not sure. 2. how to write names under each box In boxplot, names can explain each box, but here names does not work. 3. how to make staple from dash to solid line Thanks again Elaine On Tue, Sep 25, 2012 at 7:00 AM, Richard M. Heiberger r...@temple.eduwrote: ## I would do this in lattice using the panel.bwplot.intermediate.hh ## function from the HH package. ## install.packages(HH) ## if necessary library(HH) dataN - data.frame(GE_distance=rnorm(260), Diet_B=factor(rep(1:13, each=20))) Diet.colors - c(forestgreen, darkgreen,chocolate1,darkorange2, sienna2,red2,firebrick3,saddlebrown,coral4, chocolate4,darkblue,navy,grey38) bwplot(GE_distance ~ Diet_B, data=dataN, xlab=list(Diet of Breeding Ground, cex = 1.4), ylab = list( Distance between Centers of B and NB Range (1000 km), cex = 1.4), panel=panel.bwplot.intermediate.hh, col=Diet.colors, pch=rep(|,13)) On Mon, Sep 24, 2012 at 6:23 PM, Elaine Kuo elaine.kuo...@gmail.comwrote: Hello, I am making a boxplot of 13 boxes. I tried to color the box using 13 colors but failed. Only red and brown were displayed. Green, blue, and grey disappeared. Please kindly advise modification after checking the code below. Thank you in advance. Elaine R code # data input dataN -read.csv(H:/a_mig_distance_B_NB/R_data/Mig_bird_586_20120925.csv,header=T, row.names=1) dim(dataN) dataN[1,] str(dataN) # graph par(mai=c(1,1.03,0.4,0.4)) obs.group-dataN$Diet_B par(new=T) boxplot(GE_distance~Diet_B, data=dataN,xlab=Diet of Breeding Ground,ylab=, yaxt=n,type=p, pch=1,lwd=0.95, cex.lab=1.4, cex.axis=1.2, font.axis=2, cex=1.5, las=1, bty=l, col=c(forestgreen, darkgreen,chocolate1,darkorange2,sienna2, red2,firebrick3, saddlebrown,coral4,chocolate4,darkblue,navy,grey38)[obs.group])) op = par(mar = c(5,5,4,2) + 0.1) title(ylab = Distance between Centers of B and NB Range (1000 km), cex.lab = 1.4,line = 3) axis(side=2,yaxp=c(0,2,4),cex.lab=1.4, cex.axis=1.2,font.axis=2, las=1) [[alternative HTML version deleted]] __ R-help@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. [[alternative HTML version deleted]] __ R-help@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.
Re: [R] boxplot of different colors
Hello Sarah, Thanks for the suggestion of table(obs.group). I checked it and found no problems of the obs.group. As for using dput(), please kindly share some examples to display the colored graph in r-help. In fact, some colors were assigned to all types of diets, like A=red1 B=red2 C=green1 D=green4 E=darkgreen F=orange3 G=darkorange2 H=navy I=blue1 However, the boxplot displays as A=red1 B=red2 C=green1 D=green4 E=red1 F=red2 G=green1 H=green4 I=red1. I am wondering if there is any bug in showing too many colors for boxplot. Elaine On Tue, Sep 25, 2012 at 6:52 AM, Sarah Goslee sarah.gos...@gmail.comwrote: Hi Elaine, Without a reproducible example it's impossible to say, but I'd take a hard look at: table(obs.group) If that doesn't give you some insight, a small reproducible example included in your email using dput() would allow us to answer you more effectively. Sarah On Mon, Sep 24, 2012 at 6:23 PM, Elaine Kuo elaine.kuo...@gmail.com wrote: Hello, I am making a boxplot of 13 boxes. I tried to color the box using 13 colors but failed. Only red and brown were displayed. Green, blue, and grey disappeared. Please kindly advise modification after checking the code below. Thank you in advance. Elaine R code # data input dataN -read.csv(H:/a_mig_distance_B_NB/R_data/Mig_bird_586_20120925.csv,header=T, row.names=1) dim(dataN) dataN[1,] str(dataN) # graph par(mai=c(1,1.03,0.4,0.4)) obs.group-dataN$Diet_B par(new=T) boxplot(GE_distance~Diet_B, data=dataN,xlab=Diet of Breeding Ground,ylab=, yaxt=n,type=p, pch=1,lwd=0.95, cex.lab=1.4, cex.axis=1.2, font.axis=2, cex=1.5, las=1, bty=l, col=c(forestgreen, darkgreen,chocolate1,darkorange2,sienna2, red2,firebrick3, saddlebrown,coral4,chocolate4,darkblue,navy,grey38)[obs.group])) op = par(mar = c(5,5,4,2) + 0.1) title(ylab = Distance between Centers of B and NB Range (1000 km), cex.lab = 1.4,line = 3) axis(side=2,yaxp=c(0,2,4),cex.lab=1.4, cex.axis=1.2,font.axis=2, las=1) -- Sarah Goslee http://www.functionaldiversity.org [[alternative HTML version deleted]] __ R-help@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.
[R] boxplot of multi box color
Hello, I want to draw a boxplot using 13 colors for 13 boxes. Each box represents a type of diet of birds. Y axis is the breeding range of the birds. I checked the previous r-help and found a possible solution. However, it did not work by showing error in ncol(Diet_B), Diet_B not found. Please kindly help with modification and thank you. Also, if anything is unclear, please let me know. code # data input dataN -read.csv(H:/Mig_bird_586_20120925.csv,header=T, row.names=1) dataN$Diet_B -factor(dataN$Diet_B) # graph par(mai=c(1,1.03,0.4,0.4)) boxplot(GE_distance~Diet_B, data=dataN, col = rep(seq(ncol(Diet_B)) + 1, each = 1)) [[alternative HTML version deleted]] __ R-help@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.
[R] To predict Y based on only one sample of X and Y
Hello I want to predict wing length using regression commands. (lm and predict) The data details are as followed Data: Bird physiological data 1. body mass 2. body length 3. wing length Data type: Order A: consisting of 20 species, body mass and length of all 20 species are measured Order B: consisting of 2 species, body mass and length of only 1 species is measured Order C: consisting of 5 species, body mass and length of only 1 species is measured Method: 1. for order A, using predict and lm datam.lm -lm(Wing.Length~Body.mass+Body.Length) However, for order B and C, please kindly advise any method to get wing length based on body mass and length. (phylogenic relationship is tentatively neglected) Thank you Elaine [[alternative HTML version deleted]] __ R-help@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.
[R] how to generate response variables using simple regression
Hello, I have weight and wing length data of 5 kinds of birds (B1 to B5). Weight data (predictor) and wing data (response) were used to generated a simple regression. (using lm) Now some weight data are found but without wing data (B6, B7). I want to use the generated simple regression to produce wing data of B6 and B7 by their weight data. Please kindly advise R code to carry it out. Thank you. Elaine [[alternative HTML version deleted]] __ R-help@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.
Re: [R] how to print km square in the form of km2
Hello Rolf, Thank you for the response. I tried your command but it did not work. plot(1:10,ylab=y,xlab=**expression(plain(km)^2)) Please kindly advise any other method to make 2 in km2 become a uppercase number. Thanks again. Elaine On Tue, Feb 21, 2012 at 8:24 AM, Rolf Turner rolf.tur...@xtra.co.nz wrote: On 21/02/12 12:54, Elaine Kuo wrote: Hello, This is Elaine. I am drawing a plot with x-axis label with km square as the unit. Now I want to print km square in the form of km2 and output 2 as the uppercase. Please kindly help suggest command to show the uppercase. When you say as [the] uppercase I *think* you mean as a superscript. Assuming that I am correct in my supposition, you can achieve what you want via the syntax shown in the following example: plot(1:10,ylab=y,xlab=**expression(plain(km)^2)) For details on how you do this sort of thing in general see: ?plotmath Be warned --- it's tricky! I find that I always need to experiment quite a lot before I get it right. Experimentation is cheap, but. HTH cheers, Rolf Turner [[alternative HTML version deleted]] __ R-help@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.
[R] how to print km square in the form of km2
Hello, This is Elaine. I am drawing a plot with x-axis label with km square as the unit. Now I want to print km square in the form of km2 and output 2 as the uppercase. Please kindly help suggest command to show the uppercase. Thank you. Elaine [[alternative HTML version deleted]] __ R-help@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.
[R] to check if a group of values is randomly distributed
Dear list, I have 603 numbers depicting range sizes of birds in Japan. I would like to learn if the 603 range sizes are randomly distributed or not, in order to check if they meet mid-domain effects. Please kindly advise if any R package or function can check the fit. Also, any more references are highly appreciated. Thank you Elaine [[alternative HTML version deleted]] __ R-help@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.
[R] How to calculate squared R of spatial autoregressive models
Dear List, I am comparing the squared R values of linear models and its spatial autoregressive counterparts. (SARerror) (1. lm (Y~X1) 2. lm (Y~ X1+X2) 3. lm(Y~X1+X2+X3)) The squared R values of linear models are generated by command summary (lm). Similarly, I tried to produce those of spatial autoregressive models based on the squared Pearsons correlation of explanatory and response variables. It failed The code is as followed. Please kindly modify the code and thank you. 1. single predictor sar.x1 -errorsarlm(Y~X1,data=datam.std,listw=nb8.w, na.action=na.omit, method=Matrix, zero.policy=TRUE) summary(sar.x1) cor(sar.x1$X1, sar.x1$Y, method = pearson) error message error in cor(sar.x1$ X1, sar.x1$Y, method = pearson) : supply both 'x' and 'y' or a matrix-like 'x' 2. multiple predictors sar.all -errorsarlm(Y~X1+X2+X3,data=datam.std,listw=nb8.w, na.action=na.omit, method=Matrix, zero.policy=TRUE) summary(sar.all) cor(sar.all$X1+ sar.all$X2+ sar.all$X3, sar.x1$Y, method = pearson) error message error in cor(sar.all$X1+ sar.all$X2+ sar.all$X3, sar.x1$Y, method = pearson) : supply both 'x' and 'y' or a matrix-like 'x' Elaine [[alternative HTML version deleted]] __ R-help@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.
[R] discerning plot dots using colors
Dear List, I am using the command plot to present the relationship between bird richness (Y axis) and elevation (X axis). However, I would like to observe the distributions of bird richness in different administrative areas (A, B, C, ., G) in this plot. For example, the dots in area A might fall in the upper right part of the plot, while those in area B might appear in the middle of the elevation range. Please kindly advise how to differentiate the dots in distinct areas using colors. Thank you. Elaine [[alternative HTML version deleted]] __ R-help@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.
[R] delta AIC for models with 2 variables using MuMIn
Dear List, I want to ask a AIC question based on package library(MuMIn) The relative importance of 16 explanatory variables are assessed using delta AIC in a generalized linear model. Please kindly advise if it is possible to show models with any two only certain variables. Thank you. Elaine I asked a similar question and got a great help for models with only one variable as below. ~~ In effect, you want data(Cement) lm1 - lm(y ~ ., data = Cement) dd - dredge(lm1, subset = X1) want - with(dd, is.na(X) is.na(X2) is.na(X3) is.na(X4)) want ## how many models selected? sum(want) ## OK selected just 1, show it dd[want, , drop = FALSE] Oh, actually, I suppose you could automate this, so it will return all models with single variable: dd - dredge(lm1) parms - !is.na(dd[, -c(1, (ncol(dd) - c(0:7)))]) want - which(rowSums(parms) == 1) dd[want, ] Having said all this, I don't think this is a good way to do model selection. G [[alternative HTML version deleted]] __ R-help@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.
[R] Extracting data subset for plot
Dear list, I want to make a plot based on the following information, using the command plot. variable A for x axis : temperature (range: -20 degrees to 40 degree) variable B for y axis : altitude (range: 50 m to 2500 m ) The data below 0 degree of X variable wants to be erased tentatively. Please kindly advise the command to extract the data ranging from 0 degree to 40 degrees. Thank you. Elaine [[alternative HTML version deleted]] __ R-help@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.
[R] How to set the limit of abline (regression line of lm)
Dear List, I ran a regression model using lm and produced a regression line using abline. The line ranges from -20 to 20 in x axis, and the section I only want is from -20 to 0. Please kindly advise any function in abline () to set the range of x axes. Thank you Elaine [[alternative HTML version deleted]] __ R-help@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.
[R] how to show the number of each axis interval (plot)
Dear List, I am using plot for homework. The x-axis covered from 0 to 80, with 4 intervals. However, the plot only showed 0, 40, 80. 20 and 60 disappeared. Please kindly advise how to show 0, 20, 40, 60, 80 for the axis interval. Thank you. Elaine [[alternative HTML version deleted]] __ R-help@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.
Re: [R] how to plot y-axis on the right of x-axis
Thank you. The answers provides the right direction and a code was written accordingly. One more request, if the label of axis X wants to be drawn from 5 to 1 (left to right) rather than 1 to 5, is it fine to change axis (4, at = NULL) ? If so, which value should be input ? Thanks again. Elaine code plot(1:5,axes=FALSE) axis(1) axis(4) box() On Wed, Aug 25, 2010 at 5:39 PM, Jim Lemon j...@bitwrit.com.au wrote: On 08/25/2010 09:12 AM, elaine kuo wrote: Dear List, I have a richness data distributing across 20 N to 20 S latitude. (120 E-140 E longitude). I would like to draw the richness in the north hemisphere and a regression line in the plot (x-axis: latitude, y-axis: richness in the north hemisphere). The above demand is done using plot. Then, south hemisphere richness and regression are required to be generated using the same y-axis above but an x-axis on the left side of the y-axis. (The higher latitude in the south hemisphere, the left it would move) Please kindly share how to design the south plot and regression line for richness. Also, please advise if any more info is in need. Hi Elaine, Changing the position of the axes is easily done by changing the side and pos arguments of the axis function. If you want to move the y-axis to the right (or as you state it, the x axis to the left): # y axis on the left plot(1:5,axes=FALSE) axis(1) axis(2) # add a y axis one third of the way to the right xylim-par(usr) axis(2,pos=xylim[1]+diff(xylim[1:2])/3) # add another y axis two thirds of the way axis(4,pos=xylim[2]-diff(xylim[1:2])/3) # add one more on the right axis(4) You can move the x axis up and down using the same tricks. Jim [[alternative HTML version deleted]] __ R-help@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.
Re: [R] how to plot y-axis on the right of x-axis
Yes, I appreciated your answers which well hit my questions. (esp the perfect model parts). About the plot part, one more question. Is it possible to make the two plots (northern and southern richness) sharing the same Y axis (latitude = 0, the equator) ? In other words, southern richness would be on the left side of the Y axis, while northern one on the right side. Elaine Two plot panels on the same device like: layout(1:2) plot(1:100) plot(1:100) layout(1) = Yes that's what I want The second panel for southern species richness, do you mean you want the plot to go like this: plot(1:100, xlim = c(100,1)) = Yes, too. [[alternative HTML version deleted]] __ R-help@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.
[R] how to plot y-axis on the right of x-axis
Dear List, I have a richness data distributing across 20 N to 20 S latitude. (120 E-140 E longitude). I would like to draw the richness in the north hemisphere and a regression line in the plot (x-axis: latitude, y-axis: richness in the north hemisphere). The above demand is done using plot. Then, south hemisphere richness and regression are required to be generated using the same y-axis above but an x-axis on the left side of the y-axis. (The higher latitude in the south hemisphere, the left it would move) Please kindly share how to design the south plot and regression line for richness. Also, please advise if any more info is in need. Elaine [[alternative HTML version deleted]] __ R-help@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.
Re: [R] AIC in MuMIn
Please kindly advise if it is possible to show the singular model with only one certain variable using the command subset. (or maybe others) I tried the command subset=X3 but it returned multiple models including X3. The above demand might look unnecessary when visual inspection offers the solution with few exp. variables. However, it is of great importance for recognizing AIC for each variable in the model selection with more than 10 variables. No, there isn't. The object returned by dredge is a data frame so you can subset it to your hearts content, but you'll need to select rows where you specify that all your variables (except the one you are interested in) are missing (NA). Without writing this all out, I don't know of a quick way of doing this sort of subsetting. In effect, you want data(Cement) lm1 - lm(y ~ ., data = Cement) dd - dredge(lm1, subset = X1) want - with(dd, is.na(X) is.na(X2) is.na(X3) is.na(X4)) want ## how many models selected? sum(want) ## OK selected just 1, show it dd[want, , drop = FALSE] Oh, actually, I suppose you could automate this, so it will return all models with single variable: dd - dredge(lm1) parms - !is.na(dd[, -c(1, (ncol(dd) - c(0:7)))]) want - which(rowSums(parms) == 1) dd[want, ] Having said all this, I don't think this is a good way to do model selection. = Thanks for the time-efficient formula. Actually it is over my current ability to automate it, but it did save a lot of time already. Moreover, please kindly explain the command beginning with parms. data (Cement) was checked but could not ensure why the row and the column were set to be 1 and (ncol(dd) - c(0:7)). Elaine [[alternative HTML version deleted]] __ R-help@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.
Re: [R] AIC in MuMIn
Hmmm. Thinking some more, I might not have answered your (unstated) question. What do your mean by GLM? = I meant generalized linear model as well. Thanks for the references. The first one was mentioned first in my life time after keeping asking the same question. I mean the Generalized Linear Model, not the General Linear Model. The Generalized one allows for non-normal responses and different mean-variance relationships and is the GLM of Nelder and Wedderburn (1972, J. Royal Statistical Society, Series A, 135(3),370-384) and the monograph by McCullagh and Wedderburn (1989, Generalized Linear Models, Chapman Hall/CRC). The R function glm() fits these kinds of model. The General Linear Model (IIRC) was the linking of linear regression and anova into a single entity. The R function lm() fits these kinds of models. The linear model is a special case of the Generalized Linear Model when the Gaussian error is used with the identity link function. Hence a Gaussian GLM (my GLM) with the identity link fitted by glm() will give the same results as lm(), but it will do so in a very inefficient manner. As this was what your code was doing I suggested using lm() instead. = Thanks for the important suggestion. I tried both lm and glm until now but no one commented on the method. Elaine [[alternative HTML version deleted]] __ R-help@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.
Re: [R] AIC in MuMIn
Please suggest how to define subset in my case How would I know? I still haven't seen your data. You seem to be mistaken on what is and is not included in your model and you fitted it. What hope do we have...? However, given the model 'mig.stds' from above in this email: mig.stds -lm(SummerM_ratio ~ temp_max + evi_mean + topo_var + topo_mean + coast + Iso_index_0808, ## now tell R were to find the variables in formula data = datum.std) ## If you are fitting a Gaussian GLM it is better fitted with lm() If you want to consider dredged models containing temp_max, then you would do dredge(mig.stds, subset = temp_max) If you want models that contain temp_max and coast, then you'd do dredge(mig.stds, subset = temp_max coast) or dredge(mig.stds, fixed = ~ temp_max + coast) The bits you include in subset or fixed are the names of your variables that you want in or out of the models. In your case, the names of the variables as input into the model formula. With 'subset' you need to use logical operators (and [], or [|]) whilst with 'fixed' you can specify a formula of variables that should be included or excluded in the same way you'd write any R formula. But, now having been told this, please note that this is *all* discussed on the ?dredge help page if you bother to read it. I've never used this package, and, OK, I have used R for going on for 11 or 12 years now so am used to reading help pages and understand the language a bit more you perhaps do, but you do seem to be asking questions or running into problems that are all covered by the help pages. = I posted it for help, after following the manual with the command dredge but receiving an error message two days ago. command target-dredge(mig.stds, subset = temp_max) error in eval(expr, envir, enclos) : 'temp_max' not found One possible cause could be data = datam.std. datam.std was produced as the code below, which seemed to make it hard to find explanatory variables. Please kindly share your experience in R, because I am unsure if my assumption is logical or not. Also, please kindly advise how to modify the command for dredging subset if possible. ( command target-dredge(mig.stds, subset = temp_max)) Thank you in advance. Elaine code library(MuMIn) datam -read.csv(c:/migration/Mig_ratio_20100817.csv,header=T, row.names=1) # std regression model (16 indep. variables) datam.sd-scale(datam) datam.std-as.data.frame(datam.sd) summary (datam.std) mean(datam.std) # obtain standard deviation sd(datam.std) mig.stds -lm(SummerM_ratio~temp_ran+temp_mean+temp_max+temp_min+evi_ran+evi_mean+evi_max+evi_min+prec_ran+prec_mean+prec_max+prec_min+topo_var+topo_mean+coast+Iso_index_0808,data=datam.std) summary(mig.stds) [[alternative HTML version deleted]] __ R-help@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.
Re: [R] AIC in MuMIn
A cause other than data based on standardized regression was identified. It is that the manual command added with target - at the left hand side. C1 did not work but C2 did. C1 target-dredge(mig.stds, subset = temp_max) C2 dredge(mig.stds, subset = temp_max) Elaine On Wed, Aug 18, 2010 at 5:37 PM, elaine kuo elaine.kuo...@gmail.com wrote: Please suggest how to define subset in my case How would I know? I still haven't seen your data. You seem to be mistaken on what is and is not included in your model and you fitted it. What hope do we have...? However, given the model 'mig.stds' from above in this email: mig.stds -lm(SummerM_ratio ~ temp_max + evi_mean + topo_var + topo_mean + coast + Iso_index_0808, ## now tell R were to find the variables in formula data = datum.std) ## If you are fitting a Gaussian GLM it is better fitted with lm() If you want to consider dredged models containing temp_max, then you would do dredge(mig.stds, subset = temp_max) If you want models that contain temp_max and coast, then you'd do dredge(mig.stds, subset = temp_max coast) or dredge(mig.stds, fixed = ~ temp_max + coast) The bits you include in subset or fixed are the names of your variables that you want in or out of the models. In your case, the names of the variables as input into the model formula. With 'subset' you need to use logical operators (and [], or [|]) whilst with 'fixed' you can specify a formula of variables that should be included or excluded in the same way you'd write any R formula. But, now having been told this, please note that this is *all* discussed on the ?dredge help page if you bother to read it. I've never used this package, and, OK, I have used R for going on for 11 or 12 years now so am used to reading help pages and understand the language a bit more you perhaps do, but you do seem to be asking questions or running into problems that are all covered by the help pages. = I posted it for help, after following the manual with the command dredge but receiving an error message two days ago. command target-dredge(mig.stds, subset = temp_max) error in eval(expr, envir, enclos) : 'temp_max' not found One possible cause could be data = datam.std. datam.std was produced as the code below, which seemed to make it hard to find explanatory variables. Please kindly share your experience in R, because I am unsure if my assumption is logical or not. Also, please kindly advise how to modify the command for dredging subset if possible. ( command target-dredge(mig.stds, subset = temp_max)) Thank you in advance. Elaine code library(MuMIn) datam -read.csv(c:/migration/Mig_ratio_20100817.csv,header=T, row.names=1) # std regression model (16 indep. variables) datam.sd-scale(datam) datam.std-as.data.frame(datam.sd) summary (datam.std) mean(datam.std) # obtain standard deviation sd(datam.std) mig.stds -lm(SummerM_ratio~temp_ran+temp_mean+temp_max+temp_min+evi_ran+evi_mean+evi_max+evi_min+prec_ran+prec_mean+prec_max+prec_min+topo_var+topo_mean+coast+Iso_index_0808,data=datam.std) summary(mig.stds) [[alternative HTML version deleted]] __ R-help@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.
Re: [R] AIC in MuMIn
Yes, I tried the example in the ?dredge and agreed that something else caused the mistake. Aside from the cause which takes time to clarify (16 explanatory variables in the model), I would like to ask another question. Please kindly advise if it is possible to show the singular model with only one certain variable using the command subset. (or maybe others) I tried the command subset=X3 but it returned multiple models including X3. The above demand might look unnecessary when visual inspection offers the solution with few exp. variables. However, it is of great importance for recognizing AIC for each variable in the model selection with more than 10 variables. Please kindly help and thank you in advance. Elaine code library(MuMIn) data(Cement) lm1 - lm(y ~ ., data = Cement) dd - dredge(lm1, beta = FALSE, eval = TRUE, rank = AIC) X3-dredge(lm1, rank = AIC, subset=X3) On Wed, Aug 18, 2010 at 9:18 PM, Gavin Simpson gavin.simp...@ucl.ac.ukwrote: On Wed, 2010-08-18 at 21:11 +0800, elaine kuo wrote: A cause other than data based on standardized regression was identified. It is that the manual command added with target - at the left hand side. C1 did not work but C2 did. C1 target-dredge(mig.stds, subset = temp_max) C2 dredge(mig.stds, subset = temp_max) Glad you have this working, but that can't possibly be the reason for the error. There must be something else going on. The only difference between the two calls is that you are storing the result somewhere, yet the error was coming from within the running of the dredge function. If everything works from within a new, clean R session then great. G Elaine On Wed, Aug 18, 2010 at 5:37 PM, elaine kuo elaine.kuo...@gmail.com wrote: Please suggest how to define subset in my case How would I know? I still haven't seen your data. You seem to be mistaken on what is and is not included in your model and you fitted it. What hope do we have...? However, given the model 'mig.stds' from above in this email: mig.stds -lm(SummerM_ratio ~ temp_max + evi_mean + topo_var + topo_mean + coast + Iso_index_0808, ## now tell R were to find the variables in formula data = datum.std) ## If you are fitting a Gaussian GLM it is better fitted with lm() If you want to consider dredged models containing temp_max, then you would do dredge(mig.stds, subset = temp_max) If you want models that contain temp_max and coast, then you'd do dredge(mig.stds, subset = temp_max coast) or dredge(mig.stds, fixed = ~ temp_max + coast) The bits you include in subset or fixed are the names of your variables that you want in or out of the models. In your case, the names of the variables as input into the model formula. With 'subset' you need to use logical operators (and [], or [|]) whilst with 'fixed' you can specify a formula of variables that should be included or excluded in the same way you'd write any R formula. But, now having been told this, please note that this is *all* discussed on the ?dredge help page if you bother to read it. I've never used this package, and, OK, I have used R for going on for 11 or 12 years now so am used to reading help pages and understand the language a bit more you perhaps do, but you do seem to be asking questions or running into problems that are all covered by the help pages. = I posted it for help, after following the manual with the command dredge but receiving an error message two days ago. command target-dredge(mig.stds, subset = temp_max) error in eval(expr, envir, enclos) : 'temp_max' not found One possible cause could be data = datam.std. datam.std was produced as the code below, which seemed to make it hard to find explanatory variables. Please kindly share your experience in R, because I am unsure if my assumption is logical or not. Also, please kindly advise how to modify
[R] AIC in MuMIn
Hello, I am using package MuMIn to calculate AIC for a full model with 10 explanatory variables. Thanks in advance in sharing your experience. Q1 In the AIC list of all models, each model is differentiated by model number. Please kindly advise if it is possible to find the corresponding explanatory variable(s) for the model number. Q2 error message I tried to display sub-model with only temp_ran using the code below but failed. Please kindly suggest the potential failure cause. code rm(list=ls()) library(MuMIn) datam -read.csv(c:/migration/Mig_ratio_20100817.csv,header=T, row.names=1) mig.stds -glm(datam.std$SummerM_ratio~ datam.std$temp_max++datam.std$evi_mean+datam.std$topo_var+datam.std$topo_mean+datam.std$coast+datam.std$Iso_index_0808,data=datam.std,family=gaussian) target.model - dredge(mig.stds, subset=datam.std$temp_ran) error in eval(expr, envir, enclos), 'temp_ran' not found Q3 showing sub-models for two assigned explanatory variables The manual only explains how to exclude two variables. Please advise how to contain submodels regarding certain two or more variables. Elaine [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] AIC in MuMIn
Thank you. Most of the answers solved the puzzles. Q2 I tried to display sub-model with only temp_ran using the code below but failed. Please kindly suggest the potential failure cause. code library(MuMIn) datam -read.csv(c:/migration/Mig_ratio_20100817.csv,header=T, row.names=1) mig.stds -lm(SummerM_ratio ~ temp_max + evi_mean + topo_var + topo_mean + coast + Iso_index_0808, ## now tell R were to find the variables in formula data = datum.std) ## If you are fitting a Gaussian GLM it is better fitted with lm() = Please explain why fitted lm is better for GLM. But temp_ran is not in your model... error in eval(expr, envir, enclos), 'temp_ran' not found When used properly (none of this datam.std$ business), subset will do what you want: dd2 - dredge(lm1, subset = X1) dd2 Global model: lm(formula = y ~ ., data = Cement) --- Model selection table (Int)X X1 X2 X3 X4 k R.sq Adj.R.sq RSS 3 52.58 1.4680 0.6623 4 0.9787 0.9744 57.90 = Please suggest how to define subset in my case Finally, it would be highly appreciated to recommend any references of R for a beginner like me. Elaine [[alternative HTML version deleted]] __ R-help@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.
[R] AIC for model selection in Package ‘MuMIn ’
Dear List, Ben's recommendation to MuMIn is of great importance to research with over ten independent variables. However, the criteria in this package for model selection are AICc (second-order AIC) and QAIC (quasi-AIC). Please kindly share if it is possible to carry AIC rather than the metrics above using this package. Thank you. Elaine [[alternative HTML version deleted]] __ R-help@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.
Re: [R] AIC for model selection in Package â� �MuMInâ��
Thanks for Ben. Model selection by AIC is feasible by the code below. One more question, when is it appropriate to carry out model averaging and parameter averaging? code library(MuMIn) data(Cement) lm1 - lm(y ~ ., data = Cement) dd - dredge(lm1, beta = TRUE, eval = TRUE, rank = AIC) print(dd) Elaine On Mon, Aug 16, 2010 at 9:21 PM, Ben Bolker bbol...@gmail.com wrote: elaine kuo elaine.kuo.tw at gmail.com writes: [re: MuMIn package] However, the criteria in this package for model selection are AICc (second-order AIC) and QAIC (quasi-AIC). Please kindly share if it is possible to carry AIC rather than the metrics above using this package. Thank you. I think you're misunderstanding the documentation. The reason that AICc and QAIC are explicitly included in the package, and the package documentation, is that (unlike AIC and BIC) they are *not* implemented in base R. If you simply use dredge(...,rank=AIC) that should work. good luck. __ R-help@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. [[alternative HTML version deleted]] __ R-help@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.
[R] Independent variables omitted in lm and glm
Dear List, Some independent variable were missing in calculation using lm and glm (gaussian). (X= Y1+Y2+ ..+Y16, Independent number: 16 variable) However, those variables did work well in cor(X, Y) respectively. str(dataframe) was also run to ensure that the variables were all numbers. Moreover, the missing variables were different in lm and glm. In lm, 3 factors were not taken into consideration. In glm, only one of them was omitted. (attached 2 shots) Please kindly advise whether further info is in need to solve the issue. Also, if similar problems have been encountered, please kindly share your experience. Thank you. Elaine Code rm(list=ls()) library(MuMIn) datam -read.csv(c:/migration/Mig_ratio_20100817.csv,header=T, row.names=1) dim(datam) datam[1,] # original regression model (16 indep. variables) Mig.lm -lm(datam$SummerM_ratio~datam$temp_ran+datam$temp_mean+datam$temp_max+datam$temp_min+datam$evi_ran+datam$evi_mean+datam$evi_max+datam$evi_min+datam$prec_ran+datam$prec_mean+datam$prec_max+datam$prec_min+datam$topo_var+datam$topo_mean+datam$coast+datam$Iso_index_0808,data=datam) summary(mig.lm) mig.glm -glm(datam$SummerM_ratio~datam$temp_ran+datam$temp_mean+datam$temp_max+datam$temp_min+datam$evi_ran+datam$evi_mean+datam$evi_max+datam$evi_min+datam$prec_ran+datam$prec_mean+datam$prec_max+datam$prec_min+datam$topo_var+datam$topo_mean+datam$coast+datam$Iso_index_0808,data=datam,family=gaussian) summary(mig.glm) [[alternative HTML version deleted]] __ R-help@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.
Re: [R] Independent variables omitted in lm and glm
sorry I forget the attachments Dear List, Some independent variable were missing in calculation using lm and glm (gaussian). (X= Y1+Y2+…..+Y16, Independent number: 16 variable) However, those variables did work well in cor(X, Y) respectively. str(dataframe) was also run to ensure that the variables were all numbers. Moreover, the missing variables were different in lm and glm. In lm, 3 factors were not taken into consideration. In glm, only one of them was omitted. (attached 2 shots) Please kindly advise whether further info is in need to solve the issue. Also, if similar problems have been encountered, please kindly share your experience. Thank you. Elaine Code rm(list=ls()) library(MuMIn) datam -read.csv(c:/migration/Mig_ratio_20100817.csv,header=T, row.names=1) dim(datam) datam[1,] # original regression model (16 indep. variables) Mig.lm -lm(datam$SummerM_ratio~datam$temp_ran+datam$temp_mean+datam$temp_max+datam$temp_min+datam$evi_ran+datam$evi_mean+datam$evi_max+datam$evi_min+datam$prec_ran+datam$prec_mean+datam$prec_max+datam$prec_min+datam$topo_var+datam$topo_mean+datam$coast+datam$Iso_index_0808,data=datam) summary(mig.lm) mig.glm -glm(datam$SummerM_ratio~datam$temp_ran+datam$temp_mean+datam$temp_max+datam$temp_min+datam$evi_ran+datam$evi_mean+datam$evi_max+datam$evi_min+datam$prec_ran+datam$prec_mean+datam$prec_max+datam$prec_min+datam$topo_var+datam$topo_mean+datam$coast+datam$Iso_index_0808,data=datam,family=gaussian) summary(mig.glm) __ R-help@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.
[R] how to display delta AIC of all models
Dear all, I am making model selection of generalised linear models based on delta AIC, using the command step(AIC). Also, I would like to learn the explanatory powers of each independent variable. To phrase differently, it is in need to show the delta AIC of all models rather than the final model with the least delta AIC. Please kindly advise if it is possible to exhibit all delta AIC of different combinations of the independent variables. Thank you. Elaine [[alternative HTML version deleted]] __ R-help@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.
Re: [R] what is scaling in plot
code rm(list=ls()) library(vegan) library(MASS) data(varespec) print(varespec) str(varespec) #PCA vare.pca - rda(varespec) vare.pca plot(vare.pca) sum(apply(varespec, 2, var)) biplot(vare.pca, scaling = -1) Elaine On Sat, Aug 14, 2010 at 10:48 AM, Ben Bolker bbol...@gmail.com wrote: elaine kuo elaine.kuo.tw at gmail.com writes: Pls kindly advise what scaling is in plot. Sometime it could be negative but sometimes it might be positive .(I guess it is the proportion between the plot and the margin) Your question is unclear. Please give more context and/or details. __ R-help@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. [[alternative HTML version deleted]] __ R-help@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.
