Hi R-listers,
In plyr I am using coding I have used before but an error seems to be
apparent. Has the function join been replaced by another word? I tried
this before and it didn't work and then worked for me. But now it is not
working again.
Please advise, Jean
data.to.analyze -
Thank you Michael,
Another new and useful function for me. In brief, str() gave me:
$ Aeventexhumed: chr A A A A ...
$ Aeventexhumed: Factor w/ 4 levels ,A,B,C: 2 2 2 2 2 2 2 2 2 2 ...
I think on the data sheet there are two columns for Aeventexhumed and only
one of them was converted to a
Hi R-listers,
I am wondering if the function aov() in plyr is appropriate for two
different types of tests:
1) summary(aov(EDI ~ VegIndex, data=data.to.analyze))
AND
2) summary(aov(HSuccess ~ VegIndex + Aeventexhumed +
VegIndex:Aeventexhumed, data=data.to.analyze))
the later inclusive of
Hi R-listers,
I would like to do an ANOVA with HSuccess ~ each individual Vegetation index
(0-5m, 6-10m, 11-15m, 16-20m, 21-25m, 26-30m, 31-35m) and alternatively
HSuccess ~ HTLIndex (-5-(-1m), 0-5m, 6-10m, 11-15m, 16-20m, 21-25m, 26-30m).
I'm not sure how to write the script for it. I have
Thank you!
Is there a way to obtain R2 value?
I am doing it manually but unsure about including residuals etc. in the
SS(total)... There must be a way...
Jean
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Thank you for letting me know. It may be where I hit reply but I typically
hit the latest comment. I'm sorry but I only know how to post my Q on
nabble. If there is another way to post, please let me know.
Thanks, Jean
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Hi R-listers,
Is there a way to get the mean SD value after creating an ANOVA table?
This is what I've been using to create an anova table.
summary(aov(HSuccess ~ HTLIndex*Aeventexhumed, data=data.to.analyze))
Best, Jean
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Hi R-listers,
I am trying to compare sections of the beach separated from the HTL to the
Veg (east to west), separated into indices (-5 to 30m), HTLIndex. Cross
parallel (north to south) are major beach sections (Rayos 1, 2, 3, 4 and
MNB). I am thinking to do an ANOVA for each independent
and Assurance R-sig forum I should
subscribe to? I don't understand. Please explain.
Jean
On 8-Oct-12, at 8:55 AM, Michael Weylandt [via R] wrote:
On Mon, Oct 8, 2012 at 10:03 AM, Jhope [hidden email] wrote:
Thank you for letting me know. It may be where I hit reply but I
typically
hit
Thank you for the replies.
I am actually trying to gain p-values and f values, and tried the below
script but unsuccessful.
1) I have read in another forum to use the package lmer but apparently it
does not exist.
2) Then I tried the pvals.fnc but it is not a function.
3) I read also that a
Hi R-listers,
I am receiving an error - see below. Aeventexhumed is the event in which
nesting occured, so it is defined by A, B, C. I thought as a factor was ok,
tried to change it to as.character but it still gave me the same error. Is
there something I should do about this error or just ignore
Hi R-listers,
I just tried updating my R and now I can't even open it and it is prompting
me to relaunch then relaunch just reappears. And it will not open R. I am
afraid I may have lost my scripts.
What should I do? I am running a MacBook OS X Version 10.5.8
1) Restore the entire system to
Thank you! That has worked for me when creating graphs. In plyr I used the
script:
# Veg Index
data.to.analyze$VegIndex - cut(data.to.analyze$Veg,
breaks=seq(0, 35, 5), include.lowest=TRUE)
VegIndex - data.to.analyze$VegIndex
plot(VegIndex)
But the vegetation distances on the x-axis in
Hi R-listers,
I am trying to do an ANOVA for the following scatterplot and received the
following error:
library(car)
scatterplot(HSuccess ~ Veg,
data = data.to.analyze,
xlab = Vegetation border (m),
ylab = Hatching success (%))
anova(HSuccess ~ Veg,
Hi Thanks to all for posting!
In plyr I did try something similar, a combination of what I learned from
all who replied. It seemed to work. If anyone knows of any criticism about
the grouping structure please let me know. I need this to be accurate.
Grouping defined by (0-5m) (6-10m) (11-15m)
Hi,
I have tried the script posted but received the following errors. I hope I
copied it correctly. I'm sorry but I don't know how to alter the script
myself.
Please advise, Jean
x - 0:30 + runif(124)
data.to.analyze$VegIndex - cut(x, breaks = seq(0, 35, 5))
Error in `$-.data.frame`(`*tmp*`,
Hi R listers,
I am trying to group distances of nests to the vegetation into classes that
are define by (0-5m, 6-10m, 11-15m, 16-20m, 21-25m, 26-30m, 31-35m, 36-40m,
41-45m, 46-50m, 51-55m, 56-60m). Each row is a nest and all the distances to
the vegetation is in a column.
In plyr, I have
Hi,
Allow me to recap my question. In plyr I am trying to group distances of
nests to the vegetation into classes that are defined by (0-5m, 6-10m,
11-15m, 16-20m, 21-25m, 26-30m, 31-35m). Each row is a nest and all the
distances to the vegetation is in a column.
As well I would like to create
Hi R-listers,
I am in plyr and using the script below and when I try to pull up the .csv
file with head() it does not show up. I am not sure where I am going wrong.
I have also checked the file box for turtlehatch.csv and it still does not
show up when I head(turtlehatch.csv). Am I missing a
Hi R-listers,
I am trying to group my HTL data, this is a column of data of Distances to
the HTL data = turtlehatch. I would like to create an Index of distances
(0-5m, 6-10, 11-15, 16-20... up to 60). And then create a new file with this
HTLIndex in a column.
So far I have gotten this far:
Hi R-listers,
I am trying to group my HTL data, this is a column of data of Distances to
the HTL data = turtlehatch. I would like to create an Index of distances
(0-5m, 6-10, 11-15, 16-20... up to 60). And then create a new file with this
HTLIndex in a column.
So far I have gotten this far:
Thank you Rui,
I am trying to create a column in the data file turtlehatch.csv
Saludos, Jean
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Hi R-listers,
I am having trouble plotting the values for the R2 line, lowess smooth,
smothered conditional spread, outlier identification.
I have tried the function text and legend but was unsuccessful. Please see
below.
Your help would be appreciated. Thanks in advance.
Jean
library(car)
HI R-listers,
Thanks for the replies I am convinced of Q 1 and 2.
Q 3 - I am still unsuccessful. Aeventexhumed has three events A, B and C. I
am unable to make 3 windows of scatterplot graphs side by side showing the
difference in regression of each event. With and without lattice I have
Hi R-listers,
Q1) What is the difference between the scatterplot and plot function?
Q2) I am able to make a graph with the scatterplot function:
scatterplot(DevelopIndex ~ Veg,
+ data = Turtle,
+ xlab = Vegetation border (m),
+ ylab = Embryonic development
Thank you Simon,
Yes this was in the library(car). There were no negative values in the
scatterplot graph or negative limits displayed.
Q-2 Are you sure the lines from the scatterplot are not this?:
solid green line: linear regression
solid red line: non-linear regression
upper dashed red line:
Hi R-listers,
I am trying to make a trellis boxplot with the HSuccess (y-axis) in each
Rayos (beach sections) (x-axis), for each Aeventexhumed (A, B, C) - nesting
event. I am not able to do so and keep receiving:
Error in eval(expr, envir, enclos) : object 'Rayos' not found
Please advise,
Hi R Listers,
I am trying to upload a data file and I received this message. It seems that
I am still able to make graphs and Aeventexhumed still works in the
analysis. Can I ignore this message or do I need to do something about this?
Jean
require(plyr)
Loading required package: plyr
Hi R-listers,
1) I am having trouble understanding why the means I have calculated from
Aeventexhumed (A, B, and C) are different from the means showing on the
boxplot I generated (see attached). I have added the script as to how my
data is organized.
2) Also when I went through the data
Hi R-listers,
I am using the package plyr. I am just trying to get the hatching success
mean of each nesting event and have typed in the following and received the
below results:
tapply(HSuccess, Aeventexhumed, mean)
AB C
0.2156265 0.1288559
I was able to make a scatterplot but ...
1) what does the 86 mean? The 86 shows up on the graph as well.
scatterplot (Shells/TotalEggs ~ Sector, data = data.to.analyze)
[1] 86
2) Also how do you change the Y axis title? I don't want it to read
Shells/TotalEggs, instead I would like it to read
I've originally made 48 GLM binomial models and compare the AIC values. But
dispersion was very large:
Example: Residual deviance: 8811.6 on 118 degrees of freedom
I was suggested to do a quasibinomial afterwards but found that it did not
help the dispersion factor of models and received a
After looking at 48 glm binomial models I decided to try the quasibinomial
with the top model 25 (lowest AIC). To try to account for overdispersion
(residual deviance 2679.7/68 d.f.) After doing so the dispersion factor is
the same for the quasibinomial and less sectors of the beach were
Thank you everyone for your dedication to improving 'R' - its function to
statistical analysis and comments.
I have now 48 models (unique combinations of 1 to 6 variables) and have put
them into a list and gained the results for all models. Below is a sample of
my script results:
m$model48 -
Hi R- listeners,
I should add that I would like also to compare my field data to an index
model. The index was created by using the following script:
devel.index - function(values, weights=c(1, 2, 3, 4, 5, 6)) {
foo - values*weights
return(apply(foo, 1, sum) / apply(values, 1, sum))
}
I ask the question about when to stop adding another variable even though it
lowers the AIC because each time I add a variable the AIC is lower. How do I
know when the model is a good fit? When to stop adding variables, keeping
the model simple?
Thanks, J
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Hi R-listers,
I have developed 47 GLM models with different combinations of interactions
from 1 variable to 5 variables. I have manually made each model separately
and put them into individual tables (organized by the number of variables)
showing the AIC score. I want to compare all of these
Hi , I am trying to do a 3 variable interaction and received this warning
message. Can someone please interpret?
Model31.glm - glm(cbind(Shells, TotalEggs-Shells) ~
Aeventexhumed:HTL:Sector, data=data.to.analyze, family = binomial)
Warning message:
glm.fit: fitted probabilities numerically 0 or
Hi All, I am wondering if anyone can tell me what the warning message below
the model means?
J
add1(DTA.glm,~ Aeventexhumed + Veg + Berm + HTL + Estuary + Rayos)
Single term additions
Model:
cbind(MaxHatch, TotalEggs - MaxHatch) ~ Aeventexhumed + Veg +
Berm + HTL
Df Deviance
Thank you Prof Ripley, I understand and changed Rayos into a factor.
Can someone please tell me how to change the:
Model:
cbind(MaxHatch, TotalEggs - MaxHatch) ~ Aeventexhumed + Veg +
Berm + HTL
Into a model that has?:
Model:
cbind(MaxHatch, TotalEggs - MaxHatch) ~ 1
Best, J
--
Hi everyone,
I just did a GLM binomial regression. I am wondering how do I know when my
responses are fixed?
I have found that an interaction between two factors is the most significant
predictor amongst other factors by comparing the AIC and add1 with each
factor. Does this mean that the
Hi everyone,
Does anyone have any suggestions on how to display GLM model fitting in a
report? I'm working with binomial biological data. I would like to make sure
biologists readers can interpret the response of different environments.
If possible an example would be great!
Thanks, J
--
I am wondering if anyone can tell me what the error I'm receiving means
below. I thought it said that Aeventexhumed should be converted to a factor,
so I tried to do so and received the following error.
Please advise. J
-
Thank you, I am new to R, and this forum. Aevent does not exist. I will also
try to post a better subject next time.
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I am a beginner too to R and this forum! I signed onto this forum yesterday
and received help overnight! I have also learn a bit by reading the posts. I
took someone's suggestion and made a rule for my Inbox to filter the R
emails into this folder and the listserve is now working very well for me.
Hi All,
I am a beginner to R and a prof helped me with some script. I am having
trouble understanding the below line. Is it finding the file
turtlehatch.csv? I do not have my working directory set to this file. If so
I tried (file.choose) and it did not work. R did nothing in response, no
error
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