[R] HELP relevel INTERCEPT-COMPARISONS

2017-10-28 Thread CHIRIBOGA Xavier
Dear colleagues,


How can I do to "relevel" the intercept?

I need that the treatment "Db" be the intercept, and have p-values for the 
comparisons with the others treatments.

I used the function "relevel" but it did not work out to have what I want.

Thanks for your help,


Xavier


T1 <- read.table(file.choose(), h=T)
> head(T1)
  treatment replicate Time Ebcg
1   CHA0+Db 11  9681172
2   CHA0+Db 21  5599000
3   CHA0+Db 31 10280480
4   CHA0+Db 41  1004526
5   CHA0+Db 51 12942018
6   CHA0+Db 61  7478773
> attach(T1)
> summary(T1)
   treatment   replicate  TimeEbcg
 CHA0   :6   Min.   :1.000   Min.   :1   Min.   :   0
 CHA0+Db:9   1st Qu.:2.750   1st Qu.:1   1st Qu.: 1000922
 Db :9   Median :4.500   Median :1   Median : 4044094
 Healthy:9   Mean   :4.625   Mean   :1   Mean   : 5699717
 PCL:6   3rd Qu.:6.250   3rd Qu.:1   3rd Qu.: 7785782
 PCL+Db :9   Max.   :9.000   Max.   :1   Max.   :24736254
> hist(Ebcg)
> treatment<-relevel(treatment,ref="Db")
> mT1<-lm(sqrt(Ebcg)~treatment,data=T1)
> summary(mT1)

Call:
lm(formula = sqrt(Ebcg) ~ treatment, data = T1)

Residuals:
 Min   1Q   Median   3Q  Max
-1748.12  -540.19 0.97   545.14  1949.22

Coefficients:
 Estimate Std. Error t value 
Pr(>|t|)
(Intercept) 532.5  384.4   1.385 
0.173296
treatmentCHA0+Db   2048.5  496.3   4.128 0.000170 ***
treatmentDb2491.9  496.3   5.021 9.93e-06 
***
treatmentHealthy   1215.6  496.3   2.450 0.018552 *
treatmentPCL120.4  543.6   0.221 0.825816
treatmentPCL+Db2098.9  496.3   4.229 0.000124 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 941.6 on 42 degrees of freedom
Multiple R-squared:  0.5206,Adjusted R-squared:  0.4635
F-statistic: 9.121 on 5 and 42 DF,  p-value: 6.227e-06



Xavier Chiriboga M.
PhD Candidate
Fundamental and Applied Research in Chemical Ecology Lab.
Institute of Biology
University of Neuchatel

Website: https://www.unine.ch/farce/home/membres/xavier-chiriboga.html

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[R] Function Relevel DOE NOT FOUND

2017-10-28 Thread CHIRIBOGA Xavier
Dear Forum,


Which functions and packages should be installed to make work the function 
"relevel"?


treatment<-revel(treatment,ref="Db")
Error: no se pudo encontrar la funci�n "revel"


Thank you very much for your help,


Xavier Chiriboga M.
PhD Candidate
Fundamental and Applied Research in Chemical Ecology Lab.
Institute of Biology
University of Neuchatel

Website: https://www.unine.ch/farce/home/membres/xavier-chiriboga.html

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[R] GLM and POST HOC test INTERPRETATION

2017-02-08 Thread CHIRIBOGA Xavier
Dear colleagues,


I am analyzing a data set of 68 values (integers). In some treatments (exactly 
6) the values are "zero". Because I record 0 in my measurement (or really a 
small value below zero)

My experiment is designed in such a way that I record values for 6 treatments 
at 2 times. Replicates are different in each combination time-treatment.

I am running a GLM , poisson distribution, for ANOVA I used Chisq, and for the 
POST HOC test I used Tukey.

I try to detect if interaction is significant, so I build the script:
expresion~time*treatment

Effects of time, treatment are interaction are significant. However, when I run 
the script for Tukey comparisons, I only get 15 comparisons. Of course I cannot 
interpret that:

these comparisons are the same for Time 1 and Time 2, since there is a 
significant effect of time. Moreover, I got a warning message : covariate 
interactions found. I dont know if I am doing right? I dont know what to do?


Thank you for your help,


Xavier

PhD Student

University of Neuchatel


lm3=glm(expresion~time*treatment,family="poisson")
> summary(lm3)

Call:
glm(formula = expresion ~ time * treatment, family = "poisson")

Deviance Residuals:
Min   1Q   Median   3Q  Max
-5.3796  -1.4523  -0.6642   1.2277   6.3909

Coefficients:
  Estimate Std. Error z value Pr(>|z|)
(Intercept)2.099640.29508   7.115 1.12e-12 ***
time   0.202940.19255   1.054 0.291895
treatmentCHA0+Db  -0.170040.36180  -0.470 0.638356
treatmentDb1.689520.37624   4.490 7.11e-06 ***
treatmentHEALTHY   0.840350.50340   1.669 0.095049 .
treatmentPCL   0.320720.37950   0.845 0.398041
treatmentPCL+Db0.543650.34047   1.597 0.110320
time:treatmentCHA0+Db  0.873140.22626   3.859 0.000114 ***
time:treatmentDb  -0.828030.26539  -3.120 0.001808 **
time:treatmentHEALTHY -1.369870.38318  -3.575 0.000350 ***
time:treatmentPCL  0.084740.24635   0.344 0.730851
time:treatmentPCL+Db   0.392440.21521   1.824 0.068217 .
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

(Dispersion parameter for poisson family taken to be 1)

Null deviance: 1173.05  on 66  degrees of freedom
Residual deviance:  403.07  on 55  degrees of freedom
AIC: 707.95

Number of Fisher Scoring iterations: 5


> anova(lm3,test="Chisq")
Analysis of Deviance Table

Model: poisson, link: log

Response: expresion

Terms added sequentially (first to last)


   Df Deviance Resid. Df Resid. Dev  Pr(>Chi)
NULL  661173.05
time1   100.55651072.50 < 2.2e-16 ***
treatment   5   561.6960 510.81 < 2.2e-16 ***
time:treatment  5   107.7555 403.07 < 2.2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1


> summary(glht(lm3, mcp(treatment="Tukey")))

 Simultaneous Tests for General Linear Hypotheses

Multiple Comparisons of Means: Tukey Contrasts


Fit: glm(formula = expresion ~ time * treatment, family = "poisson")

Linear Hypotheses:
   Estimate Std. Error z value Pr(>|z|)
CHA0+Db - CHA0 == 0 -0.1700 0.3618  -0.470   0.9970
Db - CHA0 == 0   1.6895 0.3762   4.490   <0.001 ***
HEALTHY - CHA0 == 0  0.8404 0.5034   1.669   0.5402
PCL - CHA0 == 0  0.3207 0.3795   0.845   0.9568
PCL+Db - CHA0 == 0   0.5437 0.3405   1.597   0.5892
Db - CHA0+Db == 01.8596 0.3135   5.931   <0.001 ***
HEALTHY - CHA0+Db == 0   1.0104 0.4584   2.204   0.2266
PCL - CHA0+Db == 0   0.4908 0.3174   1.546   0.6231
PCL+Db - CHA0+Db == 00.7137 0.2696   2.648   0.0817 .
HEALTHY - Db == 0   -0.8492 0.4699  -1.807   0.4491
PCL - Db == 0   -1.3688 0.3338  -4.101   <0.001 ***
PCL+Db - Db == 0-1.1459 0.2887  -3.969   <0.001 ***
PCL - HEALTHY == 0  -0.5196 0.4725  -1.100   0.8764
PCL+Db - HEALTHY == 0   -0.2967 0.4418  -0.672   0.9842
PCL+Db - PCL == 00.2229 0.2929   0.761   0.9725
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
(Adjusted p values reported -- single-step method)

Warning message:
In mcp2matrix(model, linfct = linfct) :
  covariate interactions found -- default contrast might be inappropriate


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[R] GLM HELP NEEDED!

2017-02-01 Thread CHIRIBOGA Xavier
Dear colleagues,


I am trying to perform a GLM. I tried again without using attach()...but still 
is not working.

Do you have any idea to help me?


Thank you again,


Xavier



a <- read.table(file.choose(), h<-T)
> head(a)
  time treatment transinduc
11   CHA0+Db 1,0768
21   CHA0+Db 1,0706
31   CHA0+Db 1,0752
41   CHA0+Db 1,0689
51   CHA0+Db 1,1829
61PCL+Db 1,1423
> summary(a)
  time treatmenttransinduc
 Min.   :1.000   CHA0   :10   1,0488 : 6
 1st Qu.:1.000   CHA0+Db: 9   1,0724 : 4
 Median :1.000   Db : 9   1,0752 : 3
 Mean   :1.433   HEALTHY:15   1,0954 : 3
 3rd Qu.:2.000   PCL:10   1,0001 : 2
 Max.   :2.000   PCL+Db :14   1,0005 : 2
  (Other):47
> m1<-glm(a$transinduc~a$time*a$treatment,data=a,family="poisson")
Error in if (any(y < 0)) stop("negative values not allowed for the 'Poisson' 
family") :
  valor ausente donde TRUE/FALSE es necesario
Adem�s: Warning message:
In Ops.factor(y, 0) : '<' not meaningful for factors


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[R] HELP with GLM

2017-01-31 Thread CHIRIBOGA Xavier
Dear colleagues,


I am trying to perform GLM ..but I got some objects masked: and an error 
message below


a <- read.table(file.choose(), h<-T)
> head(a)
  time treatment transinduc
11   CHA0+Db 1,0768
21   CHA0+Db 1,0706
31   CHA0+Db 1,0752
41   CHA0+Db 1,0689
51   CHA0+Db 1,1829
61PCL+Db 1,1423
> attach(a)
The following objects are masked from a (pos = 12):

time, transinduc, treatment

The following objects are masked from a (pos = 13):

time, treatment

The following objects are masked from a (pos = 14):

time, treatment

> summary(a)
  time treatmenttransinduc
 Min.   :1.000   CHA0   :10   1,0488 : 6
 1st Qu.:1.000   CHA0+Db: 9   1,0724 : 4
 Median :1.000   Db : 9   1,0752 : 3
 Mean   :1.433   HEALTHY:15   1,0954 : 3
 3rd Qu.:2.000   PCL:10   1,0001 : 2
 Max.   :2.000   PCL+Db :14   1,0005 : 2
  (Other):47


m1<-glm(transinduc~time*treatment,data=a,family="poisson")
Error in if (any(y < 0)) stop("negative values not allowed for the 'Poisson' 
family") :
  valor ausente donde TRUE/FALSE es necesario
Adem�s: Warning message:
In Ops.factor(y, 0) : '<' not meaningful for factors


I DO NOT HAVE NEGATIVE VALUES IN MY DATASET, Do you know what is going wrong?


Thank you for you help,


Xavier

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[R] HELP GLM

2017-01-30 Thread CHIRIBOGA Xavier
Dear colleagues,


I am trying to perform GLM but I got the following message.


 m2<-glm(induction~time+plant,data=b)
Error in glm.fit(x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,  :
  NA/NaN/Inf in 'y'
Adem�s: Warning messages:
1: In Ops.factor(y, mu) : '-' not meaningful for factors
2: In Ops.factor(eta, offset) : '-' not meaningful for factors
3: In Ops.factor(y, mu) : '-' not meaningful for factors


Do you know why it is not working?


Thank you for your help,


Xavier

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Re: [R] HELP lme4 & lmerTest INSTALLATION

2017-01-25 Thread CHIRIBOGA Xavier
Dear Thierry,


So, does it mean that I have to install "nlme" instead of "lme4"? or first 
"nlme" and after "lme4"???


I also need"lmerTest" and when I installed it, I got the following message:


install.packages("lmerTest")
Installing package into 'C:/Users/Hp/Documents/R/win-library/3.3'
(as 'lib' is unspecified)
probando la URL 
'http://cran.espol.edu.ec/bin/windows/contrib/3.3/lmerTest_2.0-33.zip'
Content type 'application/zip' length 1149547 bytes (1.1 MB)
downloaded 1.1 MB

package 'lmerTest' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\Hp\AppData\Local\Temp\Rtmp6D0iIu\downloaded_packages
> library(lmerTest)
Loading required package: Matrix
Loading required package: lme4

Attaching package: 'lme4'

The following object is masked from 'package:nlme':

lmList


Attaching package: 'lmerTest'

The following object is masked from 'package:lme4':

lmer


THANK YOU FOR YOUR REPLY,


Xavier


From: Thierry Onkelinx <thierry.onkel...@inbo.be>
Sent: Wednesday, January 25, 2017 12:42 PM
To: Rui Barradas
Cc: CHIRIBOGA Xavier; r-help@r-project.org
Subject: Re: [R] HELP lme4 & lmerTest INSTALLATION

Dear Rui,

nlme is a recommended package, lme4 is (currently) not. You need to install it.

Best regards,

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and 
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium

To call in the statistician after the experiment is done may be no more than 
asking him to perform a post-mortem examination: he may be able to say what the 
experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not ensure 
that a reasonable answer can be extracted from a given body of data. ~ John 
Tukey

2017-01-25 11:45 GMT+01:00 Rui Barradas 
<ruipbarra...@sapo.pt<mailto:ruipbarra...@sapo.pt>>:

You don't need to install lme4, it comes with base R.

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[R] HELP lme4 & lmerTest INSTALLATION

2017-01-24 Thread CHIRIBOGA Xavier
Dear colleagues,


I am having trouble installing lme4 package and this leads me to problems 
installing lmerTest, when I try to do I got this Error messages:

>install.packages("lme4")
Installing package into 'C:/Users/Hp/Documents/R/win-library/3.3'
(as 'lib' is unspecified)
probando la URL 
'http://cran.espol.edu.ec/bin/windows/contrib/3.3/lme4_1.1-12.zip'
Content type 'application/zip' length 4745943 bytes (4.5 MB)
downloaded 4.5 MB

package 'lme4' successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package 'lme4'

The downloaded binary packages are in
C:\Users\Hp\AppData\Local\Temp\RtmpWKmMgm\downloaded_packages
> library(lme4)
Error in library(lme4) : there is no package called 'lme4'
> install.packages("lmerTest")
Installing package into 'C:/Users/Hp/Documents/R/win-library/3.3'
(as 'lib' is unspecified)
also installing the dependency 'lme4'

probando la URL 
'http://cran.espol.edu.ec/bin/windows/contrib/3.3/lme4_1.1-12.zip'
Content type 'application/zip' length 4745943 bytes (4.5 MB)
downloaded 4.5 MB

probando la URL 
'http://cran.espol.edu.ec/bin/windows/contrib/3.3/lmerTest_2.0-33.zip'
Content type 'application/zip' length 1149636 bytes (1.1 MB)
downloaded 1.1 MB

package 'lme4' successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package 'lme4'
package 'lmerTest' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\Hp\AppData\Local\Temp\RtmpWKmMgm\downloaded_packages
> library(lmerTest)
Loading required package: Matrix
Error: package 'lme4' required by 'lmerTest' could not be found
Adem�s: Warning message:
In read.dcf(file.path(p, "DESCRIPTION"), c("Package", "Version")) :
  cannot open compressed file 
'C:/Users/Hp/Documents/R/win-library/3.3/lme4/DESCRIPTION', probable reason 'No 
such file or directory'



Could yo please help me?

What to do? I am using latest version : R 3.3.2.


Thank you very much,

Xavier


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[R] ERROR in make.link(link)

2016-03-20 Thread CHIRIBOGA Xavier
Dear all,


I am using R version 3.1.3. I want to run this model:

m1<-glmer(hours~soil*volatile+(1|replicate),  data=data,family=Gamma(link = 
"inv"))


But I got this:

Erreur within make.link(link) : 'inv' link not recognised


What to do in this case?


THANK YOU for help!


Xavier

PhD candidate

Biology

UNINE, Switzerlnad

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[R] package Formula????

2016-03-11 Thread CHIRIBOGA Xavier
Dear all, again me


I have already updated my version of R. But still appears this message:


plot(ctree(Surv(hours,state)~soil+volatile, data=data))
Error in loadNamespace(name) : there is no package called 'Formula'


I cannot find a package "Formula" in my list of packages. What to do in that 
case?


Thank you,

Xavier

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[R] How to install package effects

2016-03-11 Thread CHIRIBOGA Xavier
Dear all,

How to install function effects in R 3.1.2.? I got this:

 plot(effect("soil:volatile", model1))
Error in plot(effect("soil:volatile", model1)) :
  could not find function "effect"
Error in find.package(if (is.null(package)) loadedNamespaces() else package,  :
  there is no package called ''

Thank you very much,

Xavier

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[R] CANNOT RUN ctree

2016-03-10 Thread CHIRIBOGA Xavier
Dear all,
Sorry for question again, but I am desesperating..
I installed already "partykit" But there is stille a message (see below):
the package "partykit" has been compiled with the version R3.1.3.
What should I do now?

I run my function and appears this:

Error in loadNamespace(name) : there is no package called 'Formula'

THANK YOU for ur assistance,

Xavier


install.packages("partykit") Installing package into 
'C:/Users/chiribogax/Documents/R/win-library/3.1' (as 'lib' is unspecified) 
trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.1/partykit_1.0-5.zip' 
Content type 'application/zip' length 1215105 bytes (1.2 Mb) opened URL 
downloaded 1.2 Mb package 'partykit' successfully unpacked and MD5 sums checked 
The downloaded binary packages are in 
C:\Users\chiribogax\AppData\Local\Temp\RtmpyugH55\downloaded_packages > 
library("partykit") Le chargement a nécessité le package : grid Warning 
message: le package 'partykit' a été compilé avec la version R 3.1.3 > 
plot(ctree(Surv(hours,state)~soil+volatile, data=data)) Error in 
loadNamespace(name) : there is no package called 'Formula'

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[R] FUNCTION ctree

2016-03-10 Thread CHIRIBOGA Xavier
Dear all,


I am using Rstudio. What to do when you get this message?

Error in plot(ctree(Surv(hours, state) ~ soil + volatile, data = data)) :
  could not find function "ctree"

Thank you,


Xavier

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[R] erv.inv NOT FOUND

2015-04-20 Thread CHIRIBOGA Xavier
Dear members, in this case



Error: could not find function erf.inv



Anyone knows the package?

Thanks a lot!



Xavier

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[R] ABOUT STATS FORUM

2015-04-20 Thread CHIRIBOGA Xavier
Dear members,



Since this is not a Forum for Stats questions...does anyone can recomend me a 
good forum to post questions about statistics?



Thank you for info,



Xavier

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[R] RODBC package not found (in English)

2015-04-20 Thread CHIRIBOGA Xavier
Dear members,



What can I do if I get this message: ?



library(RODBC)
Error in library(RODBC) : any package called ‘RODBC’ was found





Thanks in advcance,



Xavier

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[R] RODBC did not found

2015-04-20 Thread CHIRIBOGA Xavier
Dear members,



What can I do if I get this message: ?



library(RODBC)
Error in library(RODBC) : aucun package nommé ‘RODBC’ n'est trouvé





Thanks in advcance,



Xavier

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[R] groupedData HELP!

2015-04-20 Thread CHIRIBOGA Xavier
Dear members,



what to do when this appears ?



Error: could not find function groupedData



Thanks a lot,

Xavier

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[R] survreg FUNCTION

2015-04-08 Thread CHIRIBOGA Xavier
Dear members,



I am trying a survival analysis , I got:



Error: could not find function survreg



I already load

the packages: survival

the function: splines



What can I do?



Thanks for you help,



Xavier

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[R] WEIBULL or EXPONENTIAL?

2015-04-03 Thread CHIRIBOGA Xavier
Dear members,



I am doing a survival analysis wiith the function coxph...however I am 
wondering how can I know if my data follows a EXPONENTIAL or WEIBULL 
distribution?

I have 3 censored datum. Using R studio.



Thanks for the suggestions,



Xavier

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and provide commented, minimal, self-contained, reproducible code.


[R] HELP Tukey

2015-02-26 Thread CHIRIBOGA Xavier
Dear all ,



I am trying to do a Tukey comparison, but a message appears:



tuk-glht(mod0,linfct=mcp(Soil=Tukey));summary(tuk)
Error: could not find function glht



Anyone knows how to fix it?



Thanks a lot!



Xavier

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and provide commented, minimal, self-contained, reproducible code.


[R] library(multcomp) does not work for loading Tukey

2015-02-26 Thread CHIRIBOGA Xavier
Dear colleagues,



For Tukey, I tried to load the function with



library(multcomp) but again a message says:



Error in library(multcomp) : any package called ‘multcomp’ has been found







Thanks for ur help,

Xavier

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[R] HELP asin transformation

2015-02-22 Thread CHIRIBOGA Xavier
Dear all,



I attempted to transform my data using asin but a WARNING message appears:



dat1$Abu.tr-asin(sqrt(dat1$Abundance/100))
Warning message:
In asin(sqrt(dat1$Abundance/100)) : NaNs produced



What does it mean? Is it a problem? How can I solve this?



Thank you!



XAVIER

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[R] groupedData FUNCTION

2015-02-22 Thread CHIRIBOGA Xavier
Dear colleagues,



I am trying to use the function groupedData. However, I got this message:



results-groupedData(Abundance~Timepoint|Repli,outer=~Soil,data=dat1)
Error: could not find function groupedData





I am puttin g all my willingness to learn R but this is really desesperating. 
One problem over another



ThANK YOU!

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[R] qq-Plot function in version 3.1.2.

2015-02-13 Thread CHIRIBOGA Xavier
Hello! SORRY PROBLEMS WITH FUNCTIONS AGAIN...



I NEED TO RUN A qqPlot ...I TRIED TO INSTALL IT , BUT A WARNING MESSAGE SAID



qqPlot is not available for version 3.1.2.







qqPlot(residuals(anc0),id.method=identify)
Error: could not find function qqPlot
 install.packages(qqPlot)
Installing package into ‘C:/Users/chiribogax/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘qqPlot’ is not available (for R version 3.1.2)



WHAT CAN ID DO?



THANK YOU,



Xavier

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[R] SIMPLE question

2015-02-12 Thread CHIRIBOGA Xavier
Hi everybody!



I want to do a boxcox transformation, but I got this:



Error: could not find function boxcox



What can I do? I am using R studio.



Thanks!!!



Xavier

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