# [R] HELP relevel INTERCEPT-COMPARISONS

Michael Dewey lists at dewey.myzen.co.uk
Sun Oct 29 13:16:18 CET 2017

```Dear Xavier

You problem comes from using attach(). Do not do that, it usually ends
in tears. Either use the data parameter to the functions which support
it or look at with() and within().

On 28/10/2017 21:11, CHIRIBOGA Xavier wrote:
> 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.
>
>
>
> Xavier
>
>
>    treatment replicate Time     Ebcg
> 1   CHA0+Db         1    1  9681172
> 2   CHA0+Db         2    1  5599000
> 3   CHA0+Db         3    1 10280480
> 4   CHA0+Db         4    1  1004526
> 5   CHA0+Db         5    1 12942018
> 6   CHA0+Db         6    1  7478773
>> attach(T1)
>> summary(T1)
>     treatment   replicate          Time        Ebcg
>   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 ***
> treatmentDb                2491.9          496.3       5.021         9.93e-06 ***
> treatmentHealthy       1215.6          496.3       2.450         0.018552 *
> treatmentPCL                120.4          543.6       0.221         0.825816
> treatmentPCL+Db        2098.9          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
>
> 	[[alternative HTML version deleted]]
>
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> and provide commented, minimal, self-contained, reproducible code.
>

--
Michael
http://www.dewey.myzen.co.uk/home.html

```