How to force R to use a specified factor level as reference in a regression

Question

How can I tell R to use a certain level as reference if I use binary explanatory variables in a regression   It s just using some level by default    lm x   y   as factor b      with b  0  1  2  3  4   Let s say I want to use 3 instead of the zero that is used by R

User · Answer

You can also manually tag the column with a contrasts attribute  which seems to be respected by the regression functions   contrasts df factorcol   lt - contr treatment levels df factorcol      base which levels df factorcol      RefLevel

User · Answer

Others have mentioned the relevel command which is the best solution if you want to change the base level for all analyses on your data  or are willing to live with changing the data    If you don t want to change the data  this is a one time change  but in the future you want the default behavior again   then you can use a combination of the C  note uppercase  function to set contrasts and the contr treatments function with the base argument for choosing which level you want to be the baseline     For example   lm  Sepal Width   C Species contr treatment 3  base 2    data iris

User · Answer

The relevel   command is a shorthand method to your question   What it does is reorder the factor so that whatever is the ref level is first   Therefore  reordering your factor levels will also have the same effect but gives you more control   Perhaps you wanted to have levels 3 4 0 1 2   In that case     bFactor  lt - factor b  levels   c 3 4 0 1 2     I prefer this method because it s easier for me to see in my code not only what the reference was but the position of the other values as well  rather than having to look at the results for that    NOTE   DO NOT make it an ordered factor   A factor with a specified order and an ordered factor are not the same thing   lm   may start to think you want polynomial contrasts if you do that

User · Answer

See the relevel   function  Here is an example   set seed 123  x  lt - rnorm 100  DF  lt - data frame x   x                   y   4    1 5 x    rnorm 100  sd   2                    b   gl 5  20   head DF  str DF   m1  lt - lm y   x   b  data   DF  summary m1    Now alter the factor b in DF by use of the relevel   function   DF  lt - within DF  b  lt - relevel b  ref   3   m2  lt - lm y   x   b  data   DF  summary m2    The models have estimated different reference levels    gt  coef m1   Intercept            x          b2          b3          b4          b5    3 2903239   1 4358520   0 6296896   0 3698343   1 0357633   0 4666219   gt  coef m2   Intercept            x          b1          b2          b4          b5   3 66015826  1 43585196 -0 36983433  0 25985529  0 66592898  0 09678759

User · Answer

For those looking for a dplyr tidyverse version  Building on Gavin Simpson solution     Create DF set seed 123  x  lt - rnorm 100  DF  lt - data frame x   x                   y   4    1 5 x    rnorm 100  sd   2                    b   gl 5  20      Change reference level DF   DF   gt   mutate b   relevel b  3    m2  lt - lm y   x   b  data   DF  summary m2

User · Answer

I know this is an old question  but I had a similar issue and found that   lm x   y   relevel b  ref    3       does exactly what you asked

[r] How to force R to use a specified factor level as reference in a regression?

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