Skip to content

How to set Manually the Reference Level in glmmTMB

2 messages · Alexandre F. Souza, Thierry Onkelinx

Original
Alexandre F. Souza
# 
Dear all,

I am running a glmm with glmmTMB in which the fixed part has two factor
varialbes, year (ano_medida) and habitat type (Grupos_Finais below). Since
I have only two years I do not mind that the model takes the first year as
a baseline. However, no habitat type is a control or a reference, and I
would like to see results for all levels of this variable. I would like to
know how to manually do this, but I am only finding in the internet
resources to change the reference level, not to cancel it. Could anyone
help me with this?

modelo2.glmm = glmmTMB(reproducao_bin ~ ano_medida +
Basal_Area_m2*Grupos_Finais + R_dens_total*Grupos_Finais + (1|numero) + (1
|bloco/transecto/parcela), family = binomial, data = dados)

My data:
'data.frame': 1428 obs. of  12 variables:
 $ numero                  : int  4006 4009 4010 4020 4022 4024 4025 4027
4035 4036 ...
 $ bloco                   : int  1 1 1 1 1 1 1 1 1 1 ...
 $ transecto               : int  1 1 1 1 1 1 1 1 1 1 ...
 $ parcela                 : int  1 1 1 1 1 1 1 1 1 1 ...
 $ Tree_Height_m_Fuste_Parc: num  8.32 8.32 8.32 8.32 8.32 ...
 $ Grupos_Finais           : Factor w/ 3 levels "Disturbed Unflooded
Forests",..: 1 1 1 1 1 1 1 1 1 1 ...
 $ ano_medida              : Factor w/ 2 levels "2016","2017": 1 1 1 1 1 1
1 1 1 1 ...
 $ Basal_Area_m2           : num  0.182 0.182 0.182 0.182 0.182 ...
 $ das_mm                  : num  185 161 167 114 164 ...
 $ reproducao              : int  3 0 0 0 0 0 0 0 0 0 ...
 $ reproducao_bin          : int  1 0 0 0 0 0 0 0 0 0 ...
 $ R_dens_total            : int  31 31 31 31 31 31 31 31 31 31 ...
Many thanks!

Alexandre
Thierry Onkelinx
# 
Dear Alexandre,

You could change the formula to

reproducao_bin ~ 0 + Grupos_Finais + ano_medida +
Basal_Area_m2*Grupos_Finais + R_dens_total*Grupos_Finais + (1|numero) +
(1|bloco/transecto/parcela)

Another option is to calculate contrasts based on the model.

Best regards,

ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkelinx at inbo.be
Havenlaan 88 bus 73, 1000 Brussel
*Postadres:* Koning Albert II-laan 15 bus 186, 1210 Brussel
*Poststukken die naar dit adres worden gestuurd, worden ingescand en
digitaal aan de geadresseerde bezorgd. Zo kan de Vlaamse overheid haar
dossiers volledig digitaal behandelen. Poststukken met de vermelding
?vertrouwelijk? worden niet ingescand, maar ongeopend aan de geadresseerde
bezorgd.*
www.inbo.be

///////////////////////////////////////////////////////////////////////////////////////////
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
///////////////////////////////////////////////////////////////////////////////////////////

<https://www.inbo.be>


Op do 28 mrt 2024 om 15:38 schreef Alexandre F. Souza <
alexsouza.cb.ufrn.br at gmail.com>: