interaction term in multilevel analysis using lmer() function - r

level 1 variable:
income - continuous
level 2 variable:
state's general whether: three leveled categorical variable: hot/moderate/cool
used effect coded, and generate two variables because it has three levels.
(weather_ef1, weather_ef2)
enrolled in university - binary : yes/no ( effect coded. yes = -1, no =1)
DV:
math score
grouping variable: household
model 1: (fixed slope)
Dv is predicted by income, enrollment, and the interaction between enrollment and income.
in this case,
lmer(y~ 1 + income + enrollment +income*enrollment+ (1|householdID), data=data)
lmer(y~ 1 + income + enrollment +income:enrollment+ (1|householdID), data=data)
: is it for interaction? or * is it for interaction?
further, do I have to do factor(enrollment)?
or is it okay because it is already effect coded?
model 2: (fixed slope)
DV is predicted by income, weather, and interaction between income and weather
lmer( y ~ 1 + income + weather_ef1 + weather_ef2 + weather_ef1*income
+ weather_ef2*income +(1|houshold_id), data)
lmer ( y ~ l + income + weather_ef1+ weather_ef2 + weather_ef1:income
+ weather_ef2:income + (1|houshold_id), data)
Still confusing * is right or: is right.
I think the effect code variables are already effect coded, so I don't have to
do use the factor(weather_ef1) things.

From the documentation (use ?formula):
The * operator denotes factor crossing: a*b interpreted as a+b+a:b.
In other words a*b adds the main effects of a and b and their interaction. So in your model when you use income*enrollment this is the same as income + enrollment +income:enrollment. The two versions you described for each model should give identical results. You could just have used:
lmer(y~ 1 + income*enrollment+ (1|householdID), data=data)
which also describes the same model.
If your variables are effect coded then you don't need to use factor but be careful about the interpretation of the effects.

Related

Plot predicted values from lmer longitudinal analysis

I'm analyzing some longitudinal data using lme4 package (lmer function) with 3 Levels: measurement points nested in individuals nested in households. I'm interested in linear and non-linear change curves surrounding a specific life event. My model has many time predictors (indicating linear change before and after the event occurs and indicating non-linear change (i.e., squared time variables) before and after the event occurs). Additionally, I have several Level-2 predictors that do not vary with time (i.e., personality traits) and some control variables (e.g., age, gender). So far I did not include any random slopes or cross-level interactions.
This is my model code:
model.RI <- lmer(outcome ~ time + female_c + age_c + age_c2 + preLin + preLin.sq + postLin + postLin.sq + per1.c + per2.c + per3.c + per4.c + per5.c + (1 | ID) + (1 | House))
outcome = my dependent variable
time = year 1, year 2, year 3 ... (until year 9); this variable symbolizes something like a testing effect
female_c = gender centered
age_c = age centered
age_c2 = age squared centered
preLin = time variable indicating time to the event (this variable is 0 after the event has occurred and is -1 e.g. one year ahead of the event, -2 two years ahead of the event etc.)
preLin.sq = squared values of preLin
postLin = time variable indicating time after the event (this variable is 0 before the event and increases after the event has occurred; e.g. is +1 one year after the event)
postLin.sq = squared values of postLin
per1.c until per5.c = personality traits on Level 2 (centered)
ID = indicating the individuum
House = indicating the household
I was wondering how I could plot the predicted values of this lmer model (e.g., using ggplot2?). I've plotted change curves using the method=gam in R. This is a rather data-driven method to inspect the data without pre-defining if the curve is linear or quadratic or whatever. I would now like to check whether my parametric lmer model is comparable to that data-driven gam-plot I already have. Do you have any advise how to do this?
I would be more than happy to get some help on this! Please also feel free to ask if I was not precise enough on my explanation of what I would like to do!
Thanks a lot!
Follow this link: This is how my gam-plot looks like and I hope to get something similar when plotting the predicted values of my lmer model!
You can use the ggpredict()-function from the ggeffects-package. If you want to plot predicted values of time (preLin), you would simply write:
ggpredict(model.RI, "preLin")
The function returns a data frame (see articles), which you can use in ggplot, but you can also directly plot the results:
ggpredict(model.RI, "preLin") %>% plot()
or
p <- ggpredict(model.RI, "preLin")
plot(p)
You could also use the sjPlot-package, however, for marginal effects / predicted values, the sjPlot::plot_model()-function internally just calls ggeffects::ggpredict(), so the results would basically be identical.
Another note to your model: if you have longitudinal data, you should also include your time-variable as random slope. I'm not sure how postLin acutally refers to preLin, but if preLin captures all your measurements, you should at least write your model like this:
model.RI <- lmer(
outcome ~ time + female_c + age_c + age_c2 + preLin + preLin.sq +
postLin + postLin.sq + per1.c + per2.c + per3.c + per4.c + per5.c +
(1 + preLin | ID) + (1 + preLin | House)
)
If you also assume a quadratic trend for each person (ID), you could even add the squared term as random slope.
As your figure example suggests using splines, you could also try this:
library(splines)
model.RI <- lmer(
outcome ~ time + female_c + age_c + age_c2 + bs(preLin)
postLin + postLin.sq + per1.c + per2.c + per3.c + per4.c + per5.c +
(1 + preLin | ID) + (1 + preLin | House)
)
p <- ggpredict(model.RI, "preLin")
plot(p)
Examples for splines are also demonstrated on the website I mentioned above.
Edit:
Another note is related to nesting: you're currently modelling a fully crossed or cross-classified model. If it's completely nested, the random parts would look like this:
... + (1 + preLin | House / ID)
(see also this small code-example).

Exposure variable in logistic regression

I have a data frame which contains some characteristics from clients and contracts and 0s and 1s showing whether a fall happened the period between 2008 and 2017. I'm using a binomial model to regress probability of fall on the characteristics. I have 38000 differents contracts.
So I'm using an binomial model like this (R-code):
formule <- y ~ Niveau_gar_incapacite + Niv_indem_mens + Regrpt_franchise + Niveau_prime + Situation_familiale + Classe_age_chute + Grde_Region + Regrpt_strate + Taille_courtier + Commission + Retention + Anciennete + Regrpt_CSP + Regrpt_sinistres + Couplage
logit <- glm(Chute_commerciale~1, data=train, family=binomial(link="logit"))
selection_asc_AIC <- step(logit, direction="forward", trace=TRUE, k=2, scope=list(upper=formule))
After some tests to find multi-collinearity, I did eliminations of variables or groupings of terms.
I have this result :
results from GLM
results from GLM 2
This results are not correct with null deviance and residual deviance.
I supposed my variable exposure that is the problem.
In fact, I have contracts beginning and finishing at differents years.
So my exposure can be 5.32 or 1.36 and I have truncation and censorship.
How can I treat this variable exposure in regression logistic binomial ?
If I duplicate my row by the number of year of exposure, there is a problem of independance of observations.

Why can't I use the dependent variable in the selection equation as an independent variable in the outcome equation?

I use the example from the sampleSelection package, where I switch the dependent variable for the outcome equation to family income, because I want the labor force participation of the woman, lfp, to be a logical determinant.
library("sampleSelection")
data( Mroz87 )
Mroz87$kids <- ( Mroz87$kids5 + Mroz87$kids618 > 0 )
selection2 <- selection(selection = lfp ~ age + I(age^2) + faminc + kids + educ,
outcome = faminc ~ lfp + wage + age + exper,
data = Mroz87, method = "2step")
My problem is that adding lfp as an independent variable in the outcome equation prevents a solution. I get:
Error in solve.default(crossprod(xMat)) :
Lapack routine dgesv: system is exactly singular: U[6,6] = 0
Removing lfp from the outcome allows a solution, but not the one I seek. I think I've read that the problem is in the matrix mathematics running underneath (singularity prevents inversion, maybe?). Is there a way to get the solution I want, a work around maybe?
This is tobit-2 model and hence you assume you observe faminc only for those who have lfp=1. So lfp is always 1 for the observed outcomes. Hence it is not be identified (separately from constant).
There is a new version of sampleSelection coming that does this (currently under r-forge in branches/treatReg). Hope to get it out in a couple of weeks.

Longitudinal Multi-group latent growth curve model with time-variant and time-invariant predictors (lavaan)

First of all, I am relatively new in using R and haven't used lavaan (or growth models) before so please excuse my ignorance.
I am doing my thesis and analyzing the U.S. financial industry during the financial crisis of 2007. I therefore have individual banks and several variables for each bank across time (from 2007-2013), some are time-variant (such as ROA or capital adequacy) and some are time-invariant (such as size or age). Some variables are also time-variant but not multi-level since they apply to all firms (such as the average ROA of the U.S. financial industry).
Fist of all, can I use lavaan's growth curve model ("growth") in this instance? The example given on the tutorial is for either time-varying variables (c) that influence the outcome (DV) or time-invariant variables (x1 & x2) which influence the slope (s) and intercept (i). What about time varying variables that influence the slope and intercept? I couldn't find an example for this syntax.
Also, how do I specify the "groups" (i.e. different banks) in my analysis? It is actually possible to do a multi-level growth curve model in lavaan (or R for that matter)?
Last but not least, I could find how to import a multilevel dataset in R. My dataset is basically a 3-dimensional matrix (different variables for different firms across time) so how do I input that via SPSS (or notepad?)?
Any help is much appreciated, I am basically lost on how to implement this model and sincerely need some assistance...
Thank you all in advance for your time!
Harry
edit: Here is the sytanx that I have come with so far. DO you think it makes sense?
ETHthesismodel <- '
# intercept and slope with fixed coefficients
i =~ 1*t1 + 1*t2 + 1*t3 + 1*t4
s =~ 0*t1 + 1*t2 + 2*t3 + 3*t4
#regressions (independent variables that influence the slope & intercept)
i ~ high_constr_2007 + high_constr_2008 + ... + low_constr_2007 + low_constr_2008 + ... + ... diff_2013
s ~ high_constr_2007 + high_constr_2008 + ... + low_constr_2007 + low_constr_2008 + ... + ... diff_2013
# time-varying covariates (control variables)
t1 ~ size_2007 + cap_adeq_2007 + brand_2007 +... + acquisitions_2007
t2 ~ size_2008 + cap_adeq_2008 + brand_2008 + ... + acquisitions_2008
...
t7 ~ size_2013 + cap_adeq_2013 + brand_2013 + ... + acquisitions_2013
'
fit <- growth(ETHthesismodel, data = inputdata,
group = "bank")
summary(fit)

specifying multiple random effects in R lmer (translating from HLM model)

I'm attempting to "translate" a model run in HLM7 software to R lmer syntax.
This is from the now-ubiquitous "Math achievement" dataset. The outcome is math achievement score, and in the dataset there are various student-level predictors (such as minority status, SES, and whether or not the student is female) and various school level predictors (such as Catholic vs. Public).
The only predictors in the model I want to fit are student-level predictors, which have all been group-mean centered to deal with dummy variables (aside: contrast codes are better). The students are nested in schools, so we should (I think) have random effects specified for all of the components of the model.
Here is the HLM model:
Level-1 Model
(note: all predictors at level one are group mean centered)
MATHACHij = β0j + β1j*(MINORITYij) + β2j*(FEMALEij) + β3j*(SESij) + rij
Level-2 Models
β0j = γ00 + u0j
β1j = γ10 + u1j
β2j = γ20 + u2j
β3j = γ30 + u3j
Mixed Model
MATHACHij = γ00 + γ10*MINORITYij + γ20*FEMALEij + γ30*SESij + u0j + u1j*MINORITYij + u2j*FEMALEij + u3j*SESij + rij
Translating it to lmer syntax, I try:
(note: _gmc means the variable has been group mean centered, the grouping factor is "school_id")
model1<-lmer(mathach~minority_gmc+female_gmc+ses_gmc+(minority_gmc|school_id)+(female_gmc|school_id)+(ses_gmc|school_id), data=data, REML=F)
When I run this model I get results that don't mesh with the HLM results. Am I specifying the random effects incorrectly?
Thanks!
When you specify your random effect structure, you can include each random effect in one parentheses. While this may not solve your result dependencies, I believe the appropriate random effects code syntax for your model is this:
lmer(mathach~minority_gmc + female_gmc + ses_gmc + (1 + minority_gmc + female_gmc + ses_gmc |school_id), data=data, REML=F)

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