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Questions tagged [vgam]

33 questions
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vglm in VGAM package for ordinal variables: what do the letters L and Q stand for?

I'm fitting a cumulative-logit model using an ordinal explicative, the coefficients I get are as following: coefficients(cum_mod_podds_ord,matrix=TRUE) logit(P[Y>=2]) logit(P[Y>=3]) (Intercept) -0.4106068 -1.2504301 depr_ord.L …
Roberto
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Compare model fits of two GAM

I have a matrix Expr with rows representing variables and columns samples. I have a categorical vector called groups (containing either "A","B", or "C") I want to test which of variables 'Expr' can be explained by the fact that the sample belong to…
Gioelelm
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Generalized ordered regression with clustered standard error using the vglm function

I am working with an ordinal outcome variable (state_prev) measuring sexual violence prevalence, using a generalized ordered regression. I fitted the model: sup_state <- vglm(state_prev ~ ext_sup + ext_f + ANIpC + GDPpC + unemployment + population,…
chf
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Shift variable with global weight and threshold variables using VGLM

I've been asked to compute a sequential logit model with threshold variables. The response v is a categorical variable with three levels. There are two covariates, both are categorical variables. w has two levels and x has three levels. We are also…
stats19
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Calling the same function using VGAM::sm.ps or sm.ps in R leads to different output

I am trying to fit a multinomial logistic regression model with a vector spline smoother on the predictors. I am using the VGAM package in R (specifically the vgam function to fit the model). I have used this numerous times before and always just…
AP30
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Generalised Impulse response functions (GIRF) for VGAMs (vector GAM) in R

I have 2 variables as time series. I'd like to build semi-parametric VGAM, then analyse GIRF from Koop, Pesaran and Potter (1996) (analogously with IRF of VAR model). Which R function should I use? Are there any R functions to plot generalised…
Sergei Kharin
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Error in environment(formula) : argument "formula" is missing with no default

I'm using the vglm function of the VGAM package. m <- vglm(log(variable+1) ~ ., tobit(Lower=0), data = dat) I was able to run the code above without any issues previously, but I'm getting this error message. Error in environment(formula) : argument…
confusedpanda
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lrtest() not working: posthoc testing for multinomial with vglm() not working with lrtest()

I am running a multinomial analysis with vglm(). It all works, but then I try to follow the instructions from the following website (https://rcompanion.org/handbook/H_08.html) to do a pairwise test, because emmeans cannot handle pairwise for vglm…
catcool7
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Warning: "Intersecting linear/additive predictors" when fitting non-proportional odds ordinal regression model with VGLM()

I am fitting a partial proportional odds cumulative logit ordinal regression model. Response is an ordinal diagnosis, predictors are two urinary biomarkers. I fit the model using the following command: fit=vglm(diagnosis ~ creatinine + LYVE1,…
Timofei
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Shape estimation in truncated Pareto in R

library(VGAM) library(fitdistrplus) fitdist(u_NI$k_u, 'truncpareto', start = list(lower=1, upper=42016, shape=1)) -> fit.k_u length(u_NI$k_u) = 637594 I got this error:
GiulioGCantone
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Need help, I stuck when install (VGAM) and how to use mlogit. I don't understand from that pdf example

I need help for my problems. I have 2 problems. I can't install library (VGAM) on my RStudio. Have any idea for another regression logistic ordinal package or have solution for my problem? I Stuck for the first step when used mlogit. I have…
Yip
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Bug with VGAM? vglm family=posnegbinomial => "Error in if (take.half.step) { : missing value where TRUE/FALSE needed"

I have some actual data that I am afraid is somewhat nasty. It's essentially a Positive Negative Binomial distribution (without any zero counts). However, there are some outliers that seem to cause some bad calculations to occur (maybe underflow or…
Clem Wang
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Tobit : Error in lm.fit(X.vlm, y = z.vlm, ...) : NA/NaN/Inf in 'x' (simulated data)

I'm conducting a Monte Carlo study. I have a linear model with heteroskedasticity and left censoring of the dependent variable at 0. The mean of censoring rates is 25.9. I get the error Error in lm.fit(X.vlm, y = z.vlm, ...) : NA/NaN/Inf in…
Victor
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method of moments: beta binomial distribution

I am attempting to work through the method of moments estimation of alpha and beta for a beta binomial distribution. Taking the steps found at: http://en.wikipedia.org/wiki/Beta-binomial_distribution#Maximum_likelihood_estimation I have think I have…
user3266890
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Link "identity" function to gamma distribution in VGAM package of R

I'm using the VGAM package to do a regression between two samples which are Gamma distributed. Is it possible to choose the identity function for the link? If yes, how? I'm using these code line and it works: fit <- vglm(Y ~ X , family = gammaR,…
Didi86
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