Stack Overflow
Stack Overflow

Questions tagged [logistf]

17 questions
5
votes
1 answer

Extracting data from logistf in R

I cannot figure out how to extract the standard error "sd(coef)" information from the logistf() regression model. These models are of class logistf and the manual states that data can be extracted this way: The following generic methods are…
Lel
  • 139
  • 1
  • 2
  • 13
5
votes
1 answer

R - Separation issue in binary response models - glm, brglm, logistf

I am encountering some issues with my data and need some help. I am trying to run glm analysis with a presence/absence variable as response variable and several explanatory variable (time, location, presence/absence data, abundance data). First I…
Xochitl C.
  • 201
  • 2
  • 7
4
votes
2 answers

error: 'object not found' in nested functions

I was writing a function using the logistf::logistf and logistf::forward function. I will give here a minimum working example using sex2 from the logistf package. data(sex2) fwSel <- function(datamod) { fitnull <- logistf(case ~ 1, data = datamod,…
tnaake
  • 469
  • 5
  • 17
2
votes
1 answer

Plots with error bars using logistf object

I initially did a logistic model using the glm package but wanted to correct for separation so I have used the logistf function and I'm now trying to redo my plots. I'm unsure how to make a plot like the one below with a logistf object. A lot of…
Farida El Kafrawy
  • 43
  • 5
2
votes
0 answers

Difference between brglm & logistf?

I am currently fitting a penalized logistic regression model using the package logistf (due to quasi-complete separation). I chose this package over brglm because I found much more recommendations for logistf. However, the brglm seems to integrate…
elehna
  • 106
  • 5
2
votes
1 answer

Forest plot from logistf

I have run a few models in for the penalized logistic model in R using the logistf package. I however wish to plot some forest plots for the data. The sjPlot package : http://www.strengejacke.de/sjPlot/custplot/ gives excellent function for the glm…
Edwin
  • 35
  • 5
1
vote
1 answer

Loading {logistf} breaks MCMCglmm()

Loading the package logistf breaks MCMCglmm(). Unloading logistf before running the command doesn't remove the error. Why is that? Is there a way to solve this? Works library(MCMCglmm) #> Loading required package: Matrix #> Loading required package:…
bretauv
  • 7,756
  • 2
  • 20
  • 57
1
vote
1 answer

Unable to perform logistic regression in R

I am trying out logistic regression on a data.frame (11359 rows, 137 columns). The data.frame contains Y (one dependent variable) and the predictors (136 independent variables). All the variables are binary. The formula I created based on "my_data"…
elpavlos
  • 35
  • 4
0
votes
0 answers

Logistic Regression in R - using package "logistf"

I used the package "logistf" to perform a logistic regression in R. df <- read.csv("data.csv",header=T,row.names=1) df <- as.data.frame(sapply(df, as.numeric)) df_split <- initial_split(df, prop = 0.9) df_train <- training(df_split) %>% …
NakataKoo
  • 11
  • 2
0
votes
1 answer

Is it correct to say that any question having the term ”Softmax function” is a duplicate copy?

I would like you to leave your comments on: If it is right to say that any question having the term ‘softmax function’ is a duplicate copy to the other questions having the term ‘softmax function’ on it?
Dr Hazael Brown
  • 9
  • 5
0
votes
1 answer

create my nribin code for logistf ,does it really work?

i need to creat my own nribin code , it can be used for logistf package outcome, i maybe work,please give me some advise!!! i change z.std = mdl.std$x[,-1] to z.std = mdl.std$x and cancle: link = mdl.std$family[[2]] and …
lewis liu
  • 1
0
votes
0 answers

Memory error when applying logistf()

I am trying to apply logistf() on a dataframe (dim:11359x139). All the variables are binary. I get the following message: "Error in logistf.fit(x = x, y = y, weight = weight, offset = offset, firth, : no memory available". Even if I take into…
elpavlos
  • 35
  • 4
0
votes
2 answers

Extracting Chisq values from logistf in R

I am running a logistf model on R fit<-logistf(data=data, Amylose_trans ~ Tissue + Species); summary(fit) logistf(formula = Amylose_trans ~ Tissue + Species, data = data) Model fitted by Penalized ML Confidence intervals and p-values by Profile…
Panos
  • 179
  • 2
  • 13
0
votes
0 answers

Firth penalized regression

I'm modelling a logistic regression with the Firth's correction, using logistf package in R. When I use the command DROP1/ADD1, R help says it is based on the penalized likelihood ratio. But is the penalization it says actually the Firth's…
Claudio
  • 1
0
votes
0 answers

R - Logistf vs glm vs clogit for studies with matched pairs

I'm working on a database with matching pairs (1 to 5/6 matching) and am trying to obtain the Odds Ratio (95% confidence interval) for my variables using conditional logistic…
Shaun
  • 1
  • 1
1
2