Situation
I am fitting a series of evolving regression models. For the purposes of this question, we can think of these models in terms of Model A, Model B, and Model C. All models share at least one same covariate.
I am also fitting these models for two separate years of data. Again, for the purposes of this question, the years will be 2000 and 2010.
In an attempt to simplify the reporting of results, I am attempting to combine the reporting of the regressions into a single table that would have some kind of the following format:
2000 2010
Model A
Coef Ex1
Model B
Coef Ex1
Coef Ex2
Model C
Coef Ex1
Coef Ex2
Coef Ex3
The idea being that someone can look quickly at Coef Ex1 across several models and years.
What Have I Tried
I have tried to achieve the above table using both R stargazer and kable packages. With stargazer I can get the fully formatted table for a single model formulation across many years (e.g., stargazer(modelA2000, modelA2010), but I cannot figure out how to stack additional model formulations on the rows.
For kable I have been able to stack horizontal models, but I have not been able to add in additional years (e.g., coefs <- bind_rows(tidy(modelA2000), tidy(modelB2000), tidy(modelC2000)); coefs %>% kable()).
Question: how can I use stargazer or kable to report evolving regression models (which share the same covariates) in the rows but also with year of cross section on the column? I think I can somehow extend the answer posted here, although I'm not sure how.
Reproducible example
# Load the data
mtcars <- mtcars
# Create example results for models A, B, and C for 2000
modelA2000 <- lm(mpg ~ cyl, data = mtcars)
modelB2000 <- lm(mpg ~ cyl + wt, data = mtcars)
modelC2000 <- lm(mpg ~ cyl + wt + disp, data = mtcars)
# Slightly modify data for second set of results
mtcars$cyl <- mtcars$cyl*runif(1)
# Fit second set of results. Same models, pretending it's a different year.
modelA2010 <- lm(mpg ~ cyl, data = mtcars)
modelB2010 <- lm(mpg ~ cyl + wt, data = mtcars)
modelC2010 <- lm(mpg ~ cyl + wt + disp, data = mtcars)
Two notes before starting:
You want a pretty "custom" table, so it is almost inevitable that some manual operations will be required.
My answer relies on the development version of modelsummary, which you can install like this:
library(remotes)
install_github("vincentarelbundock/modelsummary")
We will need 4 concepts, many of them related to the broom package:
broom::tidy a function that takes a statistical model and returns a data.frame of estimates with one row per coefficient.
broom::glance a function that takes a statistical model and returns a one-row data.frame with model characteristics (e.g., number of observations)
modelsummary_list a list with 2 elements called "tidy" and "glance", and with a class name of "modelsummary_list".
The modelsummary package allows you to draw regression tables. Under the hood, it uses broom::tidy and broom::glance to extract information from those models. Users can also supply their own information about a model by supplying a list to which we assign the class modelsummary_list, as documented here.
EDIT: The recommended way to do this in modelsummary is now to use the group argument. Scroll to the end of this post for illustrative code.
Obsolete example with useful discussion
The modelsummary_wide is a function that was initially designed to "stack" results from several models with several groups of coefficients. This is useful for things like multinomial models, but it also helps us in your case, where you have multiple models in multiple groups (here: years).
First, we load packages, tweak the data, and estimate our models:
library(modelsummary)
library(broom)
library(dplyr)
mtcars2010 <- mtcars
mtcars2010$cyl <- mtcars$cyl * runif(1)
models <- list(
"A" = list(
lm(mpg ~ cyl, data = mtcars),
lm(mpg ~ cyl, data = mtcars2010)),
"B" = list(
lm(mpg ~ cyl + wt, data = mtcars),
lm(mpg ~ cyl + wt, data = mtcars2010)),
"C" = list(
lm(mpg ~ cyl + wt + disp, data = mtcars),
lm(mpg ~ cyl + wt + disp, data = mtcars2010)))
Notice that we saved our models in three groups, in a list of list.
Then, we define a tidy_model function that accepts a list of two models (one per year), combines the information on those two models, and creates a modelsummary_list object (again, please refer to the documentation). Note that we assign the "year" information to a "group" column in the tidy object.
We apply this function to each of our three groups of models using lapply.
tidy_model <- function(model_list) {
# tidy estimates
tidy_2000 <- broom::tidy(model_list[[1]])
tidy_2010 <- broom::tidy(model_list[[2]])
# create a "group" column
tidy_2000$group <- 2000
tidy_2010$group <- 2010
ti <- bind_rows(tidy_2000, tidy_2010)
# glance estimates
gl <- data.frame("N" = stats::nobs(model_list[[1]]))
# output
out <- list(tidy = ti, glance = gl)
class(out) <- "modelsummary_list"
return(out)
}
models <- lapply(models, tidy_model)
Finally, we call the modelsummary_wide with the stacking="vertical" argument to obtain this table:
modelsummary_wide(models, stacking = "vertical")
Of course, the table can be adjusted, coefficients renamed, etc. using the other arguments of the modelsummary_wide function or with kableExtra or some other package supported by the output argument.
More modern example without detailed explanation
library("modelsummary")
library("broom")
library("quantreg")
mtcars2010 <- mtcars
mtcars2010$cyl <- mtcars$cyl * runif(1)
models <- list(
"A" = list(
"2000" = rq(mpg ~ cyl, data = mtcars),
"2010" = rq(mpg ~ cyl, data = mtcars2010)),
"B" = list(
"2000" = rq(mpg ~ cyl + wt, data = mtcars),
"2010" = rq(mpg ~ cyl + wt, data = mtcars2010)),
"C" = list(
"2000" = rq(mpg ~ cyl + wt + disp, data = mtcars),
"2010" = rq(mpg ~ cyl + wt + disp, data = mtcars2010)))
tidy_model <- function(model_list) {
# tidy estimates
tidy_2000 <- broom::tidy(model_list[[1]])
tidy_2010 <- broom::tidy(model_list[[2]])
# create a "group" column
tidy_2000$group <- "2000"
tidy_2010$group <- "2010"
ti <- bind_rows(tidy_2000, tidy_2010)
# output
out <- list(tidy = ti, glance = data.frame("nobs 2010" = length(model_list[[1]]$fitted.values)))
class(out) <- "modelsummary_list"
return(out)
}
models <- lapply(models, tidy_model)
modelsummary(models,
group = model + term ~ group,
statistic = "conf.int")
2000
2010
A
(Intercept)
36.800
36.800
[30.034, 42.403]
[30.034, 42.403]
cyl
-2.700
-67.944
[-3.465, -1.792]
[-87.204, -45.102]
B
(Intercept)
38.871
38.871
[30.972, 42.896]
[30.972, 42.896]
cyl
-1.743
-43.858
[-2.154, -0.535]
[-54.215, -13.472]
wt
-2.679
-2.679
[-5.313, -1.531]
[-5.313, -1.531]
C
(Intercept)
40.683
40.683
[31.235, 47.507]
[31.235, 47.507]
cyl
-1.993
-50.162
[-3.137, -1.322]
[-78.948, -33.258]
wt
-2.937
-2.937
[-5.443, -1.362]
[-5.443, -1.362]
disp
0.003
0.003
[-0.009, 0.035]
[-0.009, 0.035]
This question already has answers here:
Creating a loop through a list of variables for an LM model in R
(2 answers)
Closed 2 years ago.
Just as the title.
There is an simple example.
If I want to explore the relationship between vs(dependent variable) and mpg, cyl, and disp(independent variables), respectively, I can code like this:
library(tidyverse)
mtcars <- as_tibble(mtcars) %>%
mutate(mpg10 = mpg*10, cyl10 = cyl*10, disp10 = disp*10)
x = c('mpg', 'cyl', 'disp')
# y ~ x style
models <- map(x, ~ lm(substitute(vs ~ i, list(i = as.name(.))), data = mtcars))
Now I want to do more further. If mpg in the model, mpg10 also should be put in. If cyl in the model, also cyl10 should be put in, etc. Like this:
# y ~ x1 + x2 style
model1 <- lm(vs ~ mpg + mpg10, data = mtcars)
model2 <- lm(vs ~ cyl + cyl10, data = mtcars)
model3 <- lm(vs ~ disp + disp10, data = mtcars)
I don't know how to do this with map() function or for loop.
Any help will be highly appreciated!
You can use grep to find all the column names with the same name and use reformulate to create formula to use in lm.
purrr::map(x, ~lm(reformulate(grep(.x, names(mtcars), value = TRUE),
'vs'), data = mtcars))
I am trying to plot marginal effects in r based on a logistic regression. For example:
data <- mtcars
mod <- glm(am ~ cyl + hp + wt + mpg, family = binomial, data = data)
library(margins)
marg <- margins(mod, atmeans = TRUE)
summary(marg)
I can run the margins plot command:
plot(marg)
which plots marginal effects and confidence intervals for all of the IVs. I only want to include in the plot cyl and hp, my explanatory variables of interest. According to r documentation, this can be accomplished using the 'which' argument, which takes a character vector. However, the documentation doesn't say how to use this argument. Does anyone know how to use the 'which' argument to ask margins.plot to plot only select marginal effects? Unfortunately, the margins plot help page, linked above, does not have any examples.
plot image
Before plotting, we can specify variables of interest with the variables option within the margins()function.
mod <- glm(am ~ cyl + hp + wt + mpg, family=binomial, data=mtcars)
library(margins)
marg <- margins(mod, variables=c("cyl", "hp"))
plot(marg)
Gives:
I want to run a whole batch of regressions over every variable in a data frame, and then store the residual deviance value from each regression in a new vector as the loop goes along.
The frame is called "cw". The first few variables are just metadata, so ignore those. I try the following:
deviances<-c()
for (x in colnames(cw)[1:8]){deviances[x]<-NA}
for (x in colnames(cw)[8:27]){
model<-glm(cwonset ~ x, fmaily = binomial, data = cw)
append(deviances, model$deviance)
}
However, it gives the error:
Error in model.frame.default(formula = cwonset ~ x, data = cw, drop.unused.levels = TRUE) :
variable lengths differ (found for 'x')
Any idea why?
without data, i had to rely on mtcars to help you out, no need of for loop also. I assumed mpg as the dependent variable
Logic : sapply helps me o loop through each colname at a time and then I just regress that. It internally is a for loop though
sapply(colnames(mtcars[-1]), function(x) {
form <- as.formula(paste0("mpg~", x))
model <- glm(form, data = mtcars)
model$deviance})
# cyl disp hp drat wt qsec vs am gear carb
# 308.3342 317.1587 447.6743 603.5667 278.3219 928.6553 629.5193 720.8966 866.2980 784.2711
Take mtcars for example:
> reg <- lm(mpg ~ cyl + disp + hp + drat + wt, data = mtcars)
> sigvar <- data.frame(summary(reg)$coef[summary(reg)$coef[,4] <= .05, 4]) #extracts significant variables with p-values
> rownames <- rownames(sig) #extracts the variables only
I hope to put the rownames on the x-axis of a barplot and the height of the barplot would be the average of the said rownames. Thanks.
I'm unclear what you want the heights of the bars to be in the barplot. However:
reg = lm(mpg ~ cyl + disp + hp + drat + wt, data = mtcars)
## extracts significant variables with p-values
## note the -1 means you skip the intercept
sigvar = summary(reg)$coef[-1,4] <= .05
If I understand what you want, you want a barplot of the average value of those variables which are significant as the height of your bar. You need to match up the significant variables with the variable names in the data frame
i = match(names(sigvar)[sigvar], names(mtcars))
i now contains the columns of the original data frame that correspond to the significant variable. Unfortunately for the mtcars data, this means mtcars[,i] only returns one column, so normally I would do something like
barplot(sapply(mtcars[,i], mean))
but that doesn't do the right thing here because mtcars[,i] returns a vector. Let's assume for argument that i = c(5,6), then this will work
i = 5:6
barplot(sapply(mtcars[,i], mean))