When fitting a generalized additive model with smoothed splines stargazer only returns the main effects and not the smooth terms which you can see in summary(pros.gam). Can stargazer return these as well? Or is there another function or package that can do the job?
library(ElemStatLearn)
library(mgcv)
library(stargazer)
pros.gam=gam(lpsa~s(lcavol)+s(lweight)+s(age)+s(lbph)+svi
+s(lcp)+gleason+s(pgg45),data=prostate)
summary(pros.gam) # Table should include the smooth terms that are visible here
stargazer(pros.gam,summary=TRUE)
toLatex of the utils package does the job:
require(utils)
toLatex(summary(pros.gam)$s.table)
Output:
# \begin{tabular}{lD{.}{.}{7}D{.}{.}{7}D{.}{.}{7}D{.}{.}{7}}
# \toprule
# & \multicolumn{1}{c}{edf} & \multicolumn{1}{c}{Ref.df} & \multicolumn{1}{c}{F} & \multicolumn{1}{c}{p-value} \\
# \midrule
# s(lcavol) & 1.0000000 & 1.0000000 & 48.8654347 & 0.0000000 \\
# s(lweight) & 7.4334733 & 8.3759397 & 2.9521585 & 0.0054553 \\
# s(age) & 1.7609527 & 2.1888342 & 3.2466098 & 0.0402275 \\
# s(lbph) & 1.7480193 & 2.1293872 & 2.3329425 & 0.0998080 \\
# s(lcp) & 3.3087460 & 4.0189658 & 1.3792509 & 0.2484695 \\
# s(pgg45) & 1.1277962 & 1.2388741 & 0.2681440 & 0.6563885 \\
# \bottomrule
# \end{tabular}
I was having the same problem converting the output of GAM models (mgcv package), I got what I wanted with the "itsadug" package authored by R. Harald Baayen.
Convert model summary into Latex / HTML table for knitr / R Markdown reports.
data(simdat)
Model with random effect and interactions:
m1 <- bam(Y ~ Group+te(Time, Trial, by=Group),data=simdat)
summary(m1)
gamtabs(m1, caption='Summary of m1')
See for more examples:
vignette("inspect", package="itsadug")
Related
I am trying to add a caption to a table output from the package "tables" in R followed by additional formatting using kableExtra.
Although other threads have found ways to add caption headers by using additional LaTeX code (Caption not appearing for LaTeX table when knitting using Hmisc LaTeX Function and Hmisc::latex not printing caption w/ tabular object), these solutions do not appear compatible with the more recent toKable() function which allows additional formatting with kableExtra.
Typically a caption would be added during when kable(x, caption = "mycaption") is used. However when it is genereated as following, an error will occur (Error in toKable(., booktabs = T) : 'table' must be a 'tabular' object.). It appears if I try to add any additional formatting through latex(), such as adding a caption, the object type will change making it unusable with the toKable() function. Any insight into how to use toKable() with additional LaTeX formatting that has been passed through latex() would be greatly appreciated!
library(tables)
library(magrittr)
library(kableExtra)
tabular((Species + 1) ~ (n=1) + Format(digits=2)* (Sepal.Length + Sepal.Width)*(mean + sd), data=iris) %>%
latex(., options = list(tabular = "longtable",
toprule = "\\caption{Table 1. My favorite caption}\\\\\\toprule")) %>%
toKable(., booktabs = T)
The LaTeX output before being passed to toKable():
\begin{longtable}{lccccc}
\caption{Table 1. My favorite caption}\\\toprule
& & \multicolumn{2}{c}{Sepal.Length} & \multicolumn{2}{c}{Sepal.Width} \\
Species & n & mean & sd & mean & \multicolumn{1}{c}{sd} \\
\hline
setosa & $\phantom{0}50$ & $5.01$ & $0.35$ & $3.43$ & $0.38$ \\
versicolor & $\phantom{0}50$ & $5.94$ & $0.52$ & $2.77$ & $0.31$ \\
virginica & $\phantom{0}50$ & $6.59$ & $0.64$ & $2.97$ & $0.32$ \\
All & $150$ & $5.84$ & $0.83$ & $3.06$ & $0.44$ \\
\hline
\end{longtable}
After tinkering around a bit with the code and trying to understand how each works... I tried pasting the options list directly into toKable. This seemed to work and it appears toKable shared similar options to those of latex().
tabular((Species + 1) ~ (n=1) + Format(digits=2)* (Sepal.Length + Sepal.Width)*(mean + sd),
data=iris) %>%
toKable(., booktabs = T,
options = list(tabular = "longtable",
toprule = "\\caption{My favorite caption}\\\\\\toprule"))
This spits out the following LaTex code correctly, as desired above:
\begin{longtable}{lccccc}
\caption{Table 1. My favorite caption}\\\toprule
& & \multicolumn{2}{c}{Sepal.Length} & \multicolumn{2}{c}{Sepal.Width} \\ \cmidrule(lr){3-4}\cmidrule(lr){5-6}
Species & n & mean & sd & mean & \multicolumn{1}{c}{sd} \\
\midrule
setosa & $\phantom{0}50$ & $5.01$ & $0.35$ & $3.43$ & $0.38$ \\
versicolor & $\phantom{0}50$ & $5.94$ & $0.52$ & $2.77$ & $0.31$ \\
virginica & $\phantom{0}50$ & $6.59$ & $0.64$ & $2.97$ & $0.32$ \\
All & $150$ & $5.84$ & $0.83$ & $3.06$ & $0.44$ \\
\bottomrule
\end{longtable}
The LaTeX code can then be presented as needed in reports or otherwise. In a Rmarkdown document converted to PDF this can look like (remember to call the tables andkableExtra packages):
Thank you for sharing, I was looking for exactly this. I can add the caption as above but it still appears just as normal body text and without a table reference when I render the Latex doc. SO in case useful for anyone else
What worked for me was to use the latexTable function from the vignette:
tab1<-latexTable(tabular((Species + 1) ~ (n=1) + Format(digits=2)
(Sepal.Length + Sepal.Width)*(mean + sd),data=iris), caption = "Iris sepal data", label = "sepals")
and then and just treated it as a kable object and could add headers, etc
tab1 %>% add_header_above(c("Blah" = 1, "Bing" = 2, "Bong" = 2)) %>% save_kable(paste0(resultspath,"tab1.tex"), float = FALSE)
I'm trying to compile a LaTeX report using RStudio and knitr. I'm having a hard time getting the packages booktabs and dcolumn to work with my texreg-generated table.
As an example, I am trying to recreate Table 2 in this example:.
My attempt as a .Rnw -file is below:
\documentclass{article}
\usepackage{booktabs}
\usepackage{dcolumn}
<<setup, include=FALSE >>=
library(texreg)
#
\begin{document}
<<analysis, include=FALSE>>=
ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
group <- gl(2,10,20, labels=c("Ctl","Trt"))
weight <- c(ctl, trt)
m1 <- lm(weight ~ group)
m2 <- lm(weight ~ group - 1) # omitting intercept
#
<<table, results='asis'>>=
texreg(m2)
#
\end{document}
However, the generated LaTex table (below) includes neither the booktabs horizontal lines nor the dcolumn alignment. How to incorporate them? Many thanks for help!
\begin{table}
\begin{center}
\begin{tabular}{l c }
\hline
& Model 1 \\
\hline
groupCtl & $5.03^{***}$ \\
& $(0.22)$ \\
groupTrt & $4.66^{***}$ \\
& $(0.22)$ \\
\hline
R$^2$ & 0.98 \\
Adj. R$^2$ & 0.98 \\
Num. obs. & 20 \\
\hline
\multicolumn{2}{l}{\scriptsize{$^{***}p<0.001$, $^{**}p<0.01$, $^*p<0.05$}}
\end{tabular}
\caption{Statistical models}
\label{table:coefficients}
\end{center}
\end{table}
Just to clarify: the crucial part in Robert's solution is the argument use.packages=FALSE not the seperation of code into two chunks.
The reason is the following: The way you call texreg() now makes it include the following in the tex output it produces:
\usepackage{booktabs}
\usepackage{dcolumn}
Saving the output in an object and then using cat() does not solve this.
You cannot use \usepackage()' outside the preamble. Knitr still compiles a PDF but apparently this use of\usepackage{}' in the document body screws up the use of booktabs and dcolumn even if you've loaded them in the preamble.
Add the argument use.packages=FALSE in texreg() - if set to FALSE, the use package statements are omitted from the output. Write the use package statements into the preamble of your document yourself and you'll have the regression table with booktabs and aligned numbers.
Try this:
\begin{document}
<<analysis, include=FALSE>>=
ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
group <- gl(2,10,20, labels=c("Ctl","Trt"))
weight <- c(ctl, trt)
m1 <- lm(weight ~ group)
m2 <- lm(weight ~ group - 1) # omitting intercept
table = texreg(m2,booktabs = TRUE,dcolumn = TRUE,use.packages=FALSE)
table2=texreg(list(m1,m2),booktabs = TRUE,dcolumn = TRUE,use.packages=FALSE)
#
<<table, results='asis',echo=FALSE>>=
cat(table)
cat(table2)
#
\end{document}
Say I have the following program in R to generate a LaTeX longtable:
library(xtable)
tabela <- xtabs(Temp ~ Month, airquality)
xtabela <- xtable(tabela)
print.xtable(xtabela, tabular.environment = 'longtable', floating = FALSE)
Which yields
\begin{longtable}{rr}
\hline
& Month \\
\hline
5 & 2032.00 \\
6 & 2373.00 \\
7 & 2601.00 \\
8 & 2603.00 \\
9 & 2307.00 \\
\hline
\hline
\end{longtable}
However, I want this table to be completely aligned to the right. In LaTeX, I just need to use \begin{longtable}[r]{rr} in order to accomplish this, but how do I pass this [r] argument through R's print.xtable? Alternatively, how do I achieve the same result through other methods (I've tried \raggedleft, but it only works with regular tabular objects)?
As a very rough method, you could do:
cat(paste(c("\\begin{longtable}[r]{", align(xt), "}\n"), collapse=""))
print(xtabella, only.contents=T)
cat("\\end{longtable}\n")
When constructing documents with Sweave and R, I make use of the stargazer library for tables.
When using stargazer, is there a mechanism to display the degrees of freedom associated with the residual deviance for a model constructed with glm?
Minimal code:
library(stargazer)
set.seed(1234)
data <- data.frame(x=1:10)
data$y <- data$x + rnorm(10, 0, 0.2)
model <- glm(y~x, data=data, family=gaussian)
summary(model)
stargazer(model,title="A test", align=T,label="Tab:test",style="all2")
Resultant stargazer table will have Observations, Log Likelihood, AIC, Residual Deviance and Null Deviance but no d.f. I can work out d.f. but would have thought this could be displayed directly. Also see:
https://sites.google.com/site/marekhlavac/stargazer
Update #1:
Thank you Marek for your response. For the benefit of others that encounter this, here is the process that lets you form the work around:
Obtain version 4.0 (not 4.5 - I'll come back to this) from http://cran.r-project.org/src/contrib/Archive/stargazer/
Within the package directory structure under R, edit "stargazer-internal.R" as per the instructions in the answer below.
Ensure that the library is not loaded in your R session
Ensure that you have removed any existing stargazer lib
Install the edited version of the stargazer package.
Reload the library in R and compile as per usual.
Here are the commands:
detach("package:stargazer", unload=TRUE)
remove.packages("stargazer")
From the command line:
R CMD INSTALL -l <path to library directory> stargazer
Finally (assuming you have a few models at hand),
library(stargazer)
stargazer(model6,model7,model8, title="Logistic model summary",align=T,label="Tab:logmod1", font.size="footnotesize", style="all2")
Result:
% Table created by stargazer v.4.0 by Marek Hlavac, Harvard University. E-mail: hlavac at fas.harvard.edu
% Date and time: Tue, Sep 24, 2013 - 17:17:17
% Requires LaTeX packages: dcolumn
\begin{table}[!htbp] \centering
\caption{Logistic model summary}
\label{Tab:logmod1}
\footnotesize
\begin{tabular}{#{\extracolsep{5pt}}lD{.}{.}{-3} D{.}{.}{-3} D{.}{.}{-3} }
\\[-1.8ex]\hline
\hline \\[-1.8ex]
& \multicolumn{3}{c}{\textit{Dependent variable:}} \\
\cline{2-4}
\\[-1.8ex] & \multicolumn{3}{c}{whalesighted} \\
\\[-1.8ex] & \multicolumn{1}{c}{\textit{logistic}} & \multicolumn{1}{c}{\textit{probit}} & \multicolumn{1}{c}{\textit{glm: binomial}} \\
& \multicolumn{1}{c}{\textit{}} & \multicolumn{1}{c}{\textit{}} & \multicolumn{1}{c}{\textit{link = cloglog}} \\
\\[-1.8ex] & \multicolumn{1}{c}{(1)} & \multicolumn{1}{c}{(2)} & \multicolumn{1}{c}{(3)}\\
\hline \\[-1.8ex]
visibility & 0.392^{***} & 0.226^{***} & 0.216^{***} \\
& (0.051) & (0.027) & (0.026) \\
Constant & -1.251^{***} & -0.745^{***} & -1.149^{***} \\
& (0.246) & (0.144) & (0.182) \\
\hline \\[-1.8ex]
Observations & \multicolumn{1}{c}{232} & \multicolumn{1}{c}{232} & \multicolumn{1}{c}{232} \\
Log Likelihood & \multicolumn{1}{c}{-110.485} & \multicolumn{1}{c}{-110.888} & \multicolumn{1}{c}{-112.694} \\
Akaike Inf. Crit. & \multicolumn{1}{c}{224.970} & \multicolumn{1}{c}{225.775} & \multicolumn{1}{c}{229.388} \\
Residual Deviance (df = 230) & \multicolumn{1}{c}{220.970} & \multicolumn{1}{c}{221.775} & \multicolumn{1}{c}{225.388} \\
Null Deviance (df = 231) & \multicolumn{1}{c}{310.759} & \multicolumn{1}{c}{310.759} & \multicolumn{1}{c}{310.759} \\
\hline
\hline \\[-1.8ex]
\textit{Note:} & \multicolumn{3}{r}{$^{*}$p$<$0.1; $^{**}$p$<$0.05; $^{***}$p$<$0.01} \\
\normalsize
\end{tabular}
\end{table}
Returning to the error I get when I implement the workaround based on the 4.5 code. I actually get the same error when I install from the mac binary (version 4.5.1) (http://cran.r-project.org/web/packages/stargazer/index.html) and simply try to use stargazer, see below.
> install.packages("stargazer")
trying URL 'http://cran.ms.unimelb.edu.au/bin/macosx/contrib/3.0/stargazer_4.5.1.tgz'
Content type 'application/x-tar' length 332917 bytes (325 Kb)
opened URL
==================================================
downloaded 325 Kb
> stargazer(model6,model7,model8,
+ title="Logistic model summary",
+ align=T,
+ label="Tab:logmod1",
+ font.size="footnotesize",
+ style="all2")
Error in `rownames<-`(`*tmp*`, value = "visibility") :
length of 'dimnames' [1] not equal to array extent
Marek, for your reference I will email the results traceback() to you.
Cheers.
Stargazer author here. It looks like the package's default is not to output degrees of freedom for residual and null deviance. I will consider changing the default in a future release.
As a quick fix for now, you might wish to use the source package (from CRAN), and modify the function .adjust.settings.style in stargazer-internal.R to contain the following:
if (style == "all") {
.format.table.parts <<- c("=!","dependent variable label","dependent variables","models","columns","numbers","-","coefficients","-","omit","-","additional","N","R-squared","adjusted R-squared","max R-squared","log likelihood","sigma2","theta(se)*(p)", "SER(df)","F statistic(df)*(p)","chi2(df)*(p)","Wald(df)*(p)","LR(df)*(p)","logrank(df)*(p)","AIC","BIC","UBRE","rho(se)*(p)","Mills(se)*(p)","residual deviance(df)*","null deviance(df)*","=!","notes")
.format.coefficient.table.parts <<- c("variable name","coefficient*","standard error","t-stat","p-value")
}
else if (style == "all2") {
.format.table.parts <<- c("=!","dependent variable label","dependent variables","models","columns","numbers","-","coefficients","-","omit","-","additional","N","R-squared","adjusted R-squared","max R-squared","log likelihood","sigma2","theta(se)*(p)", "SER(df)","F statistic(df)*(p)","chi2(df)*(p)","Wald(df)*(p)","LR(df)*(p)","logrank(df)*(p)","AIC","BIC","UBRE","rho(se)*(p)","Mills(se)*(p)","residual deviance(df)*","null deviance(df)*","=!","notes")
.format.coefficient.table.parts <<- c("variable name","coefficient*","standard error")
}
Note that the only change here is that I added "(df)*" to "residual deviance" and "null deviance".
I'm currently doing some data analysis on population data, so reporting the standard errors in the tables of parameter coefficients just doesn't really make statistical sense. I've done a fair bit of searching and can't find any way to customize the xtable output to remove it. Can anyone point me in the right direction?
Thanks a lot, I didn't post this lightly; if it's something obvious, I apologize for having wasted time!
so after my (other) whole long-winded answer... this works too:
xtable(summary(model1)$coefficients[,c(1,3,4)])
Or more generically:
sm <- summary(SomeModel)
SE.indx <- which(colnames(sm$coefficients) == "Std. Error") # find which column is Std. Error (usually 2nd)
sm$coefficients <- sm$coefficients[, -SE.indx] # Remove it
xtable(sm$coefficients) # call xtable on just the coefficients table
Results:
% latex table generated in R 2.15.1 by xtable 1.7-0 package
% Sun Dec 9 00:01:46 2012
\begin{table}[ht]
\begin{center}
\begin{tabular}{rrrr}
\hline
& Estimate & t value & Pr($>$$|$t$|$) \\
\hline
(Intercept) & 29.80 & 30.70 & 0.00 \\
crim & -0.31 & -6.91 & 0.00 \\
age & -0.09 & -6.50 & 0.00 \\
\hline
\end{tabular}
\end{center}
\end{table}
Using the first example in help(lm):
xtable(as.matrix(coef(lm.D9)))
% latex table generated in R 2.15.2 by xtable 1.7-0 package
% Sat Dec 8 19:53:09 2012
\begin{table}[ht]
\begin{center}
\begin{tabular}{rr}
\hline
& x \\
\hline
(Intercept) & 5.03 \\
groupTrt & -0.37 \\
\hline
\end{tabular}
\end{center}
\end{table}
I agreed with not using std erros if this were descriptions of a population and not just a sample. By that reasoning, however, you would not want to leave in p-values or t-statistics. That was the reason I only included the coefficients. To remove the standard error column only from the summary coefficient matrix:
xtable( coef(summary(lm.D9))[,-2] )
% latex table generated in R 2.15.2 by xtable 1.7-0 package
% Sat Dec 8 21:02:17 2012
\begin{table}[ht]
\begin{center}
\begin{tabular}{rrrr}
\hline
& Estimate & t value & Pr($>$$|$t$|$) \\
\hline
(Intercept) & 5.03 & 22.85 & 0.00 \\
groupTrt & -0.37 & -1.19 & 0.25 \\
\hline
\end{tabular}
\end{center}
\end{table}
Looking at str(summary(Model1)) we see that $coefficients has the Std. Error value we want to remove.
lesserSummary <- function(x) {
## returns same as summary(x), but with "Std. Error" remove from coefficients.
## and class of object is "modifiedSummary"
# grab the summary
sm <- summary(x)
# find which column is std error
SE.indx <- which(colnames(sm$coefficients) == "Std. Error")
# remove it
sm$coefficients <- sm$coefficients[, -SE.indx]
# give it some class
class(sm) <- "modifiedSummary"
# return it
sm
}
xtable.modifiedSummary <-
function (x, caption = NULL, label = NULL, align = NULL, digits = NULL, display = NULL, ...) {
# x is a modifiedSummary object
# This function is a modification of xtable:::xtable.summary.lm
# Key Difference is simply the number of columns that x$coef is expected to have
# (Here 3. Originally 4)
x <- data.frame(x$coef, check.names = FALSE)
class(x) <- c("xtable", "data.frame")
caption(x) <- caption
label(x) <- label
align(x) <- switch(1 + is.null(align), align, c("r", "r", "r", "r"))
digits(x) <- switch(1 + is.null(digits), digits, c(0, 4, 2, 4))
display(x) <- switch(1 + is.null(display), display, c("s", "f", "f", "f"))
return(x)
}
xtable_mod <- function(x) {
# Wrapper function to xtable.modified summary, calling first lesserSummary on x
xtable(lesserSummary(x))
}
EXAMPLE:
xtable_mod(model1)
% latex table generated in R 2.15.1 by xtable 1.7-0 package
% Sat Dec 8 23:44:54 2012
\begin{table}[ht]
\begin{center}
\begin{tabular}{rrrr}
\hline
& Estimate & t value & Pr($>$$|$t$|$) \\
\hline
(Intercept) & 29.8007 & 30.70 & 0.0000 \\
crim & -0.3118 & -6.91 & 0.0000 \\
age & -0.0896 & -6.50 & 0.0000 \\
\hline
\end{tabular}
\end{center}
\end{table}
Below are the steps taken to arrive at the above conclusion.
You can likely modify the call to xtable, but you first need to follow it down a bit:
start by looking at the source for xtable:
xtable
# function (x, caption = NULL, label = NULL, align = NULL, digits = NULL,
# display = NULL, ...)
# {
# UseMethod("xtable")
# }
# <environment: namespace:xtable>
We see that it simply has a call to UseMethod(). So lets see which methods are available:
methods(xtable)
# [1] xtable.anova* xtable.aov* xtable.aovlist*
# [4] xtable.coxph* xtable.data.frame* xtable.glm*
# [7] xtable.lm* xtable.matrix* xtable.prcomp*
# [10] xtable.summary.aov* xtable.summary.aovlist* xtable.summary.glm*
# [13] xtable.summary.lm* xtable.summary.prcomp* xtable.table*
# [16] xtable.ts* xtable.zoo*
There are several. Note that the ones with an asterisk * are non-visible.
The method called is determined by the class of the object we are calling xtable on.
Let's say our output is Model1 We take a look at its class: '
class(Model1)
# [1] "lm"
So the source we want to look at is xtable.lm.
xtable.lm
# Error: object 'xtable.lm' not found
Error? That's right, it is non-visible. So we use the package name with triple-colons. Note: please be sure to read the notice in the help file ?":::"
xtable:::xtable.lm
# function (x, caption = NULL, label = NULL, align = NULL, digits = NULL,
# display = NULL, ...)
# {
# return(xtable.summary.lm(summary(x), caption = caption, label = label,
# align = align, digits = digits, display = display))
# }
# <environment: namespace:xtable>
We notice that xtable.lm calls xtable.summary.lm and passes as its first argument a summary(x), where x is our model.
So that leads us to two place to investigate: summary and xtable.summary.lm