In this post I will present a simple way how to export your regression results (or output) from R into Microsoft Word. Previously, I have written a tutorial how to create Table 1 with study characteristics and to export into Microsoft Word. These posts are especially useful for researchers who prepare their manuscript for publication in peer-reviewed journals.
Get the results from Cox Regression Analysis
As an example to illustrate this post, I will compute a survival analysis. Survival analysis is statistical methods for analyzing data where the outcome variable is the time until the occurrence of an event. The event can be a occurrence of a disease or death, etc. In R we compute the survival analysis with the
survival package. The function for Cox regression analysis is
coxph(). I will use the
veteran data which come with
## Load survival package library(survival) # Load veteran data data(veteran) # Show first 6 rows head(veteran) trt celltype time status karno diagtime age prior 1 1 squamous 72 1 60 7 69 0 2 1 squamous 411 1 70 5 64 10 3 1 squamous 228 1 60 3 38 0 4 1 squamous 126 1 60 9 63 10 5 1 squamous 118 1 70 11 65 10 6 1 squamous 10 1 20 5 49 0 # Data description help(veteran, package="survival") trt: 1=standard 2=test celltype: 1=squamous, 2=smallcell, 3=adeno, 4=large time: survival time status: censoring status karno: Karnofsky performance score (100=good) diagtime: months from diagnosis to randomisation age: in years prior: prior therapy 0=no, 1=yes
Now let say that we are interested to know the risk of dying (status) from different cell type (celltype) and treatment (trt) when we adjust for other variables (karno, age prior, diagtime).
This is the model:
# Fit the COX model fit = coxph(Surv(time, status) ~ age + celltype + prior + karno + diagtime + trt, data=veteran)
And the output:
summary(fit) Call: coxph(formula = Surv(time, status) ~ age + celltype + prior + karno + diagtime + trt, data = veteran) n= 137, number of events= 128 coef exp(coef) se(coef) z Pr(>|z|) age -8.706e-03 9.913e-01 9.300e-03 -0.936 0.34920 celltypesmallcell 8.616e-01 2.367e+00 2.753e-01 3.130 0.00175 ** celltypeadeno 1.196e+00 3.307e+00 3.009e-01 3.975 7.05e-05 *** celltypelarge 4.013e-01 1.494e+00 2.827e-01 1.420 0.15574 prior 7.159e-03 1.007e+00 2.323e-02 0.308 0.75794 karno -3.282e-02 9.677e-01 5.508e-03 -5.958 2.55e-09 *** diagtime 8.132e-05 1.000e+00 9.136e-03 0.009 0.99290 trt 2.946e-01 1.343e+00 2.075e-01 1.419 0.15577 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 exp(coef) exp(-coef) lower .95 upper .95 age 0.9913 1.0087 0.9734 1.0096 celltypesmallcell 2.3669 0.4225 1.3799 4.0597 celltypeadeno 3.3071 0.3024 1.8336 5.9647 celltypelarge 1.4938 0.6695 0.8583 2.5996 prior 1.0072 0.9929 0.9624 1.0541 karno 0.9677 1.0334 0.9573 0.9782 diagtime 1.0001 0.9999 0.9823 1.0182 trt 1.3426 0.7448 0.8939 2.0166 Concordance= 0.736 (se = 0.03 ) Rsquare= 0.364 (max possible= 0.999 ) Likelihood ratio test= 62.1 on 8 df, p=1.799e-10 Wald test = 62.37 on 8 df, p=1.596e-10 Score (logrank) test = 66.74 on 8 df, p=2.186e-11
As we see there are “a lot” of results. In manuscript we often report only the Hazard ratio and 95% Confidence interval and only for the variables of interest. For example in this case I am interested for the cell types and treatment. Note: I will not comment for the regression coefficients since is not the aim of this post.
Prepare the table by creating the columns
# Prepare the columns HR
Select variables of interest from the table
As I mentioned earlier, I am interested only for 2 variables (cell type and treatment). With the code below I will select those variables.
# select variables you want to present in table table2
Format the table
In the manuscript we present the confidence intervals within brackets. Therefore, with the code below I will add the brackets.
# add brackes and line for later use in table table2$a
Finalize the table and make it ready for Microsoft Word
The table is almost ready, now I will merge in one column by using package
tidyr with function
# Merge all columns in one library(tidyr) table2 = unite(table2, "HR (95%CI)", c(HR, a, Lower, b, Higher, c), sep = "", remove=T) # add space between the estimates of HR and CI table2[,1]
Export Table from R to Microsoft Word
To export table from R to Microsoft Word I will use the function
FlexTable() from the package ReporteRs. I found a very good script in StackOverflow to achieve this task. I am sharing the code below. (Credits to the author in StackOverflow).
# Load the packages library(ReporteRs) library(magrittr) # The script docx( ) %>% addFlexTable(table2 %>% FlexTable(header.cell.props = cellProperties( background.color = "#003366"), header.text.props = textBold(color = "white"), add.rownames = TRUE ) %>% setZebraStyle(odd = "#DDDDDD", even = "#FFFFFF")) %>% writeDoc(file = "table2.docx")
If you have any comment or feedback feel free to post a comment below.