R markdown Knitting to Pdf issue: r code results are different from the pdf output

Question

The title of this post is pretty self-explanatory, so I will not waste your time reading more into this question.

I have tried to clean the r memory, to restart my laptop, delete the rmarkdown file, make a new file, and then knit to pdf.

The result is still the same: r code output is the different from pdf output.

---
title: "Mockup"
date: "`r format(Sys.time(), '%m/%d/%Y')`"
output: 
  pdf_document:
    fig_caption: yes
    fig_crop: no
    highlight: zenburn
    keep_tex: yes
    number_sections: false
    toc: yes
    toc_depth: 2
header-includes:
- \usepackage{example}
- \usepackage{nicematrix}
- \usepackage{hyperref}
- \usepackage{mathtools}
- \usepackage{amssymb}
- \usepackage{lettrine}
- \usepackage{amsmath}
- \usepackage{yfonts,color}
- \usepackage {titling}
- \usepackage{blkarray}
- \usepackage{fancyhdr}
- \pagestyle{fancy}
- \fancyhead[R,R]{Mockup}
- \fancyhead[L,L]{Mockup}
- \fancyfoot[C,C]{Mockup}
- \fancyfoot[L,R]{\thepage}
---

```{r setup, include=FALSE, message=FALSE}
library(knitr)
library("DAAG")
library(tree)
library(MASS)
knitr::opts_chunk$set(echo = TRUE, fig.pos= "h", comment = NA, tidy=TRUE, tidy.opts=list(width.cutoff=37))
data(spam7, data ="DAAG")
Spam <- spam7[,c("crl.tot","dollar","bang",
                 "money","n000","make","yesno")]
Spam$yesno <- as.factor(Spam$yesno)
attach(Spam)
set.seed(1234)
sample_size <- floor(0.8*nrow(Spam))
ind <- sample(seq_len(nrow(Spam)),size = sample_size)
Spam.training <- Spam[ind,]
Spam.test <- Spam[-ind,]
```

```{r,echo = FALSE}
q1.tree <- tree(yesno ~., data = Spam.training)
par(cex = .7)
plot(q1.tree)
text(q1.tree, pretty = 0)
```

R code output (within the Rmarkdown file): PDF Output:

Any tip on how to fix this?

Thank you!

Answer 1

The sample function doesn't return the same ind in Rmd and PDF. Both case I used set.seed(4).

From Rmd:

> ind <- sample(seq_len(nrow(Spam)),size = sample_size)
> print(ind)
   [1] 2696   42 1351 1276 3741 1197 3329 4163 4359  336 3465 1313  460 4378 1907 2088 4453 2678 4410 3491 3274 4565 2319
  [24] 2243 2972 3802 2206 3851 2350 2423 2593 1092 4012 2990 2203 4434 2101 2840 1773   31 4280 1105 2579  825 4122  385
  [47] 4105 4061 3294 2572 1769 3394 4074 3680 3722 1915  804  790 4055 3377 2548  324 3875 4147 1023 2852  314 2335 3651
  [70] 4405 1554 2861 1858 1566 3735 3123 1451 1997 1185  603 4117 3206 2585 4143 4549  265  207 4464  929 4192  877  572
  [93] 2433 1228 1594  379 3449 2002  163 3158 1141 2834 1199 2395 2106 2583 3005  954 4384 3636 1237 1793 1304 2213 3396
 [116] 2291 1966 3547 4086  319  640 1761 3836 1184  424 3243 4388  898 2471 1545 1826  841 4472  821 3633 3938 3129 1234
 [139] 1929   58 2512 2992 1399 4225  753 1963 2547 4342 3406 1973 1584 4503 2643 4277 1124 3767  946 1235 2130 4591 4002
 [162] 4189 1844 1483 1255  321 4535  705  669 3334 4477 2709  890 2229 4510   13 2850 1067 4529 3164  446 2683  939 3953

...

From PDF