knitting issue; object not found

rmarkdown

#1

I am writing a stats assignment in rmarkdown. It all runs fine except when I try to knit it, I get an error that an object that I defined in a prior chunk is not found. I've read a lot about this and tried some solutions but I still cannot get it to work.

Here is the code:


library(vegan)
library(magrittr)
library(labdsv)

# Load data

Oak <- read.csv("Oak_data_47x216.csv", header = TRUE, row.names = 1) 

Oak_spp <- read.csv("Oak_species_189x5.csv", header = TRUE)

## subset data ; all plots with elevation > 100
# subset explanatory and response variables

Oak.JH <- Oak[Oak$Elev.m > 100, ]
nrow(Oak.JH)/nrow(Oak) ## 75% of the plots 

Oak.JH.abund<-Oak.JH[, colnames(Oak) %in% Oak_spp$SpeciesCode]

Oak.JH.explan<-Oak.JH[, !colnames(Oak)
                      %in% Oak_spp$SpeciesCode]

Oak.JH1 <- Oak.JH.abund %>%
  vegtab(minval = 0.05 * nrow(Oak.JH.abund)) %>% # Remove rare species
  decostand("max") # Relativize by species maxima

Here is where I get the error when trying to knit

Line 83: Error in eval(expr, envir, enclose): object 'Oak.JH' not found Calls: >Anonymous>... handle -> withcallingHandelrs -> withVisible -> eval -> eval Execution halted

My working directory is set to the same spot as the .rmd file, and the code works fine when I run it normally (Ctrl+enter)

Thanks for any help


#2

I figured it out. Needed to take out eval="FALSE" and replace with results="hide" to get my desired effect.