Example spelling "mistakes"

[statzhero]

I don't understand the document and PDF examples. These words, while not in the dictionary, don't seem like mistakes. Would they get corrected?

 [1] "auth"              "CORBA"             "cpu"              
 [4] "cran"              "cron"              "css"              
 [7] "csv"               "CTRL"              "DCOM"             
[10] "de"                "dec"               "decompositions"   
[13] "dir"               "DOM"               "DSL"              
[16] "eol"               "ESC"               "facto"            
[19] "grDevices"         "httpuv"            "ignorable"        
[22] "interoperable"     "JRI"               "js"               
[25] "json"              "jsonlite"          "knitr"            
[28] "md"                "memcached"         "mydata"           
[31] "myfile"            "NaN"               "nondegenerateness"
[34] "OAuth"             "ocpu"              "opencpu"          
[37] "OpenCPU"           "pandoc"            "pb"               
[40] "php"               "png"               "prescripted"      
[43] "priori"            "protobuf"          "rApache"          
[46] "rda"               "rds"               "reproducibility"  
[49] "Reproducibility"   "RinRuby"           "RInside"          
[52] "rlm"               "rmd"               "rnorm"            
[55] "rnw"               "RPC"               "RProtoBuf"        
[58] "rpy"               "Rserve"            "RStudio"          
[61] "saveRDS"           "scalability"       "scalable"         
[64] "schemas"           "se"                "sep"              
[67] "SIGINT"            "STATA"             "stateful"         
[70] "Stateful"          "statefulness"      "stdout"           
[73] "STDOUT"            "suboptimal"        "svg"              
[76] "sweave"            "tex"               "texi"             
[79] "tmp"               "toJSON"            "urlencoded"       
[82] "www"               "xyz"    

[jeroen]

You can review and whitelist them using a custom wordlist.

[statzhero]

Thank you -- to clarify, what is the default in this example: would hunspell correct them with a high probability match here or not?

[jeroen]

hunspell does not do anything, it is a low level tool for finding unknown words, that could be mistakes. You can build on this information using e.g. the spelling package to filter this based on your own wordlist of accepted words.