SelfReported code ready for review

[mja]

https://github.com/ColemanResearchGroup/MHQ2/blob/850999b68f0d5a2ba61479cab2fa2301436a0dea/scripts/SelfReported.Rmd#L85

The regular expression should be changed to a more specific pattern like "^29000-" so that it matches field 29000 exactly, and not potential future fields like 129000 or 290000.

[JoniColeman]

Regex changed – code checked against data. Review re-requested.

[mja]

Linting

library(lintr)
mhq_lints <- linters_with_defaults(
    object_name_linter(styles = c("symbol", "CamelCase", "snake_case", "lowercase"))
)

lint("scripts/SelfReported.Rmd", linters = mhq_lints, exclude = "##")

MHQ2/scripts/SelfReported.Rmd:19:13: style: [quotes_linter] Only use double-quotes.
  comment = '',
            ^~
MHQ2/scripts/SelfReported.Rmd:22:2: style: [indentation_linter] Indentation should be 0 spaces but is 2 spaces.
  )
~^
MHQ2/scripts/SelfReported.Rmd:39:38: style: [brace_linter] There should be a space before an opening curly brace.
package_install <- function(packages){
                                     ^
MHQ2/scripts/SelfReported.Rmd:39:38: style: [paren_body_linter] There should be a space between a right parenthesis and a body expression.
package_install <- function(packages){
                                     ^
MHQ2/scripts/SelfReported.Rmd:41:4: style: [indentation_linter] Indentation should be 2 spaces but is 4 spaces.
    for(x in packages){
  ~^
MHQ2/scripts/SelfReported.Rmd:41:8: style: [spaces_left_parentheses_linter] Place a space before left parenthesis, except in a function call.
    for(x in packages){
       ^
MHQ2/scripts/SelfReported.Rmd:42:1: style: [trailing_whitespace_linter] Trailing whitespace is superfluous.

^~~~
MHQ2/scripts/SelfReported.Rmd:43:8: style: [indentation_linter] Indentation should be 4 spaces but is 8 spaces.
        install.packages(x, dependencies = TRUE)
    ~~~^
MHQ2/scripts/SelfReported.Rmd:44:1: style: [trailing_whitespace_linter] Trailing whitespace is superfluous.

^
MHQ2/scripts/SelfReported.Rmd:44:1: style: [whitespace_linter] Use spaces to indent, not tabs.

^
MHQ2/scripts/SelfReported.Rmd:45:4: style: [indentation_linter] Indentation should be 2 spaces but is 4 spaces.
    }     
  ~^
MHQ2/scripts/SelfReported.Rmd:45:6: style: [trailing_whitespace_linter] Trailing whitespace is superfluous.
    }     
     ^~~~~
MHQ2/scripts/SelfReported.Rmd:52:3: style: [commented_code_linter] Commented code should be removed.
# packages <- c("data.table","tidyverse","dplyr")
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MHQ2/scripts/SelfReported.Rmd:53:3: style: [commented_code_linter] Commented code should be removed.
# package_install(packages)
  ^~~~~~~~~~~~~~~~~~~~~~~~~
MHQ2/scripts/SelfReported.Rmd:61:28: style: [commas_linter] Commas should always have a space after.
packages <- c("data.table","tidyverse","dplyr")
                           ^
MHQ2/scripts/SelfReported.Rmd:61:40: style: [commas_linter] Commas should always have a space after.
packages <- c("data.table","tidyverse","dplyr")
                                       ^
MHQ2/scripts/SelfReported.Rmd:70:5: style: [infix_spaces_linter] Put spaces around all infix operators.
MHQ2<-fread(args[1], data.table=F)
    ^~
MHQ2/scripts/SelfReported.Rmd:70:32: style: [infix_spaces_linter] Put spaces around all infix operators.
MHQ2<-fread(args[1], data.table=F)
                               ^
MHQ2/scripts/SelfReported.Rmd:70:34: style: [T_and_F_symbol_linter] Use FALSE instead of the symbol F.
MHQ2<-fread(args[1], data.table=F)
                                ~^
MHQ2/scripts/SelfReported.Rmd:101:44: style: [infix_spaces_linter] Put spaces around all infix operators.
MHQ2$SelfReportedDiagnosisMHQ2016Compatible<- apply(MHQ2[,grep("^29000-", colnames(MHQ2))], 1, function(row) ifelse(sum(c(1:15,17:19) %in% row) > 0, 1, 0))
                                           ^~
MHQ2/scripts/SelfReported.Rmd:101:59: style: [commas_linter] Commas should always have a space after.
MHQ2$SelfReportedDiagnosisMHQ2016Compatible<- apply(MHQ2[,grep("^29000-", colnames(MHQ2))], 1, function(row) ifelse(sum(c(1:15,17:19) %in% row) > 0, 1, 0))
                                                          ^
MHQ2/scripts/SelfReported.Rmd:101:81: style: [line_length_linter] Lines should not be more than 80 characters. This line is 155 characters.
MHQ2$SelfReportedDiagnosisMHQ2016Compatible<- apply(MHQ2[,grep("^29000-", colnames(MHQ2))], 1, function(row) ifelse(sum(c(1:15,17:19) %in% row) > 0, 1, 0))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MHQ2/scripts/SelfReported.Rmd:101:128: style: [commas_linter] Commas should always have a space after.
MHQ2$SelfReportedDiagnosisMHQ2016Compatible<- apply(MHQ2[,grep("^29000-", colnames(MHQ2))], 1, function(row) ifelse(sum(c(1:15,17:19) %in% row) > 0, 1, 0))
                                                                                                                               ^
MHQ2/scripts/SelfReported.Rmd:112:49: style: [commas_linter] Commas should always have a space after.
MHQ2$SelfReportedAnxietyDisorder <- apply(MHQ2[,grep("^29000-", colnames(MHQ2))], 1, function(row) ifelse(sum(c(10:13,15) %in% row) > 0, 1, 0))
                                                ^
MHQ2/scripts/SelfReported.Rmd:112:81: style: [line_length_linter] Lines should not be more than 80 characters. This line is 143 characters.
MHQ2$SelfReportedAnxietyDisorder <- apply(MHQ2[,grep("^29000-", colnames(MHQ2))], 1, function(row) ifelse(sum(c(10:13,15) %in% row) > 0, 1, 0))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MHQ2/scripts/SelfReported.Rmd:112:119: style: [commas_linter] Commas should always have a space after.
MHQ2$SelfReportedAnxietyDisorder <- apply(MHQ2[,grep("^29000-", colnames(MHQ2))], 1, function(row) ifelse(sum(c(10:13,15) %in% row) > 0, 1, 0))
                                                                                                                      ^
MHQ2/scripts/SelfReported.Rmd:122:48: style: [commas_linter] Commas should always have a space after.
MHQ2$SelfReportedEatingDisorder <- apply(MHQ2[,grep("^29000-", colnames(MHQ2))], 1, function(row) ifelse(sum(c(17:20) %in% row) > 0, 1, 0))
                                               ^
MHQ2/scripts/SelfReported.Rmd:122:81: style: [line_length_linter] Lines should not be more than 80 characters. This line is 139 characters.
MHQ2$SelfReportedEatingDisorder <- apply(MHQ2[,grep("^29000-", colnames(MHQ2))], 1, function(row) ifelse(sum(c(17:20) %in% row) > 0, 1, 0))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MHQ2/scripts/SelfReported.Rmd:130:14: error: [error] unexpected symbol
~~TODO: This needs to be done as part of the overarching script as it relies on otuput from multiple modules~~ 
             ^
MHQ2/scripts/SelfReported.Rmd:130:81: style: [line_length_linter] Lines should not be more than 80 characters. This line is 111 characters.
~~TODO: This needs to be done as part of the overarching script as it relies on otuput from multiple modules~~ 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MHQ2/scripts/SelfReported.Rmd:130:111: style: [trailing_whitespace_linter] Trailing whitespace is superfluous.
~~TODO: This needs to be done as part of the overarching script as it relies on otuput from multiple modules~~ 
                                                                                                              ^
MHQ2/scripts/SelfReported.Rmd:131:1: style: [trailing_blank_lines_linter] Trailing blank lines are superfluous.

[JoniColeman]

Need to lintR new code and resolve issues

[JoniColeman]

Confirmed code is more efficient and gives correct output. Merging and closing.

[JoniColeman]

Markdown sections need to written such that comments are properly tabulated. This is best done by making them into lists as described here: https://www.markdownguide.org/cheat-sheet/