To have lintr ignore any of these issues, add the appropriate lines of those shown below to lint_ignore.csv at the top-level of the repository:
filename,line_number,message,line
R/genetic_association.R,44,Variable and function name style should be camelCase.,diseaseId = disease_id = snp = allele_count = count = N = vid = NULL
R/genetic_association.R,67,Commas should always have a space after.,"snpSub = intersect(colnames(genotypes),snpSub)"
R/genetic_association.R,71,Put spaces around all infix operators.,"genotypes[, snpSub, drop=FALSE])"
R/genetic_association.R,76,Commas should never have a space before.,"measure.vars = snpSub , variable.name = 'snp', value.name = 'count',"
R/genetic_association.R,133,Variable and function name style should be camelCase.,ci_lower = melt = pval = se = ci_upper = allele_count = varName = n_het = n_hom =
R/genetic_association.R,134,Variable and function name style should be camelCase.,n_total = n_wt = NULL
R/genetic_association.R,145,Variable and function name style should be camelCase.,"lmInput1[allele_count == 2, allele_count := 1]}"
R/genetic_association.R,148,Variable and function name style should be camelCase.,"lmInput1[allele_count == 1, allele_count := 0]"
R/genetic_association.R,149,Variable and function name style should be camelCase.,"lmInput1[allele_count == 2, allele_count := 1]}"
R/genetic_association.R,152,Variable and function name style should be camelCase.,"lmInput1[, allele_count := as.factor(allele_count)]"
R/genetic_association.R,168,Variable and function name style should be camelCase.,"glmStat[, ci_lower := ci[1]]"
R/genetic_association.R,169,Variable and function name style should be camelCase.,"glmStat[, ci_upper := ci[2]]}"
R/phers.R,33,Variable and function name style should be camelCase.,flag = icd = person_id = . = NULL
R/phers.R,84,Variable and function name style should be camelCase.,phecode = person_id = . = prev = w = NULL
R/phers.R,117,Variable and function name style should be camelCase.,person_id = phecode = disease_id = w = score = . = NULL
R/phers.R,157,Variable and function name style should be camelCase.,disease_id = diseaseId = resid_score = . = person_id = score = NULL
R/positive_control.R,26,Variable and function name style should be camelCase.,dx_status = entry_date = uniq_dates = . = NULL
R/positive_control.R,46,Variable and function name style should be camelCase.,"cases[, dx_status := 1]"
R/positive_control.R,55,Variable and function name style should be camelCase.,"dxStatus[is.na(dx_status), dx_status := 0]"
R/utils.R,111,Variable and function name style should be camelCase.,n_het = n_hom = n_wt = NULL
R/utils.R,114,Variable and function name style should be camelCase.,"dCounts[, n_wt := sum(lmInput$allele_count == 0)]"
R/utils.R,115,Variable and function name style should be camelCase.,"dCounts[, n_het := sum(lmInput$allele_count == 1)]"
R/utils.R,116,Variable and function name style should be camelCase.,"dCounts[, n_hom := sum(lmInput$allele_count == 2)]"
data-raw/phers_create_data.R,73,Variable and function name style should be camelCase.,IcdCodes = icdPhecodeMap[flag == flag1 & !(icd %in% diseaseDxIcdMap[disease_id == marfanId]$icd)]$icd
data-raw/phers_create_data.R,83,Variable and function name style should be camelCase.,"icdSampleAll = icdSampleAll[, entry_date := sample(entryDates, nrow(icdSampleAll))]"
data-raw/phers_create_data.R,94,Trailing blank lines are superfluous.,""
inst/extdata/run_plink.R,15,Lines should not be more than 120 characters.,plinkCmnd = glue('--simulate {plinkSimPath} --make-bed --out {plinkOut} --simulate-ncases {npop/2} --simulate-ncontrols {npop/2} --seed 1')
data-raw/phers_create_data.R line 94: Trailing blank lines are superfluous. (https://github.com/hugheylab/phers/blob/main/data-raw/phers_create_data.R#L94)
To have lintr ignore any of these issues, add the appropriate lines of those shown below to lint_ignore.csv at the top-level of the repository: