hugheylab / phers

https://phers.hugheylab.org
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lintr found issues with code #87

Closed github-actions[bot] closed 1 year ago

github-actions[bot] commented 1 year ago
  1. R/genetic_association.R line 55: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/main/R/genetic_association.R#L55)
    diseaseId = disease_id = snp = allele_count = count = N = variant_id = person_id = NULL   
  2. R/genetic_association.R line 102: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/main/R/genetic_association.R#L102)
    ci_lower = melt = pval = se = ci_upper = allele_count = varName = n_het =   
  3. R/genetic_association.R line 103: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/main/R/genetic_association.R#L103)
    n_hom = n_total = n_wt = genotype = NULL   
  4. R/genetic_diagnosis.R line 29: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/main/R/genetic_diagnosis.R#L29)
    dx_status = occurrence_age = uniq_ages = . = NULL   
  5. R/phers.R line 26: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/main/R/phers.R#L26)
    flag = icd = person_id = . = NULL   
  6. R/phers.R line 67: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/main/R/phers.R#L67)
    person_id = phecode = disease_id = w = score = . = NULL   
  7. R/phers.R line 105: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/main/R/phers.R#L105)
    disease_id = diseaseId = resid_score = . = person_id = score = NULL   
  8. R/utils.R line 186: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/main/R/utils.R#L186)
    n_het = n_hom = n_wt = NULL   
  9. R/weights.R line 2: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/main/R/weights.R#L2)
    phecode = person_id = . = pred = w = dx_status = NULL   
  10. R/weights.R line 23: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/main/R/weights.R#L23)
    phecode = person_id = . = pred = w = dx_status = NULL   
  11. R/weights.R line 49: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/main/R/weights.R#L49)
    phecode = person_id = . = w = phe = dx_status = pred = NULL   
  12. R/weights.R line 74: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/main/R/weights.R#L74)
    phecode = person_id = . = w = phe = pred = num_occurrences = NULL   
  13. R/weights.R line 96: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/main/R/weights.R#L96)
    phecode = person_id = . = w = phe = dx_status = pred = occurrence_age =   
  14. R/weights.R line 97: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/main/R/weights.R#L97)
    first_age = last_age = age2 = NULL   

    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,55,Variable and function name style should be camelCase.,diseaseId = disease_id = snp = allele_count = count = N = variant_id = person_id = NULL
    R/genetic_association.R,102,Variable and function name style should be camelCase.,ci_lower = melt = pval = se = ci_upper = allele_count = varName = n_het =
    R/genetic_association.R,103,Variable and function name style should be camelCase.,n_hom = n_total = n_wt = genotype = NULL
    R/genetic_diagnosis.R,29,Variable and function name style should be camelCase.,dx_status = occurrence_age = uniq_ages = . = NULL
    R/phers.R,26,Variable and function name style should be camelCase.,flag = icd = person_id = . = NULL
    R/phers.R,67,Variable and function name style should be camelCase.,person_id = phecode = disease_id = w = score = . = NULL
    R/phers.R,105,Variable and function name style should be camelCase.,disease_id = diseaseId = resid_score = . = person_id = score = NULL
    R/utils.R,186,Variable and function name style should be camelCase.,n_het = n_hom = n_wt = NULL
    R/weights.R,2,Variable and function name style should be camelCase.,phecode = person_id = . = pred = w = dx_status = NULL
    R/weights.R,23,Variable and function name style should be camelCase.,phecode = person_id = . = pred = w = dx_status = NULL
    R/weights.R,49,Variable and function name style should be camelCase.,phecode = person_id = . = w = phe = dx_status = pred = NULL
    R/weights.R,74,Variable and function name style should be camelCase.,phecode = person_id = . = w = phe = pred = num_occurrences = NULL
    R/weights.R,96,Variable and function name style should be camelCase.,phecode = person_id = . = w = phe = dx_status = pred = occurrence_age =
    R/weights.R,97,Variable and function name style should be camelCase.,first_age = last_age = age2 = NULL