cran-comments.md

In simrvprojects/SimRVPedigree: Simulate Pedigrees Ascertained for a Rare Disease

Resubmission February 2020

• Updated the DESCRIPTION file:
  • Updated the version number to 0.4.4 to reflect:
    • new functionality that allows users to simulate diseases with multiple disease subtypes.
    • removal of previously deprecated argument birth_range from the sim_life, sim_ped, and sim_RVped functions.
    • fixed all improper uses of class() == *, and instead switched to using inherits() or is(). Many thanks to Kurt Hornik for again pointing out this deficiency.

Test Environments prior to resubmission https://win-builder.r-project.org/ local Windows OS install, R 3.5.0

Resubmission October 2018

In this resubmission I have: - Fixed a bug in the find_mrca function and improved the tests for this function.

• We have improved the process used to simulate reproduction. The new process better models age-specific fertility. As a result, the birth_range argument has been deprecated in the sim_life, sim_ped, and sim_RVped functions. To prepare users for this change, in this resubmission, users are issued a warning if they alter the default NULL value of this argument.

• Updated the DESCRIPTION file:

  • Updated the version number to 0.3.0 to reflect:
    • the updated reproduction process, which better models age-specific fertility.
    • the deprecated argument birth_range from the sim_life, sim_ped, and sim_RVped functions.
    • the bug fix in the find_mrca function,
  • Reverted the Depends field to R (>= 3.4.0) to fix error on package check page for flavor r-oldrel-osx-x86_64.

Test Environments prior to resubmission local Windows OS install, R 3.5.0 ubuntu 14.04.5 LTS (on travis-ci), R 3.5.0

Resubmission August 2018

In this resubmission I have: - Fixed a bug in the reassign_gen function and improved the tests for this function.

• Added a new argument, called first_diagnosis, to the sim_RVped function. This argument allows users to implement new ascertainment criteria. NOTE: the default setting of the new argument ensures backwards compatibility.

• Added a function called find_mrca, which finds the most recent common ancestor of two pedigree members.

• Updated the DESCRIPTION file:

  • Updated the Depends field to R (>= 3.5.0),
  • Updated the version number to 0.2.0 to reflect:
    • the bug fix in the reassign_gen function,
    • the addition of the new argument in the sim_RVped function, called first_diagnosis, and
    • the addition of a new function called reduce_to_affected.

Test Environments prior to resubmission local Windows OS install, R 3.5.0 ubuntu 14.04.5 LTS (on travis-ci), R 3.5.0

Resubmission

In this resubmission I have:

• fixed the reference in the 'Description' field of the DESCRIPTION file to be of the form: authors (year) , and

• changed the 'Depends' field in the DESCRIPTION file to R (>= 3.4.0). Previously, it was R (>= 3.4.2).

Resubmission

In this resubmission I have updated a reference in AgeSpecififc_Hazards.Rd, which had prompted the following error message:

Found the following (possibly) invalid URLs: URL: https://www.ssa.gov/oact/NOTES/as120/TOC.html From: man/AgeSpecific_Hazards.Rd inst/doc/SimRVPedigree.html Status: Error Message: libcurl error code 35: Unknown SSL protocol error in connection to www.ssa.gov:443

• The updated reference does not contain a URL, and should therefore resolve this error.

Resubmission

In this resubmission I have:

• fixed the reference in the 'Description' field of the DESCRIPTION file to be of the form: authors (year)

Test environments

• local Windows OS install, R 3.4.3
• ubuntu 14.05.5 LTS (on travis-ci), R 3.4.2
• local OS X install, R 3.3.3
• Tested on a campus MAC, which unfortunately I did not have permission to update to more recent version of R.

R CMD check results

0 errors | 0 warnings | 1 note

Possibly mis-spelled words in DESCRIPTION: Jinko (12:9) Nieuwoudt (11:15)

These are not misspelled words, these are names of authors.

Downstream Dependencies

Currently, there are no downstream dependencies for this package.

simrvprojects/SimRVPedigree documentation built on Feb. 12, 2020, 6:12 p.m.