v1.2.5

causalPAF 1.2.5.9000

• Updated description to 1.2.5.9000
• Made changes necessary for the new development version of CRAN R being released soon as per an email from CRAN. These changes are listed below are relate to changes to the documentation.
• Changed Roxygen code for the following 5 files: causalPAFplot.R (parameter model_listArg definition removed dash dollar sign) , eval_make_formula.R (parameter model_list definition removed dash dollar sign), pointEstimate.R (parameter model_listArg definition removed dash dollar sign), sim_outnode.R (parameter model_list definition removed dash dollar sign) and sim_outnode2.R (parameter model_list definition removed dash dollar sign). In each of these files the symbols dash dollar sign were removed since these were causing errors for linux and some windows documentation compilation.
• Changed Roxygen code forNumBootstrap parameter definition in the file causalPAFplot.R to read plus or minus rather than the symbols plus or minus as it may solve issue for development version of R of linux and windows that is coming out soon that does not process documentation when there is a unicode minus character as per email received from CRAN.
• Removed minus sign in roxygen documentation in addInSplinesTo_in_out.R in definitions of parameters 'count' and 'Subset_adjustmentSet' to read `length( in_outDAG_SplinesRemoved[[2]] ) minus count'.
• In causalPAFplot.R roxygen documentation code removed hyphen in 'maximum-likelihood' and 'non-Markov' and 'Pathway-Specific ' and 'PS-PAF' and 'pathway-specific' and 'pre-fit'.
• In checkMarkovDAG.R roxygen documentation code removed hyphen in 'non Markov'.
• In indirect_PAF_Sjolander_onesimulation.R roxygen documentation code removed hyphen in 'waist hip ratio' and 'reweighted'.
• In overall_direct.R roxygen documentation code removed hyphen in 'waist hip ratio'
• In path_specific_onesimulation.R roxygen documentation code removed hyphen in 'waist hip ratio' and 'reweighted'
• In pointestimate.R roxygen documentation code removed hyphen in 'maximum likelihood' and 'non Markov' and 'pre fit'.
• In sequential_PAF.R roxygen documentation code removed hyphen in 'Monte Carlo' and 'k minus 1' and 'non Markov'.
• In strokedata.R roxygen documentation code removed hyphen in 'preexisting' and 'Preclinical' and 'no education' and 'stage wise' and 'vice versa' and 'waist to hip ratio' and 'Leisure Physical' and '6.5 yes or no' and 'disease yes or no' and '2=1 to 8, 3=9 to 12' and '2=1 to 8, 3=9 to 12' and '2=1 to 8, 3=9 to 12' and 'Waist to hip' and 'maximum likelihood'. Changed citation to Revisiting sequential attributable fractions, J Ferguson, M O'Connell, M O'Donnell, Archives of Public Health, 2020.
• In strokedata_smallSample.R roxygen documentation code removed hyphen in 'preexisting' and 'Preclinical' and 'no education' and 'stage wise' and 'vice versa' and 'waist to hip ratio' and 'Leisure Physical' and '6.5 yes or no' and 'disease yes or no' and '2=1 to 8, 3=9 to 12' and '2=1 to 8, 3=9 to 12' and '2=1 to 8, 3=9 to 12' and 'Waist to hip' and 'maximum likelihood'. Changed citation to Revisiting sequential attributable fractions, J Ferguson, M O'Connell, M O'Donnell, Archives of Public Health, 2020.

causalPAF 1.2.5.9019

• In indirect_PAF_Sjolander_onesimulation.R and path_specific_onesimulation.R, changed Roxygen wording for parameter weighting. In particular, changed the formula for case control weighting in roxygen documentation wording from latex formula format to word format as this formula was causing errors in the new R devel platforms in Windows and Linux. This addressed the errors as per email from Prof Brian D Ripley and Cran on 11th August 2022.
• Undone the change in the third bullet point above in 1.2.5.9000, by adding in the dollar sign as \eqn{$} in each of the files causalPAFplot.R, eval_make_formula.R, pointEstimate.R , sim_outnode.R and sim_outnode2.R .
• Added the published paper Pathway-specific population attributable fractions (PS-PAFs) O’Connell and Ferguson (2022) https://doi.org/10.1093/ije/dyac079 in the description file. And updated the date and number version of the description file.

causalPAF 1.2.5

• In Description changed version from 1.2.5.9019 to 1.2.5.