API update

[LittleBeannie]

In simtrial, most of the function/variable/argument name follows the camel case (e.g., the enrollRates argument in the simfix function). In modern package development, people follow snake case. For example, enrollRates should be enroll_rate in snake case. The differences between snake case and camal are summarized in https://www.freecodecamp.org/news/snake-case-vs-camel-case-vs-pascal-case-vs-kebab-case-whats-the-difference/.

Function name update:

• fixedBlockRand -> randomize_by_fixed_block @lili-ling-msd, see fixedBlockRand -> rand_by_fixed_block #32
• cutData -> cut_data_by_date @XintongLi2023, see cutData -> cut_data_by_date #33
• cutDataAtCount -> cut_data_by_event @XintongLi2023, see cutDataAtCount -> cut_data_by_event #34
• getCutDateForCount -> get_cut_date_by_event @XintongLi2023, see getCutDateForCount -> get_cut_date_by_event #35
• rpwenroll -> rpw_enroll @lili-ling-msd, see rpwenroll -> rpw_enroll #36
• pwexpfit -> fit_pwexp @lili-ling-msd, see pwexpfit -> fit_pwexp #37
• pMaxCombo -> pvalue_maxcombo @lili-ling-msd, see pMaxCombo -> pvalue_maxcombo #38
• tenFH -> wlr @lili-ling-msd, see tenFH -> wlr #39
• tenFHcorr -> will be merged into wlr given the rg @LittleBeannie
• tensurv -> counting_process @lili-ling-msd, see tensurv -> counting_process  #40
• wMB -> mb_weight @XintongLi2023 , see wMB -> mb_weight #41
• simPWSurv -> sim_pw_surv? @XintongLi2023, see simPWSurv -> sim_pw_surv #42
• simfix -> sim_fixed_n? @XintongLi2023, see simfix -> sim_fixed_n #43

Arguments to be updated:

• enrollRates -> enroll_rate @lili-ling-msd, see enrollRates -> enroll_rate and enrollTime -> enroll_time  #44
• failRates -> fail_rate, @XintongLi2023, see failRates -> fail_rate and failRate -> fail_rate and failTime -> fail_time #45
• failRate -> fail_rate @XintongLi2023, see failRates -> fail_rate and failRate -> fail_rate and failTime -> fail_time #45
• dropoutRates -> dropout_rate @lili-ling-msd, see dropoutRates -> dropout_rate and dropoutRate -> dropout_rate and dropoutTime -> dropout_time #46
• dropoutRate -> dropout_rate @lili-ling-msd, see dropoutRates -> dropout_rate and dropoutRate -> dropout_rate and dropoutTime -> dropout_time #46
• sampleSize -> sample_size @XintongLi2023 , see sampleSize -> sample_size  #47
• targetEvents -> target_event @lili-ling-msd, see targetEvents -> target_event #48
• timingType -> timing_type @XintongLi2023 , see timingType -> timing_type #49
• rg -> rho_gamma @lili-ling-msd, see rg -> rho_gamma #50
• strata -> stratum @XintongLi2023, see strata -> stratum and Stratum -> stratum #51
• Stratum -> stratum @XintongLi2023, see strata -> stratum and Stratum -> stratum #51
• Treatment -> treatment @lili-ling-msd, see Treatment -> treatment and "Control" -> "control" #52
• "Control" -> "control" @lili-ling-msd, see Treatment -> treatment and "Control" -> "control" #52
• "Experimental" -> "experimental" @lili-ling-msd, see Treatment -> treatment and "Control" -> "control" #52
• nsim -> n_sim @XintongLi2023, see nsim -> n_sim #53
• cutDate -> cut_date @lili-ling-msd, see cutDate -> cut_date  #54
• count -> event in cutDataAtCount and getCutDateForCount @XintongLi2023, see count -> event in cutDataAtCount and getCutDateForCount  #55
• dummyvar -> dummy_var in pMaxCombo @lili-ling-msd, see dummyvar -> dummy_var in pMaxCombo #56
• Z -> z in pMaxCombo @XintongLi2023 , see Z -> z in pMaxCombo  #57
• Srv -> srv in pwexpfit @lili-ling-msd, see Srv -> srv in pwexpfit #58
• returnVariance -> return_variance in tenFH @XintongLi2023 , see returnVariance -> return_variance in tenFH #59
• txval -> arm in tensurv @lili-ling-msd, see txval -> arm in tensurv #60
• wmax -> w_max in wMB @XintongLi2023 , see wmax -> w_max in wMB #61

Output variable names to be updated in tensurv:

• Stratum -> stratum (assigned to Xintong, same as strata -> stratum and Stratum -> stratum #51 )
• events -> n_event_tol @LittleBeannie, see update internal variables to follow snake case #28
• txevents -> n_event_trt @LittleBeannie, see update internal variables to follow snake case #28
• atrisk -> n_risk_tol @LittleBeannie, see update internal variables to follow snake case #28
• txatrisk -> n_risk_trt @LittleBeannie, see update internal variables to follow snake case #28
• S -> s @LittleBeannie
• OminusE -> o_minus_e @LittleBeannie, see update internal variables to follow snake case #28
• Var -> var_o_minus_e @LittleBeannie, see update internal variables to follow snake case #28

Output variable names to be updated in tenFH, tenFH:

• Z -> z (assigned to Xintong, same as Z -> z in pMaxCombo  #57)
• V1 -> v1 @LittleBeannie
  
  

Output variable names to be updated in cutData, CutDataAtCount:

• Stratum -> stratum (assigned to Xintong, same as strata -> stratum and Stratum -> stratum #51 )
• Treatment -> treatment @LittleBeannie
  

Output of pwexpfit:

• TTOT -> ttot @LittleBeannie, see update internal variables to follow snake case #28
• events -> event @LittleBeannie, see update internal variables to follow snake case #28

Output of simfix:

• Events -> event @LittleBeannie
• lnhr -> ln_hr @LittleBeannie
• Duration -> duration @LittleBeannie
• Sim -> sim @LittleBeannie
  

Output of simfix2simPWSurv and simPWSurv:

• Staratum -> stratum (assigned to Xintong, same as strata -> stratum and Stratum -> stratum #51)
• Treatment -> treatment @LittleBeannie
• enrollTime -> enroll_time (assigned to Lili, same as enrollRates -> enroll_rate and enrollTime -> enroll_time  #44)
• failTime -> fail_time (assigned to Xintong, same as failRates -> fail_rate and failRate -> fail_rate and failTime -> fail_time #45)
• dropoutTime -> dropout_time (assigned to Lili, same as dropoutRates -> dropout_rate and dropoutRate -> dropout_rate and dropoutTime -> dropout_time #46)
  
  

[nanxstats]

@LittleBeannie Yes, I think it would be the best if we can keep the style consistent. The code linter will detect all style violations, regardless if they are from internal or exported functions. I know it could be a lot of refactoring work, though!