Issue114

[nhall6]

Fixing several things outlined in #114

[jreps]

R check is showing:
"─ checking R code for possible problems ... [11s/13s] NOTE (13.4s)
cohortMethodPropensityModelServer : : no visible binding for
global variable ‘coefficient’
Undefined global functions or variables:
coefficient
"

This normally means a missing .data$ before coefficient in the code. Please add this.

[jreps]

R check is also showing multiple errors:
Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-estimation-cohort-method-covariateBalance.R:3'): (code run outside of test_that()) ──
Error in paste0("Max SDM Statistic = ", maxSdmStatistic): argument "maxSdmStatistic" is missing, with no default
Backtrace:
▆

1. ├─shiny::testServer(...) at test-estimation-cohort-method-covariateBalance.R:3:0
2. │ ├─shiny:::withMockContext(...)
3. │ │ ├─shiny::isolate(...)
4. │ │ │ ├─shiny::..stacktraceoff..(...)
5. │ │ │ └─ctx$run(...)
6. │ │ │ ├─promises::with_promise_domain(...)
7. │ │ │ │ └─domain$wrapSync(expr)
8. │ │ │ ├─shiny::withReactiveDomain(...)
9. │ │ │ │ └─promises::with_promise_domain(...)
10. │ │ │ │ └─domain$wrapSync(expr)
11. │ │ │ │ └─base::force(expr)
12. │ │ │ └─env$runWith(self, func)
13. │ │ │ └─shiny (local) contextFunc()
14. │ │ │ └─shiny::..stacktraceon..(expr)
15. │ │ ├─shiny::withReactiveDomain(...)
16. │ │ │ └─promises::with_promise_domain(...)
17. │ │ │ └─domain$wrapSync(expr)
18. │ │ │ └─base::force(expr)
19. │ │ └─withr::with_options(...)
20. │ │ └─base::force(code)
21. │ └─rlang::eval_tidy(quosure, mask, rlang::caller_env())
22. ├─OhdsiShinyModules:::plotCohortMethodCovariateBalanceScatterPlotNew(...) at test-estimation-cohort-method-covariateBalance.R:55:4
23. │ └─... %>% ...
24. ├─plotly::layout(...)
25. ├─plotly:::layout.plotly(...)
26. └─base::paste0("Max SDM Statistic = ", maxSdmStatistic)
    ── Error ('test-estimation-cohort-method-power.R:3'): (code run outside of test_that()) ──
    Error in .subset2(x, "impl")$getOutput(name): The test referenced an output that hasn't been defined yet: output$proxy1-powerTable
    Backtrace:
    ▆
27. ├─shiny::testServer(...) at test-estimation-cohort-method-power.R:3:0
28. │ ├─shiny:::withMockContext(...)
29. │ │ ├─shiny::isolate(...)
30. │ │ │ ├─shiny::..stacktraceoff..(...)
31. │ │ │ └─ctx$run(...)
32. │ │ │ ├─promises::with_promise_domain(...)
33. │ │ │ │ └─domain$wrapSync(expr)
34. │ │ │ ├─shiny::withReactiveDomain(...)
35. │ │ │ │ └─promises::with_promise_domain(...)
36. │ │ │ │ └─domain$wrapSync(expr)
37. │ │ │ │ └─base::force(expr)
38. │ │ │ └─env$runWith(self, func)
39. │ │ │ └─shiny (local) contextFunc()
40. │ │ │ └─shiny::..stacktraceon..(expr)
41. │ │ ├─shiny::withReactiveDomain(...)
42. │ │ │ └─promises::with_promise_domain(...)
43. │ │ │ └─domain$wrapSync(expr)
44. │ │ │ └─base::force(expr)
45. │ │ └─withr::with_options(...)
46. │ │ └─base::force(code)
47. │ └─rlang::eval_tidy(quosure, mask, rlang::caller_env())
48. ├─testthat::expect_true(!is.null(output$powerTable)) at test-estimation-cohort-method-power.R:52:4
49. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
50. │ └─rlang::eval_bare(expr, quo_get_env(quo))
51. ├─output$powerTable
52. └─shiny:::$.shinyoutput(output, powerTable)
53. └─.subset2(x, "impl")$getOutput(name)
    ── Error ('test-estimation-cohort-method-systematicError.R:68'): plotCohortMethodScatter ──
    Error in paste0("EASE Statistic = ", ease): argument "ease" is missing, with no default
    Backtrace:
    ▆
54. └─OhdsiShinyModules:::plotCohortMethodScatter(controlResults) at test-estimation-cohort-method-systematicError.R:68:2
55. ├─ggplot2::ggtitle(paste0("EASE Statistic = ", ease))
56. │ └─ggplot2::labs(title = label, subtitle = subtitle)
57. │ └─rlang::dots_list(...)
58. └─base::paste0("EASE Statistic = ", ease)

[ FAIL 3 | WARN 24 | SKIP 1 | PASS 451 ]

• Pleased fix these errors and confirm tests all pass by running an R check locally.

[codecov]

Codecov Report

Attention: Patch coverage is 90.90909% with 39 lines in your changes missing coverage. Please review.

Project coverage is 77.70%. Comparing base (0a22d6c) to head (e996799).
Report is 15 commits behind head on develop.

Files with missing lines	Patch %	Lines
R/characterization-riskFactors.R	50.00%	12 Missing ⚠️
R/estimation-cohort-method-propensityModel.R	60.00%	10 Missing ⚠️
R/helpers-sccsPlots.R	0.00%	7 Missing ⚠️
R/cohort-diagnostics-cohort-overlap.R	0.00%	3 Missing ⚠️
R/components-data-viewer.R	83.33%	3 Missing ⚠️
R/estimation-cohort-method-covariateBalance.R	97.77%	1 Missing ⚠️
R/estimation-cohort-method-power.R	99.24%	1 Missing ⚠️
...mation-cohort-method-propensityScoreDistribution.R	97.61%	1 Missing ⚠️
R/estimation-cohort-method-systematicError.R	98.03%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #339      +/-   ##
===========================================
+ Coverage    77.60%   77.70%   +0.10%     
===========================================
  Files           78       78              
  Lines        20627    20946     +319     
===========================================
+ Hits         16007    16277     +270     
- Misses        4620     4669      +49     

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