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harrelfe / hreport

Statistical reports in html with interactive plotly graphics, especially for clinical trials
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Trouble getting test.Rmd to run #4

Closed shannongutenkunst closed 2 months ago

shannongutenkunst commented 2 years ago

Hi. I am trying to learn how to use hreport by reproducing the example report at https://github.com/harrelfe/hreport/tree/master/inst/tests/test.Rmd

If I knit the document, I get the following error: test Rmd_knit_error

If I run the code line by line, I get a warning a line 123, which is accrualReport(enroll(edate) + randomize(rdate) ~ region(region) + country(country) + site(site), data=d, dateRange=c('2005-01-01', '2007-12-31'), targetN= data.frame(edate=c(500, 1000), rdate=c(250, 500)), targetDate=c('2006-01-01', '2007-12-31'), closeDate='2007-12-31') Warning: one argument not used by format 'The blue line depicts the cumulative frequency. The thick grayscale line represent targets.'Error in path.expand(path) : invalid 'path' argument

If I keep going line by line, I get a warning at line 159, which is exReport(~ pending(pend) + e1 + e2 + e3 + e4 + e5 + e6 + e7 + randomized(rndz) + id(subjid) + cond(e5, 'Tested', tested), erdata = erd, whenapp= c(e4='CCTA done'), data=d) #, hc=3.75, h=4) Quitting from lines 6-7 () Error in path.expand(path) : invalid 'path' argument

and another error at line 211, which is dReport(race + sex + ynbind(x1, x2, x3, x4, x5, x6, x7, label='Exclusions') ~ 1, head='Overall frequencies of categorical demographic variables and exclusions', data=d, w=4, h=4.5) Error in attr(x, "label") <- value : attempt to set an attribute on NULL

and the same error in many dReport calls after that.

I've pasted my session info below, in case that is useful. Any help you are willing to provide would be much appreciated.

Thank you, Shannon

sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.6

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] hreport_0.5-0 data.table_1.14.2 Hmisc_4.7-1 ggplot2_3.3.6 Formula_1.2-4
[6] survival_3.2-13 lattice_0.20-45

loaded via a namespace (and not attached): [1] Rcpp_1.0.9 mvtnorm_1.1-3 tidyr_1.2.1 deldir_1.0-6 zoo_1.8-11
[6] png_0.1-7 assertthat_0.2.1 digest_0.6.29 utf8_1.2.2 R6_2.5.1
[11] backports_1.4.1 MatrixModels_0.5-1 httr_1.4.4 pillar_1.8.1 rlang_1.0.6
[16] multcomp_1.4-20 lazyeval_0.2.2 rstudioapi_0.14 SparseM_1.81 rpart_4.1-15
[21] Matrix_1.5-1 checkmate_2.1.0 splines_4.1.2 stringr_1.4.1 foreign_0.8-81
[26] htmlwidgets_1.5.4 munsell_0.5.0 compiler_4.1.2 xfun_0.33 pkgconfig_2.0.3
[31] base64enc_0.1-3 htmltools_0.5.3 nnet_7.3-16 tidyselect_1.1.2 tibble_3.1.8
[36] gridExtra_2.3 htmlTable_2.4.1 codetools_0.2-18 rms_6.3-0 fansi_1.0.3
[41] viridisLite_0.4.1 dplyr_1.0.10 withr_2.5.0 MASS_7.3-54 grid_4.1.2
[46] polspline_1.1.20 nlme_3.1-153 jsonlite_1.8.2 gtable_0.3.1 lifecycle_1.0.2
[51] DBI_1.1.2 magrittr_2.0.3 scales_1.2.1 cli_3.4.1 stringi_1.7.8
[56] latticeExtra_0.6-30 generics_0.1.3 vctrs_0.4.2 sandwich_3.0-2 TH.data_1.1-1
[61] RColorBrewer_1.1-3 tools_4.1.2 interp_1.1-3 glue_1.6.2 purrr_0.3.4
[66] jpeg_0.1-9 fastmap_1.1.0 colorspace_2.0-3 cluster_2.1.2 plotly_4.10.0
[71] knitr_1.40 quantreg_5.94

harrelfe commented 2 months ago

I’m sorry I never worked on this. Please re-open if you still need help with this.