LOCATE

Analysis of the NAFLD-LOCATE randomised trial.

The data folder contains:

• synthetic trial data created using the synthpop package.
• data from the discrete choice experiment for a chronic disease screening programme.

The images folder contains images used to generate letters to GPs.

The trial sample size calculation using simulation is in NAFLD.sample.size.survival.R.

Discrete choice experiment

The files NGene Codes.txt and Nlogit codes.txt are the Ngene and Nlogit codes for analysing the discrete choice experiment.

R and package versions

We used the following version of R and packages.

R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=English_Australia.utf8  LC_CTYPE=English_Australia.utf8    LC_MONETARY=English_Australia.utf8 LC_NUMERIC=C                       LC_TIME=English_Australia.utf8    

time zone: Australia/Brisbane
tzcode source: internal

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

other attached packages:
 [1] gridExtra_2.3   mitools_2.4     nimble_1.0.1    broom_1.0.5     survminer_0.4.9 ggpubr_0.6.0    ggplot2_3.4.2   survival_3.5-5  stringr_1.5.0   janitor_2.2.0   flextable_0.9.2 tidyr_1.3.0     dplyr_1.1.2     knitr_1.43     

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.0        farver_2.1.1            fastmap_1.1.1           pracma_2.4.2            fontquiver_0.2.1        promises_1.2.0.1        digest_0.6.31           timechange_0.2.0        mime_0.12               lifecycle_1.0.3         ellipsis_0.3.2          gfonts_0.2.0            magrittr_2.0.3          compiler_4.3.1          rlang_1.1.1             tools_4.3.1             igraph_1.5.0            utf8_1.2.3              yaml_2.3.7              data.table_1.14.8       ggsignif_0.6.4          labeling_0.4.2          askpass_1.1             curl_5.0.1              xml2_1.3.4              abind_1.4-5             httpcode_0.3.0          numDeriv_2016.8-1.1     withr_2.5.0             purrr_1.0.1             grid_4.3.1              fansi_1.0.4             gdtools_0.3.3           xtable_1.8-4            colorspace_2.1-0        scales_1.2.1            crul_1.4.0              cli_3.6.1               rmarkdown_2.22          crayon_1.5.2            ragg_1.2.5             
[42] generics_0.1.3          rstudioapi_0.14         km.ci_0.5-6             commonmark_1.9.0        DBI_1.1.3               splines_4.3.1           parallel_4.3.1          survMisc_0.5.6          vctrs_0.6.3             Matrix_1.5-4.1          jsonlite_1.8.5          fontBitstreamVera_0.1.1 carData_3.0-5           car_3.1-2               rstatix_0.7.2           systemfonts_1.0.4       glue_1.6.2              codetools_0.2-19        ggtext_0.1.2            lubridate_1.9.2         stringi_1.7.12          gtable_0.3.3            later_1.3.1             munsell_0.5.0           tibble_3.2.1            pillar_1.9.0            htmltools_0.5.5         openssl_2.0.6           R6_2.5.1                KMsurv_0.1-5            textshaping_0.3.6       evaluate_0.21           shiny_1.7.4             lattice_0.21-8          highr_0.10              markdown_1.7            backports_1.4.1         gridtext_0.1.5          snakecase_0.11.0        fontLiberation_0.1.0    httpuv_1.6.11          
[83] TeachingDemos_2.12      Rcpp_1.0.10             zip_2.3.0               uuid_1.1-0              coda_0.19-4             officer_0.6.2           xfun_0.39               zoo_1.8-12              pkgconfig_2.0.3