From b11b2a462f28d47d9ee8804877089684d1f94ed5 Mon Sep 17 00:00:00 2001 From: Will Beasley Date: Sun, 29 Sep 2024 13:25:37 -0500 Subject: [PATCH] remove vignette line --- DESCRIPTION | 3 +- .../rmarkdown-1/report-1.html | 5110 +++++++++++++++-- inst/report-templates/rmarkdown-1/report-1.md | 453 +- 3 files changed, 5018 insertions(+), 548 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 990f7d4..7bae247 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -29,9 +29,8 @@ Suggests: rmarkdown, sessioninfo, testthat (>= 3.1) -VignetteBuilder: knitr Config/testthat/edition: 3 Encoding: UTF-8 Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.2 Language: en-US diff --git a/inst/report-templates/rmarkdown-1/report-1.html b/inst/report-templates/rmarkdown-1/report-1.html index 5467a99..e375254 100644 --- a/inst/report-templates/rmarkdown-1/report-1.html +++ b/inst/report-templates/rmarkdown-1/report-1.html @@ -13,51 +13,4417 @@ Trawler Report - - + + - - - - + + + + - - - - - - - - - - - - - - - - - - - - +h1.title {font-size: 38px;} +h2 {font-size: 30px;} +h3 {font-size: 24px;} +h4 {font-size: 18px;} +h5 {font-size: 16px;} +h6 {font-size: 12px;} +code {color: inherit; background-color: rgba(0, 0, 0, 0.04);} +pre:not([class]) { background-color: white } + + + + + + + + + + + + + + + + + + + + + +code{white-space: pre-wrap;} +span.smallcaps{font-variant: small-caps;} +span.underline{text-decoration: underline;} +div.column{display: inline-block; vertical-align: top; width: 50%;} +div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;} +ul.task-list{list-style: none;} + +

2.2 Rule Detail

+
## Warning: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
+## ℹ Please use `"results"` instead of `.data$results`
+## This warning is displayed once every 8 hours.
+## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
+## generated.
+
## Warning: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
+## ℹ Please use `"record_id_linked"` instead of `.data$record_id_linked`
+## This warning is displayed once every 8 hours.
+## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
+## generated.
+
## Warning: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
+## ℹ Please use `"data_collector"` instead of `.data$data_collector`
+## This warning is displayed once every 8 hours.
+## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
+## generated.
+
## Warning: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
+## ℹ Please use `"baseline_date"` instead of `.data$baseline_date`
+## This warning is displayed once every 8 hours.
+## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
+## generated.
+
+
-

2.3 Inactive Rules

+

2.3 Inactive Rules

1 rules(s) are disabled for this report:

  1. pre_albumin_levels;
-

To enable/disable a rule, set the active element in the yaml checks file to “true” or “false”.

+

To enable/disable a rule, set the active element in the +yaml checks file to “true” or “false”.

-

3 Smells

+

3 Smells

11 smells have been sniffed. 3 violation(s) were found.

-

A smell test won’t validate a specific record (like the rules above), but it will make sure the overall dataset smells as expected.

+

A smell test won’t validate a specific record (like the +rules above), but it will make sure the overall dataset smells as +expected.

-

3.1 Smell Summary

- +

3.1 Smell Summary

+
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -783,100 +5193,100 @@

3.1 Smell Summary
-

3.2 Inactive Smells

+

3.2 Inactive Smells

1 smell(s) are disabled for this report:

  1. average_serum_ferritin_levels_at_baseline;
-

To enable/disable a smell, set the active element in the yaml checks file to “true” or “false”.

+

To enable/disable a smell, set the active element in the +yaml checks file to “true” or “false”.

-

4 Configuration

-

For the sake of documentation and reproducibility, the current report was rendered in the following environment. Click the line below to expand.

+

4 Configuration

+

For the sake of documentation and reproducibility, the current report +was rendered in the following environment. Click the line below to +expand.

Environment 
## ─ Session info ───────────────────────────────────────────────────────────────
 ##  setting  value
-##  version  R version 4.1.2 (2021-11-01)
-##  os       Ubuntu 21.10
+##  version  R version 4.4.1 (2024-06-14)
+##  os       Ubuntu 24.04.1 LTS
 ##  system   x86_64, linux-gnu
 ##  ui       X11
 ##  language (EN)
 ##  collate  en_US.UTF-8
 ##  ctype    en_US.UTF-8
 ##  tz       America/Chicago
-##  date     2022-01-03
-##  pandoc   2.11.4 @ /usr/lib/rstudio/bin/pandoc/ (via rmarkdown)
+##  date     2024-09-29
+##  pandoc   3.2 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/x86_64/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date (UTC) lib source
-##  assertthat    0.2.1   2019-03-21 [1] CRAN (R 4.1.0)
-##  backports     1.4.1   2021-12-13 [1] CRAN (R 4.1.1)
-##  bslib         0.3.1   2021-10-06 [1] CRAN (R 4.1.1)
-##  checkmate     2.0.0   2020-02-06 [1] CRAN (R 4.1.0)
-##  cli           3.1.0   2021-10-27 [1] CRAN (R 4.1.1)
-##  colorspace    2.0-2   2021-06-24 [1] CRAN (R 4.1.0)
-##  crayon        1.4.2   2021-10-29 [1] CRAN (R 4.1.1)
-##  crosstalk     1.2.0   2021-11-04 [1] CRAN (R 4.1.1)
-##  DBI           1.1.2   2021-12-20 [1] CRAN (R 4.1.2)
-##  digest        0.6.29  2021-12-01 [1] CRAN (R 4.1.1)
-##  dplyr         1.0.7   2021-06-18 [1] CRAN (R 4.1.0)
-##  DT            0.20    2021-11-15 [1] CRAN (R 4.1.1)
-##  ellipsis      0.3.2   2021-04-29 [1] CRAN (R 4.1.0)
-##  evaluate      0.14    2019-05-28 [1] CRAN (R 4.1.0)
-##  fansi         0.5.0   2021-05-25 [1] CRAN (R 4.1.0)
-##  fastmap       1.1.0   2021-01-25 [1] CRAN (R 4.1.0)
-##  generics      0.1.1   2021-10-25 [1] CRAN (R 4.1.1)
-##  glue          1.6.0   2021-12-17 [1] CRAN (R 4.1.1)
-##  htmltools     0.5.2   2021-08-25 [1] CRAN (R 4.1.1)
-##  htmlwidgets   1.5.4   2021-09-08 [1] CRAN (R 4.1.1)
-##  httr          1.4.2   2020-07-20 [1] CRAN (R 4.1.0)
-##  jquerylib     0.1.4   2021-04-26 [1] CRAN (R 4.1.0)
-##  jsonlite      1.7.2   2020-12-09 [1] CRAN (R 4.1.0)
-##  kableExtra    1.3.4   2021-02-20 [1] CRAN (R 4.1.0)
-##  knitr       * 1.37    2021-12-16 [1] CRAN (R 4.1.1)
-##  lifecycle     1.0.1   2021-09-24 [1] CRAN (R 4.1.1)
-##  magrittr      2.0.1   2020-11-17 [1] CRAN (R 4.1.0)
-##  munsell       0.5.0   2018-06-12 [1] CRAN (R 4.1.0)
-##  pillar        1.6.4   2021-10-18 [1] CRAN (R 4.1.1)
-##  pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.1.0)
-##  purrr         0.3.4   2020-04-17 [1] CRAN (R 4.1.0)
-##  R6            2.5.1   2021-08-19 [1] CRAN (R 4.1.1)
-##  rlang         0.4.12  2021-10-18 [1] CRAN (R 4.1.1)
-##  rmarkdown     2.11    2021-09-14 [1] CRAN (R 4.1.1)
-##  rstudioapi    0.13    2020-11-12 [1] CRAN (R 4.1.0)
-##  rvest         1.0.2   2021-10-16 [1] CRAN (R 4.1.1)
-##  sass          0.4.0   2021-05-12 [1] CRAN (R 4.1.0)
-##  scales        1.1.1   2020-05-11 [1] CRAN (R 4.1.0)
-##  sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.1.1)
-##  stringi       1.7.6   2021-11-29 [1] CRAN (R 4.1.1)
-##  stringr       1.4.0   2019-02-10 [1] CRAN (R 4.1.0)
-##  svglite       2.0.0   2021-02-20 [1] CRAN (R 4.1.0)
-##  systemfonts   1.0.3   2021-10-13 [1] CRAN (R 4.1.1)
-##  tibble        3.1.6   2021-11-07 [1] CRAN (R 4.1.1)
-##  tidyr         1.1.4   2021-09-27 [1] CRAN (R 4.1.1)
-##  tidyselect    1.1.1   2021-04-30 [1] CRAN (R 4.1.0)
-##  utf8          1.2.2   2021-07-24 [1] CRAN (R 4.1.0)
-##  vctrs         0.3.8   2021-04-29 [1] CRAN (R 4.1.0)
-##  viridisLite   0.4.0   2021-04-13 [1] CRAN (R 4.1.0)
-##  webshot       0.5.2   2019-11-22 [1] CRAN (R 4.1.0)
-##  xfun          0.29    2021-12-14 [1] CRAN (R 4.1.1)
-##  xml2          1.3.3   2021-11-30 [1] CRAN (R 4.1.1)
-##  yaml          2.2.1   2020-02-01 [1] CRAN (R 4.1.0)
+##  backports     1.5.0   2024-05-23 [1] CRAN (R 4.4.0)
+##  bslib         0.8.0   2024-07-29 [1] CRAN (R 4.4.1)
+##  cachem        1.1.0   2024-05-16 [1] CRAN (R 4.4.0)
+##  checkmate     2.3.2   2024-07-29 [1] CRAN (R 4.4.1)
+##  cli           3.6.3   2024-06-21 [1] CRAN (R 4.4.1)
+##  colorspace    2.1-1   2024-07-26 [1] CRAN (R 4.4.1)
+##  crayon        1.5.3   2024-06-20 [1] CRAN (R 4.4.1)
+##  crosstalk     1.2.1   2023-11-23 [1] CRAN (R 4.4.0)
+##  digest        0.6.37  2024-08-19 [1] CRAN (R 4.4.1)
+##  dplyr         1.1.4   2023-11-17 [1] CRAN (R 4.4.0)
+##  DT            0.33    2024-04-04 [1] CRAN (R 4.4.0)
+##  evaluate      1.0.0   2024-09-17 [1] CRAN (R 4.4.1)
+##  fansi         1.0.6   2023-12-08 [1] CRAN (R 4.4.0)
+##  fastmap       1.2.0   2024-05-15 [1] CRAN (R 4.4.0)
+##  generics      0.1.3   2022-07-05 [1] CRAN (R 4.4.0)
+##  glue          1.7.0   2024-01-09 [1] CRAN (R 4.4.0)
+##  htmltools     0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0)
+##  htmlwidgets   1.6.4   2023-12-06 [1] CRAN (R 4.4.0)
+##  jquerylib     0.1.4   2021-04-26 [1] CRAN (R 4.4.0)
+##  jsonlite      1.8.9   2024-09-20 [1] CRAN (R 4.4.1)
+##  kableExtra    1.4.0   2024-01-24 [1] CRAN (R 4.4.0)
+##  knitr       * 1.48    2024-07-07 [1] CRAN (R 4.4.1)
+##  lifecycle     1.0.4   2023-11-07 [1] CRAN (R 4.4.0)
+##  magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.4.0)
+##  munsell       0.5.1   2024-04-01 [1] CRAN (R 4.4.0)
+##  pillar        1.9.0   2023-03-22 [1] CRAN (R 4.4.0)
+##  pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.4.0)
+##  purrr         1.0.2   2023-08-10 [1] CRAN (R 4.4.0)
+##  R6            2.5.1   2021-08-19 [1] CRAN (R 4.4.0)
+##  rlang         1.1.4   2024-06-04 [1] CRAN (R 4.4.0)
+##  rmarkdown     2.28    2024-08-17 [1] CRAN (R 4.4.1)
+##  rstudioapi    0.16.0  2024-03-24 [1] CRAN (R 4.4.0)
+##  sass          0.4.9   2024-03-15 [1] CRAN (R 4.4.0)
+##  scales        1.3.0   2023-11-28 [1] CRAN (R 4.4.0)
+##  sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.4.0)
+##  stringi       1.8.4   2024-05-06 [1] CRAN (R 4.4.0)
+##  stringr       1.5.1   2023-11-14 [1] CRAN (R 4.4.0)
+##  svglite       2.1.3   2023-12-08 [1] CRAN (R 4.4.0)
+##  systemfonts   1.1.0   2024-05-15 [1] CRAN (R 4.4.0)
+##  tibble        3.2.1   2023-03-20 [1] CRAN (R 4.4.0)
+##  tidyr         1.3.1   2024-01-24 [1] CRAN (R 4.4.0)
+##  tidyselect    1.2.1   2024-03-11 [1] CRAN (R 4.4.0)
+##  utf8          1.2.4   2023-10-22 [1] CRAN (R 4.4.0)
+##  vctrs         0.6.5   2023-12-01 [1] CRAN (R 4.4.0)
+##  viridisLite   0.4.2   2023-05-02 [1] CRAN (R 4.4.0)
+##  withr         3.0.1   2024-07-31 [1] CRAN (R 4.4.1)
+##  xfun          0.47    2024-08-17 [1] CRAN (R 4.4.1)
+##  xml2          1.3.6   2023-12-04 [1] CRAN (R 4.4.0)
+##  yaml          2.3.10  2024-07-26 [1] CRAN (R 4.4.1)
 ## 
-##  [1] /home/wibeasley/R/x86_64-pc-linux-gnu-library/4.1
+##  [1] /home/wibeasley/R/x86_64-pc-linux-gnu-library/4.4
 ##  [2] /usr/local/lib/R/site-library
 ##  [3] /usr/lib/R/site-library
 ##  [4] /usr/lib/R/library
 ## 
 ## ──────────────────────────────────────────────────────────────────────────────
-

Report rendered by wibeasley at 2022-01-03, 21:07 -0600 in 1 seconds.

+

Report rendered by wibeasley at 2024-09-29, 13:21 -0500 in 1 +seconds.

diff --git a/inst/report-templates/rmarkdown-1/report-1.md b/inst/report-templates/rmarkdown-1/report-1.md index e325d0e..7bfb516 100644 --- a/inst/report-templates/rmarkdown-1/report-1.md +++ b/inst/report-templates/rmarkdown-1/report-1.md @@ -1,6 +1,6 @@ --- title: Trawler Report -date: "Date: 2022-01-03 21:07:24" +date: "Date: 2024-09-29 13:21:12.975852" output: html_document: keep_md: true @@ -63,99 +63,132 @@ A *rule* is very exact. Each record is examined to determine if it passes each Rule Summary ----------------------------- -

+ Smell Name + Priority + The dataset smells fresh when (the)… + Legal Boundaries + Value + Pass
+ definitive diagnosis + 1 -The proportion of study participants diagnosed with malnutrition associated with Chronic Renal Disease is 100% (i.e., everyone) + +The proportion of study participants diagnosed with malnutrition +associated with Chronic Renal Disease is 100% (i.e., everyone) + [1.00, 1.00] + 1.00 + TRUE
+ dialysis adequacy + 1 -Mean Kt/V value is within the normal range (i.e., between 1.2 and 5) + +Mean Kt/V value is within the normal range (i.e., between 1.2 +and 5) + [1.2, 5.0] + 1.92 + TRUE
+ normalized protein catabolic rate + 1 + Mean Normalized Protein Catabolic Rate (nPCR) is <= 1.2g/kg/day + [0.0, 1.2] + 0.931 + TRUE
+ serum cholesterol levels at baseline + 1 + Mean cholesterol levels range is between 100 and 140mg/dl at baseline + [100, 140] + 134.1 + TRUE
+ age + 2 + Mean participant age is between 20 and 60 years + [20, 60] + 44.4 + TRUE
+ bmi at baseline + 2 + Mean BMI is between 18 and 24 + [18, 24] + 24.9 + FALSE
+ females + 2 + Proportion of female participants is about half the sample + [0.40, 0.60] + 0.444 + TRUE
+ males + 2 + Proportion of male participants is about half the sample + [0.40, 0.60] + 0.556 + TRUE
+ nutritional counseling + 2 + Most patients agreed to receiving nutritional counseling + [0.85, 0.99] + 0.889 + TRUE
+ serum creatinine level at baseline + 2 + Mean serum creatinine level is between 3mg/dl and 15mg/dl at baseline + [3, 15] + 23.2 + FALSE
+ serum prealbumin level at baseline + 2 + Mean serum pre-albumin level is between 31mg/dl and 39mg/dl at baseline + [32, 39] + 23.7 + FALSE
+ +``` +## Warning: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. +## ℹ Please use `"check_name"` instead of `.data$check_name` +## This warning is displayed once every 8 hours. +## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was +## generated. +``` + +``` +## Warning: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. +## ℹ Please use `"priority"` instead of `.data$priority` +## This warning is displayed once every 8 hours. +## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was +## generated. +``` + +``` +## Warning: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. +## ℹ Please use `"error_message"` instead of `.data$error_message` +## This warning is displayed once every 8 hours. +## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was +## generated. +``` + +``` +## Warning: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. +## ℹ Please use `"violation_count"` instead of `.data$violation_count` +## This warning is displayed once every 8 hours. +## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was +## generated. +``` + +
- - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + +
Rule Name Priority Error Message Violation Count Rule Name Priority Error Message Violation Count
baseline prealbumin levels 1 Serum pre-albumin level of all enrolled patients do not meet the study criterion 10 baseline prealbumin levels 1 Serum pre-albumin level of all enrolled patients do not meet the study criterion 10
hospitalization reason 1 Patient was hospitalized but reason and the date of hospitalization is missing 2 hospitalization reason 1 Patient was hospitalized but reason and the date of hospitalization is missing 2
missing serum marker levels 1 Relevant nutritional serum markers are missing 3 missing serum marker levels 1 Relevant nutritional serum markers are missing 3
npcr 2 NPCR at completion is missing 1 npcr 2 NPCR at completion is missing 1
optimal daily protein intake 2 Daily protein intake is optimal but one of the nutritional marker is not within the normal range 7 optimal daily protein intake 2 Daily protein intake is optimal but one of the nutritional marker is not within the normal range 7
recommended npcr range 2 NPCR values are not within the recommended range at completion 10 recommended npcr range 2 NPCR values are not within the recommended range at completion 10
serum prealbumin levels 1 2 Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit 15 serum prealbumin levels 1 2 Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit 15
serum prealbumin levels 2 2 Baseline prealbumin levels and pre-albumin levels during the 1st visit are not missing however levels in the next reading are missing 0 serum prealbumin levels 2 2 Baseline prealbumin levels and pre-albumin levels during the 1st visit are not missing however levels in the next reading are missing 0
serum prealbumin levels completion data 2 Baseline prealbumin levels are not missing however readings are not carefully monitored at completion 0 serum prealbumin levels completion data 2 Baseline prealbumin levels are not missing however readings are not carefully monitored at completion 0
baseline first visit lab parameters 3 Serum prealbumin levels are low and protein intake at baseline is less than optimal 0 baseline first visit lab parameters 3 Serum prealbumin levels are low and protein intake at baseline is less than optimal 0
daily first visit lab and workup parameters 3 In-addition to baseline & visit lab protein parameters, blood work-up npcr levels are also low 0 daily first visit lab and workup parameters 3 In-addition to baseline & visit lab protein parameters, blood work-up npcr levels are also low 0
daily protein intake 3 npcr levels in study have not improved as intended 0 daily protein intake 3 npcr levels in study have not improved as intended 0
npcr comparison 3 NPCR at completion is not greater than npcr at baseline 2 npcr comparison 3 NPCR at completion is not greater than npcr at baseline 2
serum prealbumin levels expectations 3 serum prealbumin levels are not missing however subsequent readings did not come as expected 0 serum prealbumin levels expectations 3 serum prealbumin levels are not missing however subsequent readings did not come as expected 0
@@ -163,9 +196,41 @@ Rule Summary Rule Detail ----------------------------- +``` +## Warning: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. +## ℹ Please use `"results"` instead of `.data$results` +## This warning is displayed once every 8 hours. +## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was +## generated. +``` + +``` +## Warning: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. +## ℹ Please use `"record_id_linked"` instead of `.data$record_id_linked` +## This warning is displayed once every 8 hours. +## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was +## generated. +``` + +``` +## Warning: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. +## ℹ Please use `"data_collector"` instead of `.data$data_collector` +## This warning is displayed once every 8 hours. +## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was +## generated. +``` + +``` +## Warning: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. +## ℹ Please use `"baseline_date"` instead of `.data$baseline_date` +## This warning is displayed once every 8 hours. +## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was +## generated. +``` + ```{=html} -
- +
+ ``` Inactive Rules @@ -188,105 +253,105 @@ A *smell* test won't validate a specific record (like the rules above), but it w Smell Summary ----------------------------- - +
- - - - - - + + + + + + - - - - - - + + + + + + - - - - - - + + + + + + - - - - - - + + + + + + - - - - - - + + + + + + - - - - - - + + + + + + - - - - - - + + + + + + - - - - - - + + + + + + - - - - - - + + + + + + - - - - - - + + + + + + - - - - - - + + + + + + - - - - - - + + + + + +
Smell Name Priority The dataset smells fresh when (the)... Legal Boundaries Value Pass Smell Name Priority The dataset smells fresh when (the)... Legal Boundaries Value Pass
definitive diagnosis 1 The proportion of study participants diagnosed with malnutrition associated with Chronic Renal Disease is 100% (*i.e.*, everyone) [1.00, 1.00] 1.00 TRUE definitive diagnosis 1 The proportion of study participants diagnosed with malnutrition associated with Chronic Renal Disease is 100% (*i.e.*, everyone) [1.00, 1.00] 1.00 TRUE
dialysis adequacy 1 Mean Kt/V value is within the normal range (*i.e.*, between 1.2 and 5) [1.2, 5.0] 1.92 TRUE dialysis adequacy 1 Mean Kt/V value is within the normal range (*i.e.*, between 1.2 and 5) [1.2, 5.0] 1.92 TRUE
normalized protein catabolic rate 1 Mean Normalized Protein Catabolic Rate (nPCR) is <= 1.2g/kg/day [0.0, 1.2] 0.931 TRUE normalized protein catabolic rate 1 Mean Normalized Protein Catabolic Rate (nPCR) is <= 1.2g/kg/day [0.0, 1.2] 0.931 TRUE
serum cholesterol levels at baseline 1 Mean cholesterol levels range is between 100 and 140mg/dl at baseline [100, 140] 134.1 TRUE serum cholesterol levels at baseline 1 Mean cholesterol levels range is between 100 and 140mg/dl at baseline [100, 140] 134.1 TRUE
age 2 Mean participant age is between 20 and 60 years [20, 60] 44.4 TRUE age 2 Mean participant age is between 20 and 60 years [20, 60] 44.4 TRUE
bmi at baseline 2 Mean BMI is between 18 and 24 [18, 24] 24.9 FALSE bmi at baseline 2 Mean BMI is between 18 and 24 [18, 24] 24.9 FALSE
females 2 Proportion of female participants is about half the sample [0.40, 0.60] 0.444 TRUE females 2 Proportion of female participants is about half the sample [0.40, 0.60] 0.444 TRUE
males 2 Proportion of male participants is about half the sample [0.40, 0.60] 0.556 TRUE males 2 Proportion of male participants is about half the sample [0.40, 0.60] 0.556 TRUE
nutritional counseling 2 Most patients agreed to receiving nutritional counseling [0.85, 0.99] 0.889 TRUE nutritional counseling 2 Most patients agreed to receiving nutritional counseling [0.85, 0.99] 0.889 TRUE
serum creatinine level at baseline 2 Mean serum creatinine level is between 3mg/dl and 15mg/dl at baseline [3, 15] 23.2 FALSE serum creatinine level at baseline 2 Mean serum creatinine level is between 3mg/dl and 15mg/dl at baseline [3, 15] 23.2 FALSE
serum prealbumin level at baseline 2 Mean serum pre-albumin level is between 31mg/dl and 39mg/dl at baseline [32, 39] 23.7 FALSE serum prealbumin level at baseline 2 Mean serum pre-albumin level is between 31mg/dl and 39mg/dl at baseline [32, 39] 23.7 FALSE
@@ -314,74 +379,70 @@ For the sake of documentation and reproducibility, the current report was render ``` ## ─ Session info ─────────────────────────────────────────────────────────────── ## setting value -## version R version 4.1.2 (2021-11-01) -## os Ubuntu 21.10 +## version R version 4.4.1 (2024-06-14) +## os Ubuntu 24.04.1 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz America/Chicago -## date 2022-01-03 -## pandoc 2.11.4 @ /usr/lib/rstudio/bin/pandoc/ (via rmarkdown) +## date 2024-09-29 +## pandoc 3.2 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/x86_64/ (via rmarkdown) ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date (UTC) lib source -## assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0) -## backports 1.4.1 2021-12-13 [1] CRAN (R 4.1.1) -## bslib 0.3.1 2021-10-06 [1] CRAN (R 4.1.1) -## checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.1.0) -## cli 3.1.0 2021-10-27 [1] CRAN (R 4.1.1) -## colorspace 2.0-2 2021-06-24 [1] CRAN (R 4.1.0) -## crayon 1.4.2 2021-10-29 [1] CRAN (R 4.1.1) -## crosstalk 1.2.0 2021-11-04 [1] CRAN (R 4.1.1) -## DBI 1.1.2 2021-12-20 [1] CRAN (R 4.1.2) -## digest 0.6.29 2021-12-01 [1] CRAN (R 4.1.1) -## dplyr 1.0.7 2021-06-18 [1] CRAN (R 4.1.0) -## DT 0.20 2021-11-15 [1] CRAN (R 4.1.1) -## ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0) -## evaluate 0.14 2019-05-28 [1] CRAN (R 4.1.0) -## fansi 0.5.0 2021-05-25 [1] CRAN (R 4.1.0) -## fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.0) -## generics 0.1.1 2021-10-25 [1] CRAN (R 4.1.1) -## glue 1.6.0 2021-12-17 [1] CRAN (R 4.1.1) -## htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.1.1) -## htmlwidgets 1.5.4 2021-09-08 [1] CRAN (R 4.1.1) -## httr 1.4.2 2020-07-20 [1] CRAN (R 4.1.0) -## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.1.0) -## jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.1.0) -## kableExtra 1.3.4 2021-02-20 [1] CRAN (R 4.1.0) -## knitr * 1.37 2021-12-16 [1] CRAN (R 4.1.1) -## lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.1) -## magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.1.0) -## munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0) -## pillar 1.6.4 2021-10-18 [1] CRAN (R 4.1.1) -## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0) -## purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.0) -## R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.1) -## rlang 0.4.12 2021-10-18 [1] CRAN (R 4.1.1) -## rmarkdown 2.11 2021-09-14 [1] CRAN (R 4.1.1) -## rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.0) -## rvest 1.0.2 2021-10-16 [1] CRAN (R 4.1.1) -## sass 0.4.0 2021-05-12 [1] CRAN (R 4.1.0) -## scales 1.1.1 2020-05-11 [1] CRAN (R 4.1.0) -## sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.1) -## stringi 1.7.6 2021-11-29 [1] CRAN (R 4.1.1) -## stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0) -## svglite 2.0.0 2021-02-20 [1] CRAN (R 4.1.0) -## systemfonts 1.0.3 2021-10-13 [1] CRAN (R 4.1.1) -## tibble 3.1.6 2021-11-07 [1] CRAN (R 4.1.1) -## tidyr 1.1.4 2021-09-27 [1] CRAN (R 4.1.1) -## tidyselect 1.1.1 2021-04-30 [1] CRAN (R 4.1.0) -## 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0.1.3 2022-07-05 [1] CRAN (R 4.4.0) +## glue 1.7.0 2024-01-09 [1] CRAN (R 4.4.0) +## htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0) +## htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.4.0) +## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.4.0) +## jsonlite 1.8.9 2024-09-20 [1] CRAN (R 4.4.1) +## kableExtra 1.4.0 2024-01-24 [1] CRAN (R 4.4.0) +## knitr * 1.48 2024-07-07 [1] CRAN (R 4.4.1) +## lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0) +## magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.0) +## munsell 0.5.1 2024-04-01 [1] CRAN (R 4.4.0) +## pillar 1.9.0 2023-03-22 [1] CRAN (R 4.4.0) +## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.4.0) +## purrr 1.0.2 2023-08-10 [1] CRAN (R 4.4.0) +## R6 2.5.1 2021-08-19 [1] CRAN (R 4.4.0) +## rlang 1.1.4 2024-06-04 [1] CRAN (R 4.4.0) +## rmarkdown 2.28 2024-08-17 [1] CRAN (R 4.4.1) +## rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.4.0) +## sass 0.4.9 2024-03-15 [1] CRAN (R 4.4.0) +## scales 1.3.0 2023-11-28 [1] CRAN (R 4.4.0) +## sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.0) +## stringi 1.8.4 2024-05-06 [1] CRAN (R 4.4.0) +## stringr 1.5.1 2023-11-14 [1] CRAN (R 4.4.0) +## svglite 2.1.3 2023-12-08 [1] CRAN (R 4.4.0) +## systemfonts 1.1.0 2024-05-15 [1] CRAN (R 4.4.0) +## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.4.0) +## tidyr 1.3.1 2024-01-24 [1] CRAN (R 4.4.0) +## tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.4.0) +## utf8 1.2.4 2023-10-22 [1] CRAN (R 4.4.0) +## vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.0) +## viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.4.0) +## withr 3.0.1 2024-07-31 [1] CRAN (R 4.4.1) +## xfun 0.47 2024-08-17 [1] CRAN (R 4.4.1) +## xml2 1.3.6 2023-12-04 [1] CRAN (R 4.4.0) +## yaml 2.3.10 2024-07-26 [1] CRAN (R 4.4.1) ## -## [1] /home/wibeasley/R/x86_64-pc-linux-gnu-library/4.1 +## [1] /home/wibeasley/R/x86_64-pc-linux-gnu-library/4.4 ## [2] /usr/local/lib/R/site-library ## [3] /usr/lib/R/site-library ## [4] /usr/lib/R/library @@ -392,4 +453,4 @@ For the sake of documentation and reproducibility, the current report was render -Report rendered by wibeasley at 2022-01-03, 21:07 -0600 in 1 seconds. +Report rendered by wibeasley at 2024-09-29, 13:21 -0500 in 1 seconds.