Skip to content

Commit

Permalink
more readme material
Browse files Browse the repository at this point in the history 
link to htmlpreview version of report

ref #5
  • Loading branch information
@wibeasley
wibeasley committed Dec 30, 2021
1 parent 3713540 commit d0315ba
Show file tree
Hide file tree
Showing 2 changed files with 57 additions and 70 deletions.
31 changes: 25 additions & 6 deletions README.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,18 +32,37 @@ You can install the development version of trawler from [GitHub](https://github.
devtools::install_github("OuhscBbmc/trawler")
```

## Example

This is a basic example which shows you how to solve a common problem:
## Standard Trawler Report

```{r example}
# Step 0: define paths.
# So this package example executes on every machine, temp files are used.
# Replace the two paths for your specific project
path_data <- system.file("datasets/pt-event-biochemical.rds", package = "trawler")
path_checks <- system.file("checks/checks-biochemical.yml", package = "trawler")
path_defs <- system.file("checks/checks-biochemical.yml", package = "trawler")
# In your real code, this will probably in a static directory.
# If PHI or sensitive info is contained, use a secure location.
directory_output <- file.path(tempdir(check = TRUE), "trawler")
if (!dir.exists(directory_output)) dir.create(directory_output)
path_checks <- tempfile("trawler-checks-", fileext = ".rds", tmpdir = directory_output)
# Step 1: load the check definitions and the dataset to test
ds_pt_event <- readr::read_rds(path_data)
checks <- trawler::load_checks(path_checks)
checks <- trawler::load_checks(path_defs)
# Step 2: execute the checks and save to an rds file
ds_pt_event |>
trawler::execute_checks(checks) |>
readr::write_rds(path_checks)
# Step 3: render checks as an html report with R Markdown
trawler::render_rmarkdown(path_checks, directory_output)
trawler::execute_checks(ds_pt_event, checks)
# For the sake of this example, clean up temp files.
# You probably do NOT want this line in your real code.
unlink(directory_output, recursive = TRUE)
```

The rendered html report will look similar to [this preview](https://htmlpreview.github.io/?https://github.com/OuhscBbmc/trawler/blob/main/inst/report-templates/rmarkdown-1/report-1.html).
96 changes: 32 additions & 64 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,76 +25,44 @@ You can install the development version of trawler from
devtools::install_github("OuhscBbmc/trawler")
```

## Example

This is a basic example which shows you how to solve a common problem:
## Standard Trawler Report

``` r
# Step 0: define paths.
# So this package example executes on every machine, temp files are used.

# Replace the two paths for your specific project
path_data <- system.file("datasets/pt-event-biochemical.rds", package = "trawler")
path_checks <- system.file("checks/checks-biochemical.yml", package = "trawler")
path_defs <- system.file("checks/checks-biochemical.yml", package = "trawler")

# In your real code, this will probably in a static directory.
# If PHI or sensitive info is contained, use a secure location.
directory_output <- file.path(tempdir(check = TRUE), "trawler")
if (!dir.exists(directory_output)) dir.create(directory_output)
path_checks <- tempfile("trawler-checks-", fileext = ".rds", tmpdir = directory_output)

# Step 1: load the check definitions and the dataset to test
ds_pt_event <- readr::read_rds(path_data)
checks <- trawler::load_checks(path_checks)
checks <- trawler::load_checks(path_defs)

trawler::execute_checks(ds_pt_event, checks)
#> $record_id_name
#> [1] "record_id"
#>
#> $baseline_date_name
#> [1] "date_enrolled"
#>
#> $record_id_link
#> [1] "<a href=\"https://bbmc.ouhsc.edu/redcap/redcap_v%s/DataEntry/index.php?pid=%s&arm=%s&id=%s&page=%s\" target=\"_blank\">%s</a>"
#>
#> $github_file_prefix
#> [1] "https://github.com/OuhscBbmc/validator-1/blob/master"
#>
#> $smells
#> # A tibble: 12 × 12
#> check_name pass description priority debug bound_lower bound_upper
#> <chr> <lgl> <chr> <int> <lgl> <dbl> <dbl>
#> 1 proportion_fe… TRUE Proportion femal… 2 FALSE 0.25 0.75
#> 2 proportion_ma… TRUE Proportion male … 2 FALSE 0.25 0.75
#> 3 mean_age TRUE Mean age of part… 2 FALSE 20 80
#> 4 mean_serum_pr… FALSE Mean serum pre-a… 1 FALSE 32 39
#> 5 mean_serum_cr… FALSE Mean serum creat… 1 FALSE 3 15
#> 6 average_bmi_a… FALSE Average BMI is b… 2 FALSE 18 24
#> 7 mean_serum_ch… TRUE Average Choleste… 1 FALSE 100 140
#> 8 dialysis_adeq… TRUE Normal range for… 1 FALSE 1.2 5
#> 9 average_serum… TRUE Mean serum ferri… 1 FALSE 501 1200
#> 10 nutritional_c… TRUE Most patients ag… 2 FALSE 0.85 0.99
#> 11 definitive_di… TRUE All study partic… 1 FALSE 1 1
#> 12 normalized_pr… FALSE Average Normaliz… 1 FALSE 0 0.12
#> # … with 5 more variables: bounds_template <chr>, value_template <chr>,
#> # equation <chr>, boundaries <chr>, value <dbl>
#>
#> $smell_status
#> [1] "12 smells have been sniffed. 4 violation(s) were found."
#>
#> $rules
#> # A tibble: 14 × 8
#> check_name violation_count error_message priority debug instrument
#> <chr> <int> <chr> <int> <lgl> <chr>
#> 1 baseline_pre… 10 Serum pre-albumi… 1 FALSE baseline_data
#> 2 missing_seru… 3 Relevant nutriti… 1 FALSE baseline_data
#> 3 serum_prealb… 15 Baseline prealbu… 1 FALSE baseline_data…
#> 4 serum_prealb… 0 Baseline prealbu… 1 FALSE baseline_data…
#> 5 serum_prealb… 0 Baseline prealbu… 1 FALSE baseline_data…
#> 6 serum_prealb… 0 serum prealbumin… 1 FALSE baseline_data…
#> 7 baseline_fir… 0 Serum prealbumin… 1 FALSE baseline_data…
#> 8 daily_first_… 0 In-addition to b… 1 FALSE baseline_data…
#> 9 daily_protei… 0 npcr levels in s… 1 FALSE baseline_data…
#> 10 hospitalizat… 2 Patient was hosp… 1 FALSE completion_pr…
#> 11 optimal_dail… 7 Daily protein in… 1 FALSE completion_pr…
#> 12 recommended_… 10 NPCR values are … 1 FALSE completion_da…
#> 13 npcr 1 NPCR at completi… 1 FALSE completion_da…
#> 14 npcr_compari… 2 NPCR at completi… 1 FALSE completion_da…
#> # … with 2 more variables: passing_test <chr>, results <list>
#>
#> $rule_status
#> [1] "14 rules were examined. 8 rule(s) had at least 1 violation. 50 total violation(s) were found."
# Step 2: execute the checks and save to an rds file
ds_pt_event |>
trawler::execute_checks(checks) |>
readr::write_rds(path_checks)

# Step 3: render checks as an html report with R Markdown
trawler::render_rmarkdown(path_checks, directory_output)
#> processing file: report-1.Rmd
#> Loading required namespace: DT
#> output file: report-1.knit.md
#> /usr/lib/rstudio/bin/pandoc/pandoc +RTS -K512m -RTS report-1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpy5PD2b/trawler/report-1.html --lua-filter /home/wibeasley/R/x86_64-pc-linux-gnu-library/4.1/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/wibeasley/R/x86_64-pc-linux-gnu-library/4.1/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /home/wibeasley/R/x86_64-pc-linux-gnu-library/4.1/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --number-sections --variable theme=bootstrap --include-in-header /tmp/Rtmpy5PD2b/rmarkdown-strb799437a216a.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
#>
#> attr(,"class")
#> [1] "trawler_checks"
#> Output created: /tmp/Rtmpy5PD2b/trawler/report-1.html

# For the sake of this example, clean up temp files.
# You probably do NOT want this line in your real code.
unlink(directory_output, recursive = TRUE)
```

The rendered html report will look similar to [this
preview](https://htmlpreview.github.io/?https://github.com/OuhscBbmc/trawler/blob/main/inst/report-templates/rmarkdown-1/report-1.html).

0 comments on commit d0315ba

Please sign in to comment.