Updating vignettes (#20)

* Adding hexagon and correct typos in readme

* Fixing bug in table in documentation

* Rearranging examples

* Adding brackets around package names and other minor adjustments

* Minor

* Minor

* Adding dependency {crew}

* Reverting modification of description file

* Sort snapshot results

* Reordering snapshot

README.Rmd

@@ -3,17 +3,14 @@
  always_allow_html: true
 ---
 
- <!-- README.md is generated from README.Rmd. Please edit that file -->
+# ramnog <a href="https://hta-pharma.github.io/ramnog/"><img src="man/figures/logo.png" align="right" height="138" alt="ramnog website" /></a>
 
 ```{r setup, include=FALSE}
 knitr::opts_chunk$set(echo = TRUE)
 ```
 
-# R packages for AMNOG analyses
-
-Ramnog is a collection of packages for setting up pipelines for AMNOG-style HTA analyses
-
-The aim of ramnog is that statistician/programmer can set up an AMNOG-type analyses with minimal familiarity with R.
+The {ramnog} package is a collection of packages for setting up pipelines for AMNOG-style HTA analyses.
+The aim of {ramnog} is to enable statisticians/programmers to set up an AMNOG-type analyses with minimal familiarity with `R`.
 
 # Packages
 
@@ -38,14 +35,15 @@ dt |>
 
 # Aim
 
-The aim of the ramnog framework is that a programmer has to write minimal code, and no programming to in order to set-up a new AMNOG-type analyses. For each study, the programmer will need to make, adjust, or check the following four types of code:
+The aim of {ramnog} is that a programmer has to write minimal code, and no programming to in order to set-up a new AMNOG-type analyses. For each study, the programmer will need to make, adjust, or check the following four types of code:
 
 1. The definition of each endpoint (or group of endpoints).
-2. A set of adam functions that makes any modifications to existing ADaM datasets (e.g., new age grouping in ADSL), or makes new ADaM datasets if none exist for the required output.
-3. (If needed) Define a set of criteria for when an endpoint should be included in the results. A library of these criteria are stored in the companion package {chefCriteria}
-4. A specification of the statistical functions used to summarize/analyze the data (usually found in the [chefStats](https://hta-pharma.github.io/chefStats/) package).
+2. A set of ADaM functions that makes any modifications to existing ADaM datasets (e.g., new age grouping in ADSL), or makes new ADaM datasets if none exist for the required output.
+3. (If needed) Define a set of criteria for when an endpoint should be included in the results. A library of these criteria are stored in the companion package {[chefCriteria](https://hta-pharma.github.io/chefCriteria/)}.
+4. A specification of the statistical functions used to summarize/analyze the data. A library of these functions are provided in the {[chefStats](https://hta-pharma.github.io/chefStats/)} package.
 
-A core principal of the frameworks design is __modularity__. The core functionality of the framework as specefied in the code in [chef](https://hta-pharma.github.io/chef/) should change slowly, while functionality that is subject to more frequent changes are sectioned off in other packages ([chefStats](https://hta-pharma.github.io/chefStats/) and [cheCriteria](https://hta-pharma.github.io/chefCriteria/))
+A core principal of the frameworks design is __modularity__. 
+The core functionality of the framework resides in {[chef](https://hta-pharma.github.io/chef/)} and should change slowly, while functionality that is subject to more frequent changes are sectioned off in other packages ({[chefStats](https://hta-pharma.github.io/chefStats/)} and {[chefCriteria](https://hta-pharma.github.io/chefCriteria/)}).
 
 # Contributing
 

README.md

@@ -1,13 +1,10 @@
 
-<!-- README.md is generated from README.Rmd. Please edit that file -->
+# ramnog <a href="https://hta-pharma.github.io/ramnog/"><img src="man/figures/logo.png" align="right" height="138" alt="ramnog website" /></a>
 
-# R packages for AMNOG analyses
-
-Ramnog is a collection of packages for setting up pipelines for
-AMNOG-style HTA analyses
-
-The aim of ramnog is that statistician/programmer can set up an
-AMNOG-type analyses with minimal familiarity with R.
+The {ramnog} package is a collection of packages for setting up
+pipelines for AMNOG-style HTA analyses. The aim of {ramnog} is to enable
+statisticians/programmers to set up an AMNOG-type analyses with minimal
+familiarity with `R`.
 
 # Packages
 
@@ -63,28 +60,31 @@ Wrapper package tying ecosystem together
 
 # Aim
 
-The aim of the ramnog framework is that a programmer has to write
-minimal code, and no programming to in order to set-up a new AMNOG-type
-analyses. For each study, the programmer will need to make, adjust, or
-check the following four types of code:
+The aim of {ramnog} is that a programmer has to write minimal code, and
+no programming to in order to set-up a new AMNOG-type analyses. For each
+study, the programmer will need to make, adjust, or check the following
+four types of code:
 
 1. The definition of each endpoint (or group of endpoints).
-2. A set of adam functions that makes any modifications to existing
+2. A set of ADaM functions that makes any modifications to existing
  ADaM datasets (e.g., new age grouping in ADSL), or makes new ADaM
  datasets if none exist for the required output.
 3. (If needed) Define a set of criteria for when an endpoint should be
  included in the results. A library of these criteria are stored in
- the companion package {chefCriteria}
+ the companion package
+ {[chefCriteria](https://hta-pharma.github.io/chefCriteria/)}.
 4. A specification of the statistical functions used to
- summarize/analyze the data (usually found in the
- [chefStats](https://hta-pharma.github.io/chefStats/) package).
+ summarize/analyze the data. A library of these functions are
+ provided in the
+ {[chefStats](https://hta-pharma.github.io/chefStats/)} package.
 
 A core principal of the frameworks design is **modularity**. The core
-functionality of the framework as specefied in the code in
-[chef](https://hta-pharma.github.io/chef/) should change slowly, while
-functionality that is subject to more frequent changes are sectioned off
-in other packages ([chefStats](https://hta-pharma.github.io/chefStats/)
-and [cheCriteria](https://hta-pharma.github.io/chefCriteria/))
+functionality of the framework resides in
+{[chef](https://hta-pharma.github.io/chef/)} and should change slowly,
+while functionality that is subject to more frequent changes are
+sectioned off in other packages
+({[chefStats](https://hta-pharma.github.io/chefStats/)} and
+{[chefCriteria](https://hta-pharma.github.io/chefCriteria/)}).
 
 # Contributing
 

tests/testthat/_snaps/mild_ae_by_sex.md

@@ -4,56 +4,30 @@
   ep_stat[, .(stat_filter, endpoint_group_filter, stat_result_label,
   stat_result_description, stat_result_qualifiers, stat_result_value)]
  Output
-  stat_filter
-  <char>
-  1: TOTAL_ == "total" & TRT01A == "Placebo"
-  2: TOTAL_ == "total" & TRT01A == "Placebo"
-  3: TOTAL_ == "total" & TRT01A == "Xanomeline High Dose"
-  4: TOTAL_ == "total" & TRT01A == "Xanomeline High Dose"
-  5: SEX == "F" & TRT01A == "Placebo"
-  --- 
-  4274: 
-  4275: 
-  4276: 
-  4277: 
-  4278: 
-  endpoint_group_filter
-  <char>
-  1: AESOC == "GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS" & AESEV == "MILD"
-  2: AESOC == "GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS" & AESEV == "MILD"
-  3: AESOC == "GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS" & AESEV == "MILD"
-  4: AESOC == "GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS" & AESEV == "MILD"
-  5: AESOC == "GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS" & AESEV == "MILD"
-  --- 
-  4274: AESOC == "SOCIAL CIRCUMSTANCES" & AESEV == "SEVERE"
-  4275: AESOC == "EAR AND LABYRINTH DISORDERS" & AESEV == "SEVERE"
-  4276: AESOC == "EAR AND LABYRINTH DISORDERS" & AESEV == "SEVERE"
-  4277: AESOC == "NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS)" & AESEV == "SEVERE"
-  4278: AESOC == "NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS)" & AESEV == "SEVERE"
-  stat_result_label stat_result_description
-  <char> <char>
-  1: N Number of subjects
-  2: E Number of events
-  3: N Number of subjects
-  4: E Number of events
-  5: N Number of subjects
-  --- 
-  4274: <NA> P-value interaction not conducted
-  4275: <NA> P-value interaction not conducted
-  4276: <NA> P-value interaction not conducted
-  4277: <NA> P-value interaction not conducted
-  4278: <NA> P-value interaction not conducted
-  stat_result_qualifiers stat_result_value
-  <char> <num>
-  1: <NA> 86
-  2: <NA> 36
-  3: <NA> 72
-  4: <NA> 75
-  5: <NA> 53
-  --- 
-  4274: <NA> NA
-  4275: <NA> NA
-  4276: <NA> NA
-  4277: <NA> NA
-  4278: <NA> NA
+  stat_filter endpoint_group_filter stat_result_label
+  <char> <char> <char>
+  1: <NA> <NA> <NA>
+  2: <NA> <NA> <NA>
+  3: <NA> <NA> <NA>
+  4: <NA> <NA> <NA>
+  5: <NA> <NA> <NA>
+  --- 
+  29942: <NA> <NA> <NA>
+  29943: <NA> <NA> <NA>
+  29944: <NA> <NA> <NA>
+  29945: <NA> <NA> <NA>
+  29946: <NA> <NA> <NA>
+  stat_result_description stat_result_qualifiers stat_result_value
+  <char> <char> <num>
+  1: <NA> <NA> NA
+  2: <NA> <NA> NA
+  3: <NA> <NA> NA
+  4: <NA> <NA> NA
+  5: <NA> <NA> NA
+  --- 
+  29942: <NA> <NA> NA
+  29943: <NA> <NA> NA
+  29944: <NA> <NA> NA
+  29945: <NA> <NA> NA
+  29946: <NA> <NA> NA
 

tests/testthat/test-mild_ae_by_sex.R

@@ -36,11 +36,19 @@ test_that("Complex pipeline runs without errors",
  # EXPECT ------------------------------------------------------------------
  x <- targets::tar_meta() |> data.table::as.data.table()
  targets::tar_load(ep_stat)
+ ep_stat <- ep_stat[order(c(endpoint_id,
+ strata_var,
+ fn_type,
+ fn_name,
+ stat_filter,
+ stat_result_label, 
+ stat_result_description)), ]
+
  expect_true(all(is.na(x$error)))
  expect_snapshot(ep_stat[, .(stat_filter,
  endpoint_group_filter,
  stat_result_label,
  stat_result_description,
  stat_result_qualifiers,
  stat_result_value)])
- })
+ })