Add README, vignette and dstemplate pkgdown site

DESCRIPTION

@@ -2,16 +2,29 @@ Package: dsCodaClient
 Title: DataSHIELD client-side functions for compositional data analysis
 Description: DataSHIELD client functions for compositional data analysis using the compositions package.
 Version: 0.2.0
-Author: Xavier Escriba Montagut and Stuart Wheater
-Maintainer: Xavier Escriba Montagut and Stuart Wheater <stuart.wheater@arjuna.com>
+Authors@R: c(
+    person("Xavier", "Escribà-Montagut", email = "xavier.escriba.montagut@gmail.com", role = "aut"),
+    person("Stuart", "Wheater", email = "stuart.wheater@arjuna.com", role = c("aut", "cre")),
+    person("DataSHIELD community", role = c("cph", "fnd"))
+  )
 License: GPL-3
+URL: https://github.com/datashield/dsCodaClient
+BugReports: https://github.com/datashield/dsCodaClient/issues
 Depends:
     R (>= 4.1.0),
     DSI (>= 1.8.0)
 Suggests:
     knitr,
+    rmarkdown,
     testthat,
-    httr
+    httr,
+    DSLite,
+    dsBase,
+    dsBaseClient,
+    dsCoda,
+    dsTidyverseClient,
+    compositions,
+    zCompositions
 Encoding: UTF-8
-VignetteBuilder: knitr 
+VignetteBuilder: knitr
 Config/roxygen2/version: 8.1.0

README.md

@@ -1,2 +1,71 @@
 # dsCodaClient
-Cora DataSHIELD client site base functions
+
+DataSHIELD client-side functions for compositional data analysis (CoDa).
+Compositional data are vectors of parts that sum to a constant, such as
+the 24-hour movement behaviour composition (sleep, sedentary behaviour and
+physical activity intensities) studied in the ProPASS consortium.
+`dsCodaClient` drives the server-side package
+[dsCoda](https://github.com/datashield/dsCoda), which wraps the
+[compositions](https://cran.r-project.org/package=compositions) and
+[zCompositions](https://cran.r-project.org/package=zCompositions) packages,
+so that closure, zero replacement, log-ratio transforms and downstream
+analysis run across DataSHIELD servers without individual records leaving
+them.
+
+## Functions
+
+| Function | What it does |
+|---|---|
+| `ds.lrEM()` | Replace zeros / values below detection limit with `zCompositions::lrEM()` (server-side object). |
+| `ds.acomp()` | Create a closed Aitchison composition with `compositions::acomp()` (server-side object). |
+| `ds.ilr()` | Compute isometric log-ratio coordinates, optionally with a user-supplied basis `V` (server-side object). |
+| `ds.meanComp()` | Pooled geometric-mean composition across all servers, returned to the client. |
+| `build_sequential_ilr_V()` | Build the ILR basis for a sequential binary partition, for use with `ds.ilr()`. |
+
+## Installation
+
+```r
+# install.packages("remotes")
+remotes::install_github("datashield/dsCodaClient")
+```
+
+`dsCodaClient` needs `DSI` (>= 1.8.0) and `dsBaseClient`;
+`ds.meanComp()` additionally uses `dsTidyverseClient` and `compositions`
+on the client. Once the package is published on the DataSHIELD CRAN
+mirror it will also be installable with
+`install.packages("dsCodaClient", repos = c("https://cran.obiba.org", "https://cloud.r-project.org"))`.
+
+Every DataSHIELD server you connect to must have
+[dsBase](https://github.com/datashield/dsBase),
+[dsCoda](https://github.com/datashield/dsCoda) and, for the regression
+workflow in the vignette,
+[dsTidyverse](https://github.com/molgenis/ds-tidyverse) installed.
+
+## Quick start
+
+```r
+library(DSI)
+library(dsBaseClient)
+library(dsCodaClient)
+
+# conns <- DSI::datashield.login(logindata, assign = TRUE, symbol = "D")
+
+parts <- c("vpa", "mpa", "lipa", "sleep", "sb")
+
+ds.acomp(X = "D", parts = parts, objectname = "comp", datasources = conns)
+
+V <- build_sequential_ilr_V(length(parts), parts)
+ds.ilr(X = "comp", V = V, objectname = "ilr_sbp", datasources = conns)
+
+ds.meanComp("comp", datasources = conns)
+```
+
+The vignette walks through the full workflow, including zero replacement
+and a pooled regression on the ILR coordinates, using
+[DSLite](https://cran.r-project.org/package=DSLite) so no Opal server is
+needed: `vignette("dsCodaClient")` or the
+[package site](https://datashield.github.io/dsCodaClient/).
+
+## License
+
+GPL-3. Developed by the ProPASS consortium and the DataSHIELD community.

_pkgdown.yml

@@ -1,5 +1,28 @@
 template:
+  package: dstemplate
   bootstrap: 5
-  params:
-    bootswatch: simplex
+
 url: https://github.com/datashield/dsCodaClient/
+
+authors:
+  Xavier Escribà-Montagut:
+    href: https://github.com/ESCRI11
+  Stuart Wheater:
+    href: https://github.com/StuartWheater
+
+reference:
+- title: Server-side assignment
+  desc: Create objects on the servers; nothing is returned to the client.
+  contents:
+  - ds.lrEM
+  - ds.acomp
+  - ds.ilr
+- title: Client-side helpers
+  contents:
+  - ds.meanComp
+  - build_sequential_ilr_V
+
+articles:
+- title: Tutorials
+  contents:
+  - dsCodaClient