Re-format reference vignette

Author: shikokuchuo

README.Rmd

@@ -21,7 +21,6 @@ knitr::opts_chunk$set(
 [![R-universe status](https://r-lib.r-universe.dev/badges/nanonext?color=3f72af)](https://r-lib.r-universe.dev/nanonext)
 [![R-CMD-check](https://github.com/r-lib/nanonext/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/r-lib/nanonext/actions/workflows/R-CMD-check.yaml)
 [![Codecov test coverage](https://codecov.io/gh/r-lib/nanonext/graph/badge.svg)](https://app.codecov.io/gh/r-lib/nanonext)
-[![DOI](https://zenodo.org/badge/451104675.svg)](https://doi.org/10.5281/zenodo.7903429)
 <!-- badges: end -->
 
 R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is a socket library for reliable, high-performance messaging over in-process, IPC, TCP, WebSocket and secure TLS transports. Implements 'Scalability Protocols', a standard for common communications patterns including publish/subscribe, request/reply and service discovery.

README.md

@@ -12,7 +12,6 @@ status](https://r-lib.r-universe.dev/badges/nanonext?color=3f72af)](https://r-li
 [![R-CMD-check](https://github.com/r-lib/nanonext/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/r-lib/nanonext/actions/workflows/R-CMD-check.yaml)
 [![Codecov test
 coverage](https://codecov.io/gh/r-lib/nanonext/graph/badge.svg)](https://app.codecov.io/gh/r-lib/nanonext)
-[![DOI](https://zenodo.org/badge/451104675.svg)](https://doi.org/10.5281/zenodo.7903429)
 <!-- badges: end -->
 
 R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is a

dev/vignettes/_nanonext.Rmd

@@ -15,20 +15,7 @@ knitr::opts_chunk$set(
 )
 ```
 
-### Table of Contents
-
-1. [Cross-language Exchange](#cross-language-exchange)
-2. [Async and Concurrency](#async-and-concurrency)
-3. [Synchronisation Primitives](#synchronisation-primitives)
-4. [TLS Secure Connections](#tls-secure-connections)
-5. [Request / Reply Protocol](#request-reply-protocol)
-6. [Publisher / Subscriber Protocol](#publisher-subscriber-protocol)
-7. [Surveyor / Respondent Protocol](#surveyor-respondent-protocol)
-8. [ncurl: (Async) HTTP Client](#ncurl-async-http-client)
-9. [stream: Websocket Client](#stream-websocket-client)
-10. [Options, Serialization and Statistics](#options-serialization-and-statistics)
-
-### Cross-language Exchange
+### 1. Cross-language Exchange
 
 `nanonext` provides a fast, reliable data interface between different programming languages where NNG has an implementation, including C, C++, Java, Python, Go, and Rust.
 
@@ -82,9 +69,7 @@ n$recv(mode = "double")
 n$close()
 ```
 
-[« Back to ToC](#table-of-contents)
-
-### Async and Concurrency
+### 2. Async and Concurrency
 
 `nanonext` implements true async send and receive, leveraging NNG as a massively-scalable concurrency framework.
 
@@ -162,9 +147,7 @@ close(s2)
 
 ```
 
-[« Back to ToC](#table-of-contents)
-
-### Synchronisation Primitives
+### 3. Synchronisation Primitives
 
 `nanonext` implements cross-platform synchronisation primitives from the NNG library, enabling synchronisation between NNG events and the main R execution thread.
 
@@ -232,9 +215,7 @@ When `flag = TRUE` is set for pipe notifications, `wait()` returns FALSE for pip
 
 This mechanism enables waiting simultaneously on multiple events while distinguishing between them. `pipe_notify()` can signal up to two condition variables per event for additional flexibility in concurrent applications.
 
-[« Back to ToC](#table-of-contents)
-
-### TLS Secure Connections
+### 4. TLS Secure Connections
 
 Secure connections use NNG and Mbed TLS libraries. Enable them by:
 
@@ -270,9 +251,7 @@ close(s)
 
 ```
 
-[« Back to ToC](#table-of-contents)
-
-### Request Reply Protocol
+### 5. Request Reply Protocol
 
 `nanonext` implements remote procedure calls (RPC) using NNG's req/rep protocol for distributed computing. Use this for computationally-expensive calculations or I/O-bound operations in separate server processes.
 
@@ -318,9 +297,7 @@ For server-side operations (e.g., writing to disk), calling or querying the valu
 
 The [`mirai`](https://doi.org/10.5281/zenodo.7912722) package (<https://mirai.r-lib.org/>) uses `nanonext` as the back-end to provide asynchronous execution of arbitrary R code using the RPC model.
 
-[&laquo; Back to ToC](#table-of-contents)
-
-### Publisher Subscriber Protocol
+### 6. Publisher Subscriber Protocol
 
 `nanonext` implements NNG's pub/sub protocol. Subscribers can subscribe to one or multiple topics broadcast by a publisher.
 
@@ -370,9 +347,7 @@ close(sub)
 
 ```
 
-[&laquo; Back to ToC](#table-of-contents)
-
-### Surveyor Respondent Protocol
+### 7. Surveyor Respondent Protocol
 
 Useful for service discovery and similar applications. A surveyor broadcasts a survey to all respondents, who may reply within a timeout period. Late responses are discarded.
 
@@ -415,9 +390,7 @@ close(res2)
 
 The final value resolves to a timeout error (integer 5 classed as 'errorValue'). All error codes are classed as 'errorValue' for easy distinction from integer message values.
 
-[&laquo; Back to ToC](#table-of-contents)
-
-### ncurl: Async HTTP Client
+### 8. ncurl: Async HTTP Client
 
 `ncurl()` is a minimalist http(s) client. `ncurl_aio()` performs async requests, returning immediately with an 'ncurlAio'.
 
@@ -479,9 +452,7 @@ transact(sess)
 
 ```
 
-[&laquo; Back to ToC](#table-of-contents)
-
-### stream: Websocket Client
+### 9. stream: Websocket Client
 
 `stream()` exposes NNG's low-level byte stream interface for communicating with raw sockets, including arbitrary non-NNG endpoints.
 
@@ -519,9 +490,7 @@ close(s)
 
 ```
 
-[&laquo; Back to ToC](#table-of-contents)
-
-### Options, Serialization and Statistics
+### 10. Options, Serialization and Statistics
 
 Use `opt()` and `'opt<-'()` to get and set options on Sockets, Contexts, Streams, Listeners, or Dialers. See function documentation for available options.
 
@@ -569,5 +538,3 @@ stat(s, "pipes")
 
 close(s)
 ```
-
-[&laquo; Back to ToC](#table-of-contents)

vignettes/nanonext.Rmd

@@ -8,20 +8,7 @@ vignette: >
 
 
 
-### Table of Contents
-
-1. [Cross-language Exchange](#cross-language-exchange)
-2. [Async and Concurrency](#async-and-concurrency)
-3. [Synchronisation Primitives](#synchronisation-primitives)
-4. [TLS Secure Connections](#tls-secure-connections)
-5. [Request / Reply Protocol](#request-reply-protocol)
-6. [Publisher / Subscriber Protocol](#publisher-subscriber-protocol)
-7. [Surveyor / Respondent Protocol](#surveyor-respondent-protocol)
-8. [ncurl: (Async) HTTP Client](#ncurl-async-http-client)
-9. [stream: Websocket Client](#stream-websocket-client)
-10. [Options, Serialization and Statistics](#options-serialization-and-statistics)
-
-### Cross-language Exchange
+### 1. Cross-language Exchange
 
 `nanonext` provides a fast, reliable data interface between different programming languages where NNG has an implementation, including C, C++, Java, Python, Go, and Rust.
 
@@ -78,9 +65,7 @@ n$recv(mode = "double")
 n$close()
 ```
 
-[« Back to ToC](#table-of-contents)
-
-### Async and Concurrency
+### 2. Async and Concurrency
 
 `nanonext` implements true async send and receive, leveraging NNG as a massively-scalable concurrency framework.
 
@@ -166,9 +151,7 @@ close(s2)
 
 ```
 
-[« Back to ToC](#table-of-contents)
-
-### Synchronisation Primitives
+### 3. Synchronisation Primitives
 
 `nanonext` implements cross-platform synchronisation primitives from the NNG library, enabling synchronisation between NNG events and the main R execution thread.
 
@@ -244,9 +227,7 @@ When `flag = TRUE` is set for pipe notifications, `wait()` returns FALSE for pip
 
 This mechanism enables waiting simultaneously on multiple events while distinguishing between them. `pipe_notify()` can signal up to two condition variables per event for additional flexibility in concurrent applications.
 
-[« Back to ToC](#table-of-contents)
-
-### TLS Secure Connections
+### 4. TLS Secure Connections
 
 Secure connections use NNG and Mbed TLS libraries. Enable them by:
 
@@ -266,7 +247,7 @@ The convenience function `write_cert()` generates a 4096-bit RSA key pair and se
 cert <- write_cert(cn = "127.0.0.1")
 str(cert)
 #> List of 2
-#>  $ server: chr [1:2] "-----BEGIN CERTIFICATE-----\nMIIFOTCCAyGgAwIBAgIBATANBgkqhkiG9w0BAQsFADA0MRIwEAYDVQQDDAkxMjcu\nMC4wLjExETAPBgNV"| __truncated__ "-----BEGIN RSA PRIVATE KEY-----\nMIIJJwIBAAKCAgEAjt5sNS09hjIbA7SepY8Yv+TCkvNdFDXlwVGC0AQnxWnRr/9k\nHHZTSnt85rbG"| __truncated__
+#>  $ server: chr [1:2] "-----BEGIN CERTIFICATE-----\nMIIFOTCCAyGgAwIBAgIBATANBgkqhkiG9w0BAQsFADA0MRIwEAYDVQQDDAkxMjcu\nMC4wLjExETAPBgNV"| __truncated__ "-----BEGIN RSA PRIVATE KEY-----\nMIIJKAIBAAKCAgEAwupvOgQzC3RQVt95gOTaOsDQ72tAbDzhHHLk9JfABqqWNpyl\nL7Fw3Foh7Nb9"| __truncated__
 #>  $ client: chr [1:2] "-----BEGIN CERTIFICATE-----\nMIIFOTCCAyGgAwIBAgIBATANBgkqhkiG9w0BAQsFADA0MRIwEAYDVQQDDAkxMjcu\nMC4wLjExETAPBgNV"| __truncated__ ""
 
 ser <- tls_config(server = cert$server)
@@ -287,9 +268,7 @@ close(s)
 
 ```
 
-[&laquo; Back to ToC](#table-of-contents)
-
-### Request Reply Protocol
+### 5. Request Reply Protocol
 
 `nanonext` implements remote procedure calls (RPC) using NNG's req/rep protocol for distributed computing. Use this for computationally-expensive calculations or I/O-bound operations in separate server processes.
 
@@ -327,7 +306,7 @@ When the result is needed, call the recvAio using `call_aio()` to retrieve the v
 
 ``` r
 call_aio(aio)$data |> str()
-#>  num [1:100000000] -1.0996 -0.068 -1.2462 -0.5909 -0.0194 ...
+#>  num [1:100000000] -1.532 -1.493 0.499 0.478 -0.118 ...
 ```
 
 Since `call_aio()` blocks, alternatively query `aio$data` directly, which returns 'unresolved' (logical NA) if incomplete.
@@ -336,9 +315,7 @@ For server-side operations (e.g., writing to disk), calling or querying the valu
 
 The [`mirai`](https://doi.org/10.5281/zenodo.7912722) package (<https://mirai.r-lib.org/>) uses `nanonext` as the back-end to provide asynchronous execution of arbitrary R code using the RPC model.
 
-[&laquo; Back to ToC](#table-of-contents)
-
-### Publisher Subscriber Protocol
+### 6. Publisher Subscriber Protocol
 
 `nanonext` implements NNG's pub/sub protocol. Subscribers can subscribe to one or multiple topics broadcast by a publisher.
 
@@ -403,9 +380,7 @@ close(sub)
 
 ```
 
-[&laquo; Back to ToC](#table-of-contents)
-
-### Surveyor Respondent Protocol
+### 7. Surveyor Respondent Protocol
 
 Useful for service discovery and similar applications. A surveyor broadcasts a survey to all respondents, who may reply within a timeout period. Late responses are discarded.
 
@@ -454,9 +429,7 @@ close(res2)
 
 The final value resolves to a timeout error (integer 5 classed as 'errorValue'). All error codes are classed as 'errorValue' for easy distinction from integer message values.
 
-[&laquo; Back to ToC](#table-of-contents)
-
-### ncurl: Async HTTP Client
+### 8. ncurl: Async HTTP Client
 
 `ncurl()` is a minimalist http(s) client. `ncurl_aio()` performs async requests, returning immediately with an 'ncurlAio'.
 
@@ -489,7 +462,7 @@ res
 
 call_aio(res)$headers
 #> $date
-#> [1] "Tue, 02 Dec 2025 11:11:53 GMT"
+#> [1] "Tue, 02 Dec 2025 12:02:22 GMT"
 
 res$data
 #> [1] "{\"args\":{},\"data\":{\"key\":\"value\"},\"files\":{},\"form\":{},\"headers\":{\"host\":\"postman-echo.com\",\"accept-encoding\":\"gzip, br\",\"x-forwarded-proto\":\"https\",\"content-type\":\"application/json\",\"authorization\":\"Bearer APIKEY\",\"content-length\":\"16\"},\"json\":{\"key\":\"value\"},\"url\":\"https://postman-echo.com/post\"}"
@@ -532,7 +505,7 @@ transact(sess)
 #> 
 #> $headers
 #> $headers$Date
-#> [1] "Tue, 02 Dec 2025 11:11:53 GMT"
+#> [1] "Tue, 02 Dec 2025 12:02:22 GMT"
 #> 
 #> $headers$`Content-Type`
 #> [1] "application/json; charset=utf-8"
@@ -549,9 +522,7 @@ transact(sess)
 #> [204] 2f 67 65 74 22 7d
 ```
 
-[&laquo; Back to ToC](#table-of-contents)
-
-### stream: Websocket Client
+### 9. stream: Websocket Client
 
 `stream()` exposes NNG's low-level byte stream interface for communicating with raw sockets, including arbitrary non-NNG endpoints.
 
@@ -599,9 +570,7 @@ close(s)
 
 ```
 
-[&laquo; Back to ToC](#table-of-contents)
-
-### Options, Serialization and Statistics
+### 10. Options, Serialization and Statistics
 
 Use `opt()` and `'opt<-'()` to get and set options on Sockets, Contexts, Streams, Listeners, or Dialers. See function documentation for available options.
 
@@ -653,5 +622,3 @@ stat(s, "pipes")
 
 close(s)
 ```
-
-[&laquo; Back to ToC](#table-of-contents)