Merge pull request #11 from gongcastro/test

Test
gongcastro · May 8, 2023 · 675cbcc · 675cbcc
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,63 +1,63 @@
-Package: bvq
-Title: Barcelona Vocabulary Questionnaire Database and Helper Functions
-Version: 0.2.0
-Authors@R: c(
-    person(given = "Gonzalo", family = "Garcia-Castro", 
-           email = "[email protected]",
-           role = c("cre", "aut"),
-           comment = c(ORCID = "0000-0002-8553-4209")),
-    person(given = "Daniela S. ", family = "Ávila-Varela",
-           email = "[email protected]", 
-           role = "aut",
-           comment = c(ORCID = "0000-0002-3518-8117")),
-    person(given = "Nuria", 
-           family = "Sebastian-Galles", 
-           email = "[email protected]", 
-           role = "ctb",
-           comment = c(ORCID = "0000-0001-6938-2498")))
-Maintainer: Gonzalo Garcia-Castro <[email protected]>
-Description: Download, clean, and process the Barcelona Vocabulary
-    Questionnaire (BVQ) data. BVQ is a vocabulary inventory developed for
-    assesing the vocabulary of Catalan-Spanish bilinguals infants from the
-    Metropolitan Area of Barcelona (Spain), aged 10 to 40 months. This
-    package includes functions to download the data from formr servers,
-    and return the processed data in multiple formats.
-License: MIT + file LICENSE
-URL: https://gongcastro.github.io/bvq/,
-    https://github.com/gongcastro/bvq/
-BugReports: https://github.com/gongcastro/bvq/issues
-Depends: 
-    R (>= 3.5.0),
-Imports: 
-    cli,
-    dplyr (>= 1.0.0),
-    formr (>= 0.9.1),
-    gargle,
-    googlesheets4,
-    janitor,
-    lifecycle,
-    lubridate,
-    magrittr,
-    rlang,
-    stringr,
-    tibble,
-    tidyr
-Suggests: 
-    knitr,
-    readxl,
-    rmarkdown,
-    roxygen2,
-    testthat (>= 3.0.0),
-    ggplot2 (>= 3.4.2),
-    withr
-VignetteBuilder: 
-    knitr,
-    ggplot2
-Remotes: 
-    github::rubenarslan/formr
-Config/testthat/edition: 3
-Encoding: UTF-8
-Language: en-US
-LazyData: true
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+Package: bvq
+Title: Barcelona Vocabulary Questionnaire Database and Helper Functions
+Version: 0.3.0
+Authors@R: c(
+    person(given = "Gonzalo", family = "Garcia-Castro", 
+           email = "[email protected]",
+           role = c("cre", "aut"),
+           comment = c(ORCID = "0000-0002-8553-4209")),
+    person(given = "Daniela S. ", family = "Ávila-Varela",
+           email = "[email protected]", 
+           role = "aut",
+           comment = c(ORCID = "0000-0002-3518-8117")),
+    person(given = "Nuria", 
+           family = "Sebastian-Galles", 
+           email = "[email protected]", 
+           role = "ctb",
+           comment = c(ORCID = "0000-0001-6938-2498")))
+Maintainer: Gonzalo Garcia-Castro <[email protected]>
+Description: Download, clean, and process the Barcelona Vocabulary
+    Questionnaire (BVQ) data. BVQ is a vocabulary inventory developed for
+    assesing the vocabulary of Catalan-Spanish bilinguals infants from the
+    Metropolitan Area of Barcelona (Spain), aged 10 to 40 months. This
+    package includes functions to download the data from formr servers,
+    and return the processed data in multiple formats.
+License: MIT + file LICENSE
+URL: https://gongcastro.github.io/bvq/,
+    https://github.com/gongcastro/bvq/
+BugReports: https://github.com/gongcastro/bvq/issues
+Depends: 
+    R (>= 3.5.0),
+Imports: 
+    cli,
+    dplyr (>= 1.0.0),
+    formr (>= 0.9.1),
+    gargle,
+    googlesheets4,
+    janitor,
+    lifecycle,
+    lubridate,
+    magrittr,
+    rlang,
+    stringr,
+    tibble,
+    tidyr
+Suggests: 
+    knitr,
+    readxl,
+    rmarkdown,
+    roxygen2,
+    testthat (>= 3.0.0),
+    ggplot2 (>= 3.4.2),
+    withr
+VignetteBuilder: 
+    knitr,
+    ggplot2
+Remotes: 
+    github::rubenarslan/formr
+Config/testthat/edition: 3
+Encoding: UTF-8
+Language: en-US
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+# bvq 0.3.0
+
+* Add vignettes for `bvq_connect()`, `bvq_responses()`, `bvq_vocabulary()`, and `bvq_norms()`
+* Fix citation
+* Fix `.by` argument in `bvq_vocabulary()`
+* Change base font in site
+
 # bvq 0.2.0
 
 * Package name changes from {bvqdev} to {bvq}

diff --git a/README.md b/README.md
@@ -19,7 +19,7 @@ This package also contains multiple functions that extract the data and generate
 From [r-universe](https://gongcastro.r-universe.dev/bvq) :rocket::
 
 ```r
-install.packages('bvq', repos = c('https://gongcastro.r-universe.dev',  'https://cloud.r-project.org'))
+install.packages('bvq', repos = 'https://gongcastro.r-universe.dev')
 ```
 
 From the GitHub repository:

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -7,17 +7,27 @@ template:
     bg: "white"
     fg: "black"
     primary: "#003f5c"
-    base_font: {google: "Righteous"}
-    heading_font: {google: "Roboto Slab"}
+    base_font: {google: "Roboto"}
+    heading_font: {google: "Roboto"}
     code_font: {google: "JetBrains Mono"}
 
 lang: en
 
 navbar:
   structure:
-    left:  [intro, reference, news]
+    left:  [intro, reference, articles, news]
     right: [search, github]
   components:
+    articles:
+      menu:
+      - text: "Connecting to the database"
+        href: vignettes/bvq-responses.html
+      - text: "Retrieving raw data"
+        href: vignettes/bvq-responses.html
+      - text: "Vocabulary sizes"
+        href: vignettes/bvq-vocabulary.html
+      - text: "Word acquisition norms"
+        href: vignettes/bvq-norms.html
     twitter:
       icon: fa-twitter
       href: http://twitter.com/gongcastro

diff --git a/inst/CITATION b/inst/CITATION
@@ -1,13 +1,26 @@
-citHeader("To cite bvqdev in publications use:")
+citHeader("To cite bvq in publications use:")
 
 citEntry(
   entry    = "Manual",
-  title    = "bvq: A R package for retrieving vocabualry data from the Barcelona Vocabulary Questionnaire (BVQ)",
-  author   = personList(as.person("Gonzalo Garcia-Castro")),
+  title    = "bvq: Barcelona Vocabulary Questionnaire Database and Helper Functions",
+  author   = personList(c(
+    person(given = "Gonzalo", family = "Garcia-Castro", 
+           email = "[email protected]",
+           role = c("cre", "aut"),
+           comment = c(ORCID = "0000-0002-8553-4209")),
+    person(given = "Daniela S. ", family = "Ávila-Varela",
+           email = "[email protected]", 
+           role = "aut",
+           comment = c(ORCID = "0000-0002-3518-8117")),
+    person(given = "Nuria", 
+           family = "Sebastian-Galles", 
+           email = "[email protected]", 
+           role = "ctb",
+           comment = c(ORCID = "0000-0001-6938-2498")))),
   year     = "2023",
-  snote     = "R package version 1.0.1",
+  snote     = "R package version 0.3.0",
   url      = "https://gongcastro.github.io/bvq",
    textVersion = paste(
-       "G. Garcia-Castro (2023). bvq: A R package for retrieving vocabualry data from the Barcelona Vocabulary Questionnaire (BVQ). https://gongcastro.github.io/bvq"
+       "G. Garcia-Castro, D. S. Ávila-Varela, N. Sebastian-Galles (2023). bvq: Barcelona Vocabulary Questionnaire Database and Helper Functions. https://gongcastro.github.io/bvq"
   )
 )
diff --git a/vignettes/bvq-connect.Rmd b/vignettes/bvq-connect.Rmd
@@ -1,8 +1,8 @@
 ---
-title: "Connecting to the database: `bvq_connect()`"
+title: "Connecting to the database"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{Connecting to the database: `bvq_connect()`}
+  %\VignetteIndexEntry{Connecting to the database}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---

diff --git a/vignettes/bvq-norms.Rmd b/vignettes/bvq-norms.Rmd
@@ -1,8 +1,8 @@
 ---
-title: "Word acquisition norms: `bvq_norms()`"
+title: "Word acquisition norms"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{Word acquisition norms: `bvq_norms()`}
+  %\VignetteIndexEntry{Word acquisition norms}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -12,25 +12,27 @@ knitr::opts_chunk$set(
     collapse = TRUE,
     comment = "#>"
 )
+data("pool", package = "bvq")
 ```
 
-The function `bvq_norms()` computes the proportion of children in the sample that understand or produce each item. This function returns the estimated probability of an average participant to understand or produce each item, and allows to condition this probability to the age, language profile or language dominance of participants. Proportions are adjusted for zero- and one-inflation following Gelman, Hill, and Vehtari (2020).
+The function `bvq_norms()` computes the proportion of children in the sample that understand or produce each item, sometimes called "word prevalence". This function returns the estimated probability of an average participant understanding or producing each word. The `bvq_norms()` function allows to condition this probability on the age, language profile or language dominance of participants, among other variables. Proportions are adjusted for zero- and one-inflation following Gelman, Hill, and Vehtari (2020).
 
-If argument `item` is left NULL (default), proportions are computed for all items (currently `nrow(pool)`). This may take time. If you need to compute norms for specific items, you can provide the item identifiers in the `item` argument. Available items can be consulted in the `pool` data set:
+If argument `item` is left NULL (default), proportions are computed for all items (currently `r nrow(pool)`). This may take time. If you need to compute norms for specific items, you can provide the item identifiers in the `item` argument. Available items can be consulted in the `pool` data set:
 
 ```{r pool, echo=TRUE, message=FALSE, warning=FALSE, paged.print=FALSE}
 library(bvq)
 head(pool)
 ```
 
-Let's go through an example of how to use the `bvq_norms` function for a specific set of items. 
+Let's go through an example of how to use the `bvq_norms()` function for a specific set of items. 
 
 ```{r responses, echo=TRUE, eval=FALSE, message=FALSE, warning=FALSE, paged.print=FALSE}
-library(bvq)
 
+# norms will be computed from these datasets
 participants <- bvq_participants()
 responses <- bvq_responses(participants = participants)
 
+# items we want to compute norms for
 my_items <- c("cat_gos", "cat_gat")
 
 norms <- bvq_norms(
@@ -94,11 +96,9 @@ ggplot(norms,
     scale_y_continuous(limits = c(0, 1)) +
     scale_colour_manual(values = c("#003f5c", "#ff6361")) +
     theme_minimal() +
-    theme(
-        axis.line = element_line(colour = "black"),
-        legend.position = "top",
-        panel.grid.major.x = element_blank(),
-        panel.grid.minor.x = element_blank()
-    )
+    theme(axis.line = element_line(colour = "black"),
+          legend.position = "top",
+          panel.grid.major.x = element_blank(),
+          panel.grid.minor.x = element_blank())
 
 ```
diff --git a/vignettes/bvq-responses.Rmd b/vignettes/bvq-responses.Rmd
@@ -1,8 +1,8 @@
 ---
-title: "Retrieving raw responses: `bvq_responses()` and bvq_logs()"
+title: "Retrieving raw data"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{Retrieving raw responses: `bvq_responses()` and bvq_logs()}
+  %\VignetteIndexEntry{Retrieving raw data}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---

diff --git a/vignettes/bvq-vocabulary.Rmd b/vignettes/bvq-vocabulary.Rmd
@@ -1,8 +1,8 @@
 ---
-title: "Vocabulary sizes: `bvq_vocabulary()`"
+title: "Vocabulary sizes"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{Vocabulary sizes: `bvq_vocabulary()`}
+  %\VignetteIndexEntry{Vocabulary sizes}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -16,11 +16,12 @@ knitr::opts_chunk$set(
 
 The `bvq_vocabulary()` function allows to extract vocabulary sizes for individual responses to any of the questionnaires. It takes the output of the `bvq_responses()` function as an argument, and returns several measures of vocabulary size base on such dataset.
 
-To compute vocabulary size, we first need to run `bvq_responses()` (although it this argument is not provided, `bvq_responses()` is run under the hood):
+To compute vocabulary size, we first need to run `bvq_responses()` (although if this argument is not provided, `bvq_responses()` is run under the hood):
 
 ```{r responses, echo=TRUE, eval=FALSE, message=FALSE, warning=FALSE, paged.print=FALSE}
 library(bvq)
 
+# vocabularies will be computed from these datasets
 participants <- bvq_participants()
 responses <- bvq_responses(participants = participants)