reduced png file size with cavif to remove note from R cmd check.

A2-ai · Oct 31, 2024 · 8fe4fb2 · 8fe4fb2
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diff --git a/vignettes/Integrating_reportifyr_into_report_writing.Rmd b/vignettes/Integrating_reportifyr_into_report_writing.Rmd
@@ -113,7 +113,7 @@ If you'd like more detail on the initialization of `reportifyr`, please see the
 
 To build reports with `reportifyr` you need to insert a figure or table caption using the 'Insert Caption' button under the 'References' ribbon.
 
-![](data/images/insert_caption.png){width=100%}
+![](data/images/insert_caption.avif){width=100%}
 
 This will insert a caption (either figure or table) into the Microsoft Word document. Underneath that caption, you need to add:
 
@@ -123,7 +123,7 @@ This string triggers the magic behind `reportifyr`, and inserts the figure or ta
 
 In the [vignette on integrating reportifyr into analyses](Integrating_reportifyr_into_analyses.html), we saved two figures and two tables. In the template Microsoft Word document packaged with `reportifyr`, figure and table captions, and their associated magic strings to allow insertion of figures/tables and footnotes, have already been inserted. Below is an image of the caption and magic string for the concentration time profile figure we generated:
 
-![](data/images/figure-2_caption_and_magic_string.png){width=100%}
+![](data/images/figure-2_caption_and_magic_string.avif){width=100%}
 
 We can now perform some setup and start filling in the template! The first thing we'll do is assign the input and output document names. We will be populating the `template.docx` which contains no figures or tables inserted by `reportifyr`. If the input document does contain `reportifyr` inserted objects, you'll need to remove them with `remove_tables_figures_footnotes` first.
 
@@ -159,7 +159,7 @@ add_tables(docx_in = doc_dirs$doc_clean,
 
 We can see the tables were successfully inserted:
 
-![](data/images/table_2_in_doc.png){width=100%}
+![](data/images/table_2_in_doc.avif){width=100%}
 
 Now that the tables are inserted, we can insert the figures:
 
@@ -173,7 +173,7 @@ add_plots(docx_in = doc_dirs$doc_tables,
 
 And now we can see our figures in the document as well:
 
-![](data/images/figure_2_in_doc.png){width=100%}
+![](data/images/figure_2_in_doc.avif){width=100%}
 
 Now we can add the footnotes:
 
@@ -189,8 +189,8 @@ add_footnotes(docx_in = doc_dirs$doc_tabs_figs,
 
 We now can see our figures and tables have footnotes inserted:
 
-![](data/images/fig_2_with_fn.png){width=100%}
-![](data/images/table_2_with_fn.png){width=100%}
+![](data/images/fig_2_with_fn.avif){width=100%}
+![](data/images/table_2_with_fn.avif){width=100%}
 
 Now that all the elements are inserted, we can generate a clean final report. This severs the link between `reportifyr` and the document, so please be careful using this function:
 
@@ -203,8 +203,8 @@ finalize_document(docx_in = doc_dirs$doc_draft,
 
 This creates a finalized document, free of magic strings, while also capturing the metadata for this final document. The metadata includes a file hash so you can see if this document has been updated since its creation.
 
-![](data/images/fig_2_final.png){width=100%}
-![](data/images/table_2_final.png){width=100%}
+![](data/images/fig_2_final.avif){width=100%}
+![](data/images/table_2_final.avif){width=100%}
 
 ```{r remove directories, include = FALSE}
 unlink(file.path(here::here(), "vignettes", ".venv"), recursive = TRUE)

diff --git a/vignettes/data/images/bookmarks_reference.avif b/vignettes/data/images/bookmarks_reference.avif
diff --git a/vignettes/data/images/bookmarks_reference.png b/vignettes/data/images/bookmarks_reference.png
diff --git a/vignettes/data/images/fig1_update.avif b/vignettes/data/images/fig1_update.avif
diff --git a/vignettes/data/images/fig1_update.png b/vignettes/data/images/fig1_update.png
diff --git a/vignettes/data/images/fig2_fn_ef_draft.avif b/vignettes/data/images/fig2_fn_ef_draft.avif
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diff --git a/vignettes/data/images/fig2_update.avif b/vignettes/data/images/fig2_update.avif
diff --git a/vignettes/data/images/fig2_update.png b/vignettes/data/images/fig2_update.png
diff --git a/vignettes/data/images/fig3_fn_ef_draft.avif b/vignettes/data/images/fig3_fn_ef_draft.avif
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diff --git a/vignettes/data/images/fig3_no_fn_ef.avif b/vignettes/data/images/fig3_no_fn_ef.avif
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diff --git a/vignettes/data/images/fig3_op_fn_ef_draft.avif b/vignettes/data/images/fig3_op_fn_ef_draft.avif
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diff --git a/vignettes/data/images/fig3_update.avif b/vignettes/data/images/fig3_update.avif
diff --git a/vignettes/data/images/fig3_update.png b/vignettes/data/images/fig3_update.png
diff --git a/vignettes/data/images/fig4_no_fn_ef_draft.avif b/vignettes/data/images/fig4_no_fn_ef_draft.avif
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diff --git a/vignettes/data/images/fig4_no_fn_template.avif b/vignettes/data/images/fig4_no_fn_template.avif
diff --git a/vignettes/data/images/fig4_no_fn_template.png b/vignettes/data/images/fig4_no_fn_template.png
diff --git a/vignettes/data/images/fig4_op_no_fn_ef_draft.avif b/vignettes/data/images/fig4_op_no_fn_ef_draft.avif
diff --git a/vignettes/data/images/fig4_op_no_fn_ef_draft.png b/vignettes/data/images/fig4_op_no_fn_ef_draft.png
diff --git a/vignettes/data/images/fig_2_final.avif b/vignettes/data/images/fig_2_final.avif
diff --git a/vignettes/data/images/fig_2_final.png b/vignettes/data/images/fig_2_final.png
diff --git a/vignettes/data/images/fig_2_with_fn.avif b/vignettes/data/images/fig_2_with_fn.avif
diff --git a/vignettes/data/images/fig_2_with_fn.png b/vignettes/data/images/fig_2_with_fn.png
diff --git a/vignettes/data/images/figure-1_caption_and_magic_string.avif b/vignettes/data/images/figure-1_caption_and_magic_string.avif
diff --git a/vignettes/data/images/figure-1_caption_and_magic_string.png b/vignettes/data/images/figure-1_caption_and_magic_string.png
diff --git a/vignettes/data/images/figure-2_caption_and_magic_string.avif b/vignettes/data/images/figure-2_caption_and_magic_string.avif
diff --git a/vignettes/data/images/figure-2_caption_and_magic_string.png b/vignettes/data/images/figure-2_caption_and_magic_string.png
diff --git a/vignettes/data/images/figure_1_in_doc.avif b/vignettes/data/images/figure_1_in_doc.avif
diff --git a/vignettes/data/images/figure_1_in_doc.png b/vignettes/data/images/figure_1_in_doc.png
diff --git a/vignettes/data/images/figure_1_with_fn.avif b/vignettes/data/images/figure_1_with_fn.avif
diff --git a/vignettes/data/images/figure_1_with_fn.png b/vignettes/data/images/figure_1_with_fn.png
diff --git a/vignettes/data/images/figure_2_in_doc.avif b/vignettes/data/images/figure_2_in_doc.avif
diff --git a/vignettes/data/images/figure_2_in_doc.png b/vignettes/data/images/figure_2_in_doc.png
diff --git a/vignettes/data/images/insert_caption.avif b/vignettes/data/images/insert_caption.avif
diff --git a/vignettes/data/images/insert_caption.png b/vignettes/data/images/insert_caption.png
diff --git a/vignettes/data/images/no_bk_ms.avif b/vignettes/data/images/no_bk_ms.avif
diff --git a/vignettes/data/images/no_bk_ms.png b/vignettes/data/images/no_bk_ms.png
diff --git a/vignettes/data/images/removed_bookmarks.avif b/vignettes/data/images/removed_bookmarks.avif
diff --git a/vignettes/data/images/removed_bookmarks.png b/vignettes/data/images/removed_bookmarks.png
diff --git a/vignettes/data/images/tab1_fn_ef_draft.avif b/vignettes/data/images/tab1_fn_ef_draft.avif
diff --git a/vignettes/data/images/tab1_fn_ef_draft.png b/vignettes/data/images/tab1_fn_ef_draft.png
diff --git a/vignettes/data/images/tab1_no_fn_ef.avif b/vignettes/data/images/tab1_no_fn_ef.avif
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diff --git a/vignettes/data/images/tab1_update.avif b/vignettes/data/images/tab1_update.avif
diff --git a/vignettes/data/images/tab1_update.png b/vignettes/data/images/tab1_update.png
diff --git a/vignettes/data/images/tab2_fn_ef_draft.avif b/vignettes/data/images/tab2_fn_ef_draft.avif
diff --git a/vignettes/data/images/tab2_fn_ef_draft.png b/vignettes/data/images/tab2_fn_ef_draft.png
diff --git a/vignettes/data/images/tab2_no_fn_ef.avif b/vignettes/data/images/tab2_no_fn_ef.avif
diff --git a/vignettes/data/images/tab2_no_fn_ef.png b/vignettes/data/images/tab2_no_fn_ef.png
diff --git a/vignettes/data/images/tab2_op_fn_ef_draft.avif b/vignettes/data/images/tab2_op_fn_ef_draft.avif
diff --git a/vignettes/data/images/tab2_op_fn_ef_draft.png b/vignettes/data/images/tab2_op_fn_ef_draft.png
diff --git a/vignettes/data/images/tab2_update.avif b/vignettes/data/images/tab2_update.avif
diff --git a/vignettes/data/images/tab2_update.png b/vignettes/data/images/tab2_update.png
diff --git a/vignettes/data/images/tab3_update.avif b/vignettes/data/images/tab3_update.avif
diff --git a/vignettes/data/images/tab3_update.png b/vignettes/data/images/tab3_update.png
diff --git a/vignettes/data/images/tab4_no_fn_ef_draft.avif b/vignettes/data/images/tab4_no_fn_ef_draft.avif
diff --git a/vignettes/data/images/tab4_no_fn_ef_draft.png b/vignettes/data/images/tab4_no_fn_ef_draft.png
diff --git a/vignettes/data/images/tab4_no_fn_template.avif b/vignettes/data/images/tab4_no_fn_template.avif
diff --git a/vignettes/data/images/tab4_no_fn_template.png b/vignettes/data/images/tab4_no_fn_template.png
diff --git a/vignettes/data/images/tab4_op_no_fn_ef_draft.avif b/vignettes/data/images/tab4_op_no_fn_ef_draft.avif
diff --git a/vignettes/data/images/tab4_op_no_fn_ef_draft.png b/vignettes/data/images/tab4_op_no_fn_ef_draft.png
diff --git a/vignettes/data/images/table_2_final.avif b/vignettes/data/images/table_2_final.avif
diff --git a/vignettes/data/images/table_2_final.png b/vignettes/data/images/table_2_final.png
diff --git a/vignettes/data/images/table_2_in_doc.avif b/vignettes/data/images/table_2_in_doc.avif
diff --git a/vignettes/data/images/table_2_in_doc.png b/vignettes/data/images/table_2_in_doc.png
diff --git a/vignettes/data/images/table_2_with_fn.avif b/vignettes/data/images/table_2_with_fn.avif
diff --git a/vignettes/data/images/table_2_with_fn.png b/vignettes/data/images/table_2_with_fn.png
diff --git a/vignettes/data/images/tfn_wrapper.avif b/vignettes/data/images/tfn_wrapper.avif
diff --git a/vignettes/data/images/tfn_wrapper.png b/vignettes/data/images/tfn_wrapper.png
diff --git a/vignettes/elective_footnotes.Rmd b/vignettes/elective_footnotes.Rmd
@@ -134,10 +134,10 @@ build_report(docx_in = docx_shell,
 ```
 
 This produces a report without footnotes in the entire document.
-![fig2 no fn](data/images/fig2_no_fn_ef.png){width=100%}
-![fig3 no fn](data/images/fig3_no_fn_ef.png){width=100%}
-![tab1 no fn](data/images/tab1_no_fn_ef.png){width=100%}
-![tab2 no fn](data/images/tab2_no_fn_ef.png){width=100%}
+![fig2 no fn](data/images/fig2_no_fn_ef.avif){width=100%}
+![fig3 no fn](data/images/fig3_no_fn_ef.avif){width=100%}
+![tab1 no fn](data/images/tab1_no_fn_ef.avif){width=100%}
+![tab2 no fn](data/images/tab2_no_fn_ef.avif){width=100%}
 
 If we instead want to include an appendix figure and table without footnotes, 
 but want footnotes within the rest of the report we can use the 
@@ -206,8 +206,8 @@ result <- file.copy(from = system.file("extdata/template-ef.docx", package = "re
                     to = file.path(here::here(), "vignettes", "report", "shell", "template-ef.docx"))
 ```
 
-![fig4 no fn template](data/images/fig4_no_fn_template.png){width=100%}
-![tab4 no fn template](data/images/tab4_no_fn_template.png){width=100%}
+![fig4 no fn template](data/images/fig4_no_fn_template.avif){width=100%}
+![tab4 no fn template](data/images/tab4_no_fn_template.avif){width=100%}
 
 
 ```{r}
@@ -230,12 +230,12 @@ build_report(docx_in = docx_shell,
              )
 ```
 
-![](data/images/fig2_fn_ef_draft.png){width=100%}
-![](data/images/fig3_fn_ef_draft.png){width=100%}
-![](data/images/fig4_no_fn_ef_draft.png){width=100%}
-![](data/images/tab1_fn_ef_draft.png){width=100%}
-![](data/images/tab2_fn_ef_draft.png){width=100%}
-![](data/images/tab4_no_fn_ef_draft.png){width=100%}
+![](data/images/fig2_fn_ef_draft.avif){width=100%}
+![](data/images/fig3_fn_ef_draft.avif){width=100%}
+![](data/images/fig4_no_fn_ef_draft.avif){width=100%}
+![](data/images/tab1_fn_ef_draft.avif){width=100%}
+![](data/images/tab2_fn_ef_draft.avif){width=100%}
+![](data/images/tab4_no_fn_ef_draft.avif){width=100%}
 
 We can see in the logs that theoph-pk-demographics.csv was missing metadata and 
 that default formatting was applied. We additionally see warnings about missing 
@@ -267,12 +267,12 @@ build_report(docx_in = docx_shell,
              )
 ```
 
-![](data/images/fig2_op_fn_ef_draft.png){width=100%}
-![](data/images/fig3_op_fn_ef_draft.png){width=100%}
-![](data/images/fig4_op_no_fn_ef_draft.png){width=100%}
-![](data/images/tab1_op_fn_ef_draft.png){width=100%}
-![](data/images/tab2_op_fn_ef_draft.png){width=100%}
-![](data/images/tab4_op_no_fn_ef_draft.png){width=100%}
+![](data/images/fig2_op_fn_ef_draft.avif){width=100%}
+![](data/images/fig3_op_fn_ef_draft.avif){width=100%}
+![](data/images/fig4_op_no_fn_ef_draft.avif){width=100%}
+![](data/images/tab1_op_fn_ef_draft.avif){width=100%}
+![](data/images/tab2_op_fn_ef_draft.avif){width=100%}
+![](data/images/tab4_op_no_fn_ef_draft.avif){width=100%}
 
 
 ```{r remove directories, include = FALSE}

diff --git a/vignettes/streamlined_reportifyr_workflow.Rmd b/vignettes/streamlined_reportifyr_workflow.Rmd
@@ -136,7 +136,7 @@ build_report(docx_in = docx_shell,
 This produces the same `reportifyr` draft as does the step-wise process, but with 
 only a single function call.
 
-![](data/images/tfn_wrapper.png)
+![](data/images/tfn_wrapper.avif)
 
 And we can remove the magic strings and bookmarks with the same `finalize_document` 
 function:

diff --git a/vignettes/update_report.Rmd b/vignettes/update_report.Rmd
@@ -247,17 +247,17 @@ build_report(docx_in = docx_old,
 We can see that figures 2 and 3 were updated, and table 2 was updated, while 
 table 1 and the non-`reportifyr` content were unaltered:
 
-![Figure 1 is unaltered](data/images/fig1_update.png){width=100%}
+![Figure 1 is unaltered](data/images/fig1_update.avif){width=100%}
 
-![Figure 2 is updated](data/images/fig2_update.png){width=100%}
+![Figure 2 is updated](data/images/fig2_update.avif){width=100%}
 
-![Figure 3 is updated](data/images/fig3_update.png){width=100%}
+![Figure 3 is updated](data/images/fig3_update.avif){width=100%}
 
-![Table 1 is unaltered](data/images/tab1_update.png){width=100%}
+![Table 1 is unaltered](data/images/tab1_update.avif){width=100%}
 
-![Table 2 is updated](data/images/tab2_update.png){width=100%}
+![Table 2 is updated](data/images/tab2_update.avif){width=100%}
 
-![Table 3 is unaltered](data/images/tab3_update.png){width=100%} 
+![Table 3 is unaltered](data/images/tab3_update.avif){width=100%} 
 
 ```{r, include = FALSE}
 unlink(file.path(here::here(), "vignettes", ".venv"), recursive = TRUE)