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Mark BVBRC_stats vignette Docker chunks eval=FALSE to fix CI #28

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Mark BVBRC_stats vignette Docker chunks eval=FALSE to fix CI #28

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10 changes: 5 additions & 5 deletions vignettes/BVBRC_stats.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -174,7 +174,7 @@ summarize_block <- function(df, cols, block_name) {

Here we fetch the BV-BRC bacterial metadata table, clean it, and compute four artifacts that drive the rest of the vignette: `col_stats` (one row per column with totals, missing counts, and distinct non-missing values), `host_block_stats` and `geo_block_stats` (per-block presence summaries across host and geographic columns respectively), and `diag_table` (a focused per-column view of just the host + geo columns).

```{r stats}
```{r stats, eval = FALSE}
# download the bvbrc table
bvbrc <- fetchCompleteBVBRCMetadata()

Expand Down Expand Up @@ -231,7 +231,7 @@ diag_table <- tibble(column = diag_cols) |>

The table below shows how complete each column in the BV-BRC bacterial metadata is — sorted with the most sparsely populated columns first. Columns with very high `pct_missing` are unlikely to be useful downstream and may be worth dropping from featurization.

```{r col_stats_output}
```{r col_stats_output, eval = FALSE}
cat("\n--- Per-column stats (whole table) ---\n")
print(col_stats, n = Inf)
```
Expand All @@ -240,7 +240,7 @@ print(col_stats, n = Inf)

Presence of the host-related columns (`host_common_name`, `host_group`, `host_name`) treated as a block. `n_rows_any_present` is the number of rows where at least one host field is populated; `n_rows_all_missing` is the number where every host field is empty.

```{r host_block_output}
```{r host_block_output, eval = FALSE}
cat("\n--- Host block stats ---\n")
print(host_block_stats)
```
Expand All @@ -249,7 +249,7 @@ print(host_block_stats)

Same idea as the host block, but across the geographic columns (`isolation_source`, `geographic_location`, `isolation_country`, `state_province`, `city`, `county`, `latitude`, `longitude`).

```{r geo_block_output}
```{r geo_block_output, eval = FALSE}
cat("\n--- Geographic block stats ---\n")
print(geo_block_stats)
```
Expand All @@ -258,7 +258,7 @@ print(geo_block_stats)

Column-by-column missingness for just the host and geographic fields, so you can see which specific columns drive the block-level numbers above.

```{r diag_output}
```{r diag_output, eval = FALSE}
cat("\n--- Diagnostics for host + geo columns ---\n")
print(diag_table, n = Inf)
```
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