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Make small aesthethic changes to shiny
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@jbottesini
jbottesini committed Sep 10, 2023
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8 changes: 3 additions & 5 deletions _freeze/chapters/evaluation_data_input/execute-results/html.json
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3 changes: 0 additions & 3 deletions chapters/evaluation_data_analysis.qmd
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Expand Up @@ -145,9 +145,6 @@ rename_dtstuff <- function(df){
# Need to find a way to control column width but it seems to be a problem with DT
# https://github.com/rstudio/DT/issues/29
# we didn't seem to be using all_evals_dt so I removed it to increase readability
evals_pub_df <- evals_pub %>%
# Arrange data
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13 changes: 2 additions & 11 deletions chapters/evaluation_data_input.qmd
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Expand Up @@ -411,17 +411,8 @@ all_papers_p <- all_pub_records %>%
#| include: false
#|
paper_ratings <- evals_pub %>%
select(paper_abbrev, eval_name, one_of(rating_cats), one_of(pred_cats), ends_with("_imp")) %>% # rating vars
dplyr::rename_with(.cols = c(one_of(rating_cats), one_of(pred_cats)),
.fn = gsub,
pattern = "(.+)",
replacement = "\\1_best") %>%
pivot_longer(cols = -c(paper_abbrev, eval_name),
names_pattern = "(overall|adv_knowledge|methods|logic_comms|real_world|gp_relevance|open_sci|journal_predict|merits_journal)_(.+)",
names_to = c("rating_type", ".value"))# one line per rating type
write_rds(paper_ratings, file = here("shinyapp/DataExplorer", "shiny_explorer.rds"))
evals_pub_long %>%
write_rds(file = here("shinyapp/DataExplorer", "shiny_explorer.rds"))
```

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62 changes: 22 additions & 40 deletions docs/chapters/evaluation_data_input.html
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Expand Up @@ -583,17 +583,8 @@
<span></span>
<span><span class="co">#| include: false</span></span>
<span><span class="co">#| </span></span>
<span><span class="va">paper_ratings</span> <span class="op">&lt;-</span> <span class="va">evals_pub</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html">%&gt;%</a></span> </span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">paper_abbrev</span>, <span class="va">eval_name</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/one_of.html">one_of</a></span><span class="op">(</span><span class="va">rating_cats</span><span class="op">)</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/one_of.html">one_of</a></span><span class="op">(</span><span class="va">pred_cats</span><span class="op">)</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/starts_with.html">ends_with</a></span><span class="op">(</span><span class="st">"_imp"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html">%&gt;%</a></span> <span class="co"># rating vars</span></span>
<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/rename.html">rename_with</a></span><span class="op">(</span>.cols <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/one_of.html">one_of</a></span><span class="op">(</span><span class="va">rating_cats</span><span class="op">)</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/one_of.html">one_of</a></span><span class="op">(</span><span class="va">pred_cats</span><span class="op">)</span><span class="op">)</span>,</span>
<span> .fn <span class="op">=</span> <span class="va">gsub</span>,</span>
<span> pattern <span class="op">=</span> <span class="st">"(.+)"</span>, </span>
<span> replacement <span class="op">=</span> <span class="st">"\\1_best"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html">%&gt;%</a></span> </span>
<span> <span class="fu"><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html">pivot_longer</a></span><span class="op">(</span>cols <span class="op">=</span> <span class="op">-</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="va">paper_abbrev</span>, <span class="va">eval_name</span><span class="op">)</span>,</span>
<span> names_pattern <span class="op">=</span> <span class="st">"(overall|adv_knowledge|methods|logic_comms|real_world|gp_relevance|open_sci|journal_predict|merits_journal)_(.+)"</span>,</span>
<span> names_to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"rating_type"</span>, <span class="st">".value"</span><span class="op">)</span><span class="op">)</span><span class="co"># one line per rating type</span></span>
<span></span>
<span><span class="fu"><a href="https://readr.tidyverse.org/reference/read_rds.html">write_rds</a></span><span class="op">(</span><span class="va">paper_ratings</span>, file <span class="op">=</span> <span class="fu"><a href="https://here.r-lib.org//reference/here.html">here</a></span><span class="op">(</span><span class="st">"shinyapp/DataExplorer"</span>, <span class="st">"shiny_explorer.rds"</span><span class="op">)</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span><span class="va">evals_pub_long</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html">%&gt;%</a></span> </span>
<span> <span class="fu"><a href="https://readr.tidyverse.org/reference/read_rds.html">write_rds</a></span><span class="op">(</span>file <span class="op">=</span> <span class="fu"><a href="https://here.r-lib.org//reference/here.html">here</a></span><span class="op">(</span><span class="st">"shinyapp/DataExplorer"</span>, <span class="st">"shiny_explorer.rds"</span><span class="op">)</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
<div class="cell">
Expand Down Expand Up @@ -1322,38 +1313,29 @@
<span id="cb9-416"><a href="#cb9-416" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-417"><a href="#cb9-417" aria-hidden="true" tabindex="-1"></a><span class="co">#| include: false</span></span>
<span id="cb9-418"><a href="#cb9-418" aria-hidden="true" tabindex="-1"></a><span class="co">#| </span></span>
<span id="cb9-419"><a href="#cb9-419" aria-hidden="true" tabindex="-1"></a>paper_ratings <span class="ot">&lt;-</span> evals_pub <span class="sc">%&gt;%</span> </span>
<span id="cb9-420"><a href="#cb9-420" aria-hidden="true" tabindex="-1"></a> <span class="fu">select</span>(paper_abbrev, eval_name, <span class="fu">one_of</span>(rating_cats), <span class="fu">one_of</span>(pred_cats), <span class="fu">ends_with</span>(<span class="st">"_imp"</span>)) <span class="sc">%&gt;%</span> <span class="co"># rating vars</span></span>
<span id="cb9-421"><a href="#cb9-421" aria-hidden="true" tabindex="-1"></a> dplyr<span class="sc">::</span><span class="fu">rename_with</span>(<span class="at">.cols =</span> <span class="fu">c</span>(<span class="fu">one_of</span>(rating_cats), <span class="fu">one_of</span>(pred_cats)),</span>
<span id="cb9-422"><a href="#cb9-422" aria-hidden="true" tabindex="-1"></a> <span class="at">.fn =</span> gsub,</span>
<span id="cb9-423"><a href="#cb9-423" aria-hidden="true" tabindex="-1"></a> <span class="at">pattern =</span> <span class="st">"(.+)"</span>, </span>
<span id="cb9-424"><a href="#cb9-424" aria-hidden="true" tabindex="-1"></a> <span class="at">replacement =</span> <span class="st">"</span><span class="sc">\\</span><span class="st">1_best"</span>) <span class="sc">%&gt;%</span> </span>
<span id="cb9-425"><a href="#cb9-425" aria-hidden="true" tabindex="-1"></a> <span class="fu">pivot_longer</span>(<span class="at">cols =</span> <span class="sc">-</span><span class="fu">c</span>(paper_abbrev, eval_name),</span>
<span id="cb9-426"><a href="#cb9-426" aria-hidden="true" tabindex="-1"></a> <span class="at">names_pattern =</span> <span class="st">"(overall|adv_knowledge|methods|logic_comms|real_world|gp_relevance|open_sci|journal_predict|merits_journal)_(.+)"</span>,</span>
<span id="cb9-427"><a href="#cb9-427" aria-hidden="true" tabindex="-1"></a> <span class="at">names_to =</span> <span class="fu">c</span>(<span class="st">"rating_type"</span>, <span class="st">".value"</span>))<span class="co"># one line per rating type</span></span>
<span id="cb9-419"><a href="#cb9-419" aria-hidden="true" tabindex="-1"></a>evals_pub_long <span class="sc">%&gt;%</span> </span>
<span id="cb9-420"><a href="#cb9-420" aria-hidden="true" tabindex="-1"></a> <span class="fu">write_rds</span>(<span class="at">file =</span> <span class="fu">here</span>(<span class="st">"shinyapp/DataExplorer"</span>, <span class="st">"shiny_explorer.rds"</span>))</span>
<span id="cb9-421"><a href="#cb9-421" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb9-422"><a href="#cb9-422" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
<span id="cb9-423"><a href="#cb9-423" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-424"><a href="#cb9-424" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-425"><a href="#cb9-425" aria-hidden="true" tabindex="-1"></a><span class="in">```{r save data}</span></span>
<span id="cb9-426"><a href="#cb9-426" aria-hidden="true" tabindex="-1"></a><span class="co">#| label: savedata</span></span>
<span id="cb9-427"><a href="#cb9-427" aria-hidden="true" tabindex="-1"></a><span class="co">#| code-summary: "save data for others' use"</span></span>
<span id="cb9-428"><a href="#cb9-428" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-429"><a href="#cb9-429" aria-hidden="true" tabindex="-1"></a><span class="fu">write_rds</span>(paper_ratings, <span class="at">file =</span> <span class="fu">here</span>(<span class="st">"shinyapp/DataExplorer"</span>, <span class="st">"shiny_explorer.rds"</span>))</span>
<span id="cb9-430"><a href="#cb9-430" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb9-431"><a href="#cb9-431" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
<span id="cb9-429"><a href="#cb9-429" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-430"><a href="#cb9-430" aria-hidden="true" tabindex="-1"></a>all_papers_p <span class="sc">%&gt;%</span> <span class="fu">saveRDS</span>(<span class="at">file =</span> <span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"all_papers_p.Rdata"</span>))</span>
<span id="cb9-431"><a href="#cb9-431" aria-hidden="true" tabindex="-1"></a>all_papers_p <span class="sc">%&gt;%</span> <span class="fu">write_csv</span>(<span class="at">file =</span> <span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"all_papers_p.csv"</span>))</span>
<span id="cb9-432"><a href="#cb9-432" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-433"><a href="#cb9-433" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-434"><a href="#cb9-434" aria-hidden="true" tabindex="-1"></a><span class="in">```{r save data}</span></span>
<span id="cb9-435"><a href="#cb9-435" aria-hidden="true" tabindex="-1"></a><span class="co">#| label: savedata</span></span>
<span id="cb9-436"><a href="#cb9-436" aria-hidden="true" tabindex="-1"></a><span class="co">#| code-summary: "save data for others' use"</span></span>
<span id="cb9-437"><a href="#cb9-437" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-433"><a href="#cb9-433" aria-hidden="true" tabindex="-1"></a>evals_pub <span class="sc">%&gt;%</span> <span class="fu">saveRDS</span>(<span class="at">file =</span> <span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"evals.Rdata"</span>))</span>
<span id="cb9-434"><a href="#cb9-434" aria-hidden="true" tabindex="-1"></a>evals_pub <span class="sc">%&gt;%</span> <span class="fu">write_csv</span>(<span class="at">file =</span> <span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"evals.csv"</span>))</span>
<span id="cb9-435"><a href="#cb9-435" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-436"><a href="#cb9-436" aria-hidden="true" tabindex="-1"></a>evals_pub_long <span class="sc">%&gt;%</span> <span class="fu">write_rds</span>(<span class="at">file =</span> <span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"evals_long.rds"</span>))</span>
<span id="cb9-437"><a href="#cb9-437" aria-hidden="true" tabindex="-1"></a>evals_pub_long <span class="sc">%&gt;%</span> <span class="fu">write_csv</span>(<span class="at">file =</span> <span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"evals_long.csv"</span>))</span>
<span id="cb9-438"><a href="#cb9-438" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-439"><a href="#cb9-439" aria-hidden="true" tabindex="-1"></a>all_papers_p <span class="sc">%&gt;%</span> <span class="fu">saveRDS</span>(<span class="at">file =</span> <span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"all_papers_p.Rdata"</span>))</span>
<span id="cb9-440"><a href="#cb9-440" aria-hidden="true" tabindex="-1"></a>all_papers_p <span class="sc">%&gt;%</span> <span class="fu">write_csv</span>(<span class="at">file =</span> <span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"all_papers_p.csv"</span>))</span>
<span id="cb9-441"><a href="#cb9-441" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-442"><a href="#cb9-442" aria-hidden="true" tabindex="-1"></a>evals_pub <span class="sc">%&gt;%</span> <span class="fu">saveRDS</span>(<span class="at">file =</span> <span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"evals.Rdata"</span>))</span>
<span id="cb9-443"><a href="#cb9-443" aria-hidden="true" tabindex="-1"></a>evals_pub <span class="sc">%&gt;%</span> <span class="fu">write_csv</span>(<span class="at">file =</span> <span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"evals.csv"</span>))</span>
<span id="cb9-444"><a href="#cb9-444" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-445"><a href="#cb9-445" aria-hidden="true" tabindex="-1"></a>evals_pub_long <span class="sc">%&gt;%</span> <span class="fu">write_rds</span>(<span class="at">file =</span> <span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"evals_long.rds"</span>))</span>
<span id="cb9-446"><a href="#cb9-446" aria-hidden="true" tabindex="-1"></a>evals_pub_long <span class="sc">%&gt;%</span> <span class="fu">write_csv</span>(<span class="at">file =</span> <span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"evals_long.csv"</span>))</span>
<span id="cb9-447"><a href="#cb9-447" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-448"><a href="#cb9-448" aria-hidden="true" tabindex="-1"></a><span class="co">#evals_pub %&gt;% readRDS(file = here("data", "evals.Rdata"))</span></span>
<span id="cb9-449"><a href="#cb9-449" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-450"><a href="#cb9-450" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
<span id="cb9-439"><a href="#cb9-439" aria-hidden="true" tabindex="-1"></a><span class="co">#evals_pub %&gt;% readRDS(file = here("data", "evals.Rdata"))</span></span>
<span id="cb9-440"><a href="#cb9-440" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-441"><a href="#cb9-441" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
</code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div></div></div></div></div>
</div> <!-- /content -->
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19 changes: 10 additions & 9 deletions shinyapp/DataExplorer/app.R
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ my_pal = colorRampPalette(brewer.pal(8, "Set1"))(color_count)
df <- df %>%
group_by(paper_abbrev, rating_type) %>%
mutate(n_evals = n(), # number of evaluators for each paper
rating_mean = mean(best, na.rm = T)) %>% # replace with aggreCAT functions later
rating_mean = mean(est, na.rm = T)) %>% # replace with aggreCAT functions later
ungroup() %>%
nest(.by = paper_abbrev) %>%
mutate(paper_color = my_pal) %>% # give each paper its own color
Expand All @@ -35,7 +35,7 @@ ui <- fluidPage(
# Application title
titlePanel("Unjournal Evaluation Data"),

# Sidebar with a slider input for number of bins
# Sidebar with plot options
sidebarLayout(
sidebarPanel(
selectInput(inputId = "RatingType",
Expand All @@ -50,21 +50,22 @@ ui <- fluidPage(
choices = unique(df$paper_abbrev),
selected = unique(df$paper_abbrev),
inline = FALSE,
width = NULL,
width = "200px",
choiceNames = NULL,
choiceValues = NULL
)
),
),
width = 3
), fluid = F, position = "right",

# Show a plot of the generated distribution
# Show the plot with selected info
mainPanel(
plotOutput(outputId = "distPlot",
width = "100%")
)
)
)

# Define server logic required to draw a histogram
# Define server logic required to draw plot
server <- function(input, output) {

output$distPlot <- renderPlot({
Expand All @@ -79,7 +80,7 @@ server <- function(input, output) {
filter(paper_abbrev %in% input$IncludedPapers) %>%
filter(!is.na(rating_mean)) %>%
mutate(paper_abbrev = fct_reorder(paper_abbrev, rating_mean)) %>%
ggplot(aes(x = paper_abbrev, y = best, text = eval_name)) + # dont remove eval name or posdodge stops working (???)
ggplot(aes(x = paper_abbrev, y = est, text = eval_name)) + # dont remove eval name or posdodge stops working (???)
geom_point(aes(color = paper_color),
stat = "identity", size = 2, shape = 18, stroke = 1,
position = pd) +
Expand All @@ -96,7 +97,7 @@ server <- function(input, output) {
scale_x_discrete(labels = function(x) str_wrap(x, width = 20)) +
scale_color_identity() # to use paper_color as colors

}, height = 600, width = 600)
}, height = 600, width = 700)
}

# Run the application
Expand Down
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