weekly.qmd

---
title: "Weekly"
format: html
params:
  refresh_stats: true
  csv_save_path: "private"
  save_volumes_sharing_status_info: false
---

## About

These data are collected and reported on roughly a weekly basis.

```{r weekly-setup}
#| echo: FALSE
#| message: FALSE
#| warning: FALSE

knitr::opts_chunk$set(echo = FALSE,
                      message = FALSE,
                      warning = FALSE)

suppressPackageStartupMessages(library(databraryr))
suppressPackageStartupMessages(library(tidyverse))

# Source functions (quietly)
fl <- list.files(file.path(here::here(), "R"), "*.R", 
                 full.names = TRUE)
p <- purrr::map(fl, suppressPackageStartupMessages(source)) |>
  purrr::quietly()

# Login to Databrary
x <- login_db(email = Sys.getenv("DATABRARY_LOGIN"),
         password = Sys.getenv("DATABRARY_PASSWORD"),
         client_id = Sys.getenv("DATABRARY_CLIENT_ID"),
         client_secret = Sys.getenv("DATABRARY_CLIENT_SECRET"),
         store = FALSE,
         overwrite = FALSE,
         vb = TRUE)

# Graphic theme elements
ln_size <- 3
base_size <- 14
color_orange <- "#ec7751"
color_teal <- "#4CAE99"
color_purple <- "#AB00FF"

databrary_theme <-
  ggplot2::theme_classic(base_size = base_size) +
  ggplot2::theme(axis.title.x = ggplot2::element_blank()) +
  ggplot2::theme(
    legend.position = "none",
    axis.text = ggplot2::element_text(size = ggplot2::rel(0.8),
                                      colour = "black")
  ) +
  ggplot2::theme(axis.line = ggplot2::element_blank()) +
  ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5))
```

## Institutions & Authorized Users {-}

<!-- ```{r weekly-load-inst-invest} -->
<!-- # targets::tar_load(inst_invest_csv, store = '../_targets/') -->
<!-- # updated_stats <- inst_invest_csv -->
<!-- targets::tar_load(inst_invest_df, store = '../_targets/') -->
<!-- updated_stats <- inst_invest_df -->
<!-- ``` -->

```{r}
#| label: update-db-stats
#| message: false
#| warning: false
#| results: hide
#| 
assertthat::is.string(params$csv_save_path)
assertthat::is.writeable(params$csv_save_path)

fn_inst_invest <- file.path(params$csv_save_path, "institutions-investigators.csv")
x <- assertthat::is.readable(fn_inst_invest)

# Don't refresh data by default; change default in params_weekly.yml
if (params$refresh_stats) {
  db_stats_new <- databraryr::get_db_stats()
  
  db_stats_old <- readr::read_csv(fn_inst_invest)
  n_rows <- dim(db_stats_old)[1]
  
  updated_stats <- rbind(db_stats_old, db_stats_new[, 1:4])
  readr::write_csv(updated_stats, file = fn_inst_invest)
} else {
  updated_stats <- readr::read_csv(fn_inst_invest)
}
```

```{r }
#| label: weekly-calculate-delta

n_rows <- dim(updated_stats)[1]

delta_investigators <- updated_stats$investigators[n_rows] - updated_stats$investigators[n_rows - 1]
delta_institutions <- updated_stats$institutions[n_rows] - updated_stats$institutions[n_rows - 1]

# filter NAs
updated_stats <- updated_stats |>
  dplyr::filter(!is.na(affiliates),!is.na(investigators),!is.na(affiliates),!is.na(date))
```

<!-- Now, we plot the data. -->

```{r}
#| label: fig-databrary-inst-invest-timeseries
#| fig-cap: "Change over time in authorized investigators and authorizing institutions"

gathered_stats <- updated_stats |>
  tidyr::gather(key = "type", value = "count", -date) |>
  dplyr::mutate(date = lubridate::as_date(date)) |>
  dplyr::select(date, count, type) |>
  dplyr::filter(type %in% c('institutions', 'investigators')) |>
  dplyr::filter(!is.na(count))

ratio.display <- 550/250
ratio.values <- 3757/max(gathered_stats$count)

# Plot
users_plot <- gathered_stats |>
  ggplot(aes(
    x = date,
    y = count,
    color = type,
    group = type
  )) +
  scale_x_date(date_labels = "%Y", date_breaks = '1 year') +
  geom_point() +
  geom_line(linewidth = ln_size) +
  scale_colour_manual(values = c(color_orange, color_teal)) +
  ggtitle(paste("Authorizations as of", Sys.Date())) +
  ylab("Authorizations") +
  databrary_theme +
  scale_y_continuous(breaks = c(0, 300, 600, 900, 1200, 1500, 1800, 2100, 2400)) +
  coord_fixed(ratio = ratio.values / ratio.display) +
  theme(axis.text.x = element_text(angle = 90))

# ggsave("include/img/invest-inst-for-hnds-i.png", width=11, height=6.5, dpi=300)

p <- cowplot::ggdraw(users_plot) +
  cowplot::draw_label(
    paste0(
      "Investigators: ",
      updated_stats$investigators[n_rows],
      " (+",
      delta_investigators,
      ")"
    ),
    colour = color_teal,
    .3,
    .6
  ) +
  cowplot::draw_label(
    paste0(
      "Institutions: ",
      updated_stats$institutions[n_rows],
      " (+",
      delta_institutions,
      ")"
    ),
    colour = color_orange,
    .7,
    .3
  )

p
```

## Clean up

Logout from Databrary.

```{r}
#| label: clean-up-logout
#| message: false

x <- logout_db()
```