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class: title-slide
count: false

.title[
  # 09 - Workflow Analysis
]
.subtitle[
  ## Open Science Tools
]

.author[
  ### Claudio Zandonella &amp; Davide Massidda
]

.institute[

]

---
class: center, middle, inverse
# Step VIII: Workflows


---
# Run the Analysis

--

.pull-left-30[
.move-down-140[
- Single script
- Multiple scripts
- Main script
]
]
.pull-right-70[

]

---
# Run the Analysis

.pull-left-30[
.move-down-140[
- Single script
- .alpha[Multiple scripts]
- .alpha[Main script]
]
]
.pull-right-70[
.move-down-80[
```
- my-project/
    |
    |-- analysis/
    |     |-- my-analysis
    |
    |-- src/
    |     |-- data-munging
    |     |-- models
    |     |-- plots-tables
    |     |-- utils
```
]
]

---
# Run the Analysis

.pull-left-30[
.move-down-140[
- .alpha[Single script]
- Multiple scripts
- .alpha[Main script]
]
]
.pull-right-70[
.move-down-80[
```
- my-project/
    |
    |-- analysis/
    |     |-- 01-data-preparation
    |     |-- 02-experiment-A
    |     |-- 03-experiment-B
    |     |-- 04-comparison-experiments
    |     |-- 05-sensitivity-analysis
    |
    |-- src/
    |     |-- data-munging
    |     |-- models
    |     |-- plots-tables
    |     |-- utils
```
]
]

---
# Run the Analysis

.pull-left-30[
.move-down-140[
- .alpha[Single script]
- .alpha[Multiple scripts]
- Main script
]
]
.pull-right-70[
.move-down-80[
```
- my-project/
    |
    |-- analysis/
    |     |-- 01-data-preparation
    |     |-- 02-experiment-A
    |     |-- 03-experiment-B
    |     |-- 04-comparison-experiments
    |     |-- 05-sensitivity-analysis
    |     |-- main
    |
    |-- src/
    |     |-- data-munging
    |     |-- models
    |     |-- plots-tables
    |     |-- utils
```
]
]

---
# Run the Analysis

.pull-left-30[
.move-down-140[
- .alpha[Single script]
- .alpha[Multiple scripts]
- Main script
]
]
.pull-right-70[
.move-down-80[
```
- my-project/
    |
    |-- analysis/
    |     |-- 01-data-preparation
    |     |-- 02-experiment-A
    |     |-- 03-experiment-B
    |     |-- 04-comparison-experiments
    |     |-- 05-sensitivity-analysis
*   |     |-- main
    |
    |-- src/
    |     |-- data-munging
    |     |-- models
    |     |-- plots-tables
    |     |-- utils
```
]
]

---
# General Reccomendations

--

.pull-left-30[
.move-down-120[
- Documentation
- README
- Random numbers
- Session Settings
]
]
.pull-right-70[
]

---
# General Reccomendations

.pull-left-30[
.move-down-120[
- Documentation
- .alpha[README]
- .alpha[Random numbers]
- .alpha[Session Settings]
]
]
.pull-right-70[
.move-up-50[

&lt;img src="images/09-workflow/r-script.png" width="70%" style="display: block; margin: auto;" /&gt;
]
]

---
# General Reccomendations

.pull-left-30[
.move-down-120[
- .alpha[Documentation]
- README
- .alpha[Random numbers]
- .alpha[Session Settings]
]
]
.pull-right-70[
.move-left-130[
.move-down-110[
.li-smalll[
Instructions about: 

- Requirements
- Installation
- How to run
]
]
]
]

---
# General Reccomendations

.pull-left-30[
.move-down-120[
- .alpha[Documentation]
- .alpha[README]
- Random numbers
- .alpha[Session Settings]
]
]
.pull-right-70[
.move-down-110[
&lt;img src="images/09-workflow/rng.jpeg" width="100%" style="display: block; margin: auto;" /&gt;
]
]

---
# General Reccomendations

.pull-left-30[
.move-down-120[
- .alpha[Documentation]
- .alpha[README]
- .alpha[Random numbers]
- Session Settings
]
]
.pull-right-70[
.move-down-170[
- Local settings
- Explicit default options
]
]

---
# Workflow Manager

--

.pull-left-50[
.move-down-120[
- Automatically Run the Analysis
- Discover Dependencies
- Update the Analysis
- Caching System
]
]
.pull-right-50[
.move-down-120[
{{content}}
]
]

--
&lt;img src="images/09-workflow/gnu-make.png" width="100%" style="display: block; margin: auto;" /&gt;

---
class: inverse, middle, center

# Workflow in R

---
# R Reccomendations
--

.pull-left-30[
.move-down-120[
- Script Sections
- Loading Functions
- Loading R-packages
- Reproducibility
]
]
.pull-right-50[
]

---
# R Reccomendations

.pull-left-30[
.move-down-120[
- Script Sections
- .alpha[Loading Functions]
- .alpha[Loading R-packages]
- .alpha[Reproducibility]
]
]
.pull-right-70[
.move-left-100[
.move-down-120[
.code-size-12[

```r
# Section 1 ####

# Section 2 ----

#----    Section 3    ----

####   Not Valid Section   --##
```
]
]
]
]

---
# R Reccomendations

.pull-left-30[
.move-down-120[
- Script Sections
- .alpha[Loading Functions]
- .alpha[Loading R-packages]
- .alpha[Reproducibility]
]
]
.pull-right-70[
.move-up-50[
&lt;img src="images/09-workflow/script-sections.png" width="70%" style="display: block; margin: auto;" /&gt;
]
]

---
# R Reccomendations

.pull-left-30[
.move-down-120[
- Script Sections
- .alpha[Loading Functions]
- .alpha[Loading R-packages]
- .alpha[Reproducibility]
]
]
.pull-right-70[
.move-up-50[
&lt;img src="images/09-workflow/script-collapsed.png" width="70%" style="display: block; margin: auto;" /&gt;
]
]
---
# R Reccomendations

.pull-left-30[
.move-down-120[
- Script Sections
- .alpha[Loading Functions]
- .alpha[Loading R-packages]
- .alpha[Reproducibility]
]
]
.pull-right-70[
&lt;img src="images/09-workflow/nav-top.png" width="70%" style="display: block; margin: auto;" /&gt;

&lt;img src="images/09-workflow/nav-bottom.png" width="70%" style="display: block; margin: auto;" /&gt;
]

---
# R Reccomendations

.pull-left-30[
.move-down-120[
- .alpha[Script Sections]
- Loading Functions
- .alpha[Loading R-packages]
- .alpha[Reproducibility]
]
]
.pull-right-70[
.move-down-50[
.li-small[
- `source()`
]
]
.code-size-12[
{{content}}
]
]

--

```r
# List all scripts in R/
script_list &lt;- list.files("R", full.names = TRUE)

# Source scripts
invisible(sapply(script_list, source))
```

---
# R Reccomendations

.pull-left-30[
.move-down-120[
- .alpha[Script Sections]
- Loading Functions
- .alpha[Loading R-packages]
- .alpha[Reproducibility]
]
]
.pull-right-70[
.move-down-50[
.li-small[
- `source()`
]
]
.code-size-12[

```r
# List all scripts in R/
script_list &lt;- list.files("R", full.names = TRUE)

# Source scripts
invisible(sapply(script_list, source))
```
]

.move-down-50[
.li-small[
- `devtools::load_all()`  (shortcut `Ctrl/Cmd + Shift + L`)
]
]
.code-size-12[

```r
# Load functions
devtools::load_all(path = "&lt;path-to-the-project-root&gt;")
```
]
]

---
# R Reccomendations

.pull-left-30[
.move-down-120[
- .alpha[Script Sections]
- .alpha[Loading Functions]
- Loading R-packages
- .alpha[Reproducibility]
]
]
.pull-right-70[
#### `library()`
.li-small[
{{content}}
]
]
--
- Analysis Scripts
{{content}}
--
- `.Rprofile`
- `DESCRIPTION` (in the `Depends` field)
---
# R Reccomendations

.pull-left-30[
.move-down-120[
- .alpha[Script Sections]
- .alpha[Loading Functions]
- Loading R-packages
- .alpha[Reproducibility]
]
]
.pull-right-70[
#### `library()`
.li-small[
- Analysis Scripts
- `.Rprofile`
- `DESCRIPTION` (in the `Depends` field)
]

.move-down-50[
#### Conflicts
]

.li-small[
{{content}}
]
]

--

- `&lt;package&gt;::&lt;function()&gt;`
{{content}}

--

- `conflicted` https://conflicted.r-lib.org/

---
# R Reccomendations

.pull-left-30[
.move-down-120[
- .alpha[Script Sections]
- .alpha[Loading Functions]
- Loading R-packages
- .alpha[Reproducibility]
]
]
.pull-right-70[
#### `library()`
.li-small[
- Analysis Scripts
- `.Rprofile`
- `DESCRIPTION` (in the `Depends` field)
]

.move-down-50[
#### Conflicts
]

.li-small[
- `&lt;package&gt;::&lt;function()&gt;`
- `conflicted` https://conflicted.r-lib.org/

.font-size-18[
Common conflicts
]
.li-small[
- `dplyr::select()` vs `MASS::select()`
- `dplyr::filter()` vs `stats::filter()`
]
]
]

---

# R Reccomendations

.pull-left-30[
.move-down-120[
- .alpha[Script Sections]
- .alpha[Loading Functions]
- .alpha[Loading R-packages]
- Reproducibility
]
]
.pull-right-70[
.move-down-140[
{{content}}
]
]

--
- Random Number Generator `set.seed()`
{{content}}
--
- Global Options (e.g, `stringsAsFactors` or `contrasts`)
{{content}}
--
- Project Requirements

---

## `.Rprofile`

--

.pull-left-50[

```r
#----    .Rprofile    ----#

# Load custom functions
devtools::load_all()

# Load packages
library("tidyverse")
library("lme4")

# Settings ggplot
theme_set(theme_bw())
```

.center[
.font-18[
{{content}}
]
]
]
.pull-right-50[

]

--
Rely only on code declared explicitly&lt;br&gt;in the analysis script

---

## `.Rprofile`

.pull-left-50[

```r
#----    .Rprofile    ----#

# Load custom functions
devtools::load_all()

# Load packages
library("tidyverse")
library("lme4")

# Settings ggplot
theme_set(theme_bw())
```

.center[
.font-18[
Rely only on code declared explicitly&lt;br&gt;in the analysis script
]
]
]
.pull-right-50[

```r
#----    .Rprofile    ----#

# Commands for interactive and non-interactive sessions
...

# Commands only for interactive sessions
if(interactive()){
  # Load custom functions
  devtools::load_all()
  
  # Load packages
  library("tidyverse")
  library("lme4")

  # Settings ggplot
  theme_set(theme_bw())
  }
```
]

---

## `.Rprofile`

.pull-left-50[

```r
#----    .Rprofile    ----#

# Load custom functions
devtools::load_all()

# Load packages
library("tidyverse")
library("lme4")

# Settings ggplot
theme_set(theme_bw())
```

.center[
.font-18[
Rely only on code declared explicitly&lt;br&gt;in the analysis script
]
]
]
.pull-right-50[

```r
#----    .Rprofile    ----#

# Commands for interactive and non-interactive sessions
...

# Commands only for interactive sessions
*if(interactive()){
  # Load custom functions
  devtools::load_all()
  
  # Load packages
  library("tidyverse")
  library("lme4")

  # Settings ggplot
  theme_set(theme_bw())
  }
```
]
---
# Workflow Manager

--

.pull-left-30[
&lt;br&gt;

&lt;img src="images/09-workflow/targets-hex.png" width="60%" style="display: block; margin: auto;" /&gt;

.font-14[
https://github.com/ropensci/targets
]
]
.pull-right-70[
.move-up-30[
{{content}}
]
]

--
&lt;br&gt;


```r
#----    Workflow    ----
list(
  # Get data
  tar_target(raw_data_file, "data/raw-data.csv", 
             format = "file"),
  tar_target(my_data, get_my_data(raw_data_file)),
  
  # Descriptive statistics
  tar_target(plot_obs, get_plot_obs(my_data)),
  
  # Inferential statistics
  tar_target(lm_fit, get_lm_fit(my_data))
)
```

---
# Workflow Manager

.pull-left-30[
&lt;br&gt;

&lt;img src="images/09-workflow/targets-hex.png" width="60%" style="display: block; margin: auto;" /&gt;

.font-14[
https://github.com/ropensci/targets
]
]
.pull-right-70[
&lt;img src="images/09-workflow/pipeline-new-function.png" width="80%" style="display: block; margin: auto;" /&gt;

.center[
{{content}}
]
]

--

`targets::tar_make()`

---
# Workflow Manager

.pull-left-30[
&lt;br&gt;

&lt;img src="images/09-workflow/targets-hex.png" width="60%" style="display: block; margin: auto;" /&gt;

.font-14[
https://github.com/ropensci/targets
]
]
.pull-right-70[
&lt;img src="images/09-workflow/pipeline-end.png" width="80%" style="display: block; margin: auto;" /&gt;
]

---
# Workflow Manager

.pull-left-30[
&lt;br&gt;

&lt;img src="images/09-workflow/targets-hex.png" width="60%" style="display: block; margin: auto;" /&gt;

.font-14[
https://github.com/ropensci/targets
]
]
.pull-right-70[
.move-up-100[
&lt;img src="images/09-workflow/target-net.png" width="80%" style="display: block; margin: auto;" /&gt;

]
]

---
## `targets` Project Structure

--

.pull-left-30[
.move-down-110[
.code-size-12[
```
- my-project/
  |
  |-- _targets.R
  |-- _targets/
  |
  |-- data/
  |  |-- raw-data.csv
  |
  |-- R/
  |  |-- my-functions.R
  |  |-- ...
```
]
]
]
.pull-right-70[

]

---
## `targets` Project Structure

.pull-left-30[
.move-down-110[
.code-size-12[
```
- my-project/
  |
* |-- _targets.R
  |-- _targets/
  |
  |-- data/
  |  |-- raw-data.csv
  |
  |-- R/
  |  |-- my-functions.R
  |  |-- ...
```
]
]
]
.pull-right-70[
.code-size-12[

```r
#==========================#
#====    _targets.R    ====#
#==========================#

library("targets")

#----    Settings    ----

# Load packages
library("tidyverse")
library("lme4")

# Source custom functions
source("R/my-functions.R")

# Options
options(tidyverse.quiet = TRUE)

#----    Workflow    ----

list(
  # list of targets
)
```
]
]

---
## `targets` Project Structure

.pull-left-30[
.move-down-110[
.code-size-12[
```
- my-project/
  |
* |-- _targets.R
  |-- _targets/
  |
  |-- data/
  |  |-- raw-data.csv
  |
  |-- R/
  |  |-- my-functions.R
  |  |-- ...
```
]
]
]
.pull-right-70[
.code-size-12[

```r
#==========================#
#====    _targets.R    ====#
#==========================#

*library("targets")

#----    Settings    ----

# Load packages
library("tidyverse")
library("lme4")

# Source custom functions
source("R/my-functions.R")

# Options
options(tidyverse.quiet = TRUE)

#----    Workflow    ----

list(
  # list of targets
)
```
]
]

---
## `targets` Project Structure

.pull-left-30[
.move-down-110[
.code-size-12[
```
- my-project/
  |
* |-- _targets.R
  |-- _targets/
  |
  |-- data/
  |  |-- raw-data.csv
  |
  |-- R/
  |  |-- my-functions.R
  |  |-- ...
```
]
]
]
.pull-right-70[
.code-size-12[

```r
#==========================#
#====    _targets.R    ====#
#==========================#

library("targets")

#----    Settings    ----

*# Load packages
*library("tidyverse")   # Or using
*library("lme4")        # tar_option_set(packages = c("&lt;packages&gt;"))

# Source custom functions
source("R/my-functions.R")

# Options
options(tidyverse.quiet = TRUE)

#----    Workflow    ----

list(
  # list of targets
)
```
]
]

---
## `targets` Project Structure

.pull-left-30[
.move-down-110[
.code-size-12[
```
- my-project/
  |
* |-- _targets.R
  |-- _targets/
  |
  |-- data/
  |  |-- raw-data.csv
  |
  |-- R/
  |  |-- my-functions.R
  |  |-- ...
```
]
]
]
.pull-right-70[
.code-size-12[

```r
#==========================#
#====    _targets.R    ====#
#==========================#

library("targets")

#----    Settings    ----

# Load packages
library("tidyverse")
library("lme4")

*# Source custom functions
*source("R/my-functions.R")

# Options
options(tidyverse.quiet = TRUE)

#----    Workflow    ----

list(
  # list of targets
)
```
]
]

---
## `targets` Project Structure

.pull-left-30[
.move-down-110[
.code-size-12[
```
- my-project/
  |
* |-- _targets.R
  |-- _targets/
  |
  |-- data/
  |  |-- raw-data.csv
  |
  |-- R/
  |  |-- my-functions.R
  |  |-- ...
```
]
]
]
.pull-right-70[
.code-size-12[

```r
#==========================#
#====    _targets.R    ====#
#==========================#

library("targets")

#----    Settings    ----

# Load packages
library("tidyverse")
library("lme4")

# Source custom functions
source("R/my-functions.R")

*# Options
*options(tidyverse.quiet = TRUE)

#----    Workflow    ----

list(
  # list of targets
)
```
]
]

---
## `targets` Project Structure

.pull-left-30[
.move-down-110[
.code-size-12[
```
- my-project/
  |
* |-- _targets.R
  |-- _targets/
  |
  |-- data/
  |  |-- raw-data.csv
  |
  |-- R/
  |  |-- my-functions.R
  |  |-- ...
```
]
]
]
.pull-right-70[
.code-size-12[

```r
#==========================#
#====    _targets.R    ====#
#==========================#

library("targets")

#----    Settings    ----

# Load packages
library("tidyverse")
library("lme4")

# Source custom functions
source("R/my-functions.R")

# Options
options(tidyverse.quiet = TRUE)

#----    Workflow    ----

*list(
* # list of targets
*)
```
]
]

---
## `targets` Project Structure

.pull-left-30[
.move-down-110[
.code-size-12[
```
- my-project/
  |
* |-- _targets.R
  |-- _targets/
  |
  |-- data/
  |  |-- raw-data.csv
  |
  |-- R/
  |  |-- my-functions.R
  |  |-- ...
```
]
]
]
.pull-right-70[
.code-size-12[

```r
#==========================#
#====    _targets.R    ====#
#==========================#

#----    Workflow    ----

list(
  # Get data
  tar_target(raw_data_file, "data/raw-data.csv", format = "file"),
  tar_target(my_data, get_my_data(raw_data_file)),
  
  # Descriptive statistics
  tar_target(plot_obs, get_plot_obs(my_data)),
  
  # Inferential statistics
  tar_target(lm_fit, get_lm_fit(my_data))
)
```

{{content}}
]
]

--
#### Defining Targets

`tar_target(&lt;target_name&gt;, &lt;expression&gt;) `

---
## `targets` Project Structure

.pull-left-30[
.move-down-110[
.code-size-12[
```
- my-project/
  |
* |-- _targets.R
  |-- _targets/
  |
  |-- data/
  |  |-- raw-data.csv
  |
  |-- R/
  |  |-- my-functions.R
  |  |-- ...
```
]
]
]
.pull-right-70[
.code-size-12[

```r
#==========================#
#====    _targets.R    ====#
#==========================#

#----    Workflow    ----

list(
  # Get data
* tar_target(raw_data_file, "data/raw-data.csv", format = "file"),
  tar_target(my_data, get_my_data(raw_data_file)),
  
  # Descriptive statistics
  tar_target(plot_obs, get_plot_obs(my_data)),
  
  # Inferential statistics
  tar_target(lm_fit, get_lm_fit(my_data))
)
```

#### Defining Targets

`tar_target(&lt;target_name&gt;, &lt;expression&gt;) `
]
]
---
## `targets` Project Structure

.pull-left-30[
.move-down-110[
.code-size-12[
```
- my-project/
  |
  |-- _targets.R
* |-- _targets/
  |
  |-- data/
  |  |-- raw-data.csv
  |
  |-- R/
  |  |-- my-functions.R
  |  |-- ...
```
]
]
]
.pull-right-70[
.move-down-50[
.li-small[
{{content}}
]
]
]

--
#### Content

- `meta/` metadata regarding the targets
- `objects/` targets results
- `users/` store custom files

---
## `targets` Project Structure

.pull-left-30[
.move-down-110[
.code-size-12[
```
- my-project/
  |
  |-- _targets.R
* |-- _targets/
  |
  |-- data/
  |  |-- raw-data.csv
  |
  |-- R/
  |  |-- my-functions.R
  |  |-- ...
```
]
]
]
.pull-right-70[
.move-down-50[
.li-small[
#### Content
- `meta/` metadata regarding the targets
- `objects/` targets results
- `users/` store custom files
]
]

.move-down-30[
#### Details
]
.li-small[
- Automatically created
- `.gitignore` automatically added
- Only `_targets/meta/meta` is important
]
]
---
## `targets` Workflow

--

.pull-left-30[
.move-down-50[
#### Check Pipline
]
]
.pull-right-70[


]

---
## `targets` Workflow

.pull-left-30[
.move-down-50[
#### Check Pipline
.li-small[
- `tar_manifest()`
]
]
]
.pull-right-70[
.move-down-80[
.code-size-12[

```r
targets::tar_manifest(fields = "command")
## # A tibble: 4 × 2
##   name          command                       
##   &lt;chr&gt;         &lt;chr&gt;                         
## 1 raw_data_file "\"data/raw-data.csv\""       
## 2 my_data       "get_my_data(raw_data_file)"  
## 3 plot_obs      "get_plot_obs(data = my_data)"
## 4 lm_fit        "get_lm_fit(data = my_data)"
```
]
]
]
---
## `targets` Workflow

.pull-left-30[
.move-down-50[
#### Check Pipline
.li-small[
- `tar_manifest()`
- `tar_visnetwork()`
]
]
]
.pull-right-70[
.code-size-12[

```r
targets::tar_visnetwork()
```
]
&lt;img src="images/09-workflow/pipeline-start.png" width="70%" style="display: block; margin: auto;" /&gt;

]
---
## `targets` Workflow

.pull-left-30[
.move-down-50[
#### Check Pipline
.li-small[
- `tar_manifest()`
- `tar_visnetwork()`
]

#### Run Analyis
.li-small[
- `tar_make()`
]
]
]
.pull-right-70[
.move-down-80[
.code-size-12[

```r
targets::tar_make()
## • start target raw_data_file
## • built target raw_data_file
## • start target my_data
## • built target my_data
## • start target plot_obs
## • built target plot_obs
## • start target lm_fit
## • built target lm_fit
## • end pipeline
```
]
]
]

---
## `targets` Workflow

.pull-left-30[
.move-down-50[
#### Check Pipline
.li-small[
- `tar_manifest()`
- `tar_visnetwork()`
]

#### Run Analyis
.li-small[
- `tar_make()`
]
]
]
.pull-right-70[
.code-size-12[

```r
targets::tar_visnetwork()
```
]
&lt;img src="images/09-workflow/pipeline-end.png" width="70%" style="display: block; margin: auto;" /&gt;

]

---
## `targets` Workflow

.pull-left-30[
.move-down-50[
#### Check Pipline
.li-small[
- `tar_manifest()`
- `tar_visnetwork()`
]

#### Run Analyis
.li-small[
- `tar_make()`
]
]
]
.pull-right-70[
.code-size-12[

```r
targets::tar_visnetwork()
```
]
&lt;img src="images/09-workflow/pipeline-new-function.png" width="70%" style="display: block; margin: auto;" /&gt;

]
---
## `targets` Workflow

.pull-left-30[
.move-down-50[
#### Check Pipline
.li-small[
- `tar_manifest()`
- `tar_visnetwork()`
]

#### Run Analyis
.li-small[
- `tar_make()`
]
]
]
.pull-right-70[
.move-down-80[
.code-size-12[

```r
targets::tar_make()
## ✔ skip target raw_data_file
## ✔ skip target my_data
## ✔ skip target plot_obs
## • start target lm_fit
## • built target lm_fit
## • end pipeline
```
]
]
]

---
## `targets` Workflow

.pull-left-30[
.move-down-50[
#### Check Pipline
.li-small[
- `tar_manifest()`
- `tar_visnetwork()`
]

#### Run Analyis
.li-small[
- `tar_make()`
]

#### Load Results
]
]
.pull-right-70[

]
---
## `targets` Workflow

.pull-left-30[
.move-down-50[
#### Check Pipline
.li-small[
- `tar_manifest()`
- `tar_visnetwork()`
]

#### Run Analyis
.li-small[
- `tar_make()`
]

#### Load Results
.li-small[
- `tar_read()`
]
]
]
.pull-right-70[
.code-size-12[

```r
targets::tar_read(plot_obs)
```

&lt;img src="images/09-workflow/plot-obs-1.png" width="80%" style="display: block; margin: auto;" /&gt;
]
]

---
## `targets` Workflow

.pull-left-30[
.move-down-50[
#### Check Pipline
.li-small[
- `tar_manifest()`
- `tar_visnetwork()`
]

#### Run Analyis
.li-small[
- `tar_make()`
]

#### Load Results
.li-small[
- `tar_read()`
- `tar_load()`
]
]
]
.pull-right-70[
.code-size-12[

```r
targets::tar_load(lm_fit)
summary(lm_fit)
## 
## Call:
## lm(formula = y ~ x, data = data)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -1.83060 -0.70935  0.08828  0.64521  1.82840 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(&gt;|t|)    
## (Intercept)   1.2076     0.2225   5.428 3.47e-06 ***
## xB           -1.4478     0.3146  -4.601 4.58e-05 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.995 on 38 degrees of freedom
## Multiple R-squared:  0.3578, Adjusted R-squared:  0.3409 
## F-statistic: 21.17 on 1 and 38 DF,  p-value: 4.575e-05
```
]
]

---
## `targets` Advanced Features

--

.pull-left-30[
.move-down-110[
.li-small[
- My Proj Structure
- R Markdown
- Reproducibility
- Branching
- Load All Targets
]
]
]
.pull-right-70[
]

---
## `targets` Advanced Features

.pull-left-30[
.move-down-110[
.li-small[
- My Proj Structure
- .alpha[R Markdown]
- .alpha[Reproducibility]
- .alpha[Branching]
- .alpha[Load All Targets]
]
]
]
.pull-right-70[
.pull-left-50[
.move-down-50[
.code-size-12[

```
- my-project/
  |
  |
  |
  |
  |-- _targets.R
  |
  |-- _targets/
  |
  |-- data/
  |  |-- raw-data.csv
  |
  |-- R/
  |  |-- my-functions.R
  |  |-- ...
```
]
]
]
.pull-right-50[

]
]
---
## `targets` Advanced Features

.pull-left-30[
.move-down-110[
.li-small[
- My Proj Structure
- .alpha[R Markdown]
- .alpha[Reproducibility]
- .alpha[Branching]
- .alpha[Load All Targets]
]
]
]
.pull-right-70[
.pull-left-50[
.move-down-50[
.code-size-12[

```
- my-project/
  |
  |
  |
  |
* |-- _targets.R
  |
* |-- _targets/
  |
  |-- data/
  |  |-- raw-data.csv
  |
  |-- R/
  |  |-- my-functions.R
  |  |-- ...
```
]
]
]
.pull-right-50[

]
]

---
## `targets` Advanced Features

.pull-left-30[
.move-down-110[
.li-small[
- My Proj Structure
- .alpha[R Markdown]
- .alpha[Reproducibility]
- .alpha[Branching]
- .alpha[Load All Targets]
]
]
]
.pull-right-70[
.pull-left-50[
.move-down-50[
.code-size-12[

```
- my-project/
  |
  |
  |
  |
  |-- _targets.R
  |
  |-- _targets/
  |
  |-- data/
  |  |-- raw-data.csv
  |
  |-- R/
  |  |-- my-functions.R
  |  |-- ...
```
]
]
]
.pull-right-50[
.move-down-50[
.code-size-12[
```
- my-project/
  |
  |-- _targets.yaml
  |
  |-- analysis/
  |   |-- targets-workflow.R
  |   |-- targets-analysis.R
  |   |-- _targets/
  |
  |-- data/
  |   |-- raw-data.csv
  |
  |-- R/
  |   |-- my-functions.R
  |   |-- ...
```
]
]
]
]

---
## `targets` Advanced Features

.pull-left-30[
.move-down-110[
.li-small[
- My Proj Structure
- .alpha[R Markdown]
- .alpha[Reproducibility]
- .alpha[Branching]
- .alpha[Load All Targets]
]
]
]
.pull-right-70[
.pull-left-50[
.move-down-50[
.code-size-12[

```
- my-project/
  |
  |
  |
  |
* |-- _targets.R
  |
  |-- _targets/
  |
  |-- data/
  |  |-- raw-data.csv
  |
  |-- R/
  |  |-- my-functions.R
  |  |-- ...
```
]
]
]
.pull-right-50[
.move-down-50[
.code-size-12[
```
- my-project/
  |
  |-- _targets.yaml
  |
* |-- analysis/
* |   |-- targets-workflow.R
  |   |-- targets-analysis.R
  |   |-- _targets/
  |
  |-- data/
  |   |-- raw-data.csv
  |
  |-- R/
  |   |-- my-functions.R
  |   |-- ...
```
]
]
]
]

---
## `targets` Advanced Features

.pull-left-30[
.move-down-110[
.li-small[
- My Proj Structure
- .alpha[R Markdown]
- .alpha[Reproducibility]
- .alpha[Branching]
- .alpha[Load All Targets]
]
]
]
.pull-right-70[
.pull-left-50[
.move-down-50[
.code-size-12[

```
- my-project/
  |
  |
  |
  |
  |-- _targets.R
  |
* |-- _targets/
  |
  |-- data/
  |  |-- raw-data.csv
  |
  |-- R/
  |  |-- my-functions.R
  |  |-- ...
```
]
]
]
.pull-right-50[
.move-down-50[
.code-size-12[
```
- my-project/
  |
  |-- _targets.yaml
  |
* |-- analysis/
  |   |-- targets-workflow.R
  |   |-- targets-analysis.R
* |   |-- _targets/
  |
  |-- data/
  |   |-- raw-data.csv
  |
  |-- R/
  |   |-- my-functions.R
  |   |-- ...
```
]
]
]
]

---
## `targets` Advanced Features

.pull-left-30[
.move-down-110[
.li-small[
- My Proj Structure
- .alpha[R Markdown]
- .alpha[Reproducibility]
- .alpha[Branching]
- .alpha[Load All Targets]
]
]
]
.pull-right-70[
.pull-left-50[
.move-down-50[
.code-size-12[

```
- my-project/
  |
  |
  |
  |
  |-- _targets.R
  |
  |-- _targets/
  |
  |-- data/
  |  |-- raw-data.csv
  |
  |-- R/
  |  |-- my-functions.R
  |  |-- ...
```
]
]
]
.pull-right-50[
.move-down-50[
.code-size-12[
```
- my-project/
  |
  |-- _targets.yaml
  |
  |-- analysis/
  |   |-- targets-workflow.R
* |   |-- targets-analysis.R
  |   |-- _targets/
  |
  |-- data/
  |   |-- raw-data.csv
  |
  |-- R/
  |   |-- my-functions.R
  |   |-- ...
```
]
]
]
]

---
## `targets` Advanced Features

.pull-left-30[
.move-down-110[
.li-small[
- My Proj Structure
- .alpha[R Markdown]
- .alpha[Reproducibility]
- .alpha[Branching]
- .alpha[Load All Targets]
]
]
]
.pull-right-70[
.pull-left-50[
.move-down-50[
.code-size-12[

```
- my-project/
  |
  |
  |
  |
  |-- _targets.R
  |
  |-- _targets/
  |
  |-- data/
  |  |-- raw-data.csv
  |
  |-- R/
  |  |-- my-functions.R
  |  |-- ...
```
]
]
]
.pull-right-50[
.move-down-50[
.code-size-12[
```
- my-project/
  |
* |-- _targets.yaml
  |
  |-- analysis/
  |   |-- targets-workflow.R
* |   |-- targets-analysis.R
  |   |-- _targets/
  |
  |-- data/
  |   |-- raw-data.csv
  |
  |-- R/
  |   |-- my-functions.R
  |   |-- ...
```
]
]
]
]

---
## `targets` Advanced Features

.pull-left-30[
.move-down-110[
.li-small[
- My Proj Structure
- .alpha[R Markdown]
- .alpha[Reproducibility]
- .alpha[Branching]
- .alpha[Load All Targets]
]
]
]
.pull-right-70[
.move-down-80[
.code-size-12[

```r
# Targets settings
targets::tar_config_set(script = "analysis/targets-workflow.R",
                        store = "analysis/_targets/")
```
]
]

.move-down-50[
.code-size-12[
{{content}}
]
]
]

--
```yaml
#----    _targets.yaml    ----#
main:
  script: analysis/targets-workflow.R
  store: analysis/_targets/
```

---
## `targets` Advanced Features

.pull-left-30[
.move-down-110[
.li-small[
- My Proj Structure
- .alpha[R Markdown]
- .alpha[Reproducibility]
- .alpha[Branching]
- .alpha[Load All Targets]
]
]
]
.pull-right-70[
.move-down-30[
.code-size-12[

```r
#----    targets-analysis.R    ----#

# Targets settings
targets::tar_config_set(script = "analysis/targets-workflow.R",
                        store = "analysis/_targets/")

#----    Analysis    ----

# Check workflow
targets::tar_manifest(fields = "command")
targets::tar_visnetwork()

# Run analysis
targets::tar_make()

# End
targets::tar_visnetwork()


#----    Results    ----
# Load the results
...

```
]
]
]

---
## `targets` Advanced Features

.pull-left-30[
.move-down-110[
.li-small[
- My Proj Structure
- .alpha[R Markdown]
- .alpha[Reproducibility]
- .alpha[Branching]
- .alpha[Load All Targets]
]
]
]
.pull-right-70[
.move-down-30[
.code-size-12[

```r
#----    targets-analysis.R    ----#

# Targets settings
script = "analysis/targets-workflow.R"
store = "analysis/_targets/"

#----    Analysis    ----

# Check workflow
targets::tar_manifest(fields = "command", script = script)
targets::tar_visnetwork(script = script, store = store)

# Run analysis
targets::tar_make(script = script, store = store)

# End
targets::tar_visnetwork(script = script, store = store)


#----    Results    ----
# Load the results
...

```
]
]
]

---
## `targets` Advanced Features

.pull-left-30[
.move-down-110[
.li-small[
- .alpha[My Proj Structure]
- R Markdown
- .alpha[Reproducibility]
- .alpha[Branching]
- .alpha[Load All Targets]
]
]
]
.pull-right-70[
]

---
## `targets` Advanced Features

.pull-left-30[
.move-down-110[
.li-small[
- .alpha[My Proj Structure]
- R Markdown
- .alpha[Reproducibility]
- .alpha[Branching]
- .alpha[Load All Targets]
]
]
]
.pull-right-70[
.move-down-80[

.li-small[

- **R Markdown as Primary Script**&lt;br&gt;Pipeline defined and managed within R Markdown&lt;br&gt;https://books.ropensci.org/targets/markdown.html

&lt;br&gt;

{{content}}
]
]
]
--
- **R Markdown as Target**&lt;br&gt;R Markdown considered as target in the pipeline&lt;br&gt;https://books.ropensci.org/targets/literate-programming.html

---
# R Markdown as Target

--

.pull-left-50[

`documents/report.Rmd`

&lt;img src="images/09-workflow/report-analysis.png" width="80%" style="display: block; margin: auto;" /&gt;
]
.pull-right-50[
.code-size-12[
{{content}}
]
]

--


```r
#----    Targets-workflow.R    ----#

list(
  ...
  
  tarchetypes::tar_render(
    report, "documents/report.Rmd"
  ),
)
```


{{content}}

--

&lt;img src="images/09-workflow/pipeline-report.png" width="90%" style="display: block; margin: auto;" /&gt;

---
# R Markdown as Target

.pull-left-50[

`documents/report.Rmd`

&lt;img src="images/09-workflow/report-analysis.png" width="80%" style="display: block; margin: auto;" /&gt;
]
.pull-right-50[
.code-size-12[

```r
#----    Targets-workflow.R    ----#

list(
  ...
  
* tarchetypes::tar_render(
    report, "documents/report.Rmd"
  ),
)
```

&lt;img src="images/09-workflow/pipeline-report.png" width="90%" style="display: block; margin: auto;" /&gt;

]
]

---
# R Markdown as Target

.pull-left-50[

`documents/report.Rmd`

&lt;img src="images/09-workflow/report-analysis.png" width="80%" style="display: block; margin: auto;" /&gt;
]
.pull-right-50[
.move-down-50[
Compile Report

.li-small[
{{content}}
]
]
]

--

- `targets::tar_make()`
{{content}}

--
- `Knit`

---
# R Markdown as Target

.pull-left-50[

`documents/report.Rmd`

&lt;img src="images/09-workflow/report-analysis.png" width="80%" style="display: block; margin: auto;" /&gt;
]
.pull-right-50[
.move-down-50[
Compile Report

.li-small[
- `targets::tar_make()`
- `Knit`
]

.font-18[
Specify `_targets/` position with `tar_config_set()`
]

.code-size-12[
{{content}}
]
]
]

--
```
#----    documents/_targets.yaml    ----#
main:
  store: ../analysis/_targets/
```

---
## `targets` Advanced Features

.pull-left-30[
.move-down-110[
.li-small[
- .alpha[My Proj Structure]
- .alpha[R Markdown]
- Reproducibility
- .alpha[Branching]
- .alpha[Load All Targets]
]
]
]
.pull-right-70[
.move-down-110[
{{content}}
]
]

--
- Random Number Generator

{{content}}
--
- Global Settings

{{content}}
--
- Project Requirements

---
## `targets` Advanced Features

.pull-left-30[
.move-down-110[
.li-small[
- .alpha[My Proj Structure]
- .alpha[R Markdown]
- .alpha[Reproducibility]
- Branching
- .alpha[Load All Targets]
]
]
]
.pull-right-70[
.move-down-80[
{{content}}
]
]

--
&lt;img src="images/09-workflow/target-branching.png" width="100%" style="display: block; margin: auto;" /&gt;
---
## `targets` Advanced Features

.pull-left-30[
.move-down-110[
.li-small[
- .alpha[My Proj Structure]
- .alpha[R Markdown]
- .alpha[Reproducibility]
- Branching
- .alpha[Load All Targets]
]
]
]
.pull-right-70[
.move-down-110[
.li-small[
- **Dynamic Branching** - New targets are defined dynamically&lt;br&gt;https://books.ropensci.org/targets/dynamic.html

&lt;br&gt;
{{content}}
]
]
]

--
- **Static Branching** - New targets are defined a priori&lt;br&gt;https://books.ropensci.org/targets/static.html

---
## `targets` Advanced Features

.pull-left-30[
.move-down-110[
.li-small[
- .alpha[My Proj Structure]
- .alpha[R Markdown]
- .alpha[Reproducibility]
- .alpha[Branching]
- Load All Targets
]
]
]
.pull-right-70[
.code-size-12[
{{content}}
]
]

--

```r
#----    R/Targets-utils.R    ----#

#----    load_glob_env    ----

# Load targets in the global environment
load_glob_env &lt;- function(..., 
                          store = targets::tar_config_get("store")){
  targets::tar_load(..., envir = globalenv(), store = store)
}

#----    tar_load_all    ----

# Load listed targets
tar_load_all &lt;- function(store = targets::tar_config_get("store")){
  targets &lt;- c("my_data", "lm_fit", "plot_obs", 
               "&lt;other-targets&gt;", "...")

  # load
  sapply(targets, load_glob_env, store = store)

  return(cat("Tartgets loaded!\n"))
}
```

---
## `targets` Advanced Features

.pull-left-30[
.move-down-110[
.li-small[
- .alpha[My Proj Structure]
- .alpha[R Markdown]
- .alpha[Reproducibility]
- .alpha[Branching]
- Load All Targets
]
]
]
.pull-right-70[
.code-size-12[

```r
#----    R/Targets-utils.R    ----#

*#----    load_glob_env    ----

# Load targets in the global environment
load_glob_env &lt;- function(..., 
                          store = targets::tar_config_get("store")){
  targets::tar_load(..., envir = globalenv(), store = store)
}

#----    tar_load_all    ----

# Load listed targets
tar_load_all &lt;- function(store = targets::tar_config_get("store")){
  targets &lt;- c("my_data", "lm_fit", "plot_obs", 
               "&lt;other-targets&gt;", "...")

  # load
  sapply(targets, load_glob_env, store = store)

  return(cat("Tartgets loaded!\n"))
}
```
]
]

---
## `targets` Advanced Features

.pull-left-30[
.move-down-110[
.li-small[
- .alpha[My Proj Structure]
- .alpha[R Markdown]
- .alpha[Reproducibility]
- .alpha[Branching]
- Load All Targets
]
]
]
.pull-right-70[
.code-size-12[

```r
#----    R/Targets-utils.R    ----#

#----    load_glob_env    ----

# Load targets in the global environment
load_glob_env &lt;- function(..., 
                          store = targets::tar_config_get("store")){
  targets::tar_load(..., envir = globalenv(), store = store)
}

*#----    tar_load_all    ----

# Load listed targets
tar_load_all &lt;- function(store = targets::tar_config_get("store")){
  targets &lt;- c("my_data", "lm_fit", "plot_obs", 
               "&lt;other-targets&gt;", "...")

  # load
  sapply(targets, load_glob_env, store = store)

  return(cat("Tartgets loaded!\n"))
}
```
]
]

---
## `targets` Advanced Features

.pull-left-30[
.move-down-110[
.li-small[
- .alpha[My Proj Structure]
- .alpha[R Markdown]
- .alpha[Reproducibility]
- .alpha[Branching]
- Load All Targets
]
]
]
.pull-right-70[
.code-size-12[

```r
#----    .Rprofile    ----#

...

# Commands only for interactive sessions
if(interactive()){
    
    ...
  
    # Load custom function
    source("R/targets-utils.R")
    
    # alternatively devtools::load_all()
  
    # Load targets
    tar_load_all()
    
    ...
  }
```

]
]
---
class: inverse, center, middle

# Aim at the Target!

## Moving to the next step...
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