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update folder strcuture in d6 post
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@z3tt
z3tt committed Dec 4, 2023
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102 changes: 52 additions & 50 deletions _posts/d6package/d6package.Rmd
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Expand Up @@ -38,23 +38,23 @@ There are five main functionalities:
<br>The function [`simple_load()` is a utility function](#simple-load-packages) that is currently in an experimental state. It allows you to install (if not yet) and load a set of packages—even a combination of CRAN and GitHub packages—in a single step.

<br>
matches our "lab identity"
------------------------------------------------------------------------

---

<br>

## Installation

The package is not on CRAN and needs to be installed from GitHub. To do
so, open Rstudio and run the following two lines in the console. In case
the `{devtools}` package is already installed, skip that step.
the `{remotes}` package is already installed, skip that step.

```{r}
install.packages("devtools")
devtools::install_github("EcoDynIZW/d6")
install.packages("remotes")
remotes::install_github("EcoDynIZW/d6")
```

(Note: If you are asked if you want to update other packgaes either
(Note: If you are asked if you want to update other packages either
press “No” (option 3) and continue or update the packages before running
the install command again.)

Expand Down Expand Up @@ -89,43 +89,45 @@ countries](https://www.iban.com/country-codes).
The main folders created in the root folder (here
`unicornus_wl_sdm_smith_j`) are the following:

``` text
```{text}
.
└── unicornus_wl_sdm_smith_j
├── data-raw
├── data
├── docs
├── output
├── plots
└── R
└── scripts
```

The full scaffolding structure including all subdirectories and
The full scaffolding structure including all sub directories and
additional files looks like this:

``` text
```{text}
.
└── unicornus_wl_sdm_smith_j
├── .Rproj.user — Rproject files
├── data-raw — raw data (tabular data in root folder)
│ └── geo-raw — raw spatial data
├── docs — documents
│ ├── admin — adminstrative docs, e.g. permits
│ ├── literature — literature used for parameterization + ms
│ ├── manuscript — manuscript drafts (main + supplement)
│ ├── presentations — talks and poster presentations
│ └── reports — rendered reports
├── output — everything that is computed (except plots)
│ ├── data-proc — processed tabular data
│ └── geo-proc — processed spatial data
├── plots — plot output
├── R — scripts
│ ├── 00_start.R — first script to run
│ └── XX_submit.R — final script to run
├── .gitignore — contains which files to ignore for version control
├── .Rbuildignore — contains which files to ignore for package builds
├── DESCRIPTION — contains project details and package dependencies
├── NAMESPACE — contains context for R objects
└── project.Rproj — Rproject file: use to start your project
├── .Rproj.user — Rproject files
├── data — main folder data
│ ├── geo — main folder spatial data (if `geo = TRUE`)
│ │ ├── processed — processed spatial data files
│ │ └── raw — raw spatial data files
│ ├── processed — processed tabular data files
│ └── raw — raw tabular data files
├── docs — documents main folder
│ ├── admin — administrative docs, e.g. permits
│ ├── literature — literature used for parametrization + manuscript
│ ├── manuscript — manuscript drafts (main + supplement)
│ ├── presentations — talks and poster presentations
│ └── reports — rendered reports
├── output — everything that is computed (except plots)
├── plots — plot output
├── scripts — script files (e.g. .R, .Rmd, .Qmd, .py, .nlogo)
│ ├── 00_start.R — first script to run after project setup
│ └── zz_submit.R — final script to run before submission
├── .gitignore — contains which files to ignore for version control
├── .Rbuildignore — contains which files to ignore for package builds
├── DESCRIPTION — contains project details and package dependencies
├── NAMESPACE — contains context for R objects
└── project.Rproj — Rproject file: use to start your project
```

#
Expand Down Expand Up @@ -203,7 +205,7 @@ department via `install_d6_packages()`:
d6::install_d6_packages()
```

Note that this function is going to check preinstalled versions and will
Note that this function is going to check pre-installed versions and will
only install packages that are not installed with your current R
version.

Expand All @@ -217,14 +219,14 @@ d6::install_d6_packages(geo = FALSE)

The default packages that are going to be installed are:

``` text
```{text}
tidyverse (tibble, dplyr, tidyr, ggplot2, readr, forcats, stringr, purrr), lubridate, here, vroom, patchwork, remotes
```

The following packages will be installed in case you specify
`geo = TRUE`:

``` text
```{text}
sf, terra, stars, tmap
```

Expand All @@ -243,7 +245,7 @@ in manuscripts, presentations, and posters.

The theme can be added to a ggplot object as usual:

```r
```{r}
library(ggplot2)
ggplot(mpg, aes(x = displ, y = cty)) +
geom_point() +
Expand All @@ -252,13 +254,13 @@ ggplot(mpg, aes(x = displ, y = cty)) +

Or set as the new global theme by overwriting the current default:

```r
```{r}
theme_set(d6::theme_d6())
```

### Typefaces

The D6 corporate theme uses the PT font superfamily and will inform you to
The D6 corporate theme uses the PT font super family and will inform you to
install the relevant files in case they are missing on your machine:

- [PT Sans](https://fonts.google.com/specimen/PT+Sans)
Expand All @@ -268,7 +270,7 @@ install the relevant files in case they are missing on your machine:
By default, the theme uses PT Sans. If you prefer serif fonts or such a
typeface is required, you can set `serif = TRUE` inside the theme:

```r
```{r}
ggplot(mpg, aes(x = displ, y = cty)) +
geom_point() +
d6::theme_d6(serif = TRUE)
Expand All @@ -277,18 +279,18 @@ ggplot(mpg, aes(x = displ, y = cty)) +

### Additional Utility Arguments

In addition to the common arguments to specify the bas settings
In addition to the common arguments to specify the base settings
(`base_family`, `base_size`, `base_line_size`, and `base_rect_size`),
we have added the following utility settings to simplify the modification
of the theme:

- `grid`: remove or add major grid lines (`"xy"` by default)
- `legend`: control legend position (`"bottom"` by default)
- `mono`: use a tabular, monospaced font for numeric scales such as x, y, and legends (`"none"` by default)
- `mono`: use a tabular, mono spaced font for numeric scales such as x, y, and legends (`"none"` by default)
- `bg`: define background color (`"transparent"` by default)
- `serif`: set main typeface (`FALSE` by default; see above)

```r
```{r}
ggplot(mpg, aes(x = class, y = hwy, color = factor(year))) +
geom_boxplot() +
d6::theme_d6(
Expand All @@ -310,7 +312,7 @@ ggplot(mpg, aes(x = class, y = hwy, color = factor(year))) +
The package also provides several templates for your scripts. In
Rstudio, navigate to `File > New File > RMarkdown... > Templates` and
choose the template you want to use. All templates come with a
preformatted YAML header and chunks for the setup.
pre-formatted YAML header and chunks for the setup.

The following templates are available for now:

Expand All @@ -329,11 +331,11 @@ The following templates are available for now:

The `render_*()` functions take care of knitting your Rmarkdown files
into HTML reports. The functions assume that your .Rmd files are saved
in the `R` directory or any subdirectory, and will store the resulting
in the `R` directory or any sub directory, and will store the resulting
.html files in the according directory, namely `./docs/reports/`.

You can render all .Rmd files that are placed in the `R` directory and
subdirectories in one step:
sub directories in one step:

```{r}
d6::render_all_reports()
Expand All @@ -360,15 +362,15 @@ are installed already, installs them if needed, and loads them via
at the same time. GitHub packages need to be specified as
"owner/repository" without any spaces.

```{r, eval=false}
d6::simple_load(pcks = c("dplyr", "ggplot2", "EcoDynIZ/d6berlin"))
```{r}
d6::simple_load(pcks = c("dplyr", "ggplot2", "EcoDynIZW/d6berlin"))
```

You can also force a reinstallation of packages. CRAN and GitHub packages
You can also force a re-installation of packages. CRAN and GitHub packages
are controlled individually via `update_cran` and `update_gh`, respectively.

```{r, eval=false}
d6::simple_load(pcks = c("dplyr", "ggplot2", "EcoDynIZ/d6berlin"),
```{r}
d6::simple_load(pcks = c("dplyr", "ggplot2", "EcoDynIZW/d6berlin"),
update_cran = TRUE, update_gh = TRUE)
```

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