diff --git a/.Rbuildignore b/.Rbuildignore
index a5d77f856db6a9e04fa31efff9ea1107d0ddda9f..c726cfaf36aca9dce8729bc6c61ae847e9f60a42 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1 +1,6 @@
^dev$
+^LICENSE\.md$
+^README\.Rmd$
+^CODE_OF_CONDUCT\.md$
+^data\.nitrates\.Rproj$
+^\.Rproj\.user$
diff --git a/.gitignore b/.gitignore
index 507e045ab5af5b8ed416b5ba33291704b2ef3e32..000e2e4d8be5c846dc013dadb7b93287d11dcd07 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,3 +3,4 @@
.RData
.DS_Store
.httr-oauth
+inst/doc
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
new file mode 100644
index 0000000000000000000000000000000000000000..85d5cd6409100569d8e285eff6cbb806bed2503d
--- /dev/null
+++ b/CODE_OF_CONDUCT.md
@@ -0,0 +1,126 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+ and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+ community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+ any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+ without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at ronan.vignard@developpement-durable.gouv.fr.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
+
+For answers to common questions about this code of conduct, see the FAQ at
+<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
+
+[homepage]: https://www.contributor-covenant.org
diff --git a/DESCRIPTION b/DESCRIPTION
new file mode 100644
index 0000000000000000000000000000000000000000..19e43c2735f2b9373ac93322c9952ac0c1740a0b
--- /dev/null
+++ b/DESCRIPTION
@@ -0,0 +1,19 @@
+Package: data.nitrates
+Title: Collecte Des Données Sur Les Nitrates
+Version: 0.0.0.9000
+Authors@R:
+ person("Ronan", "Vignard", , "ronan.vignard@developpement-durable.gouv.fr", role = c("aut", "cre"),
+ comment = c(ORCID = "0000-0000-0000-0000"))
+Description: Import des données nitrates à partir des sources ARS et
+ Hub'eau dans une base de données PostgreSQL.
+License: MIT + file LICENSE
+Suggests:
+ collectr,
+ knitr,
+ rmarkdown
+VignetteBuilder:
+ knitr
+Config/fusen/version: 0.5.2
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.1
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000000000000000000000000000000000000..6921b4cc59d464d0e6b2279207c0db0ada8e1622
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,2 @@
+YEAR: 2024
+COPYRIGHT HOLDER: Ronan Vignard
diff --git a/LICENSE.md b/LICENSE.md
new file mode 100644
index 0000000000000000000000000000000000000000..b2cd6e60b9634bd90b8599f8079941f90e2968e4
--- /dev/null
+++ b/LICENSE.md
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 Ronan Vignard
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/NAMESPACE b/NAMESPACE
new file mode 100644
index 0000000000000000000000000000000000000000..6ae926839dd1829f1016a96f766d970ff184ad97
--- /dev/null
+++ b/NAMESPACE
@@ -0,0 +1,2 @@
+# Generated by roxygen2: do not edit by hand
+
diff --git a/NEWS.md b/NEWS.md
new file mode 100644
index 0000000000000000000000000000000000000000..8ab587f3feff8f00a33fbca1788469b10572de03
--- /dev/null
+++ b/NEWS.md
@@ -0,0 +1,3 @@
+# data.nitrates (development version)
+
+* Initial CRAN submission.
diff --git a/README.Rmd b/README.Rmd
new file mode 100644
index 0000000000000000000000000000000000000000..96d24b6d854d1e134ff5b87ceecd12248f144c7a
--- /dev/null
+++ b/README.Rmd
@@ -0,0 +1,69 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+ collapse = TRUE,
+ comment = "#>",
+ fig.path = "man/figures/README-",
+ out.width = "100%"
+)
+```
+
+# data.nitrates
+
+<!-- badges: start -->
+[](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/eau-milieux-aquatiques/data.nitrates/-/releases)
+[](https://opensource.org/licenses/MIT)
+[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/eau-milieux-aquatiques/data.nitrates/-/commits/master)
+
+<!-- badges: end -->
+
+## Objectif
+
+L'objectif du package `data.nitrates` est de faciliter l'actualisation des lots de données suivants dans une base de données PostgreSQL locale.
+
+**Sources :**
+
+- Données de l'ARS : `nitrates.nitrate_data_analyse_ars`
+- Données provenant de la plateforme Hub'eau :
+ - [API "Qualité des nappes d'eau souterraine"](https://hubeau.eaufrance.fr/page/api-qualite-nappes) : `qualite_nappes_eau_souterraine.nitrate_qualite_nappes_analyses`
+ - [API "Qualité des cours d'eau"](https://hubeau.eaufrance.fr/page/api-qualite-cours-deau) : `qualite_cours_d_eau.hubeau_qualite_rivieres_station_pc`
+
+**Livrables :**
+
+- Table des prélèvements : `nitrates.nitrate_prelevement`
+- Table des analyses : `nitrates.nitrate_analyse`
+
+## Installation
+
+Installer le package `remotes` si besoin :
+
+```{r install-remotes, eval=FALSE}
+install.packages("remotes")
+```
+
+
+Installer le package `data.nitrates` :
+
+```{r install-package, eval=FALSE}
+remotes::install_gitlab('dreal-pdl/csd/eau-milieux-aquatiques/data.nitrate', host="gitlab-forge.din.developpement-durable.gouv.fr")
+```
+
+## Utilisation
+
+### Chargement du package
+Charger le package `data.nitrates` dans la session :
+
+```{r load-package, eval=FALSE}
+library(data.nitrates)
+```
+
+### Documentation
+
+La documentation du package est consultable sur ce site :
+https://dreal-pdl.gitlab-pages.din.developpement-durable.gouv.fr/csd/eau-milieux-aquatiques/data.nitrate/
diff --git a/README.md b/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..b99b734368f8b18511ccb6cbc159f491f18a0332
--- /dev/null
+++ b/README.md
@@ -0,0 +1,67 @@
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# data.nitrates
+
+<!-- badges: start -->
+
+[](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/eau-milieux-aquatiques/data.nitrates/-/releases)
+[](https://opensource.org/licenses/MIT)
+[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/eau-milieux-aquatiques/data.nitrates/-/commits/master)
+
+<!-- badges: end -->
+
+## Objectif
+
+L’objectif du package `data.nitrates` est de faciliter l’actualisation
+des lots de données suivants dans une base de données PostgreSQL locale.
+
+**Sources :**
+
+- Données de l’ARS : `nitrates.nitrate_data_analyse_ars`
+- Données provenant de la plateforme Hub’eau :
+ - [API “Qualité des nappes d’eau
+ souterraine”](https://hubeau.eaufrance.fr/page/api-qualite-nappes) :
+ `qualite_nappes_eau_souterraine.nitrate_qualite_nappes_analyses`
+ - [API “Qualité des cours
+ d’eau”](https://hubeau.eaufrance.fr/page/api-qualite-cours-deau) :
+ `qualite_cours_d_eau.hubeau_qualite_rivieres_station_pc`
+
+**Livrables :**
+
+- Table des prélèvements : `nitrates.nitrate_prelevement`
+- Table des analyses : `nitrates.nitrate_analyse`
+
+## Installation
+
+Installer le package `remotes` si besoin :
+
+``` r
+install.packages("remotes")
+```
+
+Installer le package `data.nitrates` :
+
+``` r
+remotes::install_gitlab('dreal-pdl/csd/eau-milieux-aquatiques/data.nitrate', host="gitlab-forge.din.developpement-durable.gouv.fr")
+```
+
+## Utilisation
+
+### Chargement du package
+
+Charger le package `data.nitrates` dans la session :
+
+``` r
+library(data.nitrates)
+```
+
+### Documentation
+
+La documentation du package est consultable sur ce site :
+<https://dreal-pdl.gitlab-pages.din.developpement-durable.gouv.fr/csd/eau-milieux-aquatiques/data.nitrate/>
diff --git a/data.nitrates.Rproj b/data.nitrates.Rproj
index c8daeb91df75db32b7653943a4ee2b557eddad0e..6a3ede2239ad87da09a17c21b42cb9bb5ea83810 100644
--- a/data.nitrates.Rproj
+++ b/data.nitrates.Rproj
@@ -15,3 +15,7 @@ LaTeX: pdfLaTeX
AutoAppendNewline: Yes
StripTrailingWhitespace: Yes
LineEndingConversion: Posix
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
diff --git a/dev/0-dev_history.Rmd b/dev/0-dev_history.Rmd
index 628b333c51f7927ee0bcf2f467de69d77f03bdf1..d8a08b2fc6f207bcb92ec284f2d514034b3e2f37 100644
--- a/dev/0-dev_history.Rmd
+++ b/dev/0-dev_history.Rmd
@@ -16,15 +16,15 @@ All commands that you use to use when developing packages...
fusen::fill_description(
pkg = here::here(),
fields = list(
- Title = "Build A Package From Rmarkdown File",
- Description = "Use Rmarkdown First method to build your package. Start your package with documentation. Everything can be set from a Rmarkdown file in your project.",
+ Title = "Collecte des données sur les nitrates",
+ Description = "Import des données nitrates à partir des sources ARS et Hub'eau dans une base de données PostgreSQL.",
`Authors@R` = c(
- person("John", "Doe", email = "john@email.me", role = c("aut", "cre"), comment = c(ORCID = "0000-0000-0000-0000"))
+ person("Ronan", "Vignard", email = "ronan.vignard@developpement-durable.gouv.fr", role = c("aut", "cre"), comment = c(ORCID = "0000-0000-0000-0000"))
)
)
)
# Define License with use_*_license()
-usethis::use_mit_license("John Doe")
+usethis::use_mit_license("Ronan Vignard")
```
# All-in-one function to deploy publicly on GitHub
@@ -56,7 +56,7 @@ remotes::install_local()
# README
usethis::use_readme_rmd()
# Code of Conduct
-usethis::use_code_of_conduct("contact@fake.com")
+usethis::use_code_of_conduct("ronan.vignard@developpement-durable.gouv.fr")
# NEWS
usethis::use_news_md()
```
diff --git a/dev/config_attachment.yaml b/dev/config_attachment.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..46e24ecc2173ddbd6d930225a01bb92e508508d5
--- /dev/null
+++ b/dev/config_attachment.yaml
@@ -0,0 +1,12 @@
+path.n: NAMESPACE
+path.d: DESCRIPTION
+dir.r: R
+dir.v: vignettes
+dir.t: tests
+extra.suggests: ~
+pkg_ignore: ~
+document: yes
+normalize: yes
+inside_rmd: no
+must.exist: yes
+check_if_suggests_is_installed: yes
diff --git a/dev/config_fusen.yaml b/dev/config_fusen.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..7b7d7547f62d7f7f3ab58a7da562e90667f1185e
--- /dev/null
+++ b/dev/config_fusen.yaml
@@ -0,0 +1,13 @@
+flat_import_data.Rmd:
+ path: dev/flat_import_data.Rmd
+ state: active
+ R: []
+ tests: []
+ vignettes: vignettes/import-des-donnees.Rmd
+ inflate:
+ flat_file: dev/flat_import_data.Rmd
+ vignette_name: Import des données
+ open_vignette: true
+ check: true
+ document: true
+ overwrite: ask
diff --git a/dev/flat_first.Rmd b/dev/flat_first.Rmd
deleted file mode 100644
index f902c01846178e94bc26b3be29944335a6e42a20..0000000000000000000000000000000000000000
--- a/dev/flat_first.Rmd
+++ /dev/null
@@ -1,206 +0,0 @@
----
-title: "flat_first.Rmd for working package"
-output: html_document
-editor_options:
- chunk_output_type: console
----
-
-<!-- Run this 'development' chunk -->
-<!-- Store every call to library() that you need to explore your functions -->
-
-```{r development, include=FALSE}
-library(testthat)
-```
-
-<!--
- You need to run the 'description' chunk in the '0-dev_history.Rmd' file before continuing your code there.
-
-If it is the first time you use {fusen}, after 'description', you can directly run the last chunk of the present file with inflate() inside.
--->
-
-```{r development-load}
-# Load already included functions if relevant
-pkgload::load_all(export_all = FALSE)
-```
-
-# Include some data examples in your package
-
-<!--
- Store your dataset in a directory named "inst/" at the root of your project.
- Use it for your tests in this Rmd thanks to `pkgload::load_all()` to make it available
-and `system.file()` to read it in your examples.
-
-- There already is a dataset in the "inst/" directory to be used in the examples below
--->
-
-```{r development-dataset}
-# Run all this chunk in the console directly
-# There already is a dataset in the "inst/" directory
-# Make the dataset file available to the current Rmd during development
-pkgload::load_all(path = here::here(), export_all = FALSE)
-
-# You will be able to read your example data file in each of your function examples and tests as follows - see chunks below
-datafile <- system.file("nyc_squirrels_sample.csv", package = "data.nitrates")
-nyc_squirrels <- read.csv(datafile, encoding = "UTF-8")
-
-nyc_squirrels
-```
-
-
-# The first function of the package: Calculate the median of a vector
-
-<!--
-Create a chunk for the core of the function
-
-- The chunk needs to be named `function` at least
-- It contains the code of a documented function
-- The chunk can also be named `function-my_median` to make it easily
-findable in your Rmd
-- Let the `@examples` part empty, and use the next `examples` chunk instead to present reproducible examples
-
-After inflating the template
-
-- This function code will automatically be added in a new file in the "R/" directory
--->
-
-```{r function}
-#' My median
-#'
-#' @param x Vector of Numeric values
-#' @inheritParams stats::median
-#'
-#' @return
-#' Median of vector x
-#' @export
-#'
-#' @examples
-my_median <- function(x, na.rm = TRUE) {
- if (!is.numeric(x)) {stop("x should be numeric")}
- stats::median(x, na.rm = na.rm)
-}
-```
-
-<!--
-Create a chunk with an example of use for your function
-
-- The chunk needs to be named `examples` at least
-- It contains working examples of your function
-- The chunk is better be named `examples-my_median` to be handled
-correctly when inflated as a vignette
-
-After inflating the template
-
-- This example will automatically be added in the '@examples' part of our function above in the "R/" directory
-- This example will automatically be added in the vignette created from this Rmd template
--->
-
-```{r examples}
-my_median(1:12)
-
-# Example with your dataset in "inst/"
-datafile <- system.file("nyc_squirrels_sample.csv", package = "data.nitrates")
-nyc_squirrels <- read.csv(datafile, encoding = "UTF-8")
-# Apply my function
-my_median(nyc_squirrels[,"hectare_squirrel_number"])
-```
-
-<!--
-Create a chunk with a test of use for your function
-
-- The chunk needs to be named `tests` at least
-- It contains working tests of your function
-- The chunk is better be named `tests-my_median` to be handled
-correctly when inflated as a vignette
-
-After inflating the template
-
-- This test code will automatically be added in the "tests/testthat/" directory
--->
-
-```{r tests}
-test_that("my_median works properly and show error if needed", {
- expect_true(my_median(1:12) == 6.5)
- expect_error(my_median("text"))
-})
-
-# Test with your dataset in "inst/"
-datafile <- system.file("nyc_squirrels_sample.csv", package = "data.nitrates")
-nyc_squirrels <- read.csv(datafile, encoding = "UTF-8")
-# Apply test on my function
-test_that("my_median works properly with internal dataset", {
- expect_equal(my_median(nyc_squirrels[,"hectare_squirrel_number"]), 3)
-})
-```
-
-# Calculate the mean of a vector
-
-<!--
-There can be other functions, examples and tests in your flat template.
-Each of them will be inflated in a different file, provided that there is a level-1 or level-2 section title to separate from previous functions.
--->
-
-## Use sub-functions in the same chunk
-
-```{r function-my_other_median}
-#' My Other median
-#'
-#' @param x Vector of Numeric values
-#' @inheritParams stats::median
-#'
-#' @return
-#' Median of vector x
-#' @export
-#'
-#' @examples
-my_other_median <- function(x, na.rm = TRUE) {
- if (!is.numeric(x)) {stop("x should be numeric")}
- sub_median(x, na.rm =na.rm)
-}
-
-#' Core of the median not exported
-#' @param x Vector of Numeric values
-#' @inheritParams stats::median
-sub_median <- function(x, na.rm = TRUE) {
- stats::median(x, na.rm)
-}
-```
-
-```{r examples-my_other_median}
-my_other_median(1:12)
-```
-
-```{r tests-my_other_median}
-test_that("my_median works properly and show error if needed", {
- expect_true(my_other_median(1:12) == 6.5)
- expect_error(my_other_median("text"))
-})
-```
-
-<!--
-# There can be development actions
-
-Create a chunk with 'development' actions
-
-- The chunk needs to be named `development` or `dev`
-- It contains functions that are used for package development only
-- Note that you may want to store most of these functions in the 0-dev_history.Rmd file
-
-These are only included in the present flat template file, their content will not be part of the package anywhere else.
--->
-
-```{r development-inflate, eval=FALSE}
-# Keep eval=FALSE to avoid infinite loop in case you hit the knit button
-# Execute in the console directly
-fusen::inflate(flat_file = "dev/flat_first.Rmd", vignette_name = "Get started")
-```
-
-
-# Inflate your package
-
-You're one inflate from paper to box.
-Build your package from this very Rmd using `fusen::inflate()`
-
-- Verify your `"DESCRIPTION"` file has been updated
-- Verify your function is in `"R/"` directory
-- Verify your test is in `"tests/testthat/"` directory
-- Verify this Rmd appears in `"vignettes/"` directory
diff --git a/dev/flat_import_data.Rmd b/dev/flat_import_data.Rmd
new file mode 100644
index 0000000000000000000000000000000000000000..7716cf58260decd899115f947c522def21f5821e
--- /dev/null
+++ b/dev/flat_import_data.Rmd
@@ -0,0 +1,180 @@
+---
+title: "Import des données"
+output: html_document
+editor_options:
+ chunk_output_type: console
+---
+
+```{r development, include=FALSE}
+library(testthat)
+library(xlsx)
+library(datalibaba)
+library(RPostgreSQL)
+library(sf)
+library(collectr)
+library(dplyr)
+```
+
+```{r development-1}
+# Load already included functions
+pkgload::load_all(export_all = FALSE)
+```
+
+# Présentation
+
+> Cette page contient la logique métier concernant l'import des données
+ARS et Hub'eau dans le cadre du projet Nitrates
+
+# Connexion à la base de données PostgreSQL
+
+```{r development-connect_to_db, eval=FALSE}
+# Se connecter à la base de données PostgreSQL si_eau
+connexion <- datalibaba::connect_to_db(db = "si_eau")
+```
+
+```{r development-list_schemas, eval=FALSE}
+# Lister les schémas présents dans la base
+schemas_list <- data.frame(datalibaba::list_schemas(connexion))
+
+# Renommer la variable unique en "nom_schema"
+schemas_list <- schemas_list |>
+ rename(nom_schema = unique(names(.)))
+
+# Trier le dataframe par la variable nom_schema
+schemas_list <- schemas_list |>
+ arrange(nom_schema)
+```
+
+```{r development-list_tables, eval=FALSE}
+# Lister les tables présentes dans le schéma spécifié
+tables_list <- data.frame(datalibaba::list_tables(
+ con = connexion,
+ db = "si_eau",
+ schema = "qualite_cours_d_eau"))
+
+# Renommer la variable unique en "nom_table"
+tables_list <- tables_list |>
+ rename(nom_table = names(tables_list)[1])
+
+# Trier le dataframe par la variable nom_table
+tables_list <- tables_list |>
+ arrange(nom_table)
+```
+
+# Import des données de l'ARS
+
+```{r}
+data_ars_2022 <- collectr::import_xlsx(
+ filepath = "T:\\datalab\\SRNP_DEMA_SI_EAU\\NITRATES\\DONNEES_CLIENT\\SOURCES\\ARS\\2023_06\\Nitrates 2022 pour DREAL EPNT4 2023-05-30.xlsx",
+ sheet = 1,
+ row = 2)
+```
+
+## Première approche : non concluante
+
+### Vérification de la correspondande de la structure du dataframe avec celle de la table
+
+```{r development-check_structure_table, eval=FALSE}
+collectr::check_structure_table(connexion,
+ data_ars_2022,
+ "nitrate_data_analyse_ars_test",
+ "qualite_cours_d_eau")
+```
+
+### Adaptation de la structure
+
+```{r development, eval=FALSE}
+data_ars_2022 <- data_ars_2022 |>
+ select(-coord_x,-coord_y) |>
+ mutate(eligible_ades = rep(NA, n()))
+```
+
+### Insertion des données du dataframe dans la table en base
+
+La fonction insert_into_table() doit être corrigée.
+
+```{r development-insert_into_table, eval=FALSE}
+collectr::insert_into_table(connexion,
+ data_ars_2022,
+ "nitrate_data_analyse_ars_test",
+ "qualite_cours_d_eau"
+)
+```
+
+## Deuxième approche : concluante
+
+### Création d'une table pour le nouveau millésime
+
+```{r create-nitrate_data_ars, eval=FALSE}
+poster_data(data = data_ars_2022,
+ table = "nitrate_data_ars_2022",
+ schema = "qualite_cours_d_eau",
+ db = "si_eau",
+ overwrite = TRUE)
+
+```
+
+### Modification du type des champs si besoin
+
+```{r modify_column_type, eval=FALSE}
+# Appeler la fonction pour modifier le type de colonne
+collectr::modify_column_type(connexion,
+ schema = "qualite_cours_d_eau",
+ table_name = "nitrate_data_ars_2022",
+ column_name = "plv_date ",
+ column_type = "date")
+```
+
+### Insertion des données du nouveau millésime en base dans la table globale
+
+```{r import_and_merge_tables, eval=FALSE}
+import_and_merge_tables(connexion,
+ source_table = "nitrate_data_ars_2022",
+ source_schema = "qualite_cours_d_eau",
+ target_table = "nitrate_data_analyse_ars_test",
+ target_schema = "qualite_cours_d_eau")
+
+```
+
+# Import des données Hub'eau ESU
+
+```{r create-nitrate_analyse_esu_2020, eval=FALSE}
+nitrate_analyse_esu_2020 <- get_json_data(code_parametre = "1340",
+ code_region = "52",
+ date_debut_prelevement = "2020-01-01",
+ date_fin_prelevement = "2020-12-31",
+ size = "5000")
+```
+
+```{r create-nitrate_analyse_esu_2021, eval=FALSE}
+nitrate_analyse_esu_2021 <- get_json_data(code_parametre = "1340",
+ code_region = "52",
+ date_debut_prelevement = "2021-01-01",
+ date_fin_prelevement = "2021-12-31",
+ size = "5000")
+```
+
+```{r create-nitrate_analyse_esu_2022, eval=FALSE}
+nitrate_analyse_esu_2022 <- get_json_data(code_parametre = "1340",
+ code_region = "52",
+ date_debut_prelevement = "2022-01-01",
+ date_fin_prelevement = "2022-12-31",
+ size = "5000")
+```
+
+```{r development-inflate, eval=FALSE}
+# Keep eval=FALSE to avoid infinite loop in case you hit the knit button
+# Execute in the console directly
+fusen::inflate(flat_file = "dev/flat_import_data.Rmd", vignette_name = "Import des données")
+```
+
+
+# Inflate your package
+
+You're one inflate from paper to box.
+Build your package from this very Rmd using `fusen::inflate()`
+
+- Verify your `"DESCRIPTION"` file has been updated
+- Verify your function is in `"R/"` directory
+- Verify your test is in `"tests/testthat/"` directory
+- Verify this Rmd appears in `"vignettes/"` directory
diff --git a/vignettes/import-des-donnees.Rmd b/vignettes/import-des-donnees.Rmd
new file mode 100644
index 0000000000000000000000000000000000000000..803a56a578ce8c9de978ccf4f197a970beb5f419
--- /dev/null
+++ b/vignettes/import-des-donnees.Rmd
@@ -0,0 +1,121 @@
+---
+title: "Import des données"
+output: rmarkdown::html_vignette
+vignette: >
+ %\VignetteIndexEntry{import-des-donnees}
+ %\VignetteEngine{knitr::rmarkdown}
+ %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+ collapse = TRUE,
+ comment = "#>"
+)
+```
+
+```{r setup}
+library(data.nitrates)
+```
+
+<!-- WARNING - This vignette is generated by {fusen} from dev/flat_import_data.Rmd: do not edit by hand -->
+
+# Présentation
+
+> Cette page contient la logique métier concernant l'import des données
+ARS et Hub'eau dans le cadre du projet Nitrates
+
+
+# Connexion à la base de données PostgreSQL
+
+# Import des données de l'ARS
+
+```{r}
+data_ars_2022 <- collectr::import_xlsx(
+ filepath = "T:\\datalab\\SRNP_DEMA_SI_EAU\\NITRATES\\DONNEES_CLIENT\\SOURCES\\ARS\\2023_06\\Nitrates 2022 pour DREAL EPNT4 2023-05-30.xlsx",
+ sheet = 1,
+ row = 2)
+```
+
+## Première approche : non concluante
+
+### Vérification de la correspondande de la structure du dataframe avec celle de la table
+
+### Adaptation de la structure
+
+### Insertion des données du dataframe dans la table en base
+
+La fonction insert_into_table() doit être corrigée.
+
+
+## Deuxième approche : concluante
+
+### Création d'une table pour le nouveau millésime
+
+```{r create-nitrate_data_ars, eval = FALSE}
+poster_data(data = data_ars_2022,
+ table = "nitrate_data_ars_2022",
+ schema = "qualite_cours_d_eau",
+ db = "si_eau",
+ overwrite = TRUE)
+
+```
+
+### Modification du type des champs si besoin
+
+```{r modify_column_type, eval = FALSE}
+# Appeler la fonction pour modifier le type de colonne
+collectr::modify_column_type(connexion,
+ schema = "qualite_cours_d_eau",
+ table_name = "nitrate_data_ars_2022",
+ column_name = "plv_date ",
+ column_type = "date")
+```
+
+### Insertion des données du nouveau millésime en base dans la table globale
+
+```{r import_and_merge_tables, eval = FALSE}
+import_and_merge_tables(connexion,
+ source_table = "nitrate_data_ars_2022",
+ source_schema = "qualite_cours_d_eau",
+ target_table = "nitrate_data_analyse_ars_test",
+ target_schema = "qualite_cours_d_eau")
+
+```
+
+# Import des données Hub'eau ESU
+
+```{r create-nitrate_analyse_esu_2020, eval = FALSE}
+nitrate_analyse_esu_2020 <- get_json_data(code_parametre = "1340",
+ code_region = "52",
+ date_debut_prelevement = "2020-01-01",
+ date_fin_prelevement = "2020-12-31",
+ size = "5000")
+```
+
+```{r create-nitrate_analyse_esu_2021, eval = FALSE}
+nitrate_analyse_esu_2021 <- get_json_data(code_parametre = "1340",
+ code_region = "52",
+ date_debut_prelevement = "2021-01-01",
+ date_fin_prelevement = "2021-12-31",
+ size = "5000")
+```
+
+```{r create-nitrate_analyse_esu_2022, eval = FALSE}
+nitrate_analyse_esu_2022 <- get_json_data(code_parametre = "1340",
+ code_region = "52",
+ date_debut_prelevement = "2022-01-01",
+ date_fin_prelevement = "2022-12-31",
+ size = "5000")
+```
+
+# Inflate your package
+
+You're one inflate from paper to box.
+Build your package from this very Rmd using `fusen::inflate()`
+
+- Verify your `"DESCRIPTION"` file has been updated
+- Verify your function is in `"R/"` directory
+- Verify your test is in `"tests/testthat/"` directory
+- Verify this Rmd appears in `"vignettes/"` directory
+