Commit 7fe5f4c4 authored by cedricbriandgithub's avatar cedricbriandgithub
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On redécasse tout

parent cd05ffd7
^.*\.Rproj$
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dev_history.R
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$run_dev.*
^LICENSE\.md$
^README\.Rmd$
^CODE_OF_CONDUCT\.md$
^.*\.Rproj$
^\.Rproj\.user$
^data-raw$
dev_history.R
^dev$
$run_dev.*
^LICENSE\.md$
^README\.Rmd$
^CODE_OF_CONDUCT\.md$
/credentials-config.json
/data-sources.json
/credentials-config.json
/data-sources.json
.Rproj.user
.Rhistory
.RData
.Ruserdata
stacoshiny.Rproj
/.project
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.Rproj.user
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.RData
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stacoshiny.Rproj
/.project
.settings
# 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, 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 [INSERT CONTACT
METHOD]. 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 2.0,
available at https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
Community Impact Guidelines were inspired by [Mozilla's code of conduct
enforcement ladder](https://github.com/mozilla/diversity).
[homepage]: https://www.contributor-covenant.org
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.
# 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, 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 [INSERT CONTACT
METHOD]. 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 2.0,
available at https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
Community Impact Guidelines were inspired by [Mozilla's code of conduct
enforcement ladder](https://github.com/mozilla/diversity).
[homepage]: https://www.contributor-covenant.org
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.
YEAR: 2021
COPYRIGHT HOLDER: Golem User
YEAR: 2021
COPYRIGHT HOLDER: Golem User
# MIT License
Copyright (c) 2021 Golem User
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.
# MIT License
Copyright (c) 2021 Golem User
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.
# stacoshiny 0.0.0.9000
* Added a `NEWS.md` file to track changes to the package.
# stacoshiny 0.0.0.9000
* Added a `NEWS.md` file to track changes to the package.
......@@ -12,8 +12,8 @@ app_server <- function( input, output, session ) {
DD$login_button <- mod_header_server("header_ui_1") # login_button reactive variable récupérée depuis le module
mod_left_side_bar_server("left_side_bar_ui_1",DD)
DD$button_ref_dc <- mod_ref_dc_server("ref_dc_ui_sidebar",DD)
#mod_ref_taxon_server("ref_taxon_mod_migr_multi", DD)
mod_migr_multi_server("migr_multi_ui_1",DD)
mod_ref_taxon_server("ref_taxon_mod_migr_multi", DD)
mod_annuel_server("annuel_ui_1")
mod_interannuel_server("interannuel_ui_1")
mod_espece_server("espece_ui_1")
......
#' The application User-Interface
#'
#' @param request Internal parameter for `{shiny}`.
#' DO NOT REMOVE.
#' @import shiny
#' @noRd
#' @importFrom shinydashboardPlus dashboardPage
app_ui <- function(request) {
tagList(
# Leave this function for adding external resources
golem_add_external_resources(),
# Your application UI logic
dashboardPage(
header = mod_header_ui("header_ui_1"),
sidebar = mod_left_side_bar_ui("left_side_bar_ui_1"),
body = mod_main_page_ui("main_page_ui_1")
)
)
}
#' Add external Resources to the Application
#'
#' This function is internally used to add external
#' resources inside the Shiny application.
#'
#' @import shiny
#' @importFrom golem add_resource_path activate_js favicon bundle_resources
#' @noRd
golem_add_external_resources <- function(){
add_resource_path(
'www', app_sys('app/www')
)
tags$head(
favicon(ext = 'png'),
bundle_resources(
path = app_sys('app/www'),
app_title = 'stacoshiny'
)
# Add here other external resources
# for example, you can add shinyalert::useShinyalert()
)
}
#' The application User-Interface
#'
#' @param request Internal parameter for `{shiny}`.
#' DO NOT REMOVE.
#' @import shiny
#' @noRd
#' @importFrom shinydashboardPlus dashboardPage
app_ui <- function(request) {
tagList(
# Leave this function for adding external resources
golem_add_external_resources(),
# Your application UI logic
dashboardPage(
header = mod_header_ui("header_ui_1"),
sidebar = mod_left_side_bar_ui("left_side_bar_ui_1"),
body = mod_main_page_ui("main_page_ui_1")
)
)
}
#' Add external Resources to the Application
#'
#' This function is internally used to add external
#' resources inside the Shiny application.
#'
#' @import shiny
#' @importFrom golem add_resource_path activate_js favicon bundle_resources
#' @noRd
golem_add_external_resources <- function(){
add_resource_path(
'www', app_sys('app/www')
)
tags$head(
favicon(ext = 'png'),
bundle_resources(
path = app_sys('app/www'),
app_title = 'stacoshiny'
)
# Add here other external resources
# for example, you can add shinyalert::useShinyalert()
)
}
#' Inverted versions of in, is.null and is.na
#'
#' @noRd
#'
#' @examples
#' 1 %not_in% 1:10
#' not_null(NULL)
#' @importFrom shiny reactiveValues reactiveValuesToList
`%not_in%` <- Negate(`%in%`)
not_null <- Negate(is.null)
not_na <- Negate(is.na)
#' Removes the null from a vector
#'
#' @noRd
#'
#' @example
#' drop_nulls(list(1, NULL, 2))
drop_nulls <- function(x){
x[!sapply(x, is.null)]
}
#' If x is `NULL`, return y, otherwise return x
#'
#' @param x,y Two elements to test, one potentially `NULL`
#'
#' @noRd
#'
#' @examples
#' NULL %||% 1
"%||%" <- function(x, y){
if (is.null(x)) {
y
} else {
x
}
}
#' If x is `NA`, return y, otherwise return x
#'
#' @param x,y Two elements to test, one potentially `NA`
#'
#' @noRd
#'
#' @examples
#' NA %||% 1
"%|NA|%" <- function(x, y){
if (is.na(x)) {
y
} else {
x
}
}
#' Typing reactiveValues is too long
#'
#' @inheritParams reactiveValues
#' @inheritParams reactiveValuesToList
#'
#' @noRd
rv <- reactiveValues
rvtl <- reactiveValuesToList
#' Inverted versions of in, is.null and is.na
#'
#' @noRd
#'
#' @examples
#' 1 %not_in% 1:10
#' not_null(NULL)
#' @importFrom shiny reactiveValues reactiveValuesToList
`%not_in%` <- Negate(`%in%`)
not_null <- Negate(is.null)
not_na <- Negate(is.na)
#' Removes the null from a vector
#'
#' @noRd
#'
#' @example
#' drop_nulls(list(1, NULL, 2))
drop_nulls <- function(x){
x[!sapply(x, is.null)]
}
#' If x is `NULL`, return y, otherwise return x
#'
#' @param x,y Two elements to test, one potentially `NULL`
#'
#' @noRd
#'
#' @examples
#' NULL %||% 1
"%||%" <- function(x, y){
if (is.null(x)) {
y
} else {
x
}
}
#' If x is `NA`, return y, otherwise return x
#'
#' @param x,y Two elements to test, one potentially `NA`
#'
#' @noRd
#'
#' @examples
#' NA %||% 1
"%|NA|%" <- function(x, y){
if (is.na(x)) {
y
} else {
x
}
}
#' Typing reactiveValues is too long
#'
#' @inheritParams reactiveValues
#' @inheritParams reactiveValuesToList
#'
#' @noRd
rv <- reactiveValues
rvtl <- reactiveValuesToList
#' Turn an R list into an HTML list
#'
#' @param list An R list
#' @param class a class for the list
#'
#' @return an HTML list
#' @noRd
#'
#' @examples
#' list_to_li(c("a","b"))
#'
#' @importFrom shiny tags tagAppendAttributes tagList
list_to_li <- function(list, class = NULL){
if (is.null(class)){
tagList(
lapply(
list,
tags$li
)
)
} else {
res <- lapply(
list,
tags$li
)
res <- lapply(
res,
function(x) {
tagAppendAttributes(
x,
class = class
)
}
)
tagList(res)
}
}
#' Turn an R list into corresponding HTML paragraph tags
#'
#' @param list an R list
#' @param class a class for the paragraph tags
#'
#' @return An HTML tag
#' @noRd
#'
#' @examples
#' list_to_p(c("This is the first paragraph", "this is the second paragraph"))
#'
#' @importFrom shiny tags tagAppendAttributes tagList