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6
.Rbuildignore
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6
.Rbuildignore
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^renv$
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||||||
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^renv\.lock$
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||||||
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^webResearch\.Rproj$
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||||||
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^\.Rproj\.user$
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||||||
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^LICENSE\.md$
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||||||
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^dev$
|
||||||
1
.Rprofile
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.Rprofile
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||||||
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source("renv/activate.R")
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7
.gitignore
vendored
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.gitignore
vendored
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.Rproj.user
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||||||
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dev/
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||||||
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.Rhistory
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||||||
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.Rdata
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||||||
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.httr-oauth
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||||||
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.DS_Store
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||||||
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.quarto
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26
DESCRIPTION
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DESCRIPTION
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||||||
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Package: webResearch
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Title: Browser Based Data Analysis
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||||||
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Version: 0.0.0.9000
|
||||||
|
Authors@R:
|
||||||
|
person("Andreas Gammelgaard", "Damsbo", , "agdamsbo@clin.au.dk", role = c("aut", "cre"),
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||||||
|
comment = c(ORCID = "0000-0002-7559-1154"))
|
||||||
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Description: Browser based basic data analysis and research output.
|
||||||
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License: AGPL (>= 3)
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||||||
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Encoding: UTF-8
|
||||||
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Roxygen: list(markdown = TRUE)
|
||||||
|
RoxygenNote: 7.3.2
|
||||||
|
Imports:
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||||||
|
assertthat,
|
||||||
|
dplyr,
|
||||||
|
glue,
|
||||||
|
gt,
|
||||||
|
gtsummary,
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||||||
|
haven,
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||||||
|
here,
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||||||
|
openxlsx2,
|
||||||
|
quarto,
|
||||||
|
readODS,
|
||||||
|
readr
|
||||||
|
Suggests:
|
||||||
|
MASS,
|
||||||
|
styler
|
||||||
659
LICENSE.md
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659
LICENSE.md
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@ -0,0 +1,659 @@
|
||||||
|
GNU Affero General Public License
|
||||||
|
=================================
|
||||||
|
|
||||||
|
_Version 3, 19 November 2007_
|
||||||
|
_Copyright (C) 2007 Free Software Foundation, Inc. <<https://fsf.org/>>_
|
||||||
|
|
||||||
|
Everyone is permitted to copy and distribute verbatim copies of this
|
||||||
|
license document, but changing it is not allowed.
|
||||||
|
|
||||||
|
## Preamble
|
||||||
|
|
||||||
|
The GNU Affero General Public License is a free, copyleft license for
|
||||||
|
software and other kinds of works, specifically designed to ensure
|
||||||
|
cooperation with the community in the case of network server software.
|
||||||
|
|
||||||
|
The licenses for most software and other practical works are designed
|
||||||
|
to take away your freedom to share and change the works. By contrast,
|
||||||
|
our General Public Licenses are intended to guarantee your freedom to
|
||||||
|
share and change all versions of a program--to make sure it remains
|
||||||
|
free software for all its users.
|
||||||
|
|
||||||
|
When we speak of free software, we are referring to freedom, not
|
||||||
|
price. Our General Public Licenses are designed to make sure that you
|
||||||
|
have the freedom to distribute copies of free software (and charge for
|
||||||
|
them if you wish), that you receive source code or can get it if you
|
||||||
|
want it, that you can change the software or use pieces of it in new
|
||||||
|
free programs, and that you know you can do these things.
|
||||||
|
|
||||||
|
Developers that use our General Public Licenses protect your rights
|
||||||
|
with two steps: (1) assert copyright on the software, and (2) offer
|
||||||
|
you this License which gives you legal permission to copy, distribute
|
||||||
|
and/or modify the software.
|
||||||
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|
||||||
|
A secondary benefit of defending all users' freedom is that
|
||||||
|
improvements made in alternate versions of the program, if they
|
||||||
|
receive widespread use, become available for other developers to
|
||||||
|
incorporate. Many developers of free software are heartened and
|
||||||
|
encouraged by the resulting cooperation. However, in the case of
|
||||||
|
software used on network servers, this result may fail to come about.
|
||||||
|
The GNU General Public License permits making a modified version and
|
||||||
|
letting the public access it on a server without ever releasing its
|
||||||
|
source code to the public.
|
||||||
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|
||||||
|
The GNU Affero General Public License is designed specifically to
|
||||||
|
ensure that, in such cases, the modified source code becomes available
|
||||||
|
to the community. It requires the operator of a network server to
|
||||||
|
provide the source code of the modified version running there to the
|
||||||
|
users of that server. Therefore, public use of a modified version, on
|
||||||
|
a publicly accessible server, gives the public access to the source
|
||||||
|
code of the modified version.
|
||||||
|
|
||||||
|
An older license, called the Affero General Public License and
|
||||||
|
published by Affero, was designed to accomplish similar goals. This is
|
||||||
|
a different license, not a version of the Affero GPL, but Affero has
|
||||||
|
released a new version of the Affero GPL which permits relicensing
|
||||||
|
under this license.
|
||||||
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|
||||||
|
The precise terms and conditions for copying, distribution and
|
||||||
|
modification follow.
|
||||||
|
|
||||||
|
## TERMS AND CONDITIONS
|
||||||
|
|
||||||
|
### 0. Definitions.
|
||||||
|
|
||||||
|
"This License" refers to version 3 of the GNU Affero General Public
|
||||||
|
License.
|
||||||
|
|
||||||
|
"Copyright" also means copyright-like laws that apply to other kinds
|
||||||
|
of works, such as semiconductor masks.
|
||||||
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|
||||||
|
"The Program" refers to any copyrightable work licensed under this
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License. Each licensee is addressed as "you". "Licensees" and
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"recipients" may be individuals or organizations.
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To "modify" a work means to copy from or adapt all or part of the work
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an exact copy. The resulting work is called a "modified version" of
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the earlier work or a work "based on" the earlier work.
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A "covered work" means either the unmodified Program or a work based
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on the Program.
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|
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To "propagate" a work means to do anything with it that, without
|
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permission, would make you directly or secondarily liable for
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||||||
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infringement under applicable copyright law, except executing it on a
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computer or modifying a private copy. Propagation includes copying,
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distribution (with or without modification), making available to the
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public, and in some countries other activities as well.
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To "convey" a work means any kind of propagation that enables other
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parties to make or receive copies. Mere interaction with a user
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through a computer network, with no transfer of a copy, is not
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conveying.
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An interactive user interface displays "Appropriate Legal Notices" to
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the extent that it includes a convenient and prominently visible
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the interface presents a list of user commands or options, such as a
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### 1. Source Code.
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|
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The "source code" for a work means the preferred form of the work for
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making modifications to it. "Object code" means any non-source form of
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a work.
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A "Standard Interface" means an interface that either is an official
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standard defined by a recognized standards body, or, in the case of
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interfaces specified for a particular programming language, one that
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is widely used among developers working in that language.
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The "System Libraries" of an executable work include anything, other
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than the work as a whole, that (a) is included in the normal form of
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Major Component, or to implement a Standard Interface for which an
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implementation is available to the public in source code form. A
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||||||
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"Major Component", in this context, means a major essential component
|
||||||
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(kernel, window system, and so on) of the specific operating system
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(if any) on which the executable work runs, or a compiler used to
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produce the work, or an object code interpreter used to run it.
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The "Corresponding Source" for a work in object code form means all
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the source code needed to generate, install, and (for an executable
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work) run the object code and to modify the work, including scripts to
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control those activities. However, it does not include the work's
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System Libraries, or general-purpose tools or generally available free
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programs which are used unmodified in performing those activities but
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which are not part of the work. For example, Corresponding Source
|
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includes interface definition files associated with source files for
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the work, and the source code for shared libraries and dynamically
|
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linked subprograms that the work is specifically designed to require,
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such as by intimate data communication or control flow between those
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subprograms and other parts of the work.
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|
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The Corresponding Source need not include anything that users can
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regenerate automatically from other parts of the Corresponding Source.
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|
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|
The Corresponding Source for a work in source code form is that same
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||||||
|
work.
|
||||||
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|
||||||
|
### 2. Basic Permissions.
|
||||||
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|
||||||
|
All rights granted under this License are granted for the term of
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||||||
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copyright on the Program, and are irrevocable provided the stated
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conditions are met. This License explicitly affirms your unlimited
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permission to run the unmodified Program. The output from running a
|
||||||
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covered work is covered by this License only if the output, given its
|
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content, constitutes a covered work. This License acknowledges your
|
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|
rights of fair use or other equivalent, as provided by copyright law.
|
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|
||||||
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You may make, run and propagate covered works that you do not convey,
|
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without conditions so long as your license otherwise remains in force.
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You may convey covered works to others for the sole purpose of having
|
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them make modifications exclusively for you, or provide you with
|
||||||
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facilities for running those works, provided that you comply with the
|
||||||
|
terms of this License in conveying all material for which you do not
|
||||||
|
control copyright. Those thus making or running the covered works for
|
||||||
|
you must do so exclusively on your behalf, under your direction and
|
||||||
|
control, on terms that prohibit them from making any copies of your
|
||||||
|
copyrighted material outside their relationship with you.
|
||||||
|
|
||||||
|
Conveying under any other circumstances is permitted solely under the
|
||||||
|
conditions stated below. Sublicensing is not allowed; section 10 makes
|
||||||
|
it unnecessary.
|
||||||
|
|
||||||
|
### 3. Protecting Users' Legal Rights From Anti-Circumvention Law.
|
||||||
|
|
||||||
|
No covered work shall be deemed part of an effective technological
|
||||||
|
measure under any applicable law fulfilling obligations under article
|
||||||
|
11 of the WIPO copyright treaty adopted on 20 December 1996, or
|
||||||
|
similar laws prohibiting or restricting circumvention of such
|
||||||
|
measures.
|
||||||
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|
||||||
|
When you convey a covered work, you waive any legal power to forbid
|
||||||
|
circumvention of technological measures to the extent such
|
||||||
|
circumvention is effected by exercising rights under this License with
|
||||||
|
respect to the covered work, and you disclaim any intention to limit
|
||||||
|
operation or modification of the work as a means of enforcing, against
|
||||||
|
the work's users, your or third parties' legal rights to forbid
|
||||||
|
circumvention of technological measures.
|
||||||
|
|
||||||
|
### 4. Conveying Verbatim Copies.
|
||||||
|
|
||||||
|
You may convey verbatim copies of the Program's source code as you
|
||||||
|
receive it, in any medium, provided that you conspicuously and
|
||||||
|
appropriately publish on each copy an appropriate copyright notice;
|
||||||
|
keep intact all notices stating that this License and any
|
||||||
|
non-permissive terms added in accord with section 7 apply to the code;
|
||||||
|
keep intact all notices of the absence of any warranty; and give all
|
||||||
|
recipients a copy of this License along with the Program.
|
||||||
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|
||||||
|
You may charge any price or no price for each copy that you convey,
|
||||||
|
and you may offer support or warranty protection for a fee.
|
||||||
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|
||||||
|
### 5. Conveying Modified Source Versions.
|
||||||
|
|
||||||
|
You may convey a work based on the Program, or the modifications to
|
||||||
|
produce it from the Program, in the form of source code under the
|
||||||
|
terms of section 4, provided that you also meet all of these
|
||||||
|
conditions:
|
||||||
|
|
||||||
|
- a) The work must carry prominent notices stating that you modified
|
||||||
|
it, and giving a relevant date.
|
||||||
|
- b) The work must carry prominent notices stating that it is
|
||||||
|
released under this License and any conditions added under
|
||||||
|
section 7. This requirement modifies the requirement in section 4
|
||||||
|
to "keep intact all notices".
|
||||||
|
- c) You must license the entire work, as a whole, under this
|
||||||
|
License to anyone who comes into possession of a copy. This
|
||||||
|
License will therefore apply, along with any applicable section 7
|
||||||
|
additional terms, to the whole of the work, and all its parts,
|
||||||
|
regardless of how they are packaged. This License gives no
|
||||||
|
permission to license the work in any other way, but it does not
|
||||||
|
invalidate such permission if you have separately received it.
|
||||||
|
- d) If the work has interactive user interfaces, each must display
|
||||||
|
Appropriate Legal Notices; however, if the Program has interactive
|
||||||
|
interfaces that do not display Appropriate Legal Notices, your
|
||||||
|
work need not make them do so.
|
||||||
|
|
||||||
|
A compilation of a covered work with other separate and independent
|
||||||
|
works, which are not by their nature extensions of the covered work,
|
||||||
|
and which are not combined with it such as to form a larger program,
|
||||||
|
in or on a volume of a storage or distribution medium, is called an
|
||||||
|
"aggregate" if the compilation and its resulting copyright are not
|
||||||
|
used to limit the access or legal rights of the compilation's users
|
||||||
|
beyond what the individual works permit. Inclusion of a covered work
|
||||||
|
in an aggregate does not cause this License to apply to the other
|
||||||
|
parts of the aggregate.
|
||||||
|
|
||||||
|
### 6. Conveying Non-Source Forms.
|
||||||
|
|
||||||
|
You may convey a covered work in object code form under the terms of
|
||||||
|
sections 4 and 5, provided that you also convey the machine-readable
|
||||||
|
Corresponding Source under the terms of this License, in one of these
|
||||||
|
ways:
|
||||||
|
|
||||||
|
- a) Convey the object code in, or embodied in, a physical product
|
||||||
|
(including a physical distribution medium), accompanied by the
|
||||||
|
Corresponding Source fixed on a durable physical medium
|
||||||
|
customarily used for software interchange.
|
||||||
|
- b) Convey the object code in, or embodied in, a physical product
|
||||||
|
(including a physical distribution medium), accompanied by a
|
||||||
|
written offer, valid for at least three years and valid for as
|
||||||
|
long as you offer spare parts or customer support for that product
|
||||||
|
model, to give anyone who possesses the object code either (1) a
|
||||||
|
copy of the Corresponding Source for all the software in the
|
||||||
|
product that is covered by this License, on a durable physical
|
||||||
|
medium customarily used for software interchange, for a price no
|
||||||
|
more than your reasonable cost of physically performing this
|
||||||
|
conveying of source, or (2) access to copy the Corresponding
|
||||||
|
Source from a network server at no charge.
|
||||||
|
- c) Convey individual copies of the object code with a copy of the
|
||||||
|
written offer to provide the Corresponding Source. This
|
||||||
|
alternative is allowed only occasionally and noncommercially, and
|
||||||
|
only if you received the object code with such an offer, in accord
|
||||||
|
with subsection 6b.
|
||||||
|
- d) Convey the object code by offering access from a designated
|
||||||
|
place (gratis or for a charge), and offer equivalent access to the
|
||||||
|
Corresponding Source in the same way through the same place at no
|
||||||
|
further charge. You need not require recipients to copy the
|
||||||
|
Corresponding Source along with the object code. If the place to
|
||||||
|
copy the object code is a network server, the Corresponding Source
|
||||||
|
may be on a different server (operated by you or a third party)
|
||||||
|
that supports equivalent copying facilities, provided you maintain
|
||||||
|
clear directions next to the object code saying where to find the
|
||||||
|
Corresponding Source. Regardless of what server hosts the
|
||||||
|
Corresponding Source, you remain obligated to ensure that it is
|
||||||
|
available for as long as needed to satisfy these requirements.
|
||||||
|
- e) Convey the object code using peer-to-peer transmission,
|
||||||
|
provided you inform other peers where the object code and
|
||||||
|
Corresponding Source of the work are being offered to the general
|
||||||
|
public at no charge under subsection 6d.
|
||||||
|
|
||||||
|
A separable portion of the object code, whose source code is excluded
|
||||||
|
from the Corresponding Source as a System Library, need not be
|
||||||
|
included in conveying the object code work.
|
||||||
|
|
||||||
|
A "User Product" is either (1) a "consumer product", which means any
|
||||||
|
tangible personal property which is normally used for personal,
|
||||||
|
family, or household purposes, or (2) anything designed or sold for
|
||||||
|
incorporation into a dwelling. In determining whether a product is a
|
||||||
|
consumer product, doubtful cases shall be resolved in favor of
|
||||||
|
coverage. For a particular product received by a particular user,
|
||||||
|
"normally used" refers to a typical or common use of that class of
|
||||||
|
product, regardless of the status of the particular user or of the way
|
||||||
|
in which the particular user actually uses, or expects or is expected
|
||||||
|
to use, the product. A product is a consumer product regardless of
|
||||||
|
whether the product has substantial commercial, industrial or
|
||||||
|
non-consumer uses, unless such uses represent the only significant
|
||||||
|
mode of use of the product.
|
||||||
|
|
||||||
|
"Installation Information" for a User Product means any methods,
|
||||||
|
procedures, authorization keys, or other information required to
|
||||||
|
install and execute modified versions of a covered work in that User
|
||||||
|
Product from a modified version of its Corresponding Source. The
|
||||||
|
information must suffice to ensure that the continued functioning of
|
||||||
|
the modified object code is in no case prevented or interfered with
|
||||||
|
solely because modification has been made.
|
||||||
|
|
||||||
|
If you convey an object code work under this section in, or with, or
|
||||||
|
specifically for use in, a User Product, and the conveying occurs as
|
||||||
|
part of a transaction in which the right of possession and use of the
|
||||||
|
User Product is transferred to the recipient in perpetuity or for a
|
||||||
|
fixed term (regardless of how the transaction is characterized), the
|
||||||
|
Corresponding Source conveyed under this section must be accompanied
|
||||||
|
by the Installation Information. But this requirement does not apply
|
||||||
|
if neither you nor any third party retains the ability to install
|
||||||
|
modified object code on the User Product (for example, the work has
|
||||||
|
been installed in ROM).
|
||||||
|
|
||||||
|
The requirement to provide Installation Information does not include a
|
||||||
|
requirement to continue to provide support service, warranty, or
|
||||||
|
updates for a work that has been modified or installed by the
|
||||||
|
recipient, or for the User Product in which it has been modified or
|
||||||
|
installed. Access to a network may be denied when the modification
|
||||||
|
itself materially and adversely affects the operation of the network
|
||||||
|
or violates the rules and protocols for communication across the
|
||||||
|
network.
|
||||||
|
|
||||||
|
Corresponding Source conveyed, and Installation Information provided,
|
||||||
|
in accord with this section must be in a format that is publicly
|
||||||
|
documented (and with an implementation available to the public in
|
||||||
|
source code form), and must require no special password or key for
|
||||||
|
unpacking, reading or copying.
|
||||||
|
|
||||||
|
### 7. Additional Terms.
|
||||||
|
|
||||||
|
"Additional permissions" are terms that supplement the terms of this
|
||||||
|
License by making exceptions from one or more of its conditions.
|
||||||
|
Additional permissions that are applicable to the entire Program shall
|
||||||
|
be treated as though they were included in this License, to the extent
|
||||||
|
that they are valid under applicable law. If additional permissions
|
||||||
|
apply only to part of the Program, that part may be used separately
|
||||||
|
under those permissions, but the entire Program remains governed by
|
||||||
|
this License without regard to the additional permissions.
|
||||||
|
|
||||||
|
When you convey a copy of a covered work, you may at your option
|
||||||
|
remove any additional permissions from that copy, or from any part of
|
||||||
|
it. (Additional permissions may be written to require their own
|
||||||
|
removal in certain cases when you modify the work.) You may place
|
||||||
|
additional permissions on material, added by you to a covered work,
|
||||||
|
for which you have or can give appropriate copyright permission.
|
||||||
|
|
||||||
|
Notwithstanding any other provision of this License, for material you
|
||||||
|
add to a covered work, you may (if authorized by the copyright holders
|
||||||
|
of that material) supplement the terms of this License with terms:
|
||||||
|
|
||||||
|
- a) Disclaiming warranty or limiting liability differently from the
|
||||||
|
terms of sections 15 and 16 of this License; or
|
||||||
|
- b) Requiring preservation of specified reasonable legal notices or
|
||||||
|
author attributions in that material or in the Appropriate Legal
|
||||||
|
Notices displayed by works containing it; or
|
||||||
|
- c) Prohibiting misrepresentation of the origin of that material,
|
||||||
|
or requiring that modified versions of such material be marked in
|
||||||
|
reasonable ways as different from the original version; or
|
||||||
|
- d) Limiting the use for publicity purposes of names of licensors
|
||||||
|
or authors of the material; or
|
||||||
|
- e) Declining to grant rights under trademark law for use of some
|
||||||
|
trade names, trademarks, or service marks; or
|
||||||
|
- f) Requiring indemnification of licensors and authors of that
|
||||||
|
material by anyone who conveys the material (or modified versions
|
||||||
|
of it) with contractual assumptions of liability to the recipient,
|
||||||
|
for any liability that these contractual assumptions directly
|
||||||
|
impose on those licensors and authors.
|
||||||
|
|
||||||
|
All other non-permissive additional terms are considered "further
|
||||||
|
restrictions" within the meaning of section 10. If the Program as you
|
||||||
|
received it, or any part of it, contains a notice stating that it is
|
||||||
|
governed by this License along with a term that is a further
|
||||||
|
restriction, you may remove that term. If a license document contains
|
||||||
|
a further restriction but permits relicensing or conveying under this
|
||||||
|
License, you may add to a covered work material governed by the terms
|
||||||
|
of that license document, provided that the further restriction does
|
||||||
|
not survive such relicensing or conveying.
|
||||||
|
|
||||||
|
If you add terms to a covered work in accord with this section, you
|
||||||
|
must place, in the relevant source files, a statement of the
|
||||||
|
additional terms that apply to those files, or a notice indicating
|
||||||
|
where to find the applicable terms.
|
||||||
|
|
||||||
|
Additional terms, permissive or non-permissive, may be stated in the
|
||||||
|
form of a separately written license, or stated as exceptions; the
|
||||||
|
above requirements apply either way.
|
||||||
|
|
||||||
|
### 8. Termination.
|
||||||
|
|
||||||
|
You may not propagate or modify a covered work except as expressly
|
||||||
|
provided under this License. Any attempt otherwise to propagate or
|
||||||
|
modify it is void, and will automatically terminate your rights under
|
||||||
|
this License (including any patent licenses granted under the third
|
||||||
|
paragraph of section 11).
|
||||||
|
|
||||||
|
However, if you cease all violation of this License, then your license
|
||||||
|
from a particular copyright holder is reinstated (a) provisionally,
|
||||||
|
unless and until the copyright holder explicitly and finally
|
||||||
|
terminates your license, and (b) permanently, if the copyright holder
|
||||||
|
fails to notify you of the violation by some reasonable means prior to
|
||||||
|
60 days after the cessation.
|
||||||
|
|
||||||
|
Moreover, your license from a particular copyright holder is
|
||||||
|
reinstated permanently if the copyright holder notifies you of the
|
||||||
|
violation by some reasonable means, this is the first time you have
|
||||||
|
received notice of violation of this License (for any work) from that
|
||||||
|
copyright holder, and you cure the violation prior to 30 days after
|
||||||
|
your receipt of the notice.
|
||||||
|
|
||||||
|
Termination of your rights under this section does not terminate the
|
||||||
|
licenses of parties who have received copies or rights from you under
|
||||||
|
this License. If your rights have been terminated and not permanently
|
||||||
|
reinstated, you do not qualify to receive new licenses for the same
|
||||||
|
material under section 10.
|
||||||
|
|
||||||
|
### 9. Acceptance Not Required for Having Copies.
|
||||||
|
|
||||||
|
You are not required to accept this License in order to receive or run
|
||||||
|
a copy of the Program. Ancillary propagation of a covered work
|
||||||
|
occurring solely as a consequence of using peer-to-peer transmission
|
||||||
|
to receive a copy likewise does not require acceptance. However,
|
||||||
|
nothing other than this License grants you permission to propagate or
|
||||||
|
modify any covered work. These actions infringe copyright if you do
|
||||||
|
not accept this License. Therefore, by modifying or propagating a
|
||||||
|
covered work, you indicate your acceptance of this License to do so.
|
||||||
|
|
||||||
|
### 10. Automatic Licensing of Downstream Recipients.
|
||||||
|
|
||||||
|
Each time you convey a covered work, the recipient automatically
|
||||||
|
receives a license from the original licensors, to run, modify and
|
||||||
|
propagate that work, subject to this License. You are not responsible
|
||||||
|
for enforcing compliance by third parties with this License.
|
||||||
|
|
||||||
|
An "entity transaction" is a transaction transferring control of an
|
||||||
|
organization, or substantially all assets of one, or subdividing an
|
||||||
|
organization, or merging organizations. If propagation of a covered
|
||||||
|
work results from an entity transaction, each party to that
|
||||||
|
transaction who receives a copy of the work also receives whatever
|
||||||
|
licenses to the work the party's predecessor in interest had or could
|
||||||
|
give under the previous paragraph, plus a right to possession of the
|
||||||
|
Corresponding Source of the work from the predecessor in interest, if
|
||||||
|
the predecessor has it or can get it with reasonable efforts.
|
||||||
|
|
||||||
|
You may not impose any further restrictions on the exercise of the
|
||||||
|
rights granted or affirmed under this License. For example, you may
|
||||||
|
not impose a license fee, royalty, or other charge for exercise of
|
||||||
|
rights granted under this License, and you may not initiate litigation
|
||||||
|
(including a cross-claim or counterclaim in a lawsuit) alleging that
|
||||||
|
any patent claim is infringed by making, using, selling, offering for
|
||||||
|
sale, or importing the Program or any portion of it.
|
||||||
|
|
||||||
|
### 11. Patents.
|
||||||
|
|
||||||
|
A "contributor" is a copyright holder who authorizes use under this
|
||||||
|
License of the Program or a work on which the Program is based. The
|
||||||
|
work thus licensed is called the contributor's "contributor version".
|
||||||
|
|
||||||
|
A contributor's "essential patent claims" are all patent claims owned
|
||||||
|
or controlled by the contributor, whether already acquired or
|
||||||
|
hereafter acquired, that would be infringed by some manner, permitted
|
||||||
|
by this License, of making, using, or selling its contributor version,
|
||||||
|
but do not include claims that would be infringed only as a
|
||||||
|
consequence of further modification of the contributor version. For
|
||||||
|
purposes of this definition, "control" includes the right to grant
|
||||||
|
patent sublicenses in a manner consistent with the requirements of
|
||||||
|
this License.
|
||||||
|
|
||||||
|
Each contributor grants you a non-exclusive, worldwide, royalty-free
|
||||||
|
patent license under the contributor's essential patent claims, to
|
||||||
|
make, use, sell, offer for sale, import and otherwise run, modify and
|
||||||
|
propagate the contents of its contributor version.
|
||||||
|
|
||||||
|
In the following three paragraphs, a "patent license" is any express
|
||||||
|
agreement or commitment, however denominated, not to enforce a patent
|
||||||
|
(such as an express permission to practice a patent or covenant not to
|
||||||
|
sue for patent infringement). To "grant" such a patent license to a
|
||||||
|
party means to make such an agreement or commitment not to enforce a
|
||||||
|
patent against the party.
|
||||||
|
|
||||||
|
If you convey a covered work, knowingly relying on a patent license,
|
||||||
|
and the Corresponding Source of the work is not available for anyone
|
||||||
|
to copy, free of charge and under the terms of this License, through a
|
||||||
|
publicly available network server or other readily accessible means,
|
||||||
|
then you must either (1) cause the Corresponding Source to be so
|
||||||
|
available, or (2) arrange to deprive yourself of the benefit of the
|
||||||
|
patent license for this particular work, or (3) arrange, in a manner
|
||||||
|
consistent with the requirements of this License, to extend the patent
|
||||||
|
license to downstream recipients. "Knowingly relying" means you have
|
||||||
|
actual knowledge that, but for the patent license, your conveying the
|
||||||
|
covered work in a country, or your recipient's use of the covered work
|
||||||
|
in a country, would infringe one or more identifiable patents in that
|
||||||
|
country that you have reason to believe are valid.
|
||||||
|
|
||||||
|
If, pursuant to or in connection with a single transaction or
|
||||||
|
arrangement, you convey, or propagate by procuring conveyance of, a
|
||||||
|
covered work, and grant a patent license to some of the parties
|
||||||
|
receiving the covered work authorizing them to use, propagate, modify
|
||||||
|
or convey a specific copy of the covered work, then the patent license
|
||||||
|
you grant is automatically extended to all recipients of the covered
|
||||||
|
work and works based on it.
|
||||||
|
|
||||||
|
A patent license is "discriminatory" if it does not include within the
|
||||||
|
scope of its coverage, prohibits the exercise of, or is conditioned on
|
||||||
|
the non-exercise of one or more of the rights that are specifically
|
||||||
|
granted under this License. You may not convey a covered work if you
|
||||||
|
are a party to an arrangement with a third party that is in the
|
||||||
|
business of distributing software, under which you make payment to the
|
||||||
|
third party based on the extent of your activity of conveying the
|
||||||
|
work, and under which the third party grants, to any of the parties
|
||||||
|
who would receive the covered work from you, a discriminatory patent
|
||||||
|
license (a) in connection with copies of the covered work conveyed by
|
||||||
|
you (or copies made from those copies), or (b) primarily for and in
|
||||||
|
connection with specific products or compilations that contain the
|
||||||
|
covered work, unless you entered into that arrangement, or that patent
|
||||||
|
license was granted, prior to 28 March 2007.
|
||||||
|
|
||||||
|
Nothing in this License shall be construed as excluding or limiting
|
||||||
|
any implied license or other defenses to infringement that may
|
||||||
|
otherwise be available to you under applicable patent law.
|
||||||
|
|
||||||
|
### 12. No Surrender of Others' Freedom.
|
||||||
|
|
||||||
|
If conditions are imposed on you (whether by court order, agreement or
|
||||||
|
otherwise) that contradict the conditions of this License, they do not
|
||||||
|
excuse you from the conditions of this License. If you cannot convey a
|
||||||
|
covered work so as to satisfy simultaneously your obligations under
|
||||||
|
this License and any other pertinent obligations, then as a
|
||||||
|
consequence you may not convey it at all. For example, if you agree to
|
||||||
|
terms that obligate you to collect a royalty for further conveying
|
||||||
|
from those to whom you convey the Program, the only way you could
|
||||||
|
satisfy both those terms and this License would be to refrain entirely
|
||||||
|
from conveying the Program.
|
||||||
|
|
||||||
|
### 13. Remote Network Interaction; Use with the GNU General Public License.
|
||||||
|
|
||||||
|
Notwithstanding any other provision of this License, if you modify the
|
||||||
|
Program, your modified version must prominently offer all users
|
||||||
|
interacting with it remotely through a computer network (if your
|
||||||
|
version supports such interaction) an opportunity to receive the
|
||||||
|
Corresponding Source of your version by providing access to the
|
||||||
|
Corresponding Source from a network server at no charge, through some
|
||||||
|
standard or customary means of facilitating copying of software. This
|
||||||
|
Corresponding Source shall include the Corresponding Source for any
|
||||||
|
work covered by version 3 of the GNU General Public License that is
|
||||||
|
incorporated pursuant to the following paragraph.
|
||||||
|
|
||||||
|
Notwithstanding any other provision of this License, you have
|
||||||
|
permission to link or combine any covered work with a work licensed
|
||||||
|
under version 3 of the GNU General Public License into a single
|
||||||
|
combined work, and to convey the resulting work. The terms of this
|
||||||
|
License will continue to apply to the part which is the covered work,
|
||||||
|
but the work with which it is combined will remain governed by version
|
||||||
|
3 of the GNU General Public License.
|
||||||
|
|
||||||
|
### 14. Revised Versions of this License.
|
||||||
|
|
||||||
|
The Free Software Foundation may publish revised and/or new versions
|
||||||
|
of the GNU Affero General Public License from time to time. Such new
|
||||||
|
versions will be similar in spirit to the present version, but may
|
||||||
|
differ in detail to address new problems or concerns.
|
||||||
|
|
||||||
|
Each version is given a distinguishing version number. If the Program
|
||||||
|
specifies that a certain numbered version of the GNU Affero General
|
||||||
|
Public License "or any later version" applies to it, you have the
|
||||||
|
option of following the terms and conditions either of that numbered
|
||||||
|
version or of any later version published by the Free Software
|
||||||
|
Foundation. If the Program does not specify a version number of the
|
||||||
|
GNU Affero General Public License, you may choose any version ever
|
||||||
|
published by the Free Software Foundation.
|
||||||
|
|
||||||
|
If the Program specifies that a proxy can decide which future versions
|
||||||
|
of the GNU Affero General Public License can be used, that proxy's
|
||||||
|
public statement of acceptance of a version permanently authorizes you
|
||||||
|
to choose that version for the Program.
|
||||||
|
|
||||||
|
Later license versions may give you additional or different
|
||||||
|
permissions. However, no additional obligations are imposed on any
|
||||||
|
author or copyright holder as a result of your choosing to follow a
|
||||||
|
later version.
|
||||||
|
|
||||||
|
### 15. Disclaimer of Warranty.
|
||||||
|
|
||||||
|
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
|
||||||
|
APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
|
||||||
|
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT
|
||||||
|
WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT
|
||||||
|
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
|
||||||
|
A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
|
||||||
|
PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE
|
||||||
|
DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR
|
||||||
|
CORRECTION.
|
||||||
|
|
||||||
|
### 16. Limitation of Liability.
|
||||||
|
|
||||||
|
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
|
||||||
|
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR
|
||||||
|
CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
|
||||||
|
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES
|
||||||
|
ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT
|
||||||
|
NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR
|
||||||
|
LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM
|
||||||
|
TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER
|
||||||
|
PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
|
||||||
|
|
||||||
|
### 17. Interpretation of Sections 15 and 16.
|
||||||
|
|
||||||
|
If the disclaimer of warranty and limitation of liability provided
|
||||||
|
above cannot be given local legal effect according to their terms,
|
||||||
|
reviewing courts shall apply local law that most closely approximates
|
||||||
|
an absolute waiver of all civil liability in connection with the
|
||||||
|
Program, unless a warranty or assumption of liability accompanies a
|
||||||
|
copy of the Program in return for a fee.
|
||||||
|
|
||||||
|
END OF TERMS AND CONDITIONS
|
||||||
|
|
||||||
|
## How to Apply These Terms to Your New Programs
|
||||||
|
|
||||||
|
If you develop a new program, and you want it to be of the greatest
|
||||||
|
possible use to the public, the best way to achieve this is to make it
|
||||||
|
free software which everyone can redistribute and change under these
|
||||||
|
terms.
|
||||||
|
|
||||||
|
To do so, attach the following notices to the program. It is safest to
|
||||||
|
attach them to the start of each source file to most effectively state
|
||||||
|
the exclusion of warranty; and each file should have at least the
|
||||||
|
"copyright" line and a pointer to where the full notice is found.
|
||||||
|
|
||||||
|
<one line to give the program's name and a brief idea of what it does.>
|
||||||
|
Copyright (C) <year> <name of author>
|
||||||
|
|
||||||
|
This program is free software: you can redistribute it and/or modify
|
||||||
|
it under the terms of the GNU Affero General Public License as
|
||||||
|
published by the Free Software Foundation, either version 3 of the
|
||||||
|
License, or (at your option) any later version.
|
||||||
|
|
||||||
|
This program is distributed in the hope that it will be useful,
|
||||||
|
but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||||
|
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||||
|
GNU Affero General Public License for more details.
|
||||||
|
|
||||||
|
You should have received a copy of the GNU Affero General Public License
|
||||||
|
along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||||
|
|
||||||
|
Also add information on how to contact you by electronic and paper
|
||||||
|
mail.
|
||||||
|
|
||||||
|
If your software can interact with users remotely through a computer
|
||||||
|
network, you should also make sure that it provides a way for users to
|
||||||
|
get its source. For example, if your program is a web application, its
|
||||||
|
interface could display a "Source" link that leads users to an archive
|
||||||
|
of the code. There are many ways you could offer source, and different
|
||||||
|
solutions will be better for different programs; see section 13 for
|
||||||
|
the specific requirements.
|
||||||
|
|
||||||
|
You should also get your employer (if you work as a programmer) or
|
||||||
|
school, if any, to sign a "copyright disclaimer" for the program, if
|
||||||
|
necessary. For more information on this, and how to apply and follow
|
||||||
|
the GNU AGPL, see <https://www.gnu.org/licenses/>.
|
||||||
10
NAMESPACE
Normal file
10
NAMESPACE
Normal file
|
|
@ -0,0 +1,10 @@
|
||||||
|
# Generated by roxygen2: do not edit by hand
|
||||||
|
|
||||||
|
export(baseline_table)
|
||||||
|
export(file_extension)
|
||||||
|
export(getfun)
|
||||||
|
export(read_input)
|
||||||
|
export(regression_model)
|
||||||
|
export(regression_table)
|
||||||
|
export(write_quarto)
|
||||||
|
importFrom(stats,as.formula)
|
||||||
22
R/baseline_table.R
Normal file
22
R/baseline_table.R
Normal file
|
|
@ -0,0 +1,22 @@
|
||||||
|
#' Print a flexible baseline characteristics table
|
||||||
|
#'
|
||||||
|
#' @param data data set
|
||||||
|
#' @param fun.args list of arguments passed to
|
||||||
|
#' @param fun function to
|
||||||
|
#' @param vars character vector of variables to include
|
||||||
|
#'
|
||||||
|
#' @return object of standard class for fun
|
||||||
|
#' @export
|
||||||
|
#'
|
||||||
|
#' @examples
|
||||||
|
#' mtcars |> baseline_table()
|
||||||
|
#' mtcars |> baseline_table(fun.args = list(by = "gear"))
|
||||||
|
baseline_table <- function(data, fun.args = NULL, fun = gtsummary::tbl_summary, vars = NULL) {
|
||||||
|
if (!is.null(vars)) {
|
||||||
|
data <- dplyr::select(dplyr::all_of(vars))
|
||||||
|
}
|
||||||
|
|
||||||
|
out <- do.call(fun, c(list(data = data), fun.args))
|
||||||
|
return(out)
|
||||||
|
}
|
||||||
|
|
||||||
110
R/helpers.R
Normal file
110
R/helpers.R
Normal file
|
|
@ -0,0 +1,110 @@
|
||||||
|
#' Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()'
|
||||||
|
#'
|
||||||
|
#' @description
|
||||||
|
#' This function follows the idea from this comment: https://stackoverflow.com/questions/38983179/do-call-a-function-in-r-without-loading-the-package
|
||||||
|
#' @param x function or function name
|
||||||
|
#'
|
||||||
|
#' @return function or character vector
|
||||||
|
#' @export
|
||||||
|
#'
|
||||||
|
#' @examples
|
||||||
|
#' getfun("stats::lm")
|
||||||
|
getfun <- function(x) {
|
||||||
|
if("character" %in% class(x)){
|
||||||
|
if (length(grep("::", x)) > 0) {
|
||||||
|
parts <- strsplit(x, "::")[[1]]
|
||||||
|
requireNamespace(parts[1])
|
||||||
|
getExportedValue(parts[1], parts[2])
|
||||||
|
}
|
||||||
|
}else {
|
||||||
|
x
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
#' Wrapper to save data in RDS, load into specified qmd and render
|
||||||
|
#'
|
||||||
|
#' @param data list to pass to qmd
|
||||||
|
#' @param fileformat output format. Ignored if file!=NULL
|
||||||
|
#' @param qmd.file qmd file to render. Default is 'here::here("analyses.qmd")'
|
||||||
|
#' @param file exact filename (Optional)
|
||||||
|
#' @param ... Ignored for now
|
||||||
|
#'
|
||||||
|
#' @return none
|
||||||
|
#' @export
|
||||||
|
#'
|
||||||
|
write_quarto <- function(data,fileformat,qmd.file=here::here("analyses.qmd"),file=NULL,...){
|
||||||
|
if (is.null(file)){
|
||||||
|
file <- paste0("analyses.",fileformat)
|
||||||
|
}
|
||||||
|
temp <- tempfile(fileext = ".Rds")
|
||||||
|
# write_rds(mtcars, temp)
|
||||||
|
# read_rds(temp)
|
||||||
|
web_data <- data
|
||||||
|
saveRDS(web_data,file=temp)
|
||||||
|
|
||||||
|
quarto::quarto_render(qmd.file,
|
||||||
|
output_file = file,
|
||||||
|
execute_params = list(data.file=temp)
|
||||||
|
)
|
||||||
|
}
|
||||||
|
|
||||||
|
#' Helper to import files correctly
|
||||||
|
#'
|
||||||
|
#' @param filenames file names
|
||||||
|
#'
|
||||||
|
#' @return character vector
|
||||||
|
#' @export
|
||||||
|
#'
|
||||||
|
#' @examples
|
||||||
|
#' file_extension(list.files(here::here(""))[[2]])[[1]]
|
||||||
|
#' file_extension(c("file.cd..ks", "file"))
|
||||||
|
file_extension <- function(filenames) {
|
||||||
|
sub(
|
||||||
|
pattern = "^(.*\\.|[^.]+)(?=[^.]*)", replacement = "",
|
||||||
|
filenames,
|
||||||
|
perl = TRUE
|
||||||
|
)
|
||||||
|
}
|
||||||
|
|
||||||
|
#' Flexible file import based on extension
|
||||||
|
#'
|
||||||
|
#' @param file file name
|
||||||
|
#' @param consider.na character vector of strings to consider as NAs
|
||||||
|
#'
|
||||||
|
#' @return tibble
|
||||||
|
#' @export
|
||||||
|
#'
|
||||||
|
#' @examples
|
||||||
|
#' read_input("https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/data/sample.csv")
|
||||||
|
read_input <- function(file, consider.na = c("NA", '""', "")) {
|
||||||
|
ext <- file_extension(file)
|
||||||
|
|
||||||
|
if (ext == "csv") {
|
||||||
|
df <- readr::read_csv(file = file, na = consider.na)
|
||||||
|
} else if (ext %in% c("xls", "xlsx")) {
|
||||||
|
df <- openxlsx2::read_xlsx(file = file, na.strings = consider.na)
|
||||||
|
} else if (ext == "dta") {
|
||||||
|
df <- haven::read_dta(file = file)
|
||||||
|
} else if (ext == "ods") {
|
||||||
|
df <- readODS::read_ods(file = file)
|
||||||
|
} else {
|
||||||
|
stop("Input file format has to be on of:
|
||||||
|
'.csv', '.xls', '.xlsx', '.dta' or '.ods'")
|
||||||
|
}
|
||||||
|
|
||||||
|
df
|
||||||
|
}
|
||||||
|
|
||||||
|
#' Convert string of arguments to list of arguments
|
||||||
|
#'
|
||||||
|
#' @description
|
||||||
|
#' Idea from the answer: https://stackoverflow.com/a/62979238
|
||||||
|
#'
|
||||||
|
#' @param string string to convert to list to use with do.call
|
||||||
|
#'
|
||||||
|
#' @return list
|
||||||
|
#' @export
|
||||||
|
#'
|
||||||
|
argsstring2list <- function(string){
|
||||||
|
eval(parse(text = paste0("list(", string, ")")))
|
||||||
|
}
|
||||||
99
R/regression_model.R
Normal file
99
R/regression_model.R
Normal file
|
|
@ -0,0 +1,99 @@
|
||||||
|
#' Print a flexible baseline characteristics table
|
||||||
|
#'
|
||||||
|
#' @param data data set
|
||||||
|
#' @param fun Name of function as character vector or function to use for model creation.
|
||||||
|
#' @param vars character vector of variables to include
|
||||||
|
#' @param outcome.str Name of outcome variable. Character vector.
|
||||||
|
#' @param auto.mode Make assumptions on function dependent on outcome data format.
|
||||||
|
#' @param formula.str Formula as string. Passed through 'glue::glue'. If given, 'outcome.str' and 'vars' are ignored. Optional.
|
||||||
|
#' @param args.list List of arguments passed to 'fun' with 'do.call'.
|
||||||
|
#'
|
||||||
|
#' @importFrom stats as.formula
|
||||||
|
#'
|
||||||
|
#' @return object of standard class for fun
|
||||||
|
#' @export
|
||||||
|
#'
|
||||||
|
#' @examples
|
||||||
|
#' gtsummary::trial |>
|
||||||
|
#' regression_model(outcome.str = "age")
|
||||||
|
#' gtsummary::trial |>
|
||||||
|
#' regression_model(
|
||||||
|
#' outcome.str = "age",
|
||||||
|
#' fun = "stats::lm",
|
||||||
|
#' formula.str = "{outcome.str}~.",
|
||||||
|
#' args.list = NULL
|
||||||
|
#' )
|
||||||
|
#' gtsummary::trial |> regression_model(
|
||||||
|
#' outcome.str = "trt",
|
||||||
|
#' fun = "stats::glm",
|
||||||
|
#' args.list = list(family = binomial(link = "logit"))
|
||||||
|
#' )
|
||||||
|
regression_model <- function(data,
|
||||||
|
outcome.str,
|
||||||
|
auto.mode = TRUE,
|
||||||
|
formula.str = NULL,
|
||||||
|
args.list = NULL,
|
||||||
|
fun = NULL,
|
||||||
|
vars = NULL) {
|
||||||
|
if (!is.null(formula.str)) {
|
||||||
|
formula.str <- glue::glue(formula.str)
|
||||||
|
} else {
|
||||||
|
assertthat::assert_that(outcome.str %in% names(data),
|
||||||
|
msg = "Outcome variable is not present in the provided dataset"
|
||||||
|
)
|
||||||
|
formula.str <- glue::glue("{outcome.str}~.")
|
||||||
|
|
||||||
|
if (!is.null(vars)) {
|
||||||
|
if (outcome.str %in% vars){
|
||||||
|
vars <- vars[vars %in% outcome.str]
|
||||||
|
}
|
||||||
|
data <- data |> dplyr::select(dplyr::all_of(c(vars,outcome.str)))
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
# Formatting character variables as factor
|
||||||
|
# Improvement should add a missing vector to format as NA
|
||||||
|
data <- data |> dplyr::mutate(dplyr::across(dplyr::where(is.character), as.factor))
|
||||||
|
|
||||||
|
# browser()
|
||||||
|
if (auto.mode) {
|
||||||
|
if (is.numeric(data[[outcome.str]])){
|
||||||
|
fun <- "stats::lm"
|
||||||
|
} else if (is.factor(data[[outcome.str]])){
|
||||||
|
if (length(levels(data[[outcome.str]]))==2){
|
||||||
|
fun <- "stats::glm"
|
||||||
|
args.list = list(family = binomial(link = "logit"))
|
||||||
|
|
||||||
|
} else if (length(levels(data[[outcome.str]]))>2){
|
||||||
|
fun <- "MASS::polr"
|
||||||
|
args.list = list(
|
||||||
|
Hess = TRUE,
|
||||||
|
method = "logistic"
|
||||||
|
)
|
||||||
|
} else {
|
||||||
|
stop("The provided output variable only has one level")
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
stop("Output variable should be either numeric or factor for auto.mode")
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
assertthat::assert_that("character" %in% class(fun),
|
||||||
|
msg = "Please provide the function as a character vector."
|
||||||
|
)
|
||||||
|
|
||||||
|
out <- do.call(
|
||||||
|
getfun(fun),
|
||||||
|
c(
|
||||||
|
list(data = data),
|
||||||
|
list(formula = as.formula(formula.str)),
|
||||||
|
args.list
|
||||||
|
)
|
||||||
|
)
|
||||||
|
|
||||||
|
# Recreating the call
|
||||||
|
# out$call <- match.call(definition=eval(parse(text=fun)), call(fun, data = 'data',formula = as.formula(formula.str),args.list))
|
||||||
|
|
||||||
|
return(out)
|
||||||
|
}
|
||||||
40
R/regression_table.R
Normal file
40
R/regression_table.R
Normal file
|
|
@ -0,0 +1,40 @@
|
||||||
|
#' Create table of regression model
|
||||||
|
#'
|
||||||
|
#' @param data regression model
|
||||||
|
#' @param args.list list of arguments passed to 'fun'.
|
||||||
|
#' @param fun function to use for table creation. Default is "gtsummary::tbl_regression".
|
||||||
|
#'
|
||||||
|
#' @return object of standard class for fun
|
||||||
|
#' @export
|
||||||
|
#'
|
||||||
|
#' @examples
|
||||||
|
#' gtsummary::trial |>
|
||||||
|
#' regression_model(
|
||||||
|
#' outcome.str = "stage",
|
||||||
|
#' fun = "MASS::polr"
|
||||||
|
#' ) |>
|
||||||
|
#' regression_table(args.list = list(exponentiate = TRUE))
|
||||||
|
#' gtsummary::trial |>
|
||||||
|
#' regression_model(
|
||||||
|
#' outcome.str = "age",
|
||||||
|
#' fun = "stats::lm",
|
||||||
|
#' formula.str = "{outcome.str}~.",
|
||||||
|
#' args.list = NULL
|
||||||
|
#' ) |>
|
||||||
|
#' regression_table()
|
||||||
|
#' gtsummary::trial |>
|
||||||
|
#' regression_model(
|
||||||
|
#' outcome.str = "trt",
|
||||||
|
#' fun = "stats::glm",
|
||||||
|
#' args.list = list(family = binomial(link = "logit"))
|
||||||
|
#' ) |>
|
||||||
|
#' regression_table()
|
||||||
|
regression_table <- function(data, args.list = NULL, fun = "gtsummary::tbl_regression") {
|
||||||
|
|
||||||
|
if (any(c(length(class(data))!=1, class(data)!="lm"))){
|
||||||
|
args.list <- c(args.list,list(exponentiate=TRUE))
|
||||||
|
}
|
||||||
|
|
||||||
|
out <- do.call(getfun(fun), c(list(x = data), args.list))
|
||||||
|
return(out)
|
||||||
|
}
|
||||||
20
README.md
Normal file
20
README.md
Normal file
|
|
@ -0,0 +1,20 @@
|
||||||
|
# webResearch
|
||||||
|
|
||||||
|
<!-- badges: start -->
|
||||||
|
|
||||||
|
<!-- badges: end -->
|
||||||
|
|
||||||
|
This package is the backbone of the open and freely accessible browser-based data analysis tool with project name "webResearch".
|
||||||
|
|
||||||
|
## Road map
|
||||||
|
|
||||||
|
- A minimally working example
|
||||||
|
|
||||||
|
- Table 1 of baseline characteristics
|
||||||
|
- Table 2 of main analysis results
|
||||||
|
- Figure 1 of main results (like forest plot)
|
||||||
|
- Shiny GUI implementation
|
||||||
|
|
||||||
|
- Fundraising for further development
|
||||||
|
|
||||||
|
- Implementation with different focus groups and educational formats.
|
||||||
53
analyses.qmd
Normal file
53
analyses.qmd
Normal file
|
|
@ -0,0 +1,53 @@
|
||||||
|
---
|
||||||
|
title: "webResearch analysis results"
|
||||||
|
date: today
|
||||||
|
execute:
|
||||||
|
echo: false
|
||||||
|
params:
|
||||||
|
data.file: NA
|
||||||
|
---
|
||||||
|
|
||||||
|
<!-- ## Abstract -->
|
||||||
|
|
||||||
|
<!-- ### Background -->
|
||||||
|
|
||||||
|
<!-- ### Methods -->
|
||||||
|
|
||||||
|
<!-- ### Results -->
|
||||||
|
|
||||||
|
<!-- ### Conclusion -->
|
||||||
|
|
||||||
|
|
||||||
|
```{r setup}
|
||||||
|
web_data <- readRDS(file = params$data.file)
|
||||||
|
# readr::read_rds(file = here::here("data.Rds"))
|
||||||
|
library(gtsummary)
|
||||||
|
library(gt)
|
||||||
|
```
|
||||||
|
|
||||||
|
## Introduction
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
## Methods
|
||||||
|
|
||||||
|
|
||||||
|
Analyses were conducted in R version `r paste(version["major"],version["minor"],sep=".")` using the web-based data analysis tool 'webResearcher' version `r packageVersion("webResearch")`.
|
||||||
|
|
||||||
|
## Results
|
||||||
|
|
||||||
|
Below is the baseline characteristics plotted.
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
web_data$table1
|
||||||
|
```
|
||||||
|
|
||||||
|
Here are the regression results.
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
web_data$table2
|
||||||
|
```
|
||||||
|
|
||||||
|
## Discussion
|
||||||
|
|
||||||
|
Good luck on your further work!
|
||||||
282
app/functions.R
Normal file
282
app/functions.R
Normal file
|
|
@ -0,0 +1,282 @@
|
||||||
|
|
||||||
|
|
||||||
|
########
|
||||||
|
#### Current file: R//baseline_table.R
|
||||||
|
########
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
baseline_table <- function(data, fun.args = NULL, fun = gtsummary::tbl_summary, vars = NULL) {
|
||||||
|
if (!is.null(vars)) {
|
||||||
|
data <- dplyr::select(dplyr::all_of(vars))
|
||||||
|
}
|
||||||
|
|
||||||
|
out <- do.call(fun, c(list(data = data), fun.args))
|
||||||
|
return(out)
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
########
|
||||||
|
#### Current file: R//helpers.R
|
||||||
|
########
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
getfun <- function(x) {
|
||||||
|
if("character" %in% class(x)){
|
||||||
|
if (length(grep("::", x)) > 0) {
|
||||||
|
parts <- strsplit(x, "::")[[1]]
|
||||||
|
requireNamespace(parts[1])
|
||||||
|
getExportedValue(parts[1], parts[2])
|
||||||
|
}
|
||||||
|
}else {
|
||||||
|
x
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
write_quarto <- function(data,fileformat,qmd.file=here::here("analyses.qmd"),file=NULL,...){
|
||||||
|
if (is.null(file)){
|
||||||
|
file <- paste0("analyses.",fileformat)
|
||||||
|
}
|
||||||
|
temp <- tempfile(fileext = ".Rds")
|
||||||
|
# write_rds(mtcars, temp)
|
||||||
|
# read_rds(temp)
|
||||||
|
web_data <- data
|
||||||
|
saveRDS(web_data,file=temp)
|
||||||
|
|
||||||
|
quarto::quarto_render(qmd.file,
|
||||||
|
output_file = file,
|
||||||
|
execute_params = list(data.file=temp)
|
||||||
|
)
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
file_extension <- function(filenames) {
|
||||||
|
sub(
|
||||||
|
pattern = "^(.*\\.|[^.]+)(?=[^.]*)", replacement = "",
|
||||||
|
filenames,
|
||||||
|
perl = TRUE
|
||||||
|
)
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
read_input <- function(file, consider.na = c("NA", '""', "")) {
|
||||||
|
ext <- file_extension(file)
|
||||||
|
|
||||||
|
if (ext == "csv") {
|
||||||
|
df <- readr::read_csv(file = file, na = consider.na)
|
||||||
|
} else if (ext %in% c("xls", "xlsx")) {
|
||||||
|
df <- openxlsx2::read_xlsx(file = file, na.strings = consider.na)
|
||||||
|
} else if (ext == "dta") {
|
||||||
|
df <- haven::read_dta(file = file)
|
||||||
|
} else if (ext == "ods") {
|
||||||
|
df <- readODS::read_ods(file = file)
|
||||||
|
} else {
|
||||||
|
stop("Input file format has to be on of:
|
||||||
|
'.csv', '.xls', '.xlsx', '.dta' or '.ods'")
|
||||||
|
}
|
||||||
|
|
||||||
|
df
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
########
|
||||||
|
#### Current file: R//regression_model.R
|
||||||
|
########
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
regression_model <- function(data,
|
||||||
|
outcome.str,
|
||||||
|
auto.mode = TRUE,
|
||||||
|
formula.str = NULL,
|
||||||
|
args.list = NULL,
|
||||||
|
fun = NULL,
|
||||||
|
vars = NULL) {
|
||||||
|
if (!is.null(formula.str)) {
|
||||||
|
formula.str <- glue::glue(formula.str)
|
||||||
|
} else {
|
||||||
|
assertthat::assert_that(outcome.str %in% names(data),
|
||||||
|
msg = "Outcome variable is not present in the provided dataset"
|
||||||
|
)
|
||||||
|
formula.str <- glue::glue("{outcome.str}~.")
|
||||||
|
|
||||||
|
if (!is.null(vars)) {
|
||||||
|
if (outcome.str %in% vars){
|
||||||
|
vars <- vars[vars %in% outcome.str]
|
||||||
|
}
|
||||||
|
data <- data |> dplyr::select(dplyr::all_of(c(vars,outcome.str)))
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
# Formatting character variables as factor
|
||||||
|
# Improvement should add a missing vector to format as NA
|
||||||
|
data <- data |> dplyr::mutate(dplyr::across(dplyr::where(is.character), as.factor))
|
||||||
|
|
||||||
|
# browser()
|
||||||
|
if (auto.mode) {
|
||||||
|
if (is.numeric(data[[outcome.str]])){
|
||||||
|
fun <- "stats::lm"
|
||||||
|
} else if (is.factor(data[[outcome.str]])){
|
||||||
|
if (length(levels(data[[outcome.str]]))==2){
|
||||||
|
fun <- "stats::glm"
|
||||||
|
args.list = list(family = binomial(link = "logit"))
|
||||||
|
|
||||||
|
} else if (length(levels(data[[outcome.str]]))>2){
|
||||||
|
fun <- "MASS::polr"
|
||||||
|
args.list = list(
|
||||||
|
Hess = TRUE,
|
||||||
|
method = "logistic"
|
||||||
|
)
|
||||||
|
} else {
|
||||||
|
stop("The provided output variable only has one level")
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
stop("Output variable should be either numeric or factor for auto.mode")
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
assertthat::assert_that("character" %in% class(fun),
|
||||||
|
msg = "Please provide the function as a character vector."
|
||||||
|
)
|
||||||
|
|
||||||
|
out <- do.call(
|
||||||
|
getfun(fun),
|
||||||
|
c(
|
||||||
|
list(data = data),
|
||||||
|
list(formula = as.formula(formula.str)),
|
||||||
|
args.list
|
||||||
|
)
|
||||||
|
)
|
||||||
|
|
||||||
|
# Recreating the call
|
||||||
|
# out$call <- match.call(definition=eval(parse(text=fun)), call(fun, data = 'data',formula = as.formula(formula.str),args.list))
|
||||||
|
|
||||||
|
return(out)
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
########
|
||||||
|
#### Current file: R//regression_table.R
|
||||||
|
########
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
regression_table <- function(data, args.list = NULL, fun = "gtsummary::tbl_regression") {
|
||||||
|
|
||||||
|
if (any(c(length(class(data))!=1, class(data)!="lm"))){
|
||||||
|
args.list <- c(args.list,list(exponentiate=TRUE))
|
||||||
|
}
|
||||||
|
|
||||||
|
out <- do.call(getfun(fun), c(list(x = data), args.list))
|
||||||
|
return(out)
|
||||||
|
}
|
||||||
10
app/rsconnect/shinyapps.io/agdamsbo/webResearch.dcf
Normal file
10
app/rsconnect/shinyapps.io/agdamsbo/webResearch.dcf
Normal file
|
|
@ -0,0 +1,10 @@
|
||||||
|
name: webResearch
|
||||||
|
title:
|
||||||
|
username: agdamsbo
|
||||||
|
account: agdamsbo
|
||||||
|
server: shinyapps.io
|
||||||
|
hostUrl: https://api.shinyapps.io/v1
|
||||||
|
appId: 13276335
|
||||||
|
bundleId: 9334284
|
||||||
|
url: https://agdamsbo.shinyapps.io/webResearch/
|
||||||
|
version: 1
|
||||||
116
app/server.R
Normal file
116
app/server.R
Normal file
|
|
@ -0,0 +1,116 @@
|
||||||
|
# project.aid::merge_scripts(list.files("R/",full.names = TRUE),dest = here::here("app/functions.R"))
|
||||||
|
source(here::here("app/functions.R"))
|
||||||
|
|
||||||
|
server <- function(input, output, session) {
|
||||||
|
v <- shiny::reactiveValues(
|
||||||
|
list = NULL,
|
||||||
|
ds = NULL
|
||||||
|
)
|
||||||
|
|
||||||
|
ds <- shiny::reactive({
|
||||||
|
# input$file1 will be NULL initially. After the user selects
|
||||||
|
# and uploads a file, head of that data file by default,
|
||||||
|
# or all rows if selected, will be shown.
|
||||||
|
|
||||||
|
shiny::req(input$file)
|
||||||
|
|
||||||
|
v$ds <- "present"
|
||||||
|
return(read_input(input$file$datapath))
|
||||||
|
})
|
||||||
|
|
||||||
|
output$include_vars <- shiny::renderUI({
|
||||||
|
selectizeInput(
|
||||||
|
inputId = "include_vars",
|
||||||
|
selected = NULL,
|
||||||
|
label = "Covariables to include",
|
||||||
|
choices = colnames(ds()),
|
||||||
|
multiple = TRUE
|
||||||
|
)
|
||||||
|
})
|
||||||
|
|
||||||
|
output$outcome_var <- shiny::renderUI({
|
||||||
|
selectInput(
|
||||||
|
inputId = "outcome_var",
|
||||||
|
selected = NULL,
|
||||||
|
label = "Select outcome variable",
|
||||||
|
choices = colnames(ds()),
|
||||||
|
multiple = FALSE
|
||||||
|
)
|
||||||
|
})
|
||||||
|
|
||||||
|
output$data.input <- shiny::renderTable({
|
||||||
|
shiny::req(input$file)
|
||||||
|
ds()
|
||||||
|
})
|
||||||
|
|
||||||
|
shiny::observeEvent(
|
||||||
|
{
|
||||||
|
input$load
|
||||||
|
},
|
||||||
|
{
|
||||||
|
shiny::req(input$outcome_var)
|
||||||
|
|
||||||
|
v$list <- ds() |>
|
||||||
|
(\(data){
|
||||||
|
# browser()
|
||||||
|
list(
|
||||||
|
data = data,
|
||||||
|
table1 = data |> baseline_table(),
|
||||||
|
table2 = data |>
|
||||||
|
regression_model(
|
||||||
|
outcome.str = input$outcome_var,
|
||||||
|
auto.mode = input$regression_auto == 1,
|
||||||
|
formula.str = input$regression_formula,
|
||||||
|
fun = input$regression_fun,
|
||||||
|
args.list = eval(parse(text = paste0("list(", input$regression_args, ")"))),
|
||||||
|
vars = input$include_vars
|
||||||
|
) |>
|
||||||
|
regression_table()
|
||||||
|
)
|
||||||
|
})()
|
||||||
|
|
||||||
|
output$table1 <- gt::render_gt(
|
||||||
|
v$list$table1 |>
|
||||||
|
gtsummary::as_gt()
|
||||||
|
)
|
||||||
|
|
||||||
|
output$table2 <- gt::render_gt(
|
||||||
|
v$list$table2 |>
|
||||||
|
gtsummary::as_gt()
|
||||||
|
)
|
||||||
|
|
||||||
|
}
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
|
output$uploaded <- shiny::reactive({
|
||||||
|
if (is.null(v$ds)) {
|
||||||
|
"no"
|
||||||
|
} else {
|
||||||
|
"yes"
|
||||||
|
}
|
||||||
|
})
|
||||||
|
|
||||||
|
shiny::outputOptions(output, "uploaded", suspendWhenHidden = FALSE)
|
||||||
|
|
||||||
|
#####
|
||||||
|
#### Generating output
|
||||||
|
#####
|
||||||
|
|
||||||
|
# Downloadable csv of selected dataset ----
|
||||||
|
# output$downloadData <- shiny::downloadHandler(
|
||||||
|
# filename = "index_lookup.csv",
|
||||||
|
# content = function(file) {
|
||||||
|
# write.csv(v$index, file, row.names = FALSE)
|
||||||
|
# }
|
||||||
|
# )
|
||||||
|
|
||||||
|
output$report <- downloadHandler(
|
||||||
|
filename = "analyses.html",
|
||||||
|
content = function(file) {
|
||||||
|
v$list |> write_quarto(file = file)
|
||||||
|
}
|
||||||
|
)
|
||||||
|
|
||||||
|
#
|
||||||
|
}
|
||||||
124
app/ui.R
Normal file
124
app/ui.R
Normal file
|
|
@ -0,0 +1,124 @@
|
||||||
|
require(shiny)
|
||||||
|
require(bslib)
|
||||||
|
# require(ggplot2)
|
||||||
|
# source("https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/R/index_from_raw.R")
|
||||||
|
# source("https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/R/plot_index.R")
|
||||||
|
# source(here::here("R/index_from_raw.R"))
|
||||||
|
# source(here::here("R/plot_index.R"))
|
||||||
|
|
||||||
|
# ui <- fluidPage(
|
||||||
|
|
||||||
|
cards <- list(
|
||||||
|
bslib::card(
|
||||||
|
max_height = "200px",
|
||||||
|
full_screen = TRUE,
|
||||||
|
bslib::card_header("Data overview"),
|
||||||
|
shiny::uiOutput("data.input")
|
||||||
|
),
|
||||||
|
bslib::card(
|
||||||
|
# max_height = "200px",
|
||||||
|
full_screen = TRUE,
|
||||||
|
bslib::card_header("Baseline characteristics"),
|
||||||
|
gt::gt_output(outputId = "table1")
|
||||||
|
),
|
||||||
|
bslib::card(
|
||||||
|
full_screen = TRUE,
|
||||||
|
bslib::card_header("Multivariable regression table"),
|
||||||
|
gt::gt_output(outputId = "table2")
|
||||||
|
)
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
|
ui <- bslib::page_sidebar(
|
||||||
|
theme = bslib::bs_theme(bootswatch = "minty"),
|
||||||
|
title = "webResearcher for easy data analysis",
|
||||||
|
window_title = "webResearcher",
|
||||||
|
header = h6("Welcome to the webResearcher tool. This is an early alpha version to act as a proof-of-concept and in no way intended for wider public use."),
|
||||||
|
|
||||||
|
# sidebarPanel(
|
||||||
|
sidebar = bslib::sidebar(
|
||||||
|
open = "open",
|
||||||
|
h4("Upload your dataset"),
|
||||||
|
|
||||||
|
# Input: Select a file ----
|
||||||
|
fileInput(
|
||||||
|
inputId = "file",
|
||||||
|
label = "Choose data file",
|
||||||
|
multiple = FALSE,
|
||||||
|
accept = c(
|
||||||
|
"text/csv",
|
||||||
|
"text/comma-separated-values,text/plain",
|
||||||
|
".csv",
|
||||||
|
".xlsx",
|
||||||
|
".xls",
|
||||||
|
".dta",
|
||||||
|
".ods"
|
||||||
|
)
|
||||||
|
),
|
||||||
|
conditionalPanel(
|
||||||
|
condition = "output.uploaded=='yes'",
|
||||||
|
h4("Parameter specifications"),
|
||||||
|
radioButtons(
|
||||||
|
inputId = "regression_auto",
|
||||||
|
label = "Automatically choose function",
|
||||||
|
inline = TRUE,
|
||||||
|
choiceNames = c(
|
||||||
|
"Yes",
|
||||||
|
"No"
|
||||||
|
),
|
||||||
|
choiceValues = c(1, 2)
|
||||||
|
),
|
||||||
|
conditionalPanel(
|
||||||
|
condition = "input.regression_auto==2",
|
||||||
|
textInput(
|
||||||
|
inputId = "regression_formula",
|
||||||
|
label = "Formula string to render with 'glue::glue'",
|
||||||
|
value = "{outcome.str}~."
|
||||||
|
),
|
||||||
|
textInput(
|
||||||
|
inputId = "regression_fun",
|
||||||
|
label = "Function to use for analysis (needs pasckage and name)",
|
||||||
|
value = "stats::lm"
|
||||||
|
),
|
||||||
|
textInput(
|
||||||
|
inputId = "regression_args",
|
||||||
|
label = "Arguments to pass to the function (provided as a string)",
|
||||||
|
value = ""
|
||||||
|
)
|
||||||
|
),
|
||||||
|
helpText(em("Please specify relevant columns from your data, and press 'Load data'")),
|
||||||
|
uiOutput("outcome_var"),
|
||||||
|
radioButtons(
|
||||||
|
inputId = "all",
|
||||||
|
label = "Specify covariables",
|
||||||
|
inline = TRUE, selected = 2,
|
||||||
|
choiceNames = c(
|
||||||
|
"Yes",
|
||||||
|
"No"
|
||||||
|
),
|
||||||
|
choiceValues = c(1, 2)
|
||||||
|
),
|
||||||
|
conditionalPanel(
|
||||||
|
condition = "input.all==1",
|
||||||
|
uiOutput("include_vars")
|
||||||
|
),
|
||||||
|
actionButton("load", "Analyse", class = "btn-primary")
|
||||||
|
)
|
||||||
|
# ,
|
||||||
|
|
||||||
|
# Horizontal line ----
|
||||||
|
# tags$hr(),
|
||||||
|
# h4("Download results"),
|
||||||
|
#
|
||||||
|
# # Button
|
||||||
|
# downloadButton(outputId="report",
|
||||||
|
# label= "Download",
|
||||||
|
# icon = shiny::icon("download"))
|
||||||
|
),
|
||||||
|
layout_columns(
|
||||||
|
cards[[1]]
|
||||||
|
),
|
||||||
|
layout_columns(
|
||||||
|
cards[[2]], cards[[3]]
|
||||||
|
)
|
||||||
|
)
|
||||||
BIN
data.Rds
Normal file
BIN
data.Rds
Normal file
Binary file not shown.
32
man/baseline_table.Rd
Normal file
32
man/baseline_table.Rd
Normal file
|
|
@ -0,0 +1,32 @@
|
||||||
|
% Generated by roxygen2: do not edit by hand
|
||||||
|
% Please edit documentation in R/baseline_table.R
|
||||||
|
\name{baseline_table}
|
||||||
|
\alias{baseline_table}
|
||||||
|
\title{Print a flexible baseline characteristics table}
|
||||||
|
\usage{
|
||||||
|
baseline_table(
|
||||||
|
data,
|
||||||
|
fun.args = NULL,
|
||||||
|
fun = gtsummary::tbl_summary,
|
||||||
|
vars = NULL
|
||||||
|
)
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{data}{data set}
|
||||||
|
|
||||||
|
\item{fun.args}{list of arguments passed to}
|
||||||
|
|
||||||
|
\item{fun}{function to}
|
||||||
|
|
||||||
|
\item{vars}{character vector of variables to include}
|
||||||
|
}
|
||||||
|
\value{
|
||||||
|
object of standard class for fun
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
Print a flexible baseline characteristics table
|
||||||
|
}
|
||||||
|
\examples{
|
||||||
|
mtcars |> baseline_table()
|
||||||
|
mtcars |> baseline_table(fun.args = list(by = "gear"))
|
||||||
|
}
|
||||||
21
man/file_extension.Rd
Normal file
21
man/file_extension.Rd
Normal file
|
|
@ -0,0 +1,21 @@
|
||||||
|
% Generated by roxygen2: do not edit by hand
|
||||||
|
% Please edit documentation in R/helpers.R
|
||||||
|
\name{file_extension}
|
||||||
|
\alias{file_extension}
|
||||||
|
\title{Helper to import files correctly}
|
||||||
|
\usage{
|
||||||
|
file_extension(filenames)
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{filenames}{file names}
|
||||||
|
}
|
||||||
|
\value{
|
||||||
|
character vector
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
Helper to import files correctly
|
||||||
|
}
|
||||||
|
\examples{
|
||||||
|
file_extension(list.files(here::here(""))[[2]])[[1]]
|
||||||
|
file_extension(c("file.cd..ks", "file"))
|
||||||
|
}
|
||||||
20
man/getfun.Rd
Normal file
20
man/getfun.Rd
Normal file
|
|
@ -0,0 +1,20 @@
|
||||||
|
% Generated by roxygen2: do not edit by hand
|
||||||
|
% Please edit documentation in R/helpers.R
|
||||||
|
\name{getfun}
|
||||||
|
\alias{getfun}
|
||||||
|
\title{Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()'}
|
||||||
|
\usage{
|
||||||
|
getfun(x)
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{x}{function or function name}
|
||||||
|
}
|
||||||
|
\value{
|
||||||
|
function or character vector
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
This function follows the idea from this comment: https://stackoverflow.com/questions/38983179/do-call-a-function-in-r-without-loading-the-package
|
||||||
|
}
|
||||||
|
\examples{
|
||||||
|
getfun("stats::lm")
|
||||||
|
}
|
||||||
22
man/read_input.Rd
Normal file
22
man/read_input.Rd
Normal file
|
|
@ -0,0 +1,22 @@
|
||||||
|
% Generated by roxygen2: do not edit by hand
|
||||||
|
% Please edit documentation in R/helpers.R
|
||||||
|
\name{read_input}
|
||||||
|
\alias{read_input}
|
||||||
|
\title{Flexible file import based on extension}
|
||||||
|
\usage{
|
||||||
|
read_input(file, consider.na = c("NA", "\\"\\"", ""))
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{file}{file name}
|
||||||
|
|
||||||
|
\item{consider.na}{character vector of strings to consider as NAs}
|
||||||
|
}
|
||||||
|
\value{
|
||||||
|
tibble
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
Flexible file import based on extension
|
||||||
|
}
|
||||||
|
\examples{
|
||||||
|
read_input("https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/data/sample.csv")
|
||||||
|
}
|
||||||
54
man/regression_model.Rd
Normal file
54
man/regression_model.Rd
Normal file
|
|
@ -0,0 +1,54 @@
|
||||||
|
% Generated by roxygen2: do not edit by hand
|
||||||
|
% Please edit documentation in R/regression_model.R
|
||||||
|
\name{regression_model}
|
||||||
|
\alias{regression_model}
|
||||||
|
\title{Print a flexible baseline characteristics table}
|
||||||
|
\usage{
|
||||||
|
regression_model(
|
||||||
|
data,
|
||||||
|
outcome.str = "gear",
|
||||||
|
outcome.factor = TRUE,
|
||||||
|
formula.str = NULL,
|
||||||
|
args.list = list(Hess = TRUE, method = "logistic"),
|
||||||
|
fun = "MASS::polr",
|
||||||
|
vars = NULL
|
||||||
|
)
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{data}{data set}
|
||||||
|
|
||||||
|
\item{outcome.str}{Name of outcome variable. Character vector.}
|
||||||
|
|
||||||
|
\item{outcome.factor}{Factorize outcome variable. Logical.}
|
||||||
|
|
||||||
|
\item{formula.str}{Formula as string. Passed through 'glue::glue'. If given, 'outcome.str' and 'vars' are ignored. Optional.}
|
||||||
|
|
||||||
|
\item{args.list}{List of arguments passed to 'fun' with 'do.call'.}
|
||||||
|
|
||||||
|
\item{fun}{Name of function as character vector or function to use for model creation.}
|
||||||
|
|
||||||
|
\item{vars}{character vector of variables to include}
|
||||||
|
}
|
||||||
|
\value{
|
||||||
|
object of standard class for fun
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
Print a flexible baseline characteristics table
|
||||||
|
}
|
||||||
|
\examples{
|
||||||
|
gtsummary::trial |>
|
||||||
|
regression_model(outcome.str = "stage", fun = "MASS::polr")
|
||||||
|
gtsummary::trial |>
|
||||||
|
regression_model(
|
||||||
|
outcome.str = "age",
|
||||||
|
outcome.factor = FALSE,
|
||||||
|
fun = "stats::lm",
|
||||||
|
formula.str = "{outcome.str}~.",
|
||||||
|
args.list = NULL
|
||||||
|
)
|
||||||
|
gtsummary::trial |> regression_model(
|
||||||
|
outcome.str = "trt",
|
||||||
|
fun = "stats::glm",
|
||||||
|
args.list = list(family = binomial(link = "logit"))
|
||||||
|
)
|
||||||
|
}
|
||||||
45
man/regression_table.Rd
Normal file
45
man/regression_table.Rd
Normal file
|
|
@ -0,0 +1,45 @@
|
||||||
|
% Generated by roxygen2: do not edit by hand
|
||||||
|
% Please edit documentation in R/regression_table.R
|
||||||
|
\name{regression_table}
|
||||||
|
\alias{regression_table}
|
||||||
|
\title{Create table of regression model}
|
||||||
|
\usage{
|
||||||
|
regression_table(data, args.list = NULL, fun = "gtsummary::tbl_regression")
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{data}{regression model}
|
||||||
|
|
||||||
|
\item{args.list}{list of arguments passed to 'fun'.}
|
||||||
|
|
||||||
|
\item{fun}{function to use for table creation. Default is "gtsummary::tbl_regression".}
|
||||||
|
}
|
||||||
|
\value{
|
||||||
|
object of standard class for fun
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
Create table of regression model
|
||||||
|
}
|
||||||
|
\examples{
|
||||||
|
gtsummary::trial |>
|
||||||
|
regression_model(
|
||||||
|
outcome.str = "stage",
|
||||||
|
fun = "MASS::polr"
|
||||||
|
) |>
|
||||||
|
regression_table(args.list = list(exponentiate = TRUE))
|
||||||
|
gtsummary::trial |>
|
||||||
|
regression_model(
|
||||||
|
outcome.str = "age",
|
||||||
|
outcome.factor = FALSE,
|
||||||
|
fun = "stats::lm",
|
||||||
|
formula.str = "{outcome.str}~.",
|
||||||
|
args.list = NULL
|
||||||
|
) |>
|
||||||
|
regression_table()
|
||||||
|
gtsummary::trial |>
|
||||||
|
regression_model(
|
||||||
|
outcome.str = "trt",
|
||||||
|
fun = "stats::glm",
|
||||||
|
args.list = list(family = binomial(link = "logit"))
|
||||||
|
) |>
|
||||||
|
regression_table(args.list = list(exponentiate = TRUE))
|
||||||
|
}
|
||||||
31
man/write_quarto.Rd
Normal file
31
man/write_quarto.Rd
Normal file
|
|
@ -0,0 +1,31 @@
|
||||||
|
% Generated by roxygen2: do not edit by hand
|
||||||
|
% Please edit documentation in R/helpers.R
|
||||||
|
\name{write_quarto}
|
||||||
|
\alias{write_quarto}
|
||||||
|
\title{Wrapper to save data in RDS, load into specified qmd and render}
|
||||||
|
\usage{
|
||||||
|
write_quarto(
|
||||||
|
data,
|
||||||
|
fileformat,
|
||||||
|
qmd.file = here::here("analyses.qmd"),
|
||||||
|
file = NULL,
|
||||||
|
...
|
||||||
|
)
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{data}{list to pass to qmd}
|
||||||
|
|
||||||
|
\item{fileformat}{output format. Ignored if file!=NULL}
|
||||||
|
|
||||||
|
\item{qmd.file}{qmd file to render. Default is 'here::here("analyses.qmd")'}
|
||||||
|
|
||||||
|
\item{file}{exact filename (Optional)}
|
||||||
|
|
||||||
|
\item{...}{Ignored for now}
|
||||||
|
}
|
||||||
|
\value{
|
||||||
|
none
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
Wrapper to save data in RDS, load into specified qmd and render
|
||||||
|
}
|
||||||
15
publish_shiny.R
Normal file
15
publish_shiny.R
Normal file
|
|
@ -0,0 +1,15 @@
|
||||||
|
# Prep for shiny
|
||||||
|
# system2("cat ./R/index_from_raw.R ./R/plot_index.R ./R/read_file.R > ./R/functions.R")
|
||||||
|
|
||||||
|
project.aid::merge_scripts(list.files("R/",full.names = TRUE),dest = here::here("app/functions.R"))
|
||||||
|
|
||||||
|
# Typical shiny
|
||||||
|
shiny::runApp(appDir = here::here("app/"), launch.browser = TRUE)
|
||||||
|
|
||||||
|
project.aid::deploy_shiny(
|
||||||
|
files = c("server.R", "ui.R"),
|
||||||
|
account.name = "agdamsbo",
|
||||||
|
name.app = "webResearch",
|
||||||
|
name.token = "rsconnect_agdamsbo_token",
|
||||||
|
name.secret = "rsconnect_agdamsbo_secret"
|
||||||
|
)
|
||||||
7
renv/.gitignore
vendored
Normal file
7
renv/.gitignore
vendored
Normal file
|
|
@ -0,0 +1,7 @@
|
||||||
|
library/
|
||||||
|
local/
|
||||||
|
cellar/
|
||||||
|
lock/
|
||||||
|
python/
|
||||||
|
sandbox/
|
||||||
|
staging/
|
||||||
1305
renv/activate.R
Normal file
1305
renv/activate.R
Normal file
File diff suppressed because it is too large
Load diff
1658
toPdfViaTempFile14132-0.html
Normal file
1658
toPdfViaTempFile14132-0.html
Normal file
File diff suppressed because it is too large
Load diff
0
toPdfViaTempFile14132-1.pdf
Normal file
0
toPdfViaTempFile14132-1.pdf
Normal file
22
webResearch.Rproj
Normal file
22
webResearch.Rproj
Normal file
|
|
@ -0,0 +1,22 @@
|
||||||
|
Version: 1.0
|
||||||
|
|
||||||
|
RestoreWorkspace: No
|
||||||
|
SaveWorkspace: No
|
||||||
|
AlwaysSaveHistory: Default
|
||||||
|
|
||||||
|
EnableCodeIndexing: Yes
|
||||||
|
UseSpacesForTab: Yes
|
||||||
|
NumSpacesForTab: 2
|
||||||
|
Encoding: UTF-8
|
||||||
|
|
||||||
|
RnwWeave: Sweave
|
||||||
|
LaTeX: pdfLaTeX
|
||||||
|
|
||||||
|
AutoAppendNewline: Yes
|
||||||
|
StripTrailingWhitespace: Yes
|
||||||
|
LineEndingConversion: Posix
|
||||||
|
|
||||||
|
BuildType: Package
|
||||||
|
PackageUseDevtools: Yes
|
||||||
|
PackageInstallArgs: --no-multiarch --with-keep.source
|
||||||
|
PackageRoxygenize: rd,collate,namespace
|
||||||
Loading…
Add table
Reference in a new issue