Version 3, 29 June 2007
Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
+The GNU General Public License is a free, copyleft license for software and other kinds of works.
+The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, the GNU General Public License is 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. We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also to any other work released this way by its authors. You can apply it to your programs, too.
+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.
+To protect your rights, we need to prevent others from denying you these rights or asking you to surrender the rights. Therefore, you have certain responsibilities if you distribute copies of the software, or if you modify it: responsibilities to respect the freedom of others.
+For example, if you distribute copies of such a program, whether gratis or for a fee, you must pass on to the recipients the same freedoms that you received. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights.
+Developers that use the GNU GPL protect your rights with two steps: (1) assert copyright on the software, and (2) offer you this License giving you legal permission to copy, distribute and/or modify it.
+For the developers’ and authors’ protection, the GPL clearly explains that there is no warranty for this free software. For both users’ and authors’ sake, the GPL requires that modified versions be marked as changed, so that their problems will not be attributed erroneously to authors of previous versions.
+Some devices are designed to deny users access to install or run modified versions of the software inside them, although the manufacturer can do so. This is fundamentally incompatible with the aim of protecting users’ freedom to change the software. The systematic pattern of such abuse occurs in the area of products for individuals to use, which is precisely where it is most unacceptable. Therefore, we have designed this version of the GPL to prohibit the practice for those products. If such problems arise substantially in other domains, we stand ready to extend this provision to those domains in future versions of the GPL, as needed to protect the freedom of users.
+Finally, every program is threatened constantly by software patents. States should not allow patents to restrict development and use of software on general-purpose computers, but in those that do, we wish to avoid the special danger that patents applied to a free program could make it effectively proprietary. To prevent this, the GPL assures that patents cannot be used to render the program non-free.
+The precise terms and conditions for copying, distribution and modification follow.
+“This License” refers to version 3 of the GNU General Public License.
+“Copyright” also means copyright-like laws that apply to other kinds of works, such as semiconductor masks.
+“The Program” refers to any copyrightable work licensed under this License. Each licensee is addressed as “you”. “Licensees” and “recipients” may be individuals or organizations.
+To “modify” a work means to copy from or adapt all or part of the work in a fashion requiring copyright permission, other than the making of an exact copy. The resulting work is called a “modified version” of the earlier work or a work “based on” the earlier work.
+A “covered work” means either the unmodified Program or a work based on the Program.
+To “propagate” a work means to do anything with it that, without permission, would make you directly or secondarily liable for infringement under applicable copyright law, except executing it on a computer or modifying a private copy. Propagation includes copying, distribution (with or without modification), making available to the public, and in some countries other activities as well.
+To “convey” a work means any kind of propagation that enables other parties to make or receive copies. Mere interaction with a user through a computer network, with no transfer of a copy, is not conveying.
+An interactive user interface displays “Appropriate Legal Notices” to the extent that it includes a convenient and prominently visible feature that (1) displays an appropriate copyright notice, and (2) tells the user that there is no warranty for the work (except to the extent that warranties are provided), that licensees may convey the work under this License, and how to view a copy of this License. If the interface presents a list of user commands or options, such as a menu, a prominent item in the list meets this criterion.
+The “source code” for a work means the preferred form of the work for making modifications to it. “Object code” means any non-source form of a work.
+A “Standard Interface” means an interface that either is an official standard defined by a recognized standards body, or, in the case of interfaces specified for a particular programming language, one that is widely used among developers working in that language.
+The “System Libraries” of an executable work include anything, other than the work as a whole, that (a) is included in the normal form of packaging a Major Component, but which is not part of that Major Component, and (b) serves only to enable use of the work with that Major Component, or to implement a Standard Interface for which an implementation is available to the public in source code form. A “Major Component”, in this context, means a major essential component (kernel, window system, and so on) of the specific operating system (if any) on which the executable work runs, or a compiler used to produce the work, or an object code interpreter used to run it.
+The “Corresponding Source” for a work in object code form means all the source code needed to generate, install, and (for an executable work) run the object code and to modify the work, including scripts to control those activities. However, it does not include the work’s System Libraries, or general-purpose tools or generally available free programs which are used unmodified in performing those activities but which are not part of the work. For example, Corresponding Source includes interface definition files associated with source files for the work, and the source code for shared libraries and dynamically linked subprograms that the work is specifically designed to require, such as by intimate data communication or control flow between those subprograms and other parts of the work.
+The Corresponding Source need not include anything that users can regenerate automatically from other parts of the Corresponding Source.
+The Corresponding Source for a work in source code form is that same work.
+All rights granted under this License are granted for the term of copyright on the Program, and are irrevocable provided the stated conditions are met. This License explicitly affirms your unlimited permission to run the unmodified Program. The output from running a covered work is covered by this License only if the output, given its content, constitutes a covered work. This License acknowledges your rights of fair use or other equivalent, as provided by copyright law.
+You may make, run and propagate covered works that you do not convey, without conditions so long as your license otherwise remains in force. You may convey covered works to others for the sole purpose of having them make modifications exclusively for you, or provide you with 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.
+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.
+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.
+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.
+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.
+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 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.
+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 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.
+“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:
+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.
+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.
+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.
+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.
+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.
+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.
+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 Affero 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 special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such.
+The Free Software Foundation may publish revised and/or new versions of the GNU 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 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 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 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.
+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.
+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.
+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
+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 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 General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.Also add information on how to contact you by electronic and paper mail.
+If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode:
+<program> Copyright (C) <year> <name of author>
+This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
+This is free software, and you are welcome to redistribute it
+under certain conditions; type 'show c' for details.The hypothetical commands show w and show c should show the appropriate parts of the General Public License. Of course, your program’s commands might be different; for a GUI interface, you would use an “about box”.
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 GPL, see <http://www.gnu.org/licenses/>.
+The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read <http://www.gnu.org/philosophy/why-not-lgpl.html>.
+example_mab.Rmdrsvie package
+## 1. Load package and functions This vignette explains how to use
+the rsvie package to evaluate the impact of different RSV
+intervention programmes. The package is designed to be flexible and
+allow the user to define different intervention programmes, with
+different immunological profiles, and evaluate their impact on RSV
+outcomes.
## ℹ Loading rsvie
+## Creating a new generic function for 'run' in package 'rsvie'Let’s have a more detailed look at what’s in these slots. I wouldn’t +recommend changing them, but future package iterations should allow for +more flexibility.
+With this empty class, we now add information on the economics of the +model. This includes the health outcomes considered, the risk of each +health outcome occurring per infection, and the QALY loss and cost of +each outcome. First, we define the risk of each health outcome per age +group:
+## Loading required package: EnvStats##
+## Attaching package: 'EnvStats'## The following objects are masked from 'package:stats':
+##
+## predict, predict.lmNow, we need to load the QALY loss and cost for each outcome per age +group.
+With the economics and risks defined, we can now define an +intervention programme. We have several vignettes showing how to +evaluate various types of programmes that use different products. Here +is a simple example:
+To simulate a programme, we call rsvie::run on the class
+defined above. This will simulate the programme and return a class with
+the results.
example_mat.Rmdrsvie package
+## 1. Load package and functions This vignette explains how to use
+the rsvie package to evaluate the impact of different RSV
+intervention programmes. The package is designed to be flexible and
+allow the user to define different intervention programmes, with
+different immunological profiles, and evaluate their impact on RSV
+outcomes.
## ℹ Loading rsvie
+## Creating a new generic function for 'run' in package 'rsvie'Let’s have a more detailed look at what’s in these slots. I wouldn’t +recommend changing them, but future package iterations should allow for +more flexibility.
+With this empty class, we now add information on the economics of the +model. This includes the health outcomes considered, the risk of each +health outcome occurring per infection, and the QALY loss and cost of +each outcome. First, we define the risk of each health outcome per age +group:
+## Loading required package: EnvStats##
+## Attaching package: 'EnvStats'## The following objects are masked from 'package:stats':
+##
+## predict, predict.lmNow, we need to load the QALY loss and cost for each outcome per age +group.
+With the economics and risks defined, we can now define an +intervention programme. We have several vignettes showing how to +evaluate various types of programmes that use different products. Here +is a simple example:
+To simulate a programme, we call rsvie::run on the class
+defined above. This will simulate the programme and return a class with
+the results.
example_oa.Rmdrsvie package
+## 1. Load package and functions This vignette explains how to use
+the rsvie package to evaluate the impact of different RSV
+intervention programmes. The package is designed to be flexible and
+allow the user to define different intervention programmes, with
+different immunological profiles, and evaluate their impact on RSV
+outcomes.
## ℹ Loading rsvie
+## Creating a new generic function for 'run' in package 'rsvie'Let’s have a more detailed look at what’s in these slots. I wouldn’t +recommend changing them, but future package iterations should allow for +more flexibility.
+With this empty class, we now add information on the economics of the +model. This includes the health outcomes considered, the risk of each +health outcome occurring per infection, and the QALY loss and cost of +each outcome. First, we define the risk of each health outcome per age +group:
+## Loading required package: EnvStats##
+## Attaching package: 'EnvStats'## The following objects are masked from 'package:stats':
+##
+## predict, predict.lmNow, we need to load the QALY loss and cost for each outcome per age +group.
+With the economics and risks defined, we can now define an +intervention programme. We have several vignettes showing how to +evaluate various types of programmes that use different products. Here +is a simple example:
+## Warning in read.table(system.file(package = "rsvie", "extdata", "uptakes_uk", :
+## incomplete final line found by readTableHeader on '/Users/lshdh2/Dropbox/Mac
+## (3)/Documents/research/rsv/packages/rsvie/inst/extdata/uptakes_uk/flu_oa.csv'
+## Warning in read.table(system.file(package = "rsvie", "extdata", "uptakes_uk", :
+## incomplete final line found by readTableHeader on '/Users/lshdh2/Dropbox/Mac
+## (3)/Documents/research/rsv/packages/rsvie/inst/extdata/uptakes_uk/flu_oa.csv'To simulate a programme, we call rsvie::run on the class
+defined above. This will simulate the programme and return a class with
+the results.
rsvie is a simulation package which allows users to evaluate the impact and cost-effectiveness of potential RSV intervention programmes in England and Wales. The user can define intervention program timings, products, risk of outcomes, costs, and QALYs.
First, install R.
+Then, install the development version of ‘rsvie’ by running the following commands in R.
+# install.package("devtools") only run if devtools isn't installed.
+library(devtools)
+github_install("dchodge/rsvie")
+library(rsvie)The user must define several components in order to simulate the impact of an RSV intervention programme. These are 1. add_economics, the user must define the health outcomes considered, the risk of each health outcome occurring per-infection, and the QALY loss and cost of each outcome. 2. add_programme, the user must define the programme characteristics they wish to evaluate, including the timings (start date and end date), the target age group, the product’s immunological profile, and the uptake rate.
A detailed vignette explaining defining these characteristics can be found in vignettes/example.Rmd.
We also include several vignettes showing how to evaluate various programmes. These are found in vignettes/sanity_check_*.
If you have any questions, please email me at david.hodgson@lshtm.ac.uk
+RSVProgramme-class.RdA class to represent an RSV (Respiratory Syncytial Virus) Programme.
+econ_nameA character string representing the economic name.
prog_nameA character string representing the programme name.
modelAn object of class refClass representing the model.
uk_dataA list containing UK data.
model_parA list of model parameters.
econ_parA list of economic parameters.
model_calendarA list representing the model calendar.
dose_calendarA list representing the dose calendar.
immune_profileA list representing the immune profile.
econ_dfA data.frame containing economic data.
risks_dfA data.frame containing risk data.
risks_vhr_dfA data.frame containing very high risk data.
outcomes_vecA vector of outcomes.
postA data.frame containing posterior data.
seedsA vector of seeds.
SA numeric value.
raw_inciA list of raw incidence data.
wane_func_stringA character string representing the waning function.
wane_func_string_vhrA character string representing the waning function for very high risk.
outcomesA list of outcomes.
samples_outcomesA list of sample outcomes.
samples_outcomes_VHRA list of sample outcomes for very high risk.
efficaciesA vector of efficacies.
cov_matA numeric matrix representing the covariance matrix.
full_outputA logical value indicating whether to produce full output.
add_economics-RSVProgramme-method.RdThis method adds economic data to an RSVProgramme object.
+# S4 method for class 'RSVProgramme'
+add_economics(object, econ_name, econ_raw, risks_raw, risks_vhr_raw)An object of class RSVProgramme.
A character string representing the name of the economic data.
A data frame containing the raw economic data.
A data frame containing the raw risks data.
A data frame containing the raw very high risk (VHR) data.
The updated RSVProgramme object with the added economic data.
This method performs the following steps:
Checks if the output directory for the economic data exists, and creates it if it does not.
Assigns the provided economic data and risk data to the corresponding slots in the RSVProgramme object.
Extracts unique outcomes from the economic data and assigns them to the outcomes_vec slot.
Stops execution if no outcomes are detected in the economic data.
Generates samples of outcomes and assigns them to the samples_outcomes and samples_outcomes_VHR slots.
if (FALSE) { # \dontrun{
+ rsv_programme <- new("RSVProgramme")
+ rsv_programme <- add_economics(rsv_programme, "econ_data", econ_raw_df, risks_raw_df, risks_vhr_raw_df)
+} # }
+add_economics.RdThis generic function is used to add economics data to a specified object.
+add_economics(object, econ_name, econ_raw, risks_raw, risks_vhr_raw)The object to which the economics data will be added.
A character string representing the name of the economics data.
The raw economics data to be added.
The raw risks data associated with the economics data.
The raw very high risk data associated with the economics data.
The object with the added economics data.
+add_fitted_dist.RdThis function fits a specified distribution to the data in a given data frame and adds the fitted distribution as a new column.
+add_fitted_dist(cost_df, dist)A data frame containing the data to which the distribution will be fitted. The data frame should have columns named "mean", "lb_95", and "ub_95".
A character string specifying the distribution to fit. The distribution should be one of the distributions supported by the q function in R (e.g., "norm" for normal distribution, "tri" for triangular distribution).
A data frame with an additional column named fitt_dist containing the fitted distribution for each row.
if (FALSE) { # \dontrun{
+cost_df <- data.frame(mean = c(10, 20), lb_95 = c(5, 15), ub_95 = c(15, 25))
+add_fitted_dist(cost_df, "norm")
+} # }
+
+add_programme-RSVProgramme-method.RdThis method adds a programme to an RSVProgramme object, setting various attributes and creating necessary directories.
+# S4 method for class 'RSVProgramme'
+add_programme(object, prog_name, cal, cal_vhr, immune_profile)An object of class RSVProgramme.
A character string representing the name of the programme.
A calendar object used for the programme.
A calendar object for very high-risk (VHR) groups.
A list containing the immune profile information.
The updated RSVProgramme object with the new programme added.
This function sets the programme name, checks and creates necessary directories, initializes dose and sero matrices, calculates daily uptake, converts matrices to transmission calendars, and sets various attributes in the RSVProgramme object.
add_programme.RdThis function is a generic method for adding a programme to an object.
+add_programme(object, prog_name, cal, cal_vhr, immune_profile)The object to which the programme will be added.
The name of the programme to be added.
The calendar associated with the programme.
The calendar with very high resolution associated with the programme.
The immune profile associated with the programme.
The object with the added programme.
+calculate_daily_uptake.RdThis function calculates the daily uptake for different age groups based on the provided calibration data frame.
+calculate_daily_uptake(object, cal_df)A matrix with 365 rows (days) and 25 columns (age groups) representing the daily uptake.
+The function processes each age group, calculates the start and end positions within the year, and fills the uptake matrix accordingly. +Different uptake types such as "linear", "birth_rate", "flu_oa", and "oa_2425" are handled.
+if (FALSE) { # \dontrun{
+object <- your_object_with_uk_data
+cal_df <- your_calibration_data_frame
+daily_uptake_matrix <- calculate_daily_uptake(object, cal_df)
+} # }
+checkout_incidence.RdThis function processes the incidence data from an object.
+checkout_incidence(object, rerun = FALSE)An object containing the raw incidence data.
A logical value indicating whether to rerun the rsvie::run function on the object. Default is TRUE.
none
+A data frame containing the processed incidence data with additional columns for time, age group, social group, and risk group.
+if (FALSE) { # \dontrun{
+ result <- checkout_incidence(my_object)
+} # }
+checkout_states.RdThis function processes the states of a given object and returns a data table with detailed information about each state.
+checkout_states(object)A data table with columns for time, incidence, age group, risk group, social group, model type, and state name.
+The function generates a list of state names and categorizes them into risk groups, social groups, and model types. It then runs the state function on the input object and processes the resulting states into a data frame. The data frame is then transformed into a long format and additional columns are added to provide detailed information about each state.
+compare_interventions.RdThis function compares the outcomes of a base intervention with multiple other interventions.
+compare_interventions(obj_base, obj_inter)A data frame summarizing the total cases, cases in very high-risk (VHR) groups, and total cases for each age group and outcome, for both the base and other interventions.
+convert_efficacies.RdThis function takes an immune profile and converts it into a list of efficacies for different products.
+convert_efficacies(immune_profile)A list containing immune profile information. It should have the following structure:
A list with element b representing the efficacy for very high risk (VHR) individuals.
A list with elements b and product representing the efficacy and product type for mass immunization. The product can be "lav", "mab", or "mat".
A list with the following elements:
Efficacy for monoclonal antibodies (MAB) in very high risk individuals.
Efficacy for monoclonal antibodies (MAB) in mass immunization.
Efficacy for live attenuated vaccines (LAV) in mass immunization.
Efficacy for maternal antibodies (MAT) in mass immunization.
The function initializes the efficacy list with zeros. It then checks if the immune profile contains efficacy values for VHR and mass immunization and updates the efficacy list accordingly.
+convert_mat_to_trans_cal.RdThis function converts dose and sero matrices into a transmission calendar based on the provided immune profile.
+convert_mat_to_trans_cal(
+ all_dose,
+ all_sero,
+ cal_vhr,
+ daily_uptake_vhr,
+ cal,
+ daily_uptake,
+ immune_profile
+)A matrix representing all doses.
A matrix representing all sero values.
A calendar matrix for very high risk (VHR) individuals.
A matrix representing daily uptake for VHR individuals.
A calendar matrix for the general population.
A matrix representing daily uptake for the general population.
A list containing immune profiles for VHR and general population.
A list containing updated dose and sero matrices.
The function first creates a VHR calendar if the immune profile for VHR is not "none". It then calculates the sero and dose models using the get_sero_dose_cals helper function. The results are stored in the all_sero and all_dose matrices.
The get_sero_dose_cals function calculates the dose and sero models based on the provided calendar, daily uptake, and immune profile. It considers different sero delays and coverage values.
convert_to_outcomes.RdThis function processes an object to calculate various health outcomes over time.
+convert_to_outcomes(object, yrsum = 2)A list containing the following elements:
+A data frame with weekly outcomes by age group.
A data frame with discounted costs by outcome and age group.
A data frame with discounted quality-adjusted life years (QALYs) by outcome and age group.
A vector containing the number of doses administered.
The function performs the following steps:
Extracts necessary data from the input object.
Calculates the proportion of individuals in different states over time.
Estimates the incidence of various health outcomes for vaccinated and unvaccinated groups.
Computes the protected incidence for different health outcomes.
Aggregates the results to provide weekly outcomes, costs, and QALYs by age group.
Applies discounting to costs and QALYs.
if (FALSE) { # \dontrun{
+result <- convert_to_outcomes(my_object, yrsum = 3)
+} # }
+covert_raw_to_risk.RdThis function converts raw outcome data to risk metrics based on population data and model cases sample mean.
+covert_raw_to_risk(object, outcomes_raw, model_cases_sample_mean)A data frame with calculated risk metrics for each age group and outcome.
+The function performs the following steps:
Extracts population and age group data from the input object.
Defines helper functions to check the completeness of data and calculate risk per infection.
Checks that each outcome has data for all age groups.
Combines raw outcomes data with model cases data and population data.
Calculates the risk per infection for each outcome and age group.
if (FALSE) { # \dontrun{
+ result <- covert_raw_to_risk(object, outcomes_raw, model_cases_sample_mean)
+ print(result)
+} # }
+
+get_averted_df.RdThis function calculates the number of averted cases for different interventions compared to a base scenario.
+get_averted_df(base, interventions)A data frame with the calculated averted cases and proportions, with recoded age groups and outcomes.
+The function performs the following steps:
Joins the base and intervention data frames on s, outcome, and age_group.
Calculates the total number of cases averted and the proportion of cases averted.
Recodes the age groups and outcomes to more descriptive labels.
Converts the recoded age groups and outcomes to factors with specific levels.
if (FALSE) { # \dontrun{
+base <- data.frame(s = 1:5, outcome = rep("symptomatic", 5), age_group = 1:5, cases_total = c(100, 200, 150, 120, 130))
+interventions <- data.frame(s = 1:5, outcome = rep("symptomatic", 5), age_group = 1:5, cases_total = c(90, 180, 140, 110, 120))
+get_averted_df(base, interventions)
+} # }
+get_coverage.RdThis function calculates the coverage based on the immune profile mass and calibration data.
+get_coverage(immune_profile_mass, cal)The coverage value. If the product in the immune profile mass is "mat", it returns the mean of the positive coverage values from the calibration data. Otherwise, it returns 0.
+immune_profile_mass <- data.frame(product = "mat")
+cal <- data.frame(cov = c(0.1, 0.2, 0, -0.1))
+get_coverage(immune_profile_mass, cal)
+#> [1] 0.15
+get_daily_uptake.RdThis function calculates the daily uptake based on weekly uptake data.
+get_daily_uptake(up_week_raw, start_time)A numeric vector of length 365 representing the daily uptake.
+The function first processes the weekly data to fill a weekly uptake vector, then calculates the daily uptake by interpolating the weekly data.
+if (FALSE) { # \dontrun{
+up_week_raw <- c(0.1, 0.2, 0.3, 0.4, 0.5)
+start_time <- 1
+daily_uptake <- get_daily_uptake(up_week_raw, start_time)
+} # }
+get_efficacies_sample.RdThis function retrieves a sample of efficacies from an object based on a provided seed.
+get_efficacies_sample(object, seed)A list containing the sampled efficacies for each efficacy type.
+The function initializes a list with efficacy types set to 0. It then iterates over the names of the efficacy types and checks if the length of the efficacy values for each type is greater than 1. If so, it selects the efficacy value based on the provided seed. Otherwise, it assigns the single efficacy value to the list. The function finally returns the list of sampled efficacies.
+
+ All functions+ + |
+ |
|---|---|
| + + | +RSVProgramme Class |
+
| + + | +Add Economics Data to RSVProgramme Object |
+
| + + | +Add Economics Data to an Object |
+
| + + | +Add Fitted Distribution to Data Frame |
+
| + + | +Add Programme to RSVProgramme Object |
+
| + + | +Add Programme |
+
| + + | +Calculate Daily Uptake |
+
| + + | +function to conver the incidence matrix from a run to a data.frame |
+
| + + | +Checkout States |
+
| + + | +Compare Interventions |
+
| + + | +Convert Immune Profile to Efficacies |
+
| + + | +Convert Matrices to Transmission Calendar |
+
| + + | +Convert to Outcomes |
+
| + + | +Convert Raw Outcomes to Risk |
+
| + + | +Calculate Averted Cases Data Frame |
+
| + + | +Get Coverage |
+
| + + | +Calculate Daily Uptake from Weekly Data |
+
| + + | +Get Efficacies Sample |
+
| + + | +Initialise the RunInterventions class |
+
| + + | +A constructor to make an RSVProgramme object |
+
| + + | +Generate and output samples for economic and risk data |
+
| + + | +Plot Dosing Calendar |
+
| + + | +Plot Economics Data |
+
| + + | +Plot Economic Fit |
+
| + + | +Plot Outcomes |
+
| + + | +A setMethod for the |
+
| + + | +Run Method |
+
| + + | +A setMethod for the |
+
| + + | +Run State Generic Function |
+
| + + | +Summarise Outcomes |
+
make_RunInterventions.RdInitialise the RunInterventions class
+make_RunInterventions(RunInterventions, uk_data_sum, run_burn, run_full)A classRunInterventions which is fully parameterised
+output_samples.RdThis function processes raw economic and risk data, fits distributions to the data, +generates samples, and outputs the results to a specified file.
+output_samples(econ_raw, risks_raw, file.name)A list containing sampled outcomes for risks, QALYs, and costs.
+The function performs the following steps:
Fits triangular distributions to the risk, QALY, and cost data.
Generates samples for each outcome using the fitted distributions.
Outputs the sampled outcomes to the specified file.
plot_calendar.RdThis function generates and saves a plot of the dosing calendar for different age groups.
+plot_calendar(object)None
+The function performs the following steps:
Checks if the directory for saving the plot exists, and creates it if it does not.
Extracts unique age groups from the economic data frame within the object.
Updates the column names of the dose calendar matrices to match the age groups.
Converts the dose calendar matrices into a data frame suitable for plotting.
Generates a ggplot of the dosing calendar, with days of the year on the x-axis, age groups on the y-axis, and the proportion of doses as the fill color.
Saves the plot as a PNG file in the specified directory.
if (FALSE) { # \dontrun{
+plot_calendar(my_object)
+} # }
+plot_economics.RdThis function generates and saves plots for economic data, risks data, and very high-risk data from the given object.
+plot_economics(object)The function performs the following steps:
Checks if the directory for saving plots exists, and creates it if it does not.
Processes the economic data frame (econ_df) to create a combined data frame for QALY loss and Costs.
Generates and saves a plot for the economic data with uncertainty ribbons and lines.
Generates and saves a plot for the risks data with uncertainty ribbons and lines.
Generates and saves a plot for the very high-risk data with lines.
plot_economics_fit.RdThis function generates and saves plots comparing fitted distributions to reference data for risks, QALYs, and costs across different age groups.
+plot_economics_fit(object)None. The function saves the generated plots to the specified directory.
+The function performs the following steps:
Checks if the directory for saving plots exists, and creates it if it doesn't.
Extracts unique age groups from the economic data.
Defines a helper function to extract mean and 95% uncertainty intervals for model outcomes.
Extracts fitted model outcomes for risks, QALYs, and costs.
Prepares data frames for risks, QALYs, and costs by merging reference data with fitted model outcomes.
Defines a helper function to convert data frames to long format for plotting.
Converts the prepared data frames to long format.
Generates and saves plots comparing fitted model outcomes to reference data for risks, QALYs, and costs.
if (FALSE) { # \dontrun{
+ plot_economics_fit(my_economic_model)
+} # }
+plot_outcomes.RdThis function loads the run outputs from a specified file, extracts the outcomes data, and creates a boxplot of costs and QALY (Quality-Adjusted Life Year) outcomes. The plot is saved as a PNG file.
+plot_outcomes(object)A ggplot object representing the boxplot of costs and QALY outcomes.
+The function performs the following steps:
Loads the run outputs from a file located in the "outputs" directory.
Extracts the outcomes data from the loaded object.
Binds the costs and QALY data into a single data frame.
Creates a boxplot of the costs and QALY data using ggplot2.
Saves the plot as a PNG file in the "figs" subdirectory of the "outputs" directory.
run functionrun-RSVProgramme-method.RdA setMethod for the run function
# S4 method for class 'RSVProgramme'
+run(object, direct = FALSE, filename = NULL, yr_num = 2)The object on which the operation is performed.
A logical value indicating whether to run the operation directly.
An optional character string specifying the filename.
An integer specifying the number of years, default is 2.#' @return An RSVProgramme object
run.RdGeneric function to execute a specific operation.
+run(object, direct = FALSE, filename = NULL, yr_num = 2)The result of the operation.
+run_state functionrun_state-RSVProgramme-method.RdA setMethod for the run_state function
# S4 method for class 'RSVProgramme'
+run_state(object, S_i = 1, direct = FALSE)a matrix with all the values of the state variables in the dynamic transmission model
+run_state.RdThis is a generic function for running a state.
+run_state(object, S_i = 1, direct = FALSE)The result of the state run, depending on the method implementation.
+summarise_outcomes.RdThis function takes an object x and summarises the outcomes by grouping
+by s, outcome, and age_group, then calculates the total number of cases.
summarise_outcomes(x)A data frame with the total number of cases grouped by s, outcome, and age_group.