“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.
@@ -90,7 +93,7 @@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.
@@ -99,23 +102,23 @@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:
“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:
@@ -169,24 +172,24 @@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.
@@ -197,30 +200,30 @@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/>.<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.<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>.
@@ -271,7 +274,7 @@This is a vignette to help you become familiar with using
+explain(). Check out the
+function documentation for additional background and
+examples.
explain() prints a formatted message containing the
+result of a provided expression. This function is intended to be run
+interactively in the R console to aid in code understanding, transfer
+and debugging.
Below, we will go through a few examples cases using
+explain().
We will use explain() to document data manipulations and
+checks on the derived PK data set from mrgda.
+pk_data <- readr::read_csv(system.file("derived/pk.csv", package = "mrgda"))Before performing a data manipulation, we can use
+explain() to document why it is needed. This will help
+transfer knowledge of assumptions/decisions made to future authors or
+reviewers.
For instance, if we’re planning to exclude a record we believe is an
+outlier, we can first use explain() to show where in the
+data the issue exists.
mrgda::explain("ID = 1 has outlier in PK data, will remove", {
+ pk_data %>%
+ filter(ID == 1, DVID == 2, TIME < 24) %>%
+ select(ID, TIME, TAD, DV, DVID, EVID)
+})
+
+
[36m──
[39m
[1mExplanation: ID = 1 has outlier in PK data, will remove
[22m
[36m─────────────────────
[39m
+
+
[38;5;246m# A tibble: 5 × 6
[39m
+ ID TIME TAD DV DVID EVID
+
[3m
[38;5;246m<dbl>
[39m
[23m
[3m
[38;5;246m<dbl>
[39m
[23m
[3m
[38;5;246m<dbl>
[39m
[23m
[3m
[38;5;246m<chr>
[39m
[23m
[3m
[38;5;246m<dbl>
[39m
[23m
[3m
[38;5;246m<dbl>
[39m
[23m
+
[38;5;250m1
[39m 1 -
[31m0
[39m
[31m.
[39m
[31m17
[39m -
[31m0
[39m
[31m.
[39m
[31m17
[39m . 2 2
+
[38;5;250m2
[39m 1 0.68 0.68 15000 2 0
+
[38;5;250m3
[39m 1 2.68 2.68 10.4 2 0
+
[38;5;250m4
[39m 1 4.68 4.68 9.51 2 0
+
[38;5;250m5
[39m 1 23.6 23.6 2.02 2 0
+
+
[36m────────────────────────────────────────────────────────────────────────────────
[39mThis not only explains the issue, but shows where in the data it +occurs. Additionally, the formatting of the message separates itself +from the rest of the console outputs, helping it be more easily +seen.
+Users need to provide two arguments to explain(). The
+first is a message to display in the header and the second is an
+expression to display the result of.
As shown previously, this expression could be in the form of a +data.frame.
+mrgda::explain("Show the first few records of ID = 2 from the pk_data data.frame", {
+ pk_data %>%
+ filter(ID == 2) %>%
+ select(ID, TIME, DV, EVID) %>%
+ head()
+})
+
+
[36m──
[39m
[1mExplanation: Show the first few records of ID = 2 from the pk_data data.frame
[22m
+
+
[38;5;246m# A tibble: 6 × 4
[39m
+ ID TIME DV EVID
+
[3m
[38;5;246m<dbl>
[39m
[23m
[3m
[38;5;246m<dbl>
[39m
[23m
[3m
[38;5;246m<chr>
[39m
[23m
[3m
[38;5;246m<dbl>
[39m
[23m
+
[38;5;250m1
[39m 2 -
[31m0
[39m
[31m.
[39m
[31m22
[39m . 2
+
[38;5;250m2
[39m 2 0 . 1
+
[38;5;250m3
[39m 2 0.62 67.7 0
+
[38;5;250m4
[39m 2 2.58 33.9 0
+
[38;5;250m5
[39m 2 4.62 32.7 0
+
[38;5;250m6
[39m 2 22.8 14.4 0
+
+
[36m────────────────────────────────────────────────────────────────────────────────
[39mA vector can also be provided, such as one containing all the unique +studies from the data set.
+mrgda::explain("Show a vector of all studies in the data set", {
+ pk_data %>%
+ distinct(STUDYID) %>%
+ pull(STUDYID)
+})
+
+
[36m──
[39m
[1mExplanation: Show a vector of all studies in the data set
[22m
[36m───────────────────
[39m
+
+[1] "STUDY-X" "STUDY-Y"
+
+
[36m────────────────────────────────────────────────────────────────────────────────
[39mCalculations can even be performed.
+mrgda::explain("Total number of PK records that are not BLQ and doses", {
+ nrow(pk_data %>% filter(DVID == 2, BLQ == 1)) +
+ nrow(pk_data %>% filter(DVID ==1))
+})
+
+
[36m──
[39m
[1mExplanation: Total number of PK records that are not BLQ and doses
[22m
[36m──────────
[39m
+
+[1] 1034
+
+
[36m────────────────────────────────────────────────────────────────────────────────
[39mEssentially, anything that can be evaluated in the console can be
+provided as the .expr argument.
Site built with pkgdown 2.0.9.
+Site built with pkgdown 2.0.7.
diff --git a/articles/index.html b/articles/index.html index b6e2d7a..bb75275 100644 --- a/articles/index.html +++ b/articles/index.html @@ -1,5 +1,5 @@ -NEWS.md
+ explain function was added to the package. (#220)write_derived is now protected against commas causing issues with history.csv. (#218)Site built with pkgdown 2.0.9.
+Site built with pkgdown 2.0.7.
Site built with pkgdown 2.0.9.
+Site built with pkgdown 2.0.7.
diff --git a/reference/make_v_caption.html b/reference/make_v_caption.html index 007830d..fb53f95 100644 --- a/reference/make_v_caption.html +++ b/reference/make_v_caption.html @@ -1,5 +1,5 @@ -the Rstudio viewer pane process is stopped
another v() call is executed (only one will run at a time)
you manually kill it via the steps below:
-