MIT License - -Copyright (c) 2018-2022 Carrie Daymont - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. +YEAR: 2022 +COPYRIGHT HOLDER: Carrie Daymont@@ -118,7 +102,7 @@License
vignettes/adult-algorithm.Rmd
adult-algorithm.Rmdvignettes/configuration.Rmd
configuration.Rmdref.data.path - defaults to using CDC reference data
from year 2000; supply a file path to use alternate reference data. Note
that when running from an installed growthcleanr package
-(e.g. having called library(growthcleanr)), this path does
+(e.g. having called library(growthcleanr)), this path does
not need to be specified. Developers testing the source code directly
from the source directory will need to specify this as well.
error.load.mincount - default 2;
@@ -335,7 +338,7 @@
survey
+smoothed using the svysmooth() function in the R survey
package to estimate the weight and height SD scores for each day up to
7,305 days, with a bandwidth chosen to balance between over- and
under-fitting, and interpolation between the estimates from this
diff --git a/docs/articles/developer-guidelines.html b/docs/articles/developer-guidelines.html
new file mode 100644
index 0000000..c6854bb
--- /dev/null
+++ b/docs/articles/developer-guidelines.html
@@ -0,0 +1,189 @@
+
+
+
+
+
+
+
+vignettes/developer-guidelines.Rmd
+ developer-guidelines.RmdWhen deploying updates to CRAN, here a few updates that you need to +check off before doing so:
+devtools::document()
+devtools::check():
+cran-comments.md and cannot be fixed, fix them. There
+should be no ERRORs or WARNINGs before submitting to CRAN.README.Rmd, re-knit to
+README.md
+pkgdown::build_site()
+vignettes/installation.Rmd
installation.Rmdgrowthcleanr has been developed and tested using R
-version 3.6 and more recently version 4+. It should work using R on
-Windows, macOS, or Unix/Linux, although there are some additional platform-specific notes you may wish to review.
You can install the growthcleanr package directly from
-GitHub using devtools in the R console with:
To get started with growthcleanr, install it from
+CRAN:
-install.packages("devtools")
-devtools::install_github("carriedaymont/growthcleanr", ref="main")Note that ref="main" is required; the default branch is
-“main”, and must be referred to explicitly.
If you are unable to install devtools, a similar
-function is available in the remotes package:
install.packages("growthcleanr")To install the latest development version from GitHub using
+devtools:
-install.packages("remotes")
-remotes::install_github("carriedaymont/growthcleanr", ref="main")Note that ref="main" is required; the default branch is
-“main”, and must be referred to explicitly.
growthcleanr itself has several dependencies, so it may
-take a little while to download and install everything on your
-machine.
devtools::install_github("carriedaymont/growthcleanr", ref="main")
+Installing growthcleanr will install several additional
+packages in turn.
See GitHub and source-level install for +developers for additional details.
If you want to work with and potentially change the
-growthcleanr code itself, you can download or clone the
-growthcleanr source code and then install it from source.
-To clone the source using git:
% git clone https://github.com/carriedaymont/growthcleanr.gitEither way, once you have the growthcleanr package
-source, open an R session from the growthcleanr base
-directory. Then install growthcleanr using the R devtools
-package:
You can install the growthcleanr package directly from
+GitHub using devtools in the R console with:
+install.packages("devtools")
+devtools::install_github("carriedaymont/growthcleanr", ref="main")growthcleanr itself has several dependencies, so it may
+take a little while to download and install everything on your
+machine.
Note that the ref="main" part is required; the default
+value of ref refers to a branch name that is not used in
+the growthcleanr repository, which instead uses a default
+branch called “main”.
To install a different branch, for example if you want to test a
+branch associated with a merge request, specify the branch name as the
+value of ref.
If you are unable to install devtools, a similar
+function is available in the remotes package:
+install.packages("remotes")
+remotes::install_github("carriedaymont/growthcleanr", ref="main")If you are developing the growthcleanr code itself, you
+can download or clone the growthcleanr source code and then
+install it from source. To clone the source using git:
% git clone https://github.com/carriedaymont/growthcleanr.gitOnce you have the growthcleanr package source, open an R
+session from the growthcleanr base directory. Then install
+growthcleanr using the R devtools package:
devtools::install(".")You can also install the package from an installation file if one is -obtained.
vignettes/large-data-sets.Rmd
large-data-sets.Rmd
-library(growthcleanr)
+library(growthcleanr)
count <- splitinput(syngrowth, fname = "mydata", fdir = tempdir())
count## [1] 7vignettes/next-steps.Rmd
next-steps.Rmdvignettes/output.Rmd
output.Rmdvignettes/quickstart.Rmd
quickstart.RmdTo get started with growthcleanr, the
-growthcleanr package must be installed. Installing
-growthcleanr will in turn install several additional
-packages. growthcleanr is not currently on CRAN.
One option for installation is using the devtools
-package. Install devtools and growthcleanr
-with the following commands:
growthcleanr package must be installed. To install the
+latest growthcleanr release from CRAN:
-install.packages("devtools")
-devtools::install_github("carriedaymont/growthcleanr", ref="main")If you are unable to install devtools, a similar
-function is available in the remotes package:
install.packages("growthcleanr")To install the latest development version from GitHub using
+devtools:
-install.packages("remotes")
-remotes::install_github("carriedaymont/growthcleanr", ref="main")Note that ref="main" is required whether you use
-devtools or remotes. The default
-growthcleanr code branch is “main”, and this must be
-referred to explicitly.
devtools::install_github("carriedaymont/growthcleanr", ref="main")
+Installing growthcleanr will install several additional
+packages in turn.
Further installation details and notes can be found under Installation.
source_data containing growth
data:
-library(growthcleanr)
+library(growthcleanr)
# prepare data as a data.table
data <- as.data.table(source_data)
diff --git a/docs/articles/usage.html b/docs/articles/usage.html
index db7600a..0876c26 100644
--- a/docs/articles/usage.html
+++ b/docs/articles/usage.html
@@ -33,7 +33,7 @@
vignettes/usage.Rmd
usage.Rmdlibrary(growthcleanr)vignettes/utilities.Rmd
utilities.RmdDaymont Carrie. Author. +
Daymont Carrie. Contributor, maintainer.
De los Santos Hannah. Contributor, maintainer. +
De los Santos Hannah. Contributor.