Cran fixes #221

d-morrison · 2024-07-22T13:00:59Z

No description provided.

Merge branch 'CRAN-fixes' of https://github.com/UCD-SERG/serocalculator into CRAN-fixes # Conflicts: # R/est.incidence.R

… into CRAN-fixes

…ission documentation

cleaned up `f_dev` documentation

kristinawlai · 2024-08-15T22:15:17Z

NEWS.md

+
+# serocalculator (published versions)
+
+## serocalculator 1.0.3
+* Published to CRAN
+
+## serocalculator 1.0.2
+* Updated documentation and functionality based on CRAN resubmission
+* Deleted get_additional_data.R as it is no longer used
+
+# serocalculator (development versions)
+
+## serocalculator 1.2.0


Added new updates based on CRAN submission process

kristinawlai · 2024-08-15T22:16:38Z

R/autoplot.curve_params.R

 #'
 #' curve = load_curve_params("https://osf.io/download/rtw5k/") %>%
 #'   filter(antigen_iso %in% c("HlyE_IgA", "HlyE_IgG")) %>%
 #'   slice(1:100, .by = antigen_iso)  %>% # Reduce dataset for the purposes of this example
 #'   autoplot()
 #'
 #' curve
-#'
+#'}


Added missing closing bracket

kristinawlai · 2024-08-15T22:16:51Z

R/autoplot.curve_params.R

 autoplot.curve_params = function(
    object,
-    antigen_isos = object$antigen_iso %>% unique(),
+    antigen_isos = unique(object$antigen_iso),


Updated style to avoid pipe within an argument definition

fine by me; for future reference, is this a CRAN rule, a style guide rule, or just a choice we made?

I believe this was a CRAN rule, but I haven't found it to be sure. Will update if I find it.

R/df_to_array.R

R/f_dev.r

kristinawlai · 2024-08-15T22:27:27Z

R/print.seroincidence.R

-#' \dontrun{
-#' # Estimate seroincidence
-#' seroincidence <- est.incidence.by(...)
 #'
-#' # Print the seroincidence object to the console
-#' print(seroincidence)
+#' \donttest{
 #'
-#' # Or simply type (appropriate print method will be invoked automatically)
-#' seroincidence


Removed old, unfinished code and replace with an actual example

kristinawlai · 2024-08-15T22:27:49Z

R/print.seroincidence.by.R

-#' \dontrun{
-#' # Estimate seroincidence
-#' seroincidence <- est.incidence.by(...)
 #'
-#' # Print the seroincidence object to the console
-#' print(seroincidence)
+#' \donttest{
 #'
-#' # Or simply type (appropriate print method will be invoked automatically)
-#' seroincidence


Removed old, unfinished code and replace with an actual example

kristinawlai · 2024-08-15T22:28:00Z

R/print.summary.seroincidence.by.R

-#' \dontrun{
-#' # Estimate seroincidence
-#' seroincidence <- est.incidence.by(...)
 #'
-#' # Calculate summary statistics for the seroincidence object
-#' seroincidenceSummary <- summary(seroincidence)
+#' \donttest{
 #'
-#' # Print the summary of seroincidence object to the console
-#' print(seroincidenceSummary)
+#' library(tidyverse)
 #'
-#' # Or simply type (appropriate print method will be invoked automatically)
-#' seroincidenceSummary
-#' }


Removed old, unfinished code and replace with an actual example

kristinawlai · 2024-08-15T22:31:15Z

R/warn_missing_strata.R

-#' @examples
-#' \dontrun{
-#' expected_strata <- data.frame(Species = "banana", type = "orchid")
-#'
-#' warn.missing.strata(iris, expected_strata, dataname = "iris")
-#' }
-warn.missing.strata <- function(


Remove example from unexported functions, per CRAN request

kristinawlai · 2024-08-15T22:32:26Z

vignettes/articles/enteric_fever_example.Rmd

Updated section numbering format and corrected spelling errors

kristinawlai · 2024-08-19T18:38:53Z

R/graph.decay.curves.R

@d-morrison it doesn't look like this is an exported function but is wrapped by autoplot.curve_params.R. Should some of the text under @details be moved to autoplot.curve_params.R? Also since it is not longer exported, CRAN will likely have us remove the example.

kristinawlai · 2024-08-19T19:05:15Z

man/warn.missing.strata.Rd

-\examples{
-\dontrun{
-expected_strata <- data.frame(Species = "banana", type = "orchid")
-
-warn.missing.strata(iris, expected_strata, dataname = "iris")
-}
-}


Removed examples from non-exported functions per CRAN request

kristinawlai · 2024-08-19T19:06:02Z

man/summary.seroincidence.by.Rd

-\dontrun{
-# estimate seroincidence
-seroincidence <- est.incidence.by(...)

-# calculate summary statistics for the seroincidence object
-seroincidenceSummary <- summary(seroincidence)


Removed old incomplete example

kristinawlai · 2024-08-19T20:02:52Z

NEWS.md

Updated with newest changes and added sections for published and development versions

kristinawlai · 2024-08-19T20:04:46Z

R/autoplot.seroincidence.R

-#'
-autoplot.seroincidence =
-  function(object, log_x = FALSE, ...)
-{
-  to_return = attr(object, "ll_graph")


Reformatted to align with other functions

kristinawlai · 2024-08-19T20:07:17Z

R/autoplot.seroincidence.by.R

-#'
-autoplot.seroincidence.by = function(
+#' }
+autoplot.seroincidence.by <- function(


updated to "<-" to match other functions in main branch

kristinawlai · 2024-08-19T20:14:11Z

R/graph.decay.curves.R

@@ -20,14 +20,8 @@
 #' * Setting the  `n_curves` argument to a value smaller than the number of rows in `curve_params` will cause this function to select the first `n_curves` rows to graph.
 #' * Setting `n_curves` larger than the number of rows in ` will result all curves being plotted.


@d-morrison since plot_curve_params_one_ab() is not an exported function but is wrapped by autoplot.curve_params(), should some of the text in @details be moved there?

kristinawlai · 2024-08-19T20:15:05Z

R/graph.decay.curves.R

-#' @examples
-#' library(dplyr) # loads the `%>%` operator and `dplyr::filter()`
-#'
-#' load_curve_params("https://osf.io/download/rtw5k/") %>%
-#'   dplyr::filter(antigen_iso == "HlyE_IgG") %>%
-#'   serocalculator:::plot_curve_params_one_ab()
-#'


Removed example from non-exported function, per CRAN request

kristinawlai · 2024-08-19T20:16:06Z

R/graph.decay.curves.R

-
-# ggplot() +
-#   geom_line(data = serocourse.all, aes(x= t, y = res, group = iter)) +
-#   facet_wrap(~antigen_iso, ncol=2) +
-#   scale_y_log10(limits = c(0.9, 2000), breaks = c(1, 10, 100, 1000), minor_breaks = NULL) +
-#   theme_minimal()  +
-#   theme(axis.line=element_line()) +
-#   labs(x="Days since fever onset", y="ELISA units")
-
-# mcmc %>% ungroup() %>% slice_head(by = antigen_iso, n = 10) %>% droplevels() %>% plot_curve_params_one_ab(alpha  = .4) %>% print()


Removed what appeared to be old code from the bottom of this file.

kristinawlai · 2024-08-19T21:01:04Z

@d-morrison code annotation is completed and I believe I reconciled all issues between main and the CRAN branch. Since you created the PR, let me know when you think it's ready to approve.

d-morrison · 2024-08-22T06:42:30Z

@kristinawlai thanks! will review asap

d-morrison

still reviewing; please see comments so far

d-morrison · 2024-08-22T18:04:43Z

DESCRIPTION

@@ -1,16 +1,14 @@
 Package: serocalculator
 Type: Package
 Title: Estimating Infection Rates from Serological Data
-Version: 1.2.0.9000


why did the version number go backwards?

d-morrison · 2024-08-22T18:07:16Z

NEWS.md

+## serocalculator 1.0.3
+* Published to CRAN
+
+## serocalculator 1.0.2
+* Updated documentation and functionality based on CRAN re-submission
+* Deleted get_additional_data.R as it is no longer used
+
+# serocalculator (development versions)
+
+## serocalculator 1.0.3.9000
+* Reconciled CRAN version 1.0.3 with GitHub main branch (version)
+
+## serocalculator 1.2.0


version numbers are out of order here; let's discuss how to reconcile this list

Put release version marker where it is and leave development versions as they are. Moving forward, use CRAN version numbering (from 1.2.0.9000) --> this PR will use 1.2.0.9001

d-morrison · 2024-08-22T19:46:18Z

R/autoplot.curve_params.R

@@ -10,19 +10,21 @@
 #' @return a [ggplot2::ggplot()] object
 #' @export
 #' @examples
+#' \donttest{


I'll approve the use of \donttest for now, but I have created #238 as a better long-term solution

d-morrison · 2024-08-22T21:35:01Z

DESCRIPTION

-  samples into estimates of the frequency with which seroconversions (infections) 
-  occur in the sampled populations. Replaces the previous `seroincidence` package.
+Description: Translates antibody levels measured in cross-sectional population samples into estimates of the frequency with which seroconversions (infections) occur in the sampled populations. Replaces the previous 'seroincidence' package. Methods originally published in Simonsen et al. (2009) <doi:10.1002/sim.3592> and Teunis et al. (2012) <doi:10.1002/sim.5322>, and further developed in subsequent publications by de Graaf et al. (2014) <doi:10.1016/j.epidem.2014.08.002>, Teunis et al. (2016) <doi:10.1016/j.epidem.2016.04.001>, and Teunis et al. (2020) <doi:10.1002/sim.8578>.


This description is a little longer than usual (c.f. dplyr, ggplot2); in #239, we will move this information to an article, but until then, let's keep it here.

d-morrison · 2024-08-22T21:41:51Z

R/autoplot.curve_params.R

 autoplot.curve_params = function(
    object,
-    antigen_isos = object$antigen_iso %>% unique(),
+    antigen_isos = unique(object$antigen_iso),


fine by me; for future reference, is this a CRAN rule, a style guide rule, or just a choice we made?

d-morrison · 2024-08-22T21:44:39Z

R/autoplot.seroincidence.R

+    log_x = FALSE,
+    ...)
+  {
+    to_return = attr(object, "ll_graph")


time to learn about unit testing; please add a test to cover this line

d-morrison · 2024-08-22T23:41:20Z

R/autoplot.seroincidence.R

-{
-  to_return = attr(object, "ll_graph")
+#' }
+autoplot.seroincidence <-function(


we're missing a space between <- and function here (see https://style.tidyverse.org/syntax.html#extra-spaces:~:text=%2C%20%2D%2C-,%3C%2D,-%2C%20etc.)%20should%20always)

kristinawlai and others added 30 commits May 22, 2024 14:10

fixes to llik and sim.cs

52f8ae1

Update notes before submission to CRAN

9e6ae3d

Reduce example run-time by adding \dontrun to long sections of examples.

afe705e

Reduce example run-time by adding \dontrun to long sections of examples.

012dcaf

fix merge issue

e881172

Merge branch 'CRAN-fixes' of https://github.com/UCD-SERG/serocalculator into CRAN-fixes # Conflicts: # R/est.incidence.R

further reduce examples

134602d

Further reduce examples

39bff66

Further reduce examples

720f528

Merge branch 'CRAN-fixes' of https://github.com/UCD-SERG/serocalculator…

ff58791

… into CRAN-fixes

Reduce additional example

591c778

Fix spelling in Description, reduce example runtime, update CRAN subm…

e45dd9a

…ission documentation

Add references to description as suggested by CRAN

2c0e8c8

Remove example from unexported function as requested by CRAN

5053f19

Remove directed quotation mars as requested by CRAN

8b9f395

Replace ":::" with "::" as requested by CRAN + document()

0cb57cd

Add on.exit() to reset timeout options as requested by CRAN

1c5c491

Replace print() with message() in message to user, as reauested by CRAN

f43f498

remove example from unexported function

e18e3f0

Add @return to specify output in \value, as requested by CRAN

e0a5e65

Update version with edits based on CRAN comments

3018f56

Updated CRAN comments with responses and specific changes

5528632

Replace \dontrun with \donttest in examples, as requeted by CRAN

a0acf5d

fix errors

285163a

Update NEWS and additional \donttest adjustments in examples

f0c9c67

Fixed typo

801d719

Update CRAN comments, make additional edits with Ezra's feedback

85d4e84

troubleshooting

c859481

delete get_additional_data.R, add updated examples to summary functions

246c52c

cleaned up f_dev documentation

6a8c62d

Merge pull request #169 from UCD-SERG/CRAN-fixes-em

25d2934

cleaned up `f_dev` documentation

kristinawlai reviewed Aug 15, 2024

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matching style to main

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reconcile CRAN vs main branches

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Updated with newest changes and added sections for published and development versions

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kristinawlai and others added 2 commits August 19, 2024 13:24

Fix spelling errors + revert changes to main branch

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Merge branch 'main' into CRAN-fixes

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kristinawlai marked this pull request as ready for review August 19, 2024 20:58

kristinawlai self-requested a review August 19, 2024 21:00

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revert to include example + @nord

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Cran fixes #221

Cran fixes #221

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		@@ -20,14 +20,8 @@
		#' * Setting the `n_curves` argument to a value smaller than the number of rows in `curve_params` will cause this function to select the first `n_curves` rows to graph.
		#' * Setting `n_curves` larger than the number of rows in ` will result all curves being plotted.

Cran fixes #221

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Cran fixes #221

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