prepare for another CRAN submission

Author: thomas-enzlein

.Rhistory

@@ -1,57 +1,3 @@
-alignTol = 0,
-halfWindowSize = 20)
-MALDIcellassay::getFittingParameters(res)
-calculatePeakStatistics(res@fits, res@singlePeaks)
-calculatePeakStatistics(res@fits, res@singlePeaks, spec = res@avgSpectra)
-calculatePeakStatistics(res@fits, res@avgPeaks, spec = res@avgSpectra)
-100*1e-6
-source("~/.active-rstudio-document", echo=TRUE)
-source("~/.active-rstudio-document", echo=TRUE)
-library(MALDIquant)
-spec <- suppressWarnings(
-smoothIntensity(spec,
-method = "SawitzkyGolay",
-halfWindowSize = 10)
-)
-spec <- suppressWarnings(
-smoothIntensity(spec,
-method = "SavitzkyGolay",
-halfWindowSize = 10)
-)
-spec <- suppressWarnings(
-removeBaseline(spec,
-method = "TopHat")
-)
-res <- fitCurve(spec = spec,
-unit = "nM",
-varFilterMethod = "none",
-normMz = 857.133,
-binTol = 100*1e-6,
-SinglePointRecal = TRUE,
-alignTol = 0,
-halfWindowSize = 20)
-source("~/.active-rstudio-document", echo=TRUE)
-getPeakStatistics(res)
-getPeakStatistics(res) %>%
-mutate(z = calculateZPrime(res))
-getPeakStatistics(res, TRUE) %>%
-mutate(z = calculateZPrime(res))
-stats <- getPeakStatistics(res, TRUE) %>%
-mutate(z = calculateZPrime(res),
-v = calculateVPrime(res))
-View(stats)
-res <- fitCurve(spec = spec,
-unit = "nM",
-varFilterMethod = "none",
-normMz = 857.133,
-binTol = 100*1e-6,
-SinglePointRecal = TRUE,
-alignTol = 0,
-halfWindowSize = 3)
-stats <- getPeakStatistics(res, TRUE) %>%
-mutate(z = calculateZPrime(res),
-v = calculateVPrime(res))
-View(stats)
 plotCurves(res, 87, errorbars = "sd")
 stats <- getPeakStatistics(res, TRUE) %>%
 mutate(z = round(calculateZPrime(res),2),
@@ -510,3 +456,57 @@ source("~/R/MALDIcellassay/data-raw/Koch2024mzML.R", echo=TRUE)
 MALDIquantForeign::exportMzMl(spec, file = "inst/extdata/Koch2024mzML.mzML")
 source("~/R/MALDIcellassay/data-raw/Koch2024mzML.R", echo=TRUE)
 source("~/R/MALDIcellassay/data-raw/Koch2024mzML.R", echo=TRUE)
+devtools::document()
+devtools::document()
+devtools::run_examples()
+source("~/.active-rstudio-document", echo=TRUE)
+devtools::document()
+source("~/.active-rstudio-document", echo=TRUE)
+devtools::document()
+devtools::document()
+devtools::document()
+devtools::document()
+urlchecker::url_update()
+devtools::document()
+devtools::document()
+devtools::run_examples()
+usethis::use_data(Blank2022res, overwrite = TRUE, compress = "xz")
+rhub::rhub_check()
+devtools::document()
+usethis::use_version()
+devtools::check_win_devel()
+cran <- tools::CRAN_package_db()
+desc_with_doi <- grep("doi:", cran$Description, value = TRUE)
+desc_with_doi[[1]]
+View(cran)
+devtools::check_win_devel()
+usethis::use_release_issue()
+revdepcheck::revdep_check()
+checkhelper::find_missing_tags()
+install.packages("checkhelper")
+checkhelper::find_missing_tags()
+checkhelper::find_missing_tags()
+checkhelper::find_missing_tags()
+a<-checkhelper::find_missing_tags()
+View(a)
+View(a[["functions"]])
+checkhelper::check_clean_userspace()
+all_files_remaining <- checkhelper::check_clean_userspace()
+urlchecker::url_check()
+devtools::revdep()
+usethis::use_release_issue(version = "0.4.46")
+usethis::use_cran_comments()
+urlchecker::url_check()
+devtools::check(remote = TRUE, manual = TRUE)
+devtools::document()
+Sys.which("makeindex")
+tinytex::tlmgr_install("makeindex")
+tinytex::reinstall_tinytex(repository = "illinois")
+tinytex::tlmgr_install("makeindex")
+Sys.which("makeindex")
+Sys.which("makeindex")
+devtools::check(remote = TRUE, manual = TRUE)
+devtools::submit_cran()
+withr::with_options(list(repos = c(CRAN = "https://cloud.r-project.org/")),
+{callr::default_repos()
+rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran")) })

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 0.4.45
-Date: 2024-08-17 12:09:14 UTC
-SHA: 65aeeebd03a46c08249d9aa50178bcd06dc10836
+Version: 0.4.46
+Date: 2024-08-19 16:46:10 UTC
+SHA: eef754436a6fe8ff9c160774bb88824a547cb4b4

R/example_data.R

@@ -1,6 +1,6 @@
 #' Blank2022spec
 #' @description
-#' MALDI mass spectromety data of EOC cells treated with different concentrations of SAHA.
+#' MALDI mass spectrometry data of EOC cells treated with different concentrations of SAHA.
 #' It is used to demonstrate the usage of \code{MALDIcellassay}.
 #' @details
 #' The concentrations include: 0, 0.04, 0.12, 0.37, 1.11, 3.33, 10 and 30 uM of SAHA at 4 replicates each.
@@ -12,7 +12,7 @@
 
 #' Blank2022peaks
 #' @description
-#' Peaks from MALDI mass spectromety data of EOC cells treated with different concentrations of SAHA.
+#' Peaks from MALDI mass spectrometry data of EOC cells treated with different concentrations of SAHA.
 #' It is used to demonstrate the usage of \code{MALDIcellassay}.
 #' @details
 #' The concentrations include: 0, 0.04, 0.12, 0.37, 1.11, 3.33, 10 and 30 uM of SAHA at 4 replicates each.
@@ -26,7 +26,7 @@
 
 #' Blank2022intmat
 #' @description
-#' Intensity matrix from MALDI mass spectromety data of EOC cells treated with different concentrations of SAHA.
+#' Intensity matrix from MALDI mass spectrometry data of EOC cells treated with different concentrations of SAHA.
 #' It is used to demonstrate the usage of \code{MALDIcellassay}.
 #' @details
 #' The concentrations include: 0, 0.04, 0.12, 0.37, 1.11, 3.33, 10 and 30 uM of SAHA at 4 replicates each.
@@ -40,7 +40,7 @@
 
 #' Blank2022res
 #' @description
-#' Object of class MALDIcellassay from MALDI mass spectromety data of EOC cells treated with different concentrations of SAHA.
+#' Object of class MALDIcellassay from MALDI mass spectrometry data of EOC cells treated with different concentrations of SAHA.
 #' It is used to demonstrate the usage of \code{MALDIcellassay}.
 #' @details
 #' The concentrations include: 0, 0.04, 0.12, 0.37, 1.11, 3.33, 10 and 30 uM of SAHA at 4 replicates each.

R/fitCurve.R

@@ -11,7 +11,7 @@
 #' @param alignTol            Numeric, tolerance for spectral alignment in Dalton.
 #' @param binTol              Numeric, tolerance for binning of peaks.
 #' @param SNR                 Numeric, signal to noise ratio for peak detection.
-#' @param halfWindowSize      Numeric, defines the size of the window for peak detection. See `MALDIquant::detectPeaks()`.
+#' @param halfWindowSize      2ction. See `MALDIquant::detectPeaks()`.
 #' @param allowNoMatches      Logical, if normMz can not be found in a spectrum, proceed and exclude spectrum or stop
 #' @param normMeth            Character, normalization method. Can either be "TIC", "PQM", "median" or "mz". If "mz" then the normMz is used. If none no normalization is done.
 #' @param SinglePointRecal    Logical, perform single point recalibration to normMz

R/loadSpectra.R

@@ -3,9 +3,9 @@
 #' @param Dir         Character, parent directory of spectra.
 #' @param filter      Character vector, filter out spectra which match the given vector.
 #' @param nameSpectra Logical, if TRUE the spectra in the resulting list will be named according to the dirname.
-#' @param verbose     Logical, print logs to the console.
+#' @param verbose     Logical, print logs to the console. 
 #'
-#' @return List of MALDIquant::MassSpectra
+#' @return List of MALDIquant::MassSpectra 
 #' @export
 #'
 #' @importFrom svMisc progress

R/plotCurves.R

@@ -2,7 +2,7 @@
 #'
 #' @param object    object of class MALDIassay
 #' @param mzIdx     numeric, indicies of mz values to plot (see \code{getPeakStatistics()}). Note, fc_thresh and R2_thresh filters do not apply if mzIdx is set!
-#' @param errorbars character, add error bars to plot. Either standard error of the mean (`sem`) or standard deviation (`sd`) in regards to the measurment replicates or no errorbars (`none`).
+#' @param errorbars character, add error bars to plot. Either standard error of the mean (`sem`) or standard deviation (`sd`) in regards to the measurement replicates or no errorbars (`none`).
 #'
 #' @return
 #' list of ggplot objects

cran-comments.md

@@ -2,4 +2,32 @@
 
 0 errors | 0 warnings | 1 note
 
-* This is a new release.
+>Please reduce the length of the title to less than 65 characters.
+>
+>If there are references describing the methods in your package, please add these in the description field of your DESCRIPTION file in the form
+>authors (year) <doi:...>
+>authors (year, ISBN:...)
+>or if those are not available: <https:...>
+>with no space after 'doi:', 'https:' and angle brackets for auto-linking. (If you want to add a title as well please put it in quotes: "Title")
+>
+>The Description field is intended to be a (one paragraph) description of what the package does and why it may be useful. Please add more details about the package functionality and implemented methods in your Description text.
+>
+>Please only write package and software names in single quotes.
+>-> Omit them around: un-targeted
+>
+>Please fix and resubmit.
+>
+>Best,
+>Benjamin Altmann
+
+Dear CRAN-team
+I took care about the comments above.
+
+- The new title is: "Automated MALDI Cell Assays Using Dose-Response Curve Fitting" (63 character).
+- DOI's have been added to the description field.
+- The description field was extended: "Conduct automated cell-based assays using Matrix-Assisted Laser Desorption/Ionization (MALDI) methods for high-throughput screening of signals responsive to treatments. The package efficiently identifies high variance signals and fits dose-response curves to them. Quality metrics such as Z', V', log2FC, and CRS are provided for evaluating the potential of signals as biomarkers. The methodologies were introduced by Weigt et al. (2018) <doi:10.1038/s41598-018-29677-z> and refined by Unger et al. (2021) <doi:10.1038/s41596-021-00624-z>."
+- Single quotes were removed from the title.
+
+Best regards,
+Thomas Enzlein
+