Merge pull request #3 from hannesbecher/dev

Dev
hannesbecher · Oct 21, 2021 · 7e9f476 · 7e9f476
2 parents c022ced + d191b34
commit 7e9f476
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diff --git a/Tetmer/DESCRIPTION b/Tetmer/DESCRIPTION
@@ -1,11 +1,10 @@
 Package: Tetmer
 Type: Package
 Title: Fitting Population Parameters to k-mer Spectra
-Version: 2.0.0
+Version: 2.1.0
 Author: Hannes Becher
 Maintainer: The package maintainer <hannesbecher@gmx.de>
-Description: More about what it does (maybe more than one line)
-    Use four spaces when indenting paragraphs within the Description.
+Description: This package contains a shiny app for fitting population parameters to k-mer spectra.
 License: GPL (>= 3)
 Depends: 
     R (>= 2.10),

diff --git a/Tetmer/R/data.R b/Tetmer/R/data.R
@@ -6,17 +6,19 @@
 #'
 #' @format A \code{spectrum} object containing a name and data frame:
 #' \describe{
-#'   \item{name}{The name E028}
-#'   \item{data}{A dataframe with coulmns \describe{
-#'   \item{mult}{K-mer multiplicity}
-#'   \item{count}{The number of different k-mer at a given multiplicity}
+#'   \item{`name`}{The name 'E. arctica, E028'}
+#'   \item{`k`}{The k-mer length of 27}
+#'   \item{`data`}{A dataframe with coulmns \describe{
+#'   \item{`mult`}{K-mer multiplicity}
+#'   \item{`count`}{The number of different k-mer at a given multiplicity}
 #'   }
 #'   }
 #' }
 #' @source Becher et al. (2020) \url{https://doi.org/10.1016/j.xplc.2020.100105}
 #'
 #' @examples plot(E028, log="xy")
 #' plot(E028, xlim=c(0, 200), ylim=c(0, 10000000))
+#' tetmer(E028)
 "E028"
 
 
@@ -27,16 +29,18 @@
 #'
 #' @format A \code{spectrum} object containing a name and data frame:
 #' \describe{
-#'   \item{name}{The name E028}
-#'   \item{data}{A dataframe with coulmns \describe{
-#'   \item{mult}{K-mer multiplicity}
-#'   \item{count}{The number of different k-mer at a given multiplicity}
+#'   \item{`name`}{The name 'E. anglica, E030'}
+#'   \item{`k`}{The k-mer length of 21}
+#'   \item{`data`}{A dataframe with coulmns \describe{
+#'   \item{`mult`}{K-mer multiplicity}
+#'   \item{`count`}{The number of different k-mer at a given multiplicity}
 #'   }
 #'   }
 #' }
-#' @source Becher et al. (2020) \url{https://doi.org/10.1016/j.xplc.2020.100105}
+#' @source Source!
 #'
 #' @examples plot(E030, log="xy")
 #' plot(E030, xlim=c(0, 200), ylim=c(0, 10000000))
+#' tetmer(E030)
 "E030"
 
diff --git a/Tetmer/R/formulae.R b/Tetmer/R/formulae.R
@@ -64,8 +64,10 @@ factorTraaa <- expression(
 
 factorTraab <- expression(
   c(
-    tth^(-tdiverg*tth)*(-2-4*tth+exp(tdiverg*tth)*(2+7*tth+3*tth^2)) / (2+3*tth+tth^2),
+    exp(-tdiverg*tth)*(-2-4*tth+exp(tdiverg*tth)*(2+7*tth+3*tth^2)) / (2+3*tth+tth^2),
+
     (1 + ((2*exp(-tdiverg*tth) * (tth-1))/(2+tth)))/ (1 + tth),
+
     2*exp(-tdiverg*tth) / (2 + 3*tth + tth^2)
   )
 )