various bug squashing

ApfeldLab · Jan 12, 2020 · 26a62c2 · 26a62c2
1 parent cfdc8f0
commit 26a62c2
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Showing 141 changed files with 22 additions and 7 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
diff --git a/.gitignore b/.gitignore
diff --git a/.travis.yml b/.travis.yml
diff --git a/DESCRIPTION b/DESCRIPTION
diff --git a/NAMESPACE b/NAMESPACE
diff --git a/R/Sensor_Classes.R b/R/Sensor_Classes.R
diff --git a/R/Sensor_Constructors.R b/R/Sensor_Constructors.R
diff --git a/R/Sensor_Methods.R b/R/Sensor_Methods.R
diff --git a/R/Spectra_Class.R b/R/Spectra_Class.R
@@ -1,4 +1,4 @@
-#' An S4 class to represent the emission spectrum of a 2-state sensor
+    #' An S4 class to represent the emission spectrum of a 2-state sensor
 #'
 #' @slot lambdas represents excitation wavelengths in nanometers
 #' @slot values_minimum represents the relative emission values of the sensor state

diff --git a/R/Spectra_Constructors.R b/R/Spectra_Constructors.R
diff --git a/R/Spectra_Methods.R b/R/Spectra_Methods.R
diff --git a/R/extra/error_table_from_params.R b/R/extra/error_table_from_params.R
diff --git a/R/extra/helpers_scratch.R b/R/extra/helpers_scratch.R
@@ -31,3 +31,5 @@ Error_E <- function(E, Rmin, Rmax, delta, e0, error_R, temp = 295.15) {
 
 
 
+
+
diff --git a/R/launchApp.R b/R/launchApp.R
diff --git a/R/utils.R b/R/utils.R
@@ -180,24 +180,37 @@ getDb <- function() {
 #' @import mongolite
 adjustSpectra <- function(spectra, fractionMax, fractionMin) {
     adjusted_minimum <- (
-        (spectra@values_minimum / (1-fractionMin)) -
-            (spectra@values_maximum / fractionMax)
+        (spectra@values_maximum / fractionMax) -
+            (spectra@values_minimum / fractionMin)
     ) /
         (
-            (fractionMin/(1-fractionMin)) -
-                ((1-fractionMax)/fractionMax)
+            ((1-fractionMax)/fractionMax) -
+                ((1-fractionMin)/fractionMin)
         )
 
     adjusted_maximum <- (
         (spectra@values_maximum / (1-fractionMax)) -
-            (spectra@values_minimum / fractionMin)
+            (spectra@values_minimum / (1 - fractionMin))
     ) /
         (
             (fractionMax/(1-fractionMax)) -
-                ((1-fractionMin)/fractionMin)
+                ((fractionMin/(1-fractionMin)))
         )
 
     return(new("sensorSpectra", lambdas = spectra@lambdas,
                values_minimum = adjusted_minimum,
                values_maximum = adjusted_maximum))
 }
+
+#' What is the fraction deprotenated of a certain pH, given the pKa?
+#'
+#' @param pH The pH
+#' @param pKa The pKa
+#'
+#' @export
+fraction_deprot <- function(pH, pKa) {
+    return(
+        (10^(pH - pKa)) /
+            (1 + 10^(pH - pKa))
+    )
+}
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diff --git a/inst/shinyApp/app.R b/inst/shinyApp/app.R
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diff --git a/inst/shinyApp/ui/ui_01_welcome.R b/inst/shinyApp/ui/ui_01_welcome.R
diff --git a/inst/shinyApp/ui/ui_02_customSensor.R b/inst/shinyApp/ui/ui_02_customSensor.R
diff --git a/inst/shinyApp/ui/ui_04_settings.R b/inst/shinyApp/ui/ui_04_settings.R
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diff --git a/man/Sensor-class.Rd b/man/Sensor-class.Rd
diff --git a/man/adjustSpectra.Rd b/man/adjustSpectra.Rd
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diff --git a/man/getAbsError.Rd b/man/getAbsError.Rd
diff --git a/man/getDb.Rd b/man/getDb.Rd
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diff --git a/tests/testthat/test_getErrorTable.R b/tests/testthat/test_getErrorTable.R
diff --git a/tests/testthat/test_getFractionMax.R b/tests/testthat/test_getFractionMax.R
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diff --git a/tests/testthat/test_getR.R b/tests/testthat/test_getR.R
diff --git a/tests/testthat/test_getpH.R b/tests/testthat/test_getpH.R
diff --git a/tests/testthat/test_newSensorFromSpectra.R b/tests/testthat/test_newSensorFromSpectra.R
diff --git a/tests/testthat/test_plots.R b/tests/testthat/test_plots.R
diff --git a/tests/testthat/testgetDb.R b/tests/testthat/testgetDb.R
Original file line number	Diff line number	Diff line change
Expand Up		@@ -31,3 +31,5 @@ Error_E <- function(E, Rmin, Rmax, delta, e0, error_R, temp = 295.15) {