diff --git a/MFAssignR/man/IsoFiltR.Rd b/MFAssignR/man/IsoFiltR.Rd
index 23fa3a4..ded67d6 100644
--- a/MFAssignR/man/IsoFiltR.Rd
+++ b/MFAssignR/man/IsoFiltR.Rd
@@ -4,11 +4,27 @@
 \alias{IsoFiltR}
 \title{Identifies and separates likely isotopic masses from monoisotopic masses}
 \usage{
-IsoFiltR(peaks, SN = 0, Diffrat = 0.1, Sulfrat = 30)
+IsoFiltR(peaks, SN = 0, Diffrat = 0.1, Sulfrat = 30, Sulferr = 5,
+  Carberr = 5)
 }
 \arguments{
 \item{peaks}{data frame:
 The input 2 column data frame containing abundance and peak mass}
+
+\item{SN}{numeric:
+Sets the noise cut for the data, peaks below this value will not be evaluated}
+
+\item{Diffrat}{numeric:
+A value multiplied by the minimum allowed 13C ratio to expand the allowed range}
+
+\item{Sulfrat}{numeric:
+Sets the maximum 34S ratio that is allowed for matching}
+
+\item{Sulferr}{numeric:
+Sets the maximum allowed error (ppm) for 34S mass matching, default is 5}
+
+\item{Carberr}{numeric:
+Sets the maximum allowed error (ppm) for 13C mass matching, default is 5}
 }
 \value{
 list(Monolist, Isolist):
diff --git a/MFAssignR/man/MFAssign.Rd b/MFAssignR/man/MFAssign.Rd
index 54d7d0b..cd1d776 100644
--- a/MFAssignR/man/MFAssign.Rd
+++ b/MFAssignR/man/MFAssign.Rd
@@ -8,9 +8,9 @@ MFAssign(peaks, isopeaks = "none", ionMode, lowMW = 100, highMW = 1000,
   POEx = 0, NOEx = 0, Nx = 0, Sx = 0, Px = 0, S34x = 0, N15x = 0,
   Dx = 0, Ex = 0, Clx = 0, Cl37x = 0, Fx = 0, Mx = 0, NH4x = 0,
   Zx = 1, Sval = 2, Nval = 3, S34val = 2, N15val = 3, Pval = 5,
-  Ox = 30, ppm_err = 3, SN = 0, O_Cmin = 0, O_Cmax = 2.5,
-  H_Cmin = 0.3, H_Cmax = 3, DBEOmin = -13, DBEOmax = 13, Omin = 0,
-  HetCut = "off", NMScut = "on", DeNovo = 300, nLoop = 5,
+  Ox = 30, ppm_err = 3, iso_err = 5, SN = 0, O_Cmin = 0,
+  O_Cmax = 2.5, H_Cmin = 0.3, H_Cmax = 3, DBEOmin = -13, DBEOmax = 13,
+  Omin = 0, HetCut = "off", NMScut = "on", DeNovo = 300, nLoop = 5,
   SulfCheck = "on", Ambig = "off", MSMS = "off")
 }
 \arguments{
diff --git a/MFAssignR/man/MFAssignCHO_RMD.Rd b/MFAssignR/man/MFAssignCHO_RMD.Rd
index ef49ac3..3eb1126 100644
--- a/MFAssignR/man/MFAssignCHO_RMD.Rd
+++ b/MFAssignR/man/MFAssignCHO_RMD.Rd
@@ -84,14 +84,14 @@ NMScut turns on or off the nominal mass series QA parameter. Default is “on”
 \item{DeNovo}{numeric:
 DeNovo sets the de novo cut point for the data. Default is 1000.}
 
+\item{nLoop}{numeric:
+nLoops sets the number of times the KMD and z* series assignment loops. Default is 5.}
+
 \item{Ambig}{character:
 Turns on or off increased ambiguity for assignments. Default is "off".}
 
 \item{MSMS}{character:
 Turns on or off CH2 KMD prescreening before initial assignment. Default is "off".}
-
-\item{nLoops}{numeric:
-nLoops sets the number of times the KMD and z* series assignment loops. Default is 5.}
 }
 \value{
 list(Unambig = Unambig, Ambig = Ambigout, None = unassigned, MSAssign = MZ,
diff --git a/MFAssignR/man/MFAssign_RMD.Rd b/MFAssignR/man/MFAssign_RMD.Rd
index 55848a9..3404f3e 100644
--- a/MFAssignR/man/MFAssign_RMD.Rd
+++ b/MFAssignR/man/MFAssign_RMD.Rd
@@ -8,10 +8,10 @@ MFAssign_RMD(peaks, isopeaks = "none", ionMode, lowMW = 100,
   highMW = 1000, POEx = 0, NOEx = 0, Nx = 0, Sx = 0, Px = 0,
   S34x = 0, N15x = 0, Dx = 0, Ex = 0, Clx = 0, Cl37x = 0, Fx = 0,
   Mx = 0, NH4x = 0, Zx = 1, Sval = 2, Nval = 3, S34val = 2,
-  N15val = 3, Pval = 5, Ox = 30, ppm_err = 3, SN = 0, O_Cmin = 0,
-  O_Cmax = 2.5, H_Cmin = 0.3, H_Cmax = 3, DBEOmin = -13, DBEOmax = 13,
-  Omin = 0, HetCut = "off", NMScut = "on", DeNovo = 300, nLoop = 5,
-  SulfCheck = "on", Ambig = "off", MSMS = "off")
+  N15val = 3, Pval = 5, Ox = 30, ppm_err = 3, iso_err = 5, SN = 0,
+  O_Cmin = 0, O_Cmax = 2.5, H_Cmin = 0.3, H_Cmax = 3, DBEOmin = -13,
+  DBEOmax = 13, Omin = 0, HetCut = "off", NMScut = "on", DeNovo = 300,
+  nLoop = 5, SulfCheck = "on", Ambig = "off", MSMS = "off")
 }
 \arguments{
 \item{peaks}{data frame, Monoisotopic Masses}
diff --git a/MFAssignR/man/Recal.Rd b/MFAssignR/man/Recal.Rd
index 50ca554..2d47720 100644
--- a/MFAssignR/man/Recal.Rd
+++ b/MFAssignR/man/Recal.Rd
@@ -8,8 +8,8 @@ and produces a list of the chosen recalibrants.}
 Recal(df, peaks, isopeaks = "none", mode, SN = 0, mzRange = 50,
   series1 = NA, series2 = NA, series3 = NA, series4 = NA,
   series5 = NA, series6 = NA, series7 = NA, series8 = NA,
-  series9 = NA, series10 = NA, min = 100, max = 1000, bin = 10,
-  obs = 2)
+  series9 = NA, series10 = NA, min = 100, max = 1000, bin = 14,
+  obs = 1, num = 5, opt = 1)
 }
 \arguments{
 \item{df}{data frame output from MFAssign() or MFAssignCHO()}
@@ -28,10 +28,15 @@ Recal(df, peaks, isopeaks = "none", mode, SN = 0, mzRange = 50,
 
 \item{max}{numeric - maximum mass range of the data being analyzed.}
 
-\item{bin}{numeric - sets the mass window bins to choose recalibrants from, default is 10.}
+\item{bin}{numeric - sets the mass window bins to choose recalibrants from, default is 14.}
 
-\item{obs}{numeric - sets the number of peaks to choose as recalibrants from each bin,
-default is 2}
+\item{obs}{numeric - sets the number of peaks to choose as recalibrants from each bin.
+Default is 1}
+
+\item{num}{numeric - sets the number of peaks on either side of defined recalibrant to choose
+as additional recalibrants. Default is 5.}
+
+\item{opt}{numeric - selects the recalibration option to be used, options are 1, 2, 3, or 4}
 
 \item{series(1-10)}{character the recalibrant series, "O7_Na_4" for example, default is NA}
 }