Merge pull request #1845 from fchapoton/typos_pkg_more

once again typos in packages, last such branch maybe

M2/Macaulay2/packages/Chordal/ChordalDoc.m2

@@ -915,7 +915,7 @@ doc /// --chordalElim
 
         {\bf Example 3.1 of [CP'16]}
       Text
-        (chordalElim succeds in computing the elimination ideals)
+        (chordalElim succeeds in computing the elimination ideals)
       Example
         R = QQ[x_0..x_3, MonomialOrder=>Lex];
         I = ideal {x_0^4-1, x_0^2+x_2, x_1^2+x_2, x_2^2+x_3};
@@ -937,7 +937,7 @@ doc /// --chordalElim
       Text
         {\bf Example: } 3-chromatic ideal of the cycle graph
       Text
-        (chordalElim succeds)
+        (chordalElim succeeds)
       Example
         I = chromaticIdeal(QQ, cycleGraph 10, 3);
         N = chordalNet I;

M2/Macaulay2/packages/EngineTests/LinearAlgebra.Test.all.m2

@@ -83,7 +83,7 @@ end--
 
 debug Core
 
--- QQFlint: testrank:  takes alot of time, why?
+-- QQFlint: testrank:  takes a lot of time, why?
 --    testNullspace: bus error!
 -- ZZ: determinant: fails
 -- ZZpFlint: 

M2/Macaulay2/packages/MinimalPrimes/tests.m2

@@ -195,7 +195,7 @@ TEST ///
   debug needsPackage "MinimalPrimes"
   R = ZZ/32003[a,b,c,d,e,f,g,h]
   (S,SF) = makeFiberRings {c}
-  -- TODO NOTE: S whould contain ringmaps S-->R, R-->S, S-->SF,
+  -- TODO NOTE: S should contain ringmaps S-->R, R-->S, S-->SF,
   --          : Frank has done this now.  They are all stashed in S.
   --  note: for SF-->S we have numerator, denominator
   assert ( first sort gens S == c )

M2/Macaulay2/packages/MonodromySolver/Documentation.m2

@@ -362,7 +362,7 @@ doc ///
                 potential for producing new solutions. Current supported potential functions are ", TO potentialE , " and ", 
                 TO potentialLowerBound},
                 {"SelectEdgeAndDirection: accepts either ", TO selectBestEdgeAndDirection, " or ",
-                 TO selectRandomEdgeAndDirection, ". Tthe former also requires setting a potential. Default is an internal function that selects the first available edge." },
+                 TO selectRandomEdgeAndDirection, ". The former also requires setting a potential. Default is an internal function that selects the first available edge." },
                 "StoppingCriterion: eg. stop if no progress has been made",
                 "TargetSolutionCount: expected/desired number of solutions (overrides StoppingCriterion)",
                 "Verbose: reports progress in each iteration",
@@ -570,7 +570,7 @@ doc ///
         M:Matrix
             defining polynomial system
         p0:Point
-            assoiated to a specialized system
+            associated to a specialized system
         L:List
             containing partial solutions associated to p0
     Outputs

M2/Macaulay2/packages/OpenMath/cds/integer2.m2

@@ -28,7 +28,7 @@ OMSEvaluators#"integer2"#"modulo_relation" = (args, attrs) -> (
 	(x,y) -> (mod(x, m) == mod(y,m))
 )
 OMSEvaluators#"integer2"#"ord" = (args, attrs) -> ( 
-	-- This symbol  denotes a binary function. Its first argument shoud be a prime
+	-- This symbol denotes a binary function. Its first argument should be a prime
 	-- number p, the second an integer n.
 	-- When applied to p and n, it represents the highest power of p occurring in a
 	-- factorization of n.

M2/Macaulay2/packages/PHCpack/PHCpackDoc.m2

@@ -626,7 +626,7 @@ doc ///
     flag to switch to double double or quad double precision
   Description
     Text
-      By default, all computations occur in hardward double precision.
+      By default, all computations occur in hardware double precision.
       While this precision could be large enough to obtain accurate
       results, for larger problems, one may need to increase the
       precision to double double or to quad double precision.
@@ -866,7 +866,7 @@ doc ///
     f:List
       a system of polynomials
     sols:List
-      solutions of the sytem f, each of type @TO Point@ 
+      solutions of the system f, each of type @TO Point@ 
       (from a previous calculation)
     dp:ZZ
       the number of decimal places in working precision
@@ -880,7 +880,7 @@ doc ///
     Item
       invokes the command {\tt phc -v} (with option 3),
     Item 
-      stores phc output in a termporary file,
+      stores phc output in a temporary file,
     Item 
       parses and prints the refined solutions.
   Description

M2/Macaulay2/packages/PhylogeneticTrees.m2

@@ -1098,14 +1098,14 @@ doc///
     Key
 	"CFNmodel"
     Headline
-	The model corresponging to the Cavender-Farris-Neyman model or binary Jukes Cantor
+	The model corresponding to the Cavender-Farris-Neyman model or binary Jukes Cantor
     Description
 	Text
 	    The Cavender-Farris-Neyman (CFN) Model is a Markov model of base substitution. It also known as the binary Jukes-Cantor model.
 	    It assumes the root distribution vectors describe all bases occurring uniformly in the ancestral sequence.
 	    It also assumes that the rate of all specific base changes is the same.
 
-            The transistion matrix has the form
+            The transition matrix has the form
             $$\begin{pmatrix} \alpha&\beta\\
                               \beta&\alpha \end{pmatrix}$$
 	--Example
@@ -1130,7 +1130,7 @@ doc///
 	    It also assumes that the rate of all specific base changes is the same.
 	    Thus the rates of bases changes A-G, A-T and A-C are the same.
 
-            The transistion matrix has the form
+            The transition matrix has the form
             $$\begin{pmatrix} \alpha&\beta&\beta&\beta\\ 
                               \beta&\alpha&\beta&\beta\\
                               \beta&\beta&\alpha&\beta\\
@@ -1150,15 +1150,15 @@ doc///
     Key
 	"K2Pmodel"
     Headline
-	The model corresponging to the Kimura 2-parameter model
+	The model corresponding to the Kimura 2-parameter model
     Description
         Text
 	    The Kimura 2-parameter (K2P) Model is a Markov model of base substitution. It assumes the root distribution vectors describe
 	    all bases occurring uniformly in the ancestral sequence. It allows different probabilities of transitions and transversions.
 	    This means that the rate of base changes A-C and A-T are the same (transversions), and the rate of
 	    base change A-G can differ (transitions).
 
-            The transistion matrix has the form
+            The transition matrix has the form
             $$\begin{pmatrix} \alpha&\gamma&\beta&\beta\\ 
                               \gamma&\alpha&\beta&\beta\\
                               \beta&\beta&\alpha&\gamma\\
@@ -1178,15 +1178,15 @@ doc///
     Key
 	"K3Pmodel"
     Headline
-	The model corresponging to the Kimura 3-parameter model
+	The model corresponding to the Kimura 3-parameter model
     Description
         Text
 	    The Kimura 3-parameter (K3P) Model is a Markov model of base substitution. 
 	    It assumes the root distribution vectors describe all bases occurring uniformly in the ancestral sequence. 
 	    It allows different probabilities of the base changes A-G, A-C and A-T.  
 	    This is the most general group based model on group $(\mathbb{Z}/2\mathbb{Z})^2$.
 
-            The transistion matrix has the form
+            The transition matrix has the form
             $$\begin{pmatrix} \alpha&\gamma&\beta&\delta\\ 
                               \gamma&\alpha&\delta&\beta\\
                               \beta&\delta&\alpha&\gamma\\
@@ -1414,7 +1414,7 @@ doc///
 	B:List
 	    A list of lists of which group elements have identified parameters
 	aut:List
-	    A list of pairs, assigning pairs of indentified group elements to automorphisms of the group that switch the pair
+	    A list of pairs, assigning pairs of identified group elements to automorphisms of the group that switch the pair
     Description
         Text
             The elements of $G$ must have an addition operation.  The usual choices for $G$ are the list of elements of
@@ -1674,7 +1674,7 @@ doc///
 	    A list of two @TO LeafTree@s that are subtrees of {\tt T}
     Description
         Text
-	    The funtion outputs the two subtrees of $T$ obtained by deleting edge $e$ from $T$ and then re-adding the edge
+	    The function outputs the two subtrees of $T$ obtained by deleting edge $e$ from $T$ and then re-adding the edge
 	    to each of the two resulting subtrees. Both subtrees share a copy of the edge $e$
 	    and the newly labeled leaf adjacent to $e$. Other than this overlap, they are disjoint.
 
@@ -1828,7 +1828,7 @@ assert( L == l)
 --the correct SETS. We check that leafColorings(4,CFNmodel) gives the correct
 --output set. We also check that leafColorings gives the same output
 --for the JCmodel, the K2Pmodel, and the K3Pmodel on the tree with 4 leaves,
---as this method should only depend on the group, and not the acutal model.
+--as this method should only depend on the group, and not the actual model.
 
 
 TEST ///
@@ -2250,7 +2250,7 @@ TEST ///
 --the ideal in Fourier coordinates and then forming an ideal by 
 --converting each of the generators into probablity coordinates. 
 --We assert the two ideals are equal modulo the certain linear invariants
---that are supressed when computing in the ring of Fourier coordinates.
+--that are suppressed when computing in the ring of Fourier coordinates.
 
 S = pRing(4,CFNmodel);
 L = ideal apply(8,i->(S_i - S_(15-i)))

M2/Macaulay2/packages/PrimaryDecomposition/GTZ.m2

@@ -13,7 +13,7 @@ primaryDecompositionGTZ Ideal := (I) -> (
      -- compute codimension
      -- handle some specific cases
      -- switch to lex order
-     -- compute independent sets, maybe alot of them
+     -- compute independent sets, maybe a lot of them
      primarycomps := {};
      primecomps := {};
      -- loop thru these sets, until ...

M2/Macaulay2/packages/PrimaryDecomposition/doc.m2

@@ -562,7 +562,7 @@ Node
       To use this strategy, the field @TT "Strategy"@ should be a list of two integers, indicating the
       strategy to use for finding associated primes and localizing, respectively.
 
-      {\bf Warning:} Setting the second paramter to 1 works only if the ideal is homogeneous and equidimensional.
+      {\bf Warning:} Setting the second parameter to 1 works only if the ideal is homogeneous and equidimensional.
     Example
       Q = QQ[x,y];
       I = intersect(ideal(x^2), ideal(y^2))

M2/Macaulay2/packages/ReactionNetworks/DocReactionNetworks.m2

@@ -99,7 +99,7 @@ doc ///
 	    F' = toList apply(0..length SS-1, i-> sub(SS#i,P))
 	Text
 	    Next, we create the conservation equations and assume there is no
-	    translation, i.e., the intial conditions are all zero.
+	    translation, i.e., the initial conditions are all zero.
 	Example
 	    C = conservationEquations N
 	    L = {0,0,0,0,0}
@@ -319,7 +319,7 @@ doc ///
 	Text
 	    {\bf Substitute InitialValues}
 
-	    The example below demonstrates how to substitue specific values for
+	    The example below demonstrates how to substitute specific values for
 	    the initial values in a reaction network. The list of desired values
 	    must be input in the order of the initial values; for that order use
 	    N.InitialValues, where N is the name of the reaction network.
@@ -525,7 +525,7 @@ doc ///
     	shuttle model for Wnt signaling pathway
     Description
     	Text
-	    The cannonical Wnt/beta-catenin signaling pathway is important for essential
+	    The canonical Wnt/beta-catenin signaling pathway is important for essential
 	    cellular functions such as development, homeostasis, and is implicated in many
 	    diseases [MacLean, Rosen, Byrne, Harrington]. The Wnt shuttle model includes
 	    an abstraction of the signal transduction pathway

M2/Macaulay2/packages/SCSCP/docs.m2

@@ -71,9 +71,9 @@ document {
 		"host" => String => {"The IP address of the interface to bind to (may be omitted, and defaults to binding to all interfaces) "}, 
 		"port" => {ofClass{String, ZZ}, ", providing the port number (defaults to 26133) "}
 	},
-	"The server will keep running indefinitely; it may be stoppend by sending a Ctrl-C. Furthermore,
+	"The server will keep running indefinitely; it may be stopped by sending a Ctrl-C. Furthermore,
 	the server forks for every new incoming connection, so that it can serve many clients simultaneously.
-	The amount of output printed to the screen is determined by the vaule of debugLevel.",
+	The amount of output printed to the screen is determined by the value of debugLevel.",
 	EXAMPLE { PRE ///
 i1 : debugLevel = 2;
 

M2/Macaulay2/packages/Schubert2/Stromme/letter_to_collino.txt

@@ -116,7 +116,7 @@ Trank  :=proc(C) sort(expand(subs(ranksubstring,C))) end:
 # (linear part of the) ideal generated by x0 and x1.
 
 # simpleweights(A) returns the sum of one-dimensional 
-# representations, one for each occuring weight in A. For
+# representations, one for each occurring weight in A. For
 # example, simpleweights(V[j]*V[k]) should return V[j+k].
 # This is useful for computing twists of a monomial ideal:
 # if I sub V[d], then simpleweights(I*V[1]) is the ideal I in 

M2/Macaulay2/packages/Schubert2/Stromme/toricubics.txt

@@ -29,7 +29,7 @@ rank   :=proc(C) sort(expand(subs(ranksubstring,C))) end:
 # (linear part of the) ideal generated by x0 and x1.
 
 # simpleweights(A) returns the sum of one-dimensional 
-# representations, one for each occuring weight in A. For
+# representations, one for each occurring weight in A. For
 # example, simpleweights(V[j]*V[k]) should return V[j+k].
 # This is useful for computing twists of a monomial ideal:
 # if I sub V[d], then simpleweights(I*V[1]) is the ideal I in 

M2/Macaulay2/packages/SchurFunctors/schurModule.txt

@@ -27,7 +27,7 @@
 	  }
 
       Tableaux are represented with objects of class Filling, 
-      which is a doble list whose entries are lists giving the fillings of the corresponding columns.          
+      which is a double list whose entries are lists giving the fillings of the corresponding columns.          
     Example
       M=QQ^3;
       scan(4, i-> << i+1 << "-th symmetric power of M = " << schurModule({i+1},M) << endl)

M2/Macaulay2/packages/SchurFunctors/schurModulesMap.txt

@@ -12,7 +12,7 @@
 	Schur module
     F:Function 
         The function should specify, for every SST in the basis of M, 
-	a linear comination of tableaus of the shape specified by N.
+	a linear combination of tableaux of the shape specified by N.
         The output of F should be a sequence of pairs (c,T) where c is a coefficient 
 	in ring(N) and T a tableau (not necessarily semistandard). 
   Outputs

M2/Macaulay2/packages/SemidefiniteProgramming/SDPdoc.m2

@@ -492,5 +492,5 @@ doc ///
     Description
       Text
         The package uses these mutable variables to store the paths of the executables.
-	They can be edited by the user.  The prefered way to do this is @TO changeSolver@, though.
+	They can be edited by the user. The preferred way to do this is @TO changeSolver@, though.
 ///

M2/Macaulay2/packages/VirtualResolutions/doc.m2

@@ -214,7 +214,7 @@ doc ///
             Given two positive integers {\tt d,e} and a ring {\tt F}, @TT "randomRationalCurve"@ returns the ideal of a
 	    random curve in $\PP^1\times\PP^2$ of degree {\tt (d,e)} defined over the base ring {\tt F}.
 
-            This is done by randomly generating two homogenous polynomials of degree {\tt d} and three homogenous
+            This is done by randomly generating two homogeneous polynomials of degree {\tt d} and three homogeneous
             polynomials of degree three in $F[s,t]$ defining maps $\PP^1\to\PP^1$ and $\PP^1\to\PP^2$,
             respectively. The graph of the product of these two maps in $\PP^1\times(\PP^1\times\PP^2)$ is computed,
             from which a curve of bi-degree {\tt (d,e)} in $\PP^1\times\PP^2$ over {\tt F} is obtained by