Minor changes for clean build

DESCRIPTION

@@ -39,3 +39,5 @@ LazyData: true
 RoxygenNote: 7.0.2
 Suggests: 
     testthat (>= 2.1.0)
+Imports:
+    methods

NAMESPACE

@@ -26,4 +26,5 @@ export(size)
 export(strcmp)
 export(suoritaMuutos)
 export(times)
+importFrom(methods,is)
 importFrom(stats,runif)

R/admix1.R

@@ -4,6 +4,11 @@
 #' will the required variables be retrieved from the record fields?
 #' `tietue`should contain the following elements: PARTITION, COUNTS, SUMCOUNTS,
 #' alleleCodes, adjprior, popnames, rowsFromInd, data, npops, noalle
+#' @param tietue tietue
+#' @param PARTITION PARTITION
+#' @param COUNTS COUNTS
+#' @param SUMCOUNTS SUMCOUNTS
+#' @importFrom methods is
 #' @export
 admix1 <- function(tietue, PARTITION = matrix(NA, 0, 0),
         COUNTS = matrix(NA, 0, 0), SUMCOUNTS = NA) {
@@ -20,7 +25,7 @@ admix1 <- function(tietue, PARTITION = matrix(NA, 0, 0),
             cat('---------------------------------------------------\n');
             message('Reading mixture result from: ', pathname_filename, '...')
         }
-        sys.sleep(0.0001) #ASK: what for?
+        Sys.sleep(0.0001) #ASK: what for?
 
         # ASK: what is this supposed to do? What do graphic obj have to do here?
         # h0 = findobj('Tag','filename1_text');
@@ -79,7 +84,7 @@ admix1 <- function(tietue, PARTITION = matrix(NA, 0, 0),
         ),
         definput = 5
     )
-    alaRaja <- as.num(answers)
+    alaRaja <- as.numeric(answers)
     npops <- poistaLiianPienet(npops, rowsFromInd, alaRaja)
 
     nloci <- size(COUNTS, 2)
@@ -116,7 +121,7 @@ admix1 <- function(tietue, PARTITION = matrix(NA, 0, 0),
             # Yksil?on outlier
         } else if (PARTITION[ind] != 0) {
             if (PARTITION[ind] > 0) {
-                osuusTaulu(PARTITION[ind]) <- 1
+                osuusTaulu[PARTITION[ind]] <- 1
             } else {
                 # Yksilöt, joita ei ole sijoitettu mihinkään koriin.
                 arvot <- zeros(1, npops)
@@ -181,12 +186,12 @@ admix1 <- function(tietue, PARTITION = matrix(NA, 0, 0),
             omaFreqs <- computePersonalAllFreqs(
                 ind, data, allfreqs, rowsFromInd
             )
-            osuusTaulu = zeros(1, npops)
+            osuusTaulu <- zeros(1, npops)
             if (PARTITION[ind] == 0) {
                 # Yksil?on outlier
             } else if (PARTITION[ind] != 0) {
                 if (PARTITION[ind] > 0) {
-                    osuusTaulu(PARTITION[ind]) <- 1
+                    osuusTaulu[PARTITION[ind]] <- 1
                 } else {
                     # Yksilöt, joita ei ole sijoitettu mihinkään koriin.
                     arvot <- zeros(1, npops)
@@ -388,7 +393,7 @@ admix1 <- function(tietue, PARTITION = matrix(NA, 0, 0),
             }
         }
 
-        if (!isstruct(tietue)) {
+        if (!is(tietue, "list")) {
             c$proportionsIt <- proportionsIt
             c$pvalue <- uskottavuus # Added by Jing
             c$mixtureType <- 'admix' # Jing

R/find.R

@@ -1,5 +1,6 @@
 #' @title Find indices and values of nonzero elements
 #' @description Emulates behavior of `find`
+#' @param x object or logic operation on an object
 find <- function(x) {
     if (is.logical(x)) {
         return(which(x))

R/inputdlg.R

@@ -1,7 +1,7 @@
 #' @title Gather user input
 #' @description Replicates the functionality of the homonymous function in Matlab (sans dialog box)
 #' @param prompt Text field with user instructions
-#' @param dim number of dimensions in the answwers
+#' @param dims number of dimensions in the answwers
 #' @param definput default value of the input
 #' @export
 inputdlg <- function(prompt, definput=NULL, dims=1) {

R/noIndex.R

@@ -3,6 +3,8 @@
 #' @details As input, this function takes two variables from a mixture/admixture
 #' result structure.
 #' @return puredata: a data contains no index column.
+#' @param data data
+#' @param noalle noalle
 #' @export
 noIndex <- function  (data, noalle) {
     limit <- ifelse(is(noalle, "matrix"), ncol(noalle), length(noalle))

man/admix1.Rd

@@ -12,7 +12,13 @@ admix1(
 )
 }
 \arguments{
-\item{tietue}{a named record list}
+\item{tietue}{tietue}
+
+\item{PARTITION}{PARTITION}
+
+\item{COUNTS}{COUNTS}
+
+\item{SUMCOUNTS}{SUMCOUNTS}
 }
 \description{
 Admixture analysis

man/find.Rd

@@ -6,6 +6,9 @@
 \usage{
 find(x)
 }
+\arguments{
+\item{x}{object or logic operation on an object}
+}
 \description{
 Emulates behavior of `find`
 }

man/inputdlg.Rd

@@ -11,7 +11,7 @@ inputdlg(prompt, definput = NULL, dims = 1)
 
 \item{definput}{default value of the input}
 
-\item{dim}{number of dimensions in the answwers}
+\item{dims}{number of dimensions in the answwers}
 }
 \description{
 Replicates the functionality of the homonymous function in Matlab (sans dialog box)

man/noIndex.Rd

@@ -6,6 +6,11 @@
 \usage{
 noIndex(data, noalle)
 }
+\arguments{
+\item{data}{data}
+
+\item{noalle}{noalle}
+}
 \value{
 puredata: a data contains no index column.
 }