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<p>Hi,</p>
<p>I'm using the sPCA function in adegenet, and get the warning:</p>
<p><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);
font-family: "Lucida Grande"; font-size: 13px;
font-style: normal; font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align:
-webkit-left; text-indent: 0px; text-transform: none;
white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;
background-color: rgba(0, 0, 0, 0.0745098); text-decoration:
none; display: inline !important; float: none;">This function is
now deprecated. Please use the 'multispati' function in the
'adespatial' package.</span></p>
<p>I can't find any information on what this refers to or how to fix
it. The sPCA output still appears to be what I expect, and
functions properly for downstream analyses and data plotting
(though I get similar messages for some of the other spca plotting
functions). <br>
</p>
<p>Coincidentally, a couple of the adegenet functions appear to be
incompatible with the knit function in Rmarkdown. when I try to
run my script in Rmarkdown it runs fine, but if I try to knit it
to a docx file, the sPCA function causes an error that prevents
the knit document from being completed. It produces a docx file
that opens as an image file (in Preview on my Mac instead of in MS
Word), but it's truncated at the sPCA command, and if I close it
and try to open the saved docx file, it can't open due to an "xml
parsing error". Knitting to a pdf file works fine for the sPCA
function. <br>
</p>
<p>I have verified that I can use the knit function successfully for
all of my document up to the point of running the sPCA function:</p>
<p>mySpca <- spca(obj, type=5,d1=0,d2=2,scannf=FALSE, nfposi = 5,
nfnega = 2)</p>
<p>I also get an fatal error when I try to knit to a pdf file if I
add the "screeplot" function (screeplot(mySpca)). <br>
</p>
<pre tabindex="0" class="GGHFMYIBMOB ace_text-layer ace_line GGHFMYIBPOB GGHFMYIBBU" style="font-family: Monaco !important; font-size: 10pt !important; font-style: normal; font-variant-caps: normal; font-weight: normal; font-stretch: inherit !important; line-height: 1.45; outline: none; border: none; word-break: break-all; margin: 0px; -webkit-user-select: text; white-space: pre-wrap !important; box-sizing: border-box; width: 855px; padding: 6px; caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;"><span class="GGHFMYIBMOB ace_constant ace_language" style="outline: none; border: none; word-break: break-all; margin: 0px; -webkit-user-select: text; white-space: pre-wrap !important; color: rgb(200, 0, 164);">! Package inputenc Error: Unicode character ^^U (U+15)
(inputenc) not set up for use with LaTeX.
Error: Failed to compile sPCA_SNPs_AK3WC4_test.tex. See sPCA_SNPs_AK3WC4_test.log for more info.</span></pre>
<p>The log file says about the same thing. I haven't been able to
figure out what the character is that hasn't been 'set up', or how
to set it up.</p>
<p>Phil</p>
<p><br>
</p>
<pre class="moz-signature" cols="72">--
--
Phillip A. Morin, Ph.D.
Southwest Fisheries Science Center
8901 La Jolla Shores Dr.
La Jolla, CA 92037, USA
Phone: 858-546-7165
Fax: 858-546-7003
<a class="moz-txt-link-abbreviated" href="mailto:phillip.morin@noaa.gov">phillip.morin@noaa.gov</a>
<a class="moz-txt-link-freetext" href="http://swfsc.noaa.gov/mmtd-mmgenetics">http://swfsc.noaa.gov/mmtd-mmgenetics</a></pre>
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