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List: western_monarchs
Date: Fri, 29 Sep 2017 17:46:12 -0700
From: 'Ron K. Jeffries' <rjeffries...> [western_monarchs] <western_monarchs...>
Subject: Re: [western_monarchs] How does one get full article

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The database at https://www.westernmonarchcount.org/ starts with the year
1997. It's PDF but I can contact Xerces to get a spreadsheet used to
generate the PDF.
I am especially interested in the pre-1997 data, which is not available on
the westernmonarch count site (unless I am missing something;).

The note below is from the article. Not sure if the R code includes the
data used but that would make sense if other researchers want to
re-analyize. It seems this is not available to a non-academic.

Appendix A. Supplementary data
Supporting material include (S1) R code for main analysis, (S2) test if
variance in observation error is constant over time, (S3) test if
breakpoint model for population growth rate is better than model with a
single constant growth rate, (S4) test for stationarity of mean and
variance using autocorrelation tests and ADF test for a random walk vs
stationarity in time series,(S5)RcodeforS2,S3andS4,(S6)Additional analyses
with smaller subsets of the data as well as tests of covariance between
sites, and (S7) R code for S6. Supplementary data associated with this
article can be found in the online version, at http://dx.doi.
org/10.1016/j.biocon.2017.08.019.







---
Ron K. Jeffries
805-380-5446 mobile





On Fri, Sep 29, 2017 at 4:52 PM, Francis Xavier Villablanca
<footlooseandfrancisfree...> [western_monarchs] <
<western_monarchs...> wrote:

>
>
> Hi Ron,
>
> All of the references you need to get the data are in the first paragraph
> of the methods section: the info you found, and the references to Pelton.
> Also, Cheryl's info is on the first page. Her University is listed below
> her name and her email is at the bottom of the page (if you follow the
> "*"). No one is hiding anything. Just helps to know where to look ; )
>
> Best, Francis
> San Luis Obispo
>
> On Fri, Sep 29, 2017 at 1:36 PM, 'Ron K. Jeffries' <rjeffries...>
> [western_monarchs] <western_monarchs...> wrote:
>
>>
>>
>> Amusingly, the link in your email brings up a political site. LOL
>>
>> So I looked at https://www.westernmonarchcount.org/
>>
>> They provide: wmtc-data-1997-2017.pdf obviously a PDF not a format that =
R
>> it a spreadsheet program can use as input.
>>
>> The paper uses non-thanksgiving count data. Transparency requires that
>> all data be available for use by other researchers.
>>
>> Related: I tried to get contact information for lead author of this
>> study, but on my computer nothing came up. Not sure why, but if someone =
has
>> that info and will share it would be great.
>>
>> Ron K Jeffries
>>
>> On Sep 29, 2017 11:58 AM, "Francis Villablanca
>> <footlooseandfrancisfree...> [western_monarchs]" <
>> <western_monarchs...> wrote:
>>
>>>
>>>
>>> Ron, I believe there is a link to the western monarch Count.org in the
>>> first paragraph of the method section.
>>>
>>> Francis Villablanca
>>> San Luis Obispo.
>>>
>>> On Sep 29, 2017, at 9:44 AM, 'Ron K. Jeffries' <rjeffries...>
>>> [western_monarchs] <western_monarchs...> wrote:
>>>
>>>
>>>
>>> To Xerces:
>>>
>>> Is the full year by year per site data set used by this study available
>>> in spreadsheet format?
>>>
>>> I would appreciate a link to the data.
>>>
>>>
>>> Thanks
>>>
>>> Ron K Jeffries
>>>
>>> On Sep 29, 2017 8:10 AM, "Francis Villablanca
>>> <footlooseandfrancisfree...> [western_monarchs]" <
>>> <western_monarchs...> wrote:
>>>
>>>>
>>>>
>>>> Paul, they came from informal counts. Counts pre-dating the formalized
>>>> WMTC. I am sure you are aware that there were counts happening and tha=
t
>>>> they got coordinated and centralized when the WMTC "began." Those cou=
nts
>>>> are in the Xerces database. Just to be clear, the authors analytical
>>>> methods (how the numbers are crunched) did consider variation in thing=
s
>>>> like the number of sites counted per year and so on.
>>>>
>>>> Best,
>>>> Francis Villablanca
>>>> San Luis Obispo
>>>>
>>>>
>>>> On Sep 28, 2017, at 7:25 PM, Paul Cherubini <monarch...>
>>>> [western_monarchs] <western_monarchs...> wrote:
>>>>
>>>>
>>>>
>>>> Francis, I cannot figure out where in the paper it explains where
>>>> the 10,000,000 butterflies in 1997 estimate figure came from?
>>>> http://imagizer.imageshack.us/a/img924/1042/vyJLUv.jpg
>>>> And since there were no formal Thanksgiving Counts prior to
>>>> 1997, where did the 1980=E2=80=99s and early 1990=E2=80=99s count data
>>>> shown in that same graph come from; e.g. the 100,000 butterflies
>>>> estimate for 1994?
>>>> http://imagizer.imageshack.us/a/img924/1042/vyJLUv.jpg
>>>>
>>>> If readers cannot understand how the authors arrived at their
>>>> overwintering
>>>> population estimate figures for each of the 35 years show in their gra=
ph
>>>> then they cannot duplicate what the authors did; i.e. their science
>>>> cannot
>>>> be replicated. And one of the main principles of the scientific method
>>>> is
>>>> reproducibility.
>>>>
>>>> Paul Cherubini
>>>> El Dorado, Calif.
>>>>
>>>> On Sep 28, 2017, at 5:53 PM, Francis Xavier Villablanca
>>>> <footlooseandfrancisfree...> [western_monarchs] <
>>>> <western_monarchs...> wrote:
>>>>
>>>> Paul,
>>>>
>>>> It is in the first paragraph of the Methods and Materials.
>>>> Specifically: "Our analysis includes 186 sites, with counts from 1981
>>>> *=E2=80=93*2016 (Fig. 1)." They also "We filtered the full dataset to =
include
>>>> only sites monitored at least five years (see Supplement 6)." So, they
>>>> used WMTC data.
>>>>
>>>>
>>>>
>=20
>

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<div dir=3D"ltr">The database at=C2=A0<a href=3D"https://www.westernmonarch=
count.org/" target=3D"_blank">https://www.<wbr>westernmonarchcount.org/</a>=
starts with the year 1997. It&#39;s PDF but I can contact Xerces to get a =
spreadsheet used to generate the PDF.<div>I am especially interested in the=
pre-1997 data, which is not available on the westernmonarch count site (un=
less I am missing something;).</div><div><br></div><div>The note below is f=
rom the article. Not sure if the R code includes the data used but that wou=
ld make sense if other researchers want to re-analyize. It seems this is no=
t available to a non-academic.</div><div><br></div><div><div>Appendix A. Su=
pplementary data</div><div>Supporting material include (S1) R code for main=
analysis, (S2) test if variance in observation error is constant over time=
, (S3) test if breakpoint model for population growth rate is better than m=
odel with a single constant growth rate, (S4) test for stationarity of mean=
and variance using autocorrelation tests and ADF test for a random walk vs=
stationarity in time series,(S5)RcodeforS2,S3andS4,(S6)Additional analyses=
with smaller subsets of the data as well as tests of covariance between si=
tes, and (S7) R code for S6. Supplementary data associated with this articl=
e can be found in the online version, at <a href=3D"http://dx.doi">http://d=
x.doi</a>. org/10.1016/j.biocon.2017.08.019.</div></div><div><br></div><div=
><br></div><div><br></div><div><br></div><div><br></div><div><br></div></di=
v><div class=3D"gmail_extra"><br clear=3D"all"><div><div class=3D"gmail_sig=
nature" data-smartmail=3D"gmail_signature"><div dir=3D"ltr"><div>---<br>Ron=
K. Jeffries<div><span title=3D"Call with Google Voice">805-380-5446 mobile=
</span></div><div><br><br><br><br></div></div></div></div></div>
<br><div class=3D"gmail_quote">On Fri, Sep 29, 2017 at 4:52 PM, Francis Xav=
ier Villablanca <a href=3D"mailto:<footlooseandfrancisfree...>">footlo=
<oseandfrancisfree...></a> [western_monarchs] <span dir=3D"ltr">&lt;<a=
href=3D"mailto:<western_monarchs...>" target=3D"_blank">western=
<_monarchs...></a>&gt;</span> wrote:<br><blockquote class=3D"gma=
il_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-lef=
t:1ex">


<u></u>









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<span style=3D"display:none">=C2=A0</span>


<div id=3D"m_-7417935345963066907ygrp-mlmsg">
<div id=3D"m_-7417935345963066907ygrp-msg">


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<p></p><div dir=3D"ltr">Hi Ron,<div><br></div><div>All of the referen=
ces you need to get the data are in the first paragraph of the methods sect=
ion: the info you found, and the references to Pelton. Also, Cheryl&#39;s i=
nfo is on the first page. Her University is listed below her name and her e=
mail is at the bottom of the page (if you follow the &quot;*&quot;). No one=
is hiding anything. Just helps to know where to look ; )</div><div><br></d=
iv><div>Best, Francis</div><div>San Luis Obispo</div></div><div><div class=
=3D"h5"><div class=3D"gmail_extra"><br><div class=3D"gmail_quote">On Fri, S=
ep 29, 2017 at 1:36 PM, &#39;Ron K. Jeffries&#39; <a href=3D"mailto:rjeffri=
<es...>" target=3D"_blank"><rjeffries...></a> [western_monarchs] =
<span dir=3D"ltr">&lt;<a href=3D"mailto:<western_monarchs...>" t=
arget=3D"_blank">western_monarchs@yahoogroups.<wbr>com</a>&gt;</span> wrote=
:<br><blockquote class=3D"gmail_quote" style=3D"border-left:1px #ccc solid"=
>


<u></u>









=20
<div style=3D"background-color:#fff">
<span>=C2=A0</span>


<div id=3D"m_-7417935345963066907m_3873065262311681487ygrp-mlmsg">
<div id=3D"m_-7417935345963066907m_3873065262311681487ygrp-msg">


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<p></p><div dir=3D"auto">Amusingly, the link in your email brings up =
a political site. LOL<div dir=3D"auto"><br></div><div dir=3D"auto">So I loo=
ked at=C2=A0<a href=3D"https://www.westernmonarchcount.org/" target=3D"_bla=
nk">https://www.westernmonarchc<wbr>ount.org/</a></div><div dir=3D"auto"><b=
r></div><div dir=3D"auto">They provide: wmtc-data-1997-2017.pdf obviously a=
PDF not a format that R it a spreadsheet program can use as input.</div><d=
iv dir=3D"auto"><br></div><div dir=3D"auto">The paper uses non-thanksgiving=
count data. Transparency requires that all data be available for use by ot=
her researchers.</div><div dir=3D"auto"><br></div><div dir=3D"auto">Related=
: I tried to get contact information for lead author of this study, but on =
my computer nothing came up. Not sure why, but if someone has that info and=
will share it would be great.</div><div dir=3D"auto"><br></div><div dir=3D=
"auto">Ron K Jeffries</div></div><div><div class=3D"m_-7417935345963066907h=
5"><div class=3D"gmail_extra"><br><div class=3D"gmail_quote">On Sep 29, 201=
7 11:58 AM, &quot;Francis Villablanca <a href=3D"mailto:footlooseandfrancis=
<free...>" target=3D"_blank">footlooseandfrancisfree@gmail.<wbr>com</a=
> [western_monarchs]&quot; &lt;<a href=3D"mailto:western_monarchs@yahoogrou=
ps.com" target=3D"_blank">western_monarchs@yahoogroups.<wbr>com</a>&gt; wro=
te:<br type=3D"attribution"><blockquote class=3D"gmail_quote" style=3D"bord=
er-left:1px #ccc solid">


<u></u>









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<p></p><div>Ron, I believe there is a link to the western monarch <a =
href=3D"http://Count.org" target=3D"_blank">Count.org</a>=C2=A0in the first=
paragraph of the method section.<br><br>Francis Villablanca<div>San Luis O=
bispo.</div></div><div><br>On Sep 29, 2017, at 9:44 AM, &#39;Ron K. Jeffrie=
s&#39; <a href=3D"mailto:<rjeffries...>" target=3D"_blank">rjeffries@g=
mail.com</a> [western_monarchs] &lt;<a href=3D"mailto:western_monarchs@yaho=
ogroups.com" target=3D"_blank">western_monarchs@yahoogroups.<wbr>com</a>&gt=
; wrote:<br><br></div><blockquote type=3D"cite"><div>












=20

<span>=C2=A0</span>



<div id=3D"m_-7417935345963066907m_3873065262311681487m_-11370970827316=
23274ygrp-text">
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<p></p><div dir=3D"auto">To Xerces:<div dir=3D"auto"><br></div><div d=
ir=3D"auto">Is the full year by year per site data set used by this study a=
vailable in spreadsheet format?=C2=A0</div><div dir=3D"auto"><br></div><div=
dir=3D"auto">I would appreciate a link to the data.<div dir=3D"auto"><br><=
/div><div dir=3D"auto"><br></div><div dir=3D"auto">Thanks</div><div dir=3D"=
auto"><br></div><div dir=3D"auto">Ron K Jeffries</div></div></div><div clas=
s=3D"gmail_extra"><br><div class=3D"gmail_quote">On Sep 29, 2017 8:10 AM, &=
quot;Francis Villablanca <a href=3D"mailto:<footlooseandfrancisfree...>=
m" target=3D"_blank">footlooseandfrancisfree@gmail.<wbr>com</a> [western_mo=
narchs]&quot; &lt;<a href=3D"mailto:<western_monarchs...>" targe=
t=3D"_blank">western_monarchs@yahoogroups.<wbr>com</a>&gt; wrote:<br type=
=3D"attribution"><blockquote class=3D"gmail_quote" style=3D"border-left:1px=
#ccc solid">


<u></u>









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4m_-8371934381233335884ygrp-mlmsg">
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274m_-8371934381233335884ygrp-msg">


<div id=3D"m_-7417935345963066907m_3873065262311681487m_-11370970827316=
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<p></p><div>Paul, they came from informal counts. Counts pre-dating t=
he formalized WMTC. I am sure you are aware that there were counts happenin=
g and that they got coordinated and centralized when the WMTC &quot;began.&=
quot; =C2=A0Those counts are in the Xerces database. Just to be clear, the =
authors analytical methods (how the numbers are crunched) did consider vari=
ation in things like the number of sites counted per year and so on.=C2=A0<=
/div><div id=3D"m_-7417935345963066907m_3873065262311681487m_-1137097082731=
623274m_-8371934381233335884AppleMailSignature"><br></div><div id=3D"m_-741=
7935345963066907m_3873065262311681487m_-1137097082731623274m_-8371934381233=
335884AppleMailSignature">Best,</div><div id=3D"m_-7417935345963066907m_387=
3065262311681487m_-1137097082731623274m_-8371934381233335884AppleMailSignat=
ure">Francis Villablanca</div><div id=3D"m_-7417935345963066907m_3873065262=
311681487m_-1137097082731623274m_-8371934381233335884AppleMailSignature">Sa=
n Luis Obispo<br><br></div><div><br>On Sep 28, 2017, at 7:25 PM, Paul Cheru=
bini <a href=3D"mailto:<monarch...>" target=3D"_blank"><monarch...>=
et</a> [western_monarchs] &lt;<a href=3D"mailto:western_monarchs@yahoogroup=
s.com" target=3D"_blank">western_monarchs@yahoogroups.<wbr>com</a>&gt; wrot=
e:<br><br></div><blockquote type=3D"cite"><div>












=20

<span>=C2=A0</span>



<div id=3D"m_-7417935345963066907m_3873065262311681487m_-11370970827316=
23274m_-8371934381233335884ygrp-text">
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<p>Francis, I cannot figure out where in the paper it explains where<=
/p><div>the 10,000,000 butterflies in 1997 estimate figure came from?=C2=A0=
<div><a href=3D"http://imagizer.imageshack.us/a/img924/1042/vyJLUv.jpg" tar=
get=3D"_blank">http://imagizer.imageshack.us/<wbr>a/img924/1042/vyJLUv.jpg<=
/a></div><div>And since there were no formal Thanksgiving Counts prior to=
=C2=A0</div><div>1997, where did the 1980=E2=80=99s and early 1990=E2=80=99=
s count data=C2=A0</div><div>shown in that same graph come from; e.g. the 1=
00,000 butterflies</div><div>estimate for 1994?</div><div><a href=3D"http:/=
/imagizer.imageshack.us/a/img924/1042/vyJLUv.jpg" target=3D"_blank">http://=
imagizer.imageshack.us/<wbr>a/img924/1042/vyJLUv.jpg</a></div><div><br></di=
v><div>If readers cannot understand how the authors arrived at their overwi=
ntering</div><div>population estimate figures for each of the 35 years show=
in their graph</div><div>then they cannot duplicate what the authors did; =
i.e. their science cannot=C2=A0</div><div>be replicated. And one of the mai=
n principles of the scientific method is=C2=A0</div><div>reproducibility.</=
div><div><br></div><div>Paul Cherubini</div><div>El Dorado, Calif.</div><di=
v><div><br><div><blockquote type=3D"cite"><div>On Sep 28, 2017, at 5:53 PM,=
Francis Xavier Villablanca <a href=3D"mailto:footlooseandfrancisfree@gmail=
.com" target=3D"_blank">footlooseandfrancisfree@gmail.<wbr>com</a> [western=
_monarchs] &lt;<a href=3D"mailto:<western_monarchs...>" target=
=3D"_blank">western_monarchs@yahoogroups.<wbr>com</a>&gt; wrote:</div><br c=
lass=3D"m_-7417935345963066907m_3873065262311681487m_-1137097082731623274m_=
-8371934381233335884Apple-interchange-newline"><div>Paul,<br><div dir=3D"lt=
r" style=3D"font-family:Helvetica;font-size:12px;font-style:normal;font-var=
iant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-=
indent:0px;text-transform:none;white-space:normal"><div><br></div><div>It i=
s in the first paragraph of the Methods and Materials. Specifically: &quot;=
Our analysis includes 186 sites, with counts from 1981<span class=3D"m_-741=
7935345963066907m_3873065262311681487m_-1137097082731623274m_-8371934381233=
335884gmail-s1"><b>=E2=80=93</b></span>2016 (Fig. 1).&quot; They also &quot=
;We<span class=3D"m_-7417935345963066907m_3873065262311681487m_-11370970827=
31623274m_-8371934381233335884Apple-converted-space">=C2=A0</span><span cla=
ss=3D"m_-7417935345963066907m_3873065262311681487m_-1137097082731623274m_-8=
371934381233335884gmail-s1">fi</span>ltered the full dataset to include onl=
y sites monitored at least<span class=3D"m_-7417935345963066907m_3873065262=
311681487m_-1137097082731623274m_-8371934381233335884Apple-converted-space"=
>=C2=A0</span><span class=3D"m_-7417935345963066907m_3873065262311681487m_-=
1137097082731623274m_-8371934381233335884gmail-s1">fi</span>ve years (see S=
upplement 6).&quot; So, they used WMTC data.</div></div></div></blockquote>=
</div><br></div></div></div><p></p>

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