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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hello everybody,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I've got some code which runs wilcoxon tests for each 'year' and 'hotspot_ID' combination from my data. It basically compares the densities each hotspot_Id with the densities in hotspot 0 (one of the hotspot_ID's which means 'everywhere
else that is not in a hotspot') – some test data is attached. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">It looks like this. It gives me a nice, and very big, word document with all the tests in there. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif"">d<-read.csv("F:\\Offshore_analysis1_(UK_wide_approach)<a href="file:///\\Extra_analyses\test_regularity_without_nim_numbers\3_data_for_R\6360_wn.csv">\\Extra_analyses\\test_regularity_without_nim_numbers\\3_data_for_R\\6360_wn.csv</a>",
header=T)</span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif""> </span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif""># all tests between 0 and the other groups within each year together</span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif"">for(i in 1980:2005){</span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif""> for(j in 1:34){</span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif""> tmp<- d[d$YEAR == i & d$hotspot_ID %in% c(0, j), ]</span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif""> print(c(i, j))</span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif""> try(print(wilcox.test(DENSITY~factor(hotspot_ID), data= tmp, na.action = na.omit)))</span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif""> }</span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif"">}</span><o:p></o:p></p>
<p><span style="font-family:"Arial","sans-serif""> </span><o:p></o:p></p>
<p><o:p> </o:p></p>
<p class="MsoNormal">Note that many of these did not run as there is not data for every combination of year and hotspot. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I want to be able to quickly extract which combinations ran, and of those, which had a P value less than some threshold, lets say 0.05. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">So I'd like to extract some kind of table or ideally a .csv file with 3 columns:<o:p></o:p></p>
<p class="MsoNormal">Year, Hotspot_ID, P-value. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">My attempts at altering the code to do that are here.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif"">d<-read.csv("F:\\offshore_SPAs\\1_Stage1\\2_analysis_GL1.4\\2_UK_wide\\3_data_for_R.\\220_br.csv", header=T)</span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif""> </span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif""># all tests between 0 and the other groups within each year together</span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif""> output.2<-matrix( ncol=3, nrow=3000)</span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif""> </span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif"">for(i in 1980:2005){</span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif""> for(j in 1:34){</span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif""> tmp<- d[d$YEAR == i & d$hotspot_ID %in% c(0, j), ]</span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif""> print(c(i, j))</span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif""> try(wt<-(wilcox.test(DENSITY~factor(hotspot_ID), data= tmp, na.action = na.omit)</span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif""> )</span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif""> output.2$p<-wt$p.value)</span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif""> }</span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif"">}</span><o:p></o:p></p>
<p style="margin-left:72.0pt"><span style="font-family:"Arial","sans-serif""> </span><o:p></o:p></p>
<p><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I've played around quite a bit with the placement of the output bits, <o:p></o:p></p>
<p class="MsoNormal">I'm hoping someone can spot either where I'm going wrong with my attempts, or suggest a better way of doing this. I've also played a bit with matrix, and less so with sapply, but don't really know what I'm doing with those. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Any advice greatly appreciated. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks<o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"">Kerstin<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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