Add data to estimate impact on the number of randomisation

data-raw/Soil_litter/prepare_data.R

+library(vegan)
+library(ROBITools)
+
+litere_col_clean <- readRDS("litere_col_clean.rds")
+litere_col_clean <- metabarcoding.data(reads = litere_col_clean$reads,
+                                       motus = litere_col_clean$motus,
+                                       samples = litere_col_clean$samp)
+
+litere_bac_clean <- readRDS("litere_bac_clean.rds")
+litere_bac_clean <- metabarcoding.data(reads = litere_bac_clean$reads,
+                                       motus = litere_bac_clean$motus,
+                                       samples = litere_bac_clean$samp)
+
+
+
+
+litere_ins_clean <- readRDS("litere_ins_clean.rds")
+litere_ins_clean <- metabarcoding.data(reads = litere_ins_clean$reads,
+                                       motus = litere_ins_clean$motus,
+                                       samples = litere_ins_clean$samp)
+
+litere_euk_clean <- readRDS("litere_euk_clean.rds")
+litere_euk_clean <- metabarcoding.data(reads = litere_euk_clean$reads,
+                                       motus = litere_euk_clean$motus,
+                                       samples = litere_euk_clean$samp)
+
+
+# Remove rare motus
+
+litere_col_norare <- litere_col_clean[,apply(decostand(litere_col_clean$reads,method = "total"),MARGIN = 2,max) >= 0.01]
+litere_euk_norare <- litere_euk_clean[,apply(decostand(litere_euk_clean$reads,method = "total"),MARGIN = 2,max) >= 0.01]
+litere_ins_norare <- litere_ins_clean[,apply(decostand(litere_ins_clean$reads,method = "total"),MARGIN = 2,max) >= 0.01]
+litere_bac_norare <- litere_bac_clean[,apply(decostand(litere_bac_clean$reads,method = "total"),MARGIN = 2,max) >= 0.01]

manuscript/main.aux

-\relax 
-\citation{Ramsay:84:00}
-\citation{Smilde:09:00}
-\citation{Escoufier:73:00}
-\citation{Szekely:07:00}
-\citation{SzeKely:13:00}
-\citation{Lingoes:74:00}
-\citation{Gower:71:00}
-\citation{Peres-Neto:01:00}
-\citation{Bravais:44:00}
-\newcplabel{^_1}{1}
-\@writefile{toc}{\contentsline {section}{\numberline {1}Introduction}{1}}
-\newlabel{eq:CovLs}{{1}{1}}
-\newlabel{eq:Rls}{{2}{1}}
-\@writefile{toc}{\contentsline {section}{\numberline {2}Approach}{1}}
-\citation{Robert:76:00}
-\citation{El-Ghaziri:15:00,Mayer:11:00,Smilde:09:00}
-\citation{Szekely:07:00}
-\citation{SzeKely:13:00}
-\citation{Jackson:95:00}
-\citation{Peres-Neto:01:00}
-\citation{Dixon:03:00}
-\citation{Dray:07:00}
-\newlabel{eq:SVD}{{3}{2}}
-\newlabel{eq:CovLsSVD}{{4}{2}}
-\newlabel{eq:ICovLs}{{5}{2}}
-\newlabel{eq:IRLs}{{6}{2}}
-\newlabel{eq:IRls.partial}{{7}{2}}
-\@writefile{toc}{\contentsline {section}{\numberline {3}Methods}{2}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {{3.1}}Monte-Carlo estimation of $\overline  {\rcovls  (\mathbf  {X},\mathbf  {Y})}$}{2}}
-\newlabel{eq:RCovLsMC}{{8}{2}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {{3.2}}Simulating data for testing sensibility to overfitting}{2}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {{3.3}}Empirical assessment of the coefficient of determination}{2}}
-\citation{CSoRgo:96:00}
-\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces Theoritical distribution of the shared variation between the four matrices $\mathbf  {A},\tmspace  +\thinmuskip {.1667em}\mathbf  {B},\tmspace  +\thinmuskip {.1667em}\mathbf  {C},\tmspace  +\thinmuskip {.1667em}\mathbf  {D}$, expressed in permille.}}{3}}
-\newlabel{fig:nested_shared_variation}{{1}{3}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {{3.4}}Testing significance of $\irls  (\mathbf  {X},\mathbf  {Y})$}{3}}
-\newlabel{eq:pvalue}{{9}{3}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2}{\ignorespaces A) Sensibility to overfitting for various correraltion coefficients. (A) Both simulated data sets are matrices of size $(n \times p)$ with $p > 1$. B) Correlated data sets are vectors ($p=1$) with a various number of individuals $n$ (vector length). A \& B) 100 simulations are run for each combination of parameters}}{3}}
-\newlabel{fig:h0_overfit}{{2}{3}}
-\@writefile{toc}{\contentsline {section}{\numberline {4}Results}{3}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {{4.1}}Relative sensibility of $IRLs(X,Y)$ to overfitting}{3}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {{4.2}}Evaluating the shared variation}{3}}
-\@writefile{lof}{\contentsline {figure}{\numberline {3}{\ignorespaces Shared variation ($R^2$) between two matrices is mesured with both the corrected ($\irls  $) and the original ($\rls  $) versions of the procrustean correlation coefficient. A gradiant of $R^2$ is simulated for two population sizes ($n \in \{10,24\}$) and two numbers of descriptive variables ($p \in \{10,100\}$). The black dashed line corresponds to a perfect match where measured $R^2$ equals the simulated one.}}{4}}
-\newlabel{fig:shared_variation}{{3}{4}}
-\@writefile{lof}{\contentsline {figure}{\numberline {4}{\ignorespaces Estimation error on the partial determination coefficient. Error is defined as the absolute value of the difference between the expected and the estimated partial $R^2$ using the corrected $\irls  _{partial}$ and not corrected $\rls  _{partial}$ procruste correlation coefficient.}}{4}}
-\newlabel{fig:nested_shared}{{4}{4}}
-\@writefile{lot}{\contentsline {table}{\numberline {1}{\ignorespaces $P_{values}$ of the Cramer-Von Mises test of conformity of the distribution of $P_{values}$ correlation test to $\mathcal  {U}(0,1)$ under the null hypothesis.}}{4}}
-\newlabel{tab:alpha_pvalue}{{1}{4}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {{4.3}}$p_{value}$ distribution under null hyothesis}{4}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {{4.4}}Power of the test based on randomisation}{4}}
-\bibstyle{natbib}
-\bibdata{Document}
-\global\@namedef{@lastpage@}{5}
-\@writefile{lot}{\contentsline {table}{\numberline {2}{\ignorespaces Power estimation of the procruste tests for two low level of shared variations $5\%$ and $10\%$.}}{5}}
-\newlabel{tab:power}{{2}{5}}
-\@writefile{toc}{\contentsline {section}{\numberline {5}Discussion}{5}}
-\@writefile{toc}{\contentsline {section}{\numberline {6}Conclusion}{5}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {A}Notations}{5}}

manuscript/main.bbl

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