?smartid:::idf.
+each function, e.g. ?idf.
## show available methods
idf_iae_methods()
@@ -235,18 +235,19 @@ Score Samples\(N_{i,j}\) is the counts of
feature \(i\) in cell \(j\); \(\hat
-N_{i,j}\) is \(max(0,N_{i,j}-threshold)\); \(n\) is the total number of
-documents(cells); \(n_i\) is \(\sum_{j = 1}^{n} sign(N_{i,j} >
-threshold)\).
+N_{i,j}\) is \(\max(0,N_{i,j}-threshold)\); \(n\) is the total number of
+documents(cells); \(n_i\) is \(\sum_{j = 1}^{n} \mathrm{sign}(N_{i,j} >
+\mathrm{threshold})\).
Here for labeled data, we can choose logTF * IDF_prob * IAE_prob for
marker identification: \[\mathbf{score}=\log
\mathbf{TF}*\mathbf{IDF}_{prob}*\mathbf{IAE}_{prob}\]
The probability version of IDF can be termed as: \[\mathbf{IDF_{i,j}} = \log(1+\frac{\frac{n_{i,j\in
-D}}{n_{j\in D}}}{max(\frac{n_{i,j\in \hat D}}{n_{j\in \hat D}})+
+D}}{n_{j\in D}}}{\max(\frac{n_{i,j\in \hat D}}{n_{j\in \hat D}})+
e^{-8}}\frac{n_{i,j\in D}}{n_{j\in D}})\]
-And the probability version of IAE can be termed as: \[\mathbf{IAE_{i,j}} = \log(1+\frac{mean(\hat
-N_{i,j\in D})}{max(mean(\hat N_{i,j\in \hat D}))+ e^{-8}}*mean(\hat
-N_{i,j\in D}))\]
+And the probability version of IAE can be termed as: \[\mathbf{IAE_{i,j}} =
+\log(1+\frac{\mathrm{mean}(\hat N_{i,j\in D})}{\max(\mathrm{mean}(\hat
+N_{i,j\in \hat D}))+ e^{-8}}*\mathrm{mean}(\hat N_{i,j\in
+D}))\]
Where \(D\) is the category of cell
\(j\); \(\hat
D\) is the category other than \(D\).
@@ -270,7 +271,7 @@ Score Samples)
)
#> user system elapsed
-#> 0.197 0.008 0.205
+#> 0.194 0.004 0.198
## score and tf,idf,iae all saved
assays(data_sim)
@@ -470,8 +471,8 @@ Un-labeled Data\[\mathbf{score}=\log
\mathbf{TF}*\mathbf{IDF}_{sd}*\mathbf{IAE}_{sd}\]
Where IDF and IAE can be termed as: \[\mathbf{IDF_i} =
-\log(1+SD(\mathbf{TF}_{i})*\frac{n}{n_i+1})\] \[\mathbf{IAE_i} =
-\log(1+SD(\mathbf{TF}_{i})*\frac{n}{\sum_{j=1}^{n}\hat
+\log(1+\mathrm{SD}(\mathbf{TF}_{i})*\frac{n}{n_i+1})\] \[\mathbf{IAE_i} =
+\log(1+\mathrm{SD}(\mathbf{TF}_{i})*\frac{n}{\sum_{j=1}^{n}\hat
N_{i,j}+1})\]
Score Samples
@@ -491,7 +492,7 @@ Score Samples )
)
#> user system elapsed
-#> 0.178 0.020 0.198
+#> 0.189 0.008 0.197
## new score is saved and tf,idf,iae all updated
assays(data_sim)
diff --git a/pkgdown.yml b/pkgdown.yml
index 3e958b4..c1534ba 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.7
pkgdown_sha: ~
articles:
smartid_Demo: smartid_Demo.html
-last_built: 2024-03-29T11:41Z
+last_built: 2024-03-29T12:11Z