#16 remove similarity eg from readme

ropensci-archive · Nov 19, 2020 · 0e7c9fe · 0e7c9fe
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diff --git a/README.Rmd b/README.Rmd
@@ -62,18 +62,6 @@ res <- ma_calchist(query = "And(Composite(AA.AuN=='jaime teevan'),Y>2012)",
 res$histograms$histogram
 ```
 
-## Similarity
-
-```{r}
-s1 <- "Using complementary priors, we derive a fast greedy algorithm that
-can learn deep directed belief networks one layer at a time, provided the
-top two layers form an undirected associative memory"
-s2 <- "Deepneural nets with a large number of parameters are very powerful
-machine learning systems. However, overfitting is a serious problem in
-such networks"
-ma_similarity(s1, s2)
-```
-
 ## Abstract
 
 ```{r}

diff --git a/README.md b/README.md
@@ -49,67 +49,19 @@ for help on how to construct queries - for this and other functions
 
 ```r
 ma_evaluate(query = "Y='19'...")
-#> # A tibble: 10 x 349
-#>    logprob    prob     Id Ti        Y D        CC DN    S     AA    E     BT   
-#>      <dbl>   <dbl>  <dbl> <chr> <int> <chr> <int> <chr> <lis> <lis> <chr> <chr>
-#>  1   -13.7 1.17e-6 2.12e9 imag…  1992 1992… 31562 Imag… <df[… <df[… "{\"… <NA> 
-#>  2   -13.7 1.13e-6 2.60e9 diag…  1994 1994… 99513 Diag… <NUL… <df[… "{\"… a    
-#>  3   -13.7 1.09e-6 1.86e9 stan…  1992 1992… 77188 Stan… <df[… <df[… "{\"… a    
-#>  4   -13.7 1.08e-6 2.16e9 the …  1995 1995… 29019 The … <df[… <df[… "{\"… b    
-#>  5   -13.8 9.87e-7 2.13e9 crc …  1996 1996… 36272 CRC … <df[… <df[… "{\"… b    
-#>  6   -13.8 9.71e-7 2.91e9 fuzz…  1996 1996… 42590 Fuzz… <df[… <df[… "{\"… a    
-#>  7   -13.9 9.43e-7 2.16e9 gapp…  1997 1997… 59194 Gapp… <df[… <df[… "{\"… a    
-#>  8   -13.9 9.21e-7 2.23e9 manu…  1992 1992… 28470 Manu… <df[… <df[… "{\"… <NA> 
-#>  9   -14.1 7.85e-7 2.15e9 stat…  1998 1998… 20944 Stat… <df[… <df[… "{\"… a    
-#> 10   -14.1 7.74e-7 2.99e9 part…  1995 1995…   405 Part… <df[… <df[… "{\"… p    
-#> # … with 337 more variables: PB <chr>, VFN <chr>, FP <chr>, BV <chr>,
-#> #   DOI <chr>, LP <chr>, V <chr>, I <chr>, IA.IndexLength <int>,
-#> #   IA.InvertedIndex.An <list>, IA.InvertedIndex.image <list>,
-#> #   IA.InvertedIndex.forming <list>, IA.InvertedIndex.device <list>,
-#> #   `IA.InvertedIndex.has:` <list>, IA.InvertedIndex.an <list>,
-#> #   IA.InvertedIndex.body <list>, IA.InvertedIndex.on <list>,
-#> #   IA.InvertedIndex.which <list>, IA.InvertedIndex.is <list>,
-#> #   IA.InvertedIndex.formed <list>, IA.InvertedIndex.in <list>,
-#> #   IA.InvertedIndex.a <list>, IA.InvertedIndex.state <list>,
-#> #   IA.InvertedIndex.the <list>, `IA.InvertedIndex.charged;` <list>,
-#> #   IA.InvertedIndex.charging <list>, IA.InvertedIndex.having <list>,
-#> #   IA.InvertedIndex.plural <list>, IA.InvertedIndex.discharge <list>,
-#> #   `IA.InvertedIndex.portions,` <list>, IA.InvertedIndex.and <list>,
-#> #   IA.InvertedIndex.by <list>, IA.InvertedIndex.discharging <list>,
-#> #   IA.InvertedIndex.of <list>, `IA.InvertedIndex.portions;` <list>,
-#> #   IA.InvertedIndex.control <list>, IA.InvertedIndex.section <list>,
-#> #   `IA.InvertedIndex.that,` <list>, IA.InvertedIndex.when <list>,
-#> #   `IA.InvertedIndex.body,` <list>, IA.InvertedIndex.operates <list>,
-#> #   IA.InvertedIndex.not <list>, IA.InvertedIndex.switches <list>,
-#> #   IA.InvertedIndex.between <list>, IA.InvertedIndex.operating <list>,
-#> #   IA.InvertedIndex.some <list>, IA.InvertedIndex.portions <list>,
-#> #   IA.InvertedIndex.decreasing <list>, IA.InvertedIndex.output <list>,
-#> #   IA.InvertedIndex.or <list>, IA.InvertedIndex.stopping <list>,
-#> #   IA.InvertedIndex.other <list>, IA.InvertedIndex.than <list>,
-#> #   IA.InvertedIndex.portions. <list>, IA.InvertedIndex.Setting <list>,
-#> #   IA.InvertedIndex.learning <list>, IA.InvertedIndex.problem <list>,
-#> #   IA.InvertedIndex.consistency <list>, IA.InvertedIndex.processes <list>,
-#> #   IA.InvertedIndex.bounds <list>, IA.InvertedIndex.rate <list>,
-#> #   IA.InvertedIndex.convergence <list>, IA.InvertedIndex.controlling <list>,
-#> #   IA.InvertedIndex.generalization <list>, IA.InvertedIndex.ability <list>,
-#> #   IA.InvertedIndex.constructing <list>, IA.InvertedIndex.algorithms <list>,
-#> #   IA.InvertedIndex.what <list>, IA.InvertedIndex.important <list>,
-#> #   `IA.InvertedIndex.theory?.` <list>, IA.InvertedIndex.CRC <list>,
-#> #   IA.InvertedIndex.handbook <list>, IA.InvertedIndex.chemistry <list>,
-#> #   IA.InvertedIndex.physics <list>, `IA.InvertedIndex.,` <list>,
-#> #   IA.InvertedIndex.کتابخانه <list>, IA.InvertedIndex.دیجیتال <list>,
-#> #   IA.InvertedIndex.جندی <list>, IA.InvertedIndex.شاپور <list>,
-#> #   IA.InvertedIndex.اهواز <list>, IA.InvertedIndex.The <list>,
-#> #   IA.InvertedIndex.BLAST <list>, IA.InvertedIndex.programs <list>,
-#> #   IA.InvertedIndex.are <list>, IA.InvertedIndex.widely <list>,
-#> #   IA.InvertedIndex.used <list>, IA.InvertedIndex.tools <list>,
-#> #   IA.InvertedIndex.for <list>, IA.InvertedIndex.searching <list>,
-#> #   IA.InvertedIndex.protein <list>, IA.InvertedIndex.DNA <list>,
-#> #   IA.InvertedIndex.databases <list>, IA.InvertedIndex.sequence <list>,
-#> #   IA.InvertedIndex.similarities. <list>, IA.InvertedIndex.For <list>,
-#> #   `IA.InvertedIndex.comparisons,` <list>, IA.InvertedIndex.variety <list>,
-#> #   `IA.InvertedIndex.definitional,` <list>,
-#> #   IA.InvertedIndex.algorithmic <list>, IA.InvertedIndex.statistical <list>, …
+#> # A tibble: 10 x 8
+#>    logprob     prob      Id Ti                         Y    CC AA      J.JN     
+#>      <dbl>    <dbl>   <dbl> <chr>                  <int> <int> <list>  <chr>    
+#>  1   -13.7  1.10e-6  2.12e9 image forming device    1992 32430 <df[,1… <NA>     
+#>  2   -13.8  1.04e-6  1.86e9 standard methods for …  1992 81915 <df[,1… <NA>     
+#>  3   -13.8  1.03e-6  2.16e9 the nature of statist…  1995 30098 <df[,1… <NA>     
+#>  4   -13.9  9.18e-7  2.91e9 fuzzy sets              1996 44493 <df[,1… <NA>     
+#>  5   -13.9  9.12e-7  2.16e9 gapped blast and psi …  1997 61351 <df[,1… nucleic …
+#>  6   -13.9  8.77e-7  2.23e9 manufacture of semico…  1992 29044 <df[,1… <NA>     
+#>  7   -14.1  7.44e-7  2.15e9 statistical learning …  1998 21495 <df[,1… <NA>     
+#>  8   -14.1  7.22e-7  2.12e9 neural networks a com…  1998 24498 <df[,1… <NA>     
+#>  9   -14.2  6.96e-7  1.98e9 generalized gradient …  1996 84892 <df[,1… physical…
+#> 10   -14.2  6.86e-7  2.99e9 particle swarm optimi…  1995 12985 <df[,1… <NA>
 ```
 
 ## Calchistogram
@@ -121,55 +73,41 @@ res <- ma_calchist(query = "And(Composite(AA.AuN=='jaime teevan'),Y>2012)",
 res$histograms$histogram
 #> [[1]]
 #>   value   logprob count
-#> 1  2013 -17.02788    19
-#> 2  2014 -17.16747    14
-#> 3  2015 -17.48570    15
-#> 4  2016 -17.58468    17
-#> 5  2017 -18.18386    12
-#> 6  2019 -18.32731     6
-#> 7  2018 -18.56648     7
+#> 1  2013 -17.01346    19
+#> 2  2014 -17.07550    14
+#> 3  2015 -17.42947    15
+#> 4  2016 -17.50792    17
+#> 5  2019 -17.65841     6
+#> 6  2017 -18.09004    11
+#> 7  2018 -18.47003     7
+#> 8  2020 -18.95307     4
 #> 
 #> [[2]]
 #>                         value   logprob count
-#> 1            computer science -15.74012    81
-#> 2  human computer interaction -16.51284    35
-#> 3               crowdsourcing -16.68816    24
-#> 4              world wide web -16.70398    27
-#> 5               search engine -17.07613    14
-#> 6       information retrieval -17.23533    17
-#> 7                 data mining -17.31724    12
-#> 8                  multimedia -17.38984    19
-#> 9     artificial intelligence -17.76855     8
-#> 10           search analytics -17.87745     5
-```
-
-## Similarity
-
-
-```r
-s1 <- "Using complementary priors, we derive a fast greedy algorithm that
-can learn deep directed belief networks one layer at a time, provided the
-top two layers form an undirected associative memory"
-s2 <- "Deepneural nets with a large number of parameters are very powerful
-machine learning systems. However, overfitting is a serious problem in
-such networks"
-ma_similarity(s1, s2)
-#> [1] 0.6254586
+#> 1            computer science -15.66718    75
+#> 2              world wide web -16.54773    28
+#> 3               crowdsourcing -16.63486    24
+#> 4  human computer interaction -16.85747    19
+#> 5               search engine -17.00135    14
+#> 6       information retrieval -17.29366    11
+#> 7                  multimedia -17.79757    10
+#> 8     artificial intelligence -17.81949     6
+#> 9            search analytics -17.83150     5
+#> 10               data science -17.90774    11
 ```
 
 ## Abstract
 
 
 ```r
 ma_abstract(query = "Y='19'...", count = 5)
-#> # A tibble: 5 x 2
+#> # A tibble: 4 x 2
 #>           Id abstract                                                           
 #>        <dbl> <chr>                                                              
-#> 1 2119113870 "An image forming device has: an image forming body on which an im…
-#> 2 2596886333 ""                                                                 
-#> 3 1856219842 ""                                                                 
-#> 4 2156909104 "Setting of the learning problem consistency of learning processes…
-#> 5 2132905138 "CRC handbook of chemistry and physics , CRC handbook of chemistry…
+#> 1 2119113870 An image forming device has: an image forming body on which an ima…
+#> 2 1856219842 Set your standards with these standard methods. This is it: the mo…
+#> 3 2156909104 Setting of the learning problem consistency of learning processes …
+#> 4 2158714788 The BLAST programs are widely used tools for searching protein and…
 ```