Refresh package doc, some advances on vignette
[morpheus.git] / pkg / R / plot.R
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1# extractParam
2#
3# Extract successive values of a projection of the parameter(s)
4#
5# @inheritParams plotHist
6#
7extractParam <- function(mr, x=1, y=1)
8{
9 # Obtain L vectors where L = number of res lists in mr
10 lapply( mr, function(mr_list) {
11 sapply(mr_list, function(m) m[x,y])
12 } )
13}
14
15#' plotHist
16#'
17#' Plot histogram
18#'
19#' @param mr Output of multiRun(), list of lists of functions results
20#' @param x Row index of the element inside the aggregated parameter
5fc1b9d9 21#' @param y Column index of the element inside the aggregated parameter
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22#'
23#' @examples
1b53e3a5 24#' \donttest{
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25#' β <- matrix(c(1,-2,3,1),ncol=2)
26#' mr <- multiRun(...) #see bootstrap example in ?multiRun : return lists of mu_hat
27#' μ <- normalize(β)
28#' for (i in 1:2)
29#' mr[[i]] <- alignMatrices(res[[i]], ref=μ, ls_mode="exact")
30#' plotHist(mr, 2, 1) #second row, first column}
31#' @export
32plotHist <- function(mr, x, y)
33{
34 params <- extractParam(mr, x, y)
35 L = length(params)
36 # Plot histograms side by side
37 par(mfrow=c(1,L), cex.axis=1.5, cex.lab=1.5, mar=c(4.7,5,1,1))
38 for (i in 1:L)
39 hist(params[[i]], breaks=40, freq=FALSE, xlab="Parameter value", ylab="Density")
40}
41
42#' plotBox
43#'
44#' Draw boxplot
45#'
46#' @inheritParams plotHist
47#'
48#' @examples
49#' #See example in ?plotHist
50#' @export
51plotBox <- function(mr, x, y)
52{
53 params <- extractParam(mr, x, y)
54 L = length(params)
55 # Plot boxplots side by side
56 par(mfrow=c(1,L), cex.axis=1.5, cex.lab=1.5, mar=c(4.7,5,1,1))
57 for (i in 1:L)
58 boxplot(params[[i]], ylab="Parameter value")
59}
60
61#' plotCoefs
62#'
63#' Draw coefs estimations + standard deviations
64#'
65#' @inheritParams plotHist
66#' @param params True value of parameters matrix
0527116e 67#' @param idx List index to process in mr
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68#'
69#' @examples
70#' #See example in ?plotHist
71#' @export
476a79d4 72plotCoefs <- function(mr, params, idx, xtitle="Parameter")
cbd88fe5 73{
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74 L <- nrow(mr[[1]][[1]])
75 K <- ncol(mr[[1]][[1]])
76
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77 params_hat <- matrix(nrow=L, ncol=K)
78 stdev <- matrix(nrow=L, ncol=K)
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79 for (x in 1:L)
80 {
81 for (y in 1:K)
82 {
83 estims <- extractParam(mr, x, y)
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84 params_hat[x,y] <- mean(estims[[idx]])
85# stdev[x,y] <- sqrt( mean( (estims[[idx]] - params[x,y])^2 ) )
86 # HACK remove extreme quantile in estims[[i]] before computing sd()
87 stdev[x,y] <- sd( estims[[idx]] ) #[ estims[[idx]] < max(estims[[idx]]) & estims[[idx]] > min(estims[[idx]]) ] )
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88 }
89 }
90
0527116e 91 par(cex.axis=1.5, cex.lab=1.5, mar=c(4.7,5,1,1))
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92 params <- as.double(params)
93 o <- order(params)
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94 avg_param <- as.double(params_hat)
95 std_param <- as.double(stdev)
96 matplot(cbind(params[o],avg_param[o],avg_param[o]+std_param[o],avg_param[o]-std_param[o]),
476a79d4 97 col=1, lty=c(1,5,3,3), type="l", lwd=2, xlab=xtitle, ylab="")
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98
99 #print(o) #not returning o to avoid weird Jupyter issue... (TODO:)
100}
101
102#' plotQn
103#'
104#' Draw 3D map of objective function values
105#'
106#' @param N Number of starting points
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107#' @param n Number of points in sample
108#' @param p Vector of proportions
109#' @param b Vector of biases
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110#' @param β Regression matrix (target)
111#' @param link Link function (logit or probit)
112#'
113#' @export
114plotQn <- function(N, n, p, β, b, link)
115{
116 d <- nrow(β)
117 K <- ncol(β)
118 io <- generateSampleIO(n, p, β, b, link)
119 op <- optimParams(K, link, list(X=io$X, Y=io$Y))
120 # N random starting points gaussian (TODO: around true β?)
121 res <- matrix(nrow=d*K+1, ncol=N)
122 for (i in seq_len(N))
123 {
124 β_init <- rnorm(d*K)
125 par <- op$run( c(rep(1/K,K-1), β_init, rep(0,K)) )
126 par <- op$linArgs(par)
127 Qn <- op$f(par)
128 res[,i] = c(Qn, par[K:(K+d*K-1)])
129 }
130 res #TODO: plot this, not just return it...
131}