From 7616ddc1fc563f2bfb0162fdfff450d7ea62ec82 Mon Sep 17 00:00:00 2001
From: nikosbosse <nikosbosse@gmail.com>
Date: Thu, 18 Aug 2022 22:25:13 +0200
Subject: [PATCH 1/3] fix pit histogram plot in #240

---
 R/plot.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/plot.R b/R/plot.R
index 392d0119d..bdc6f63fd 100644
--- a/R/plot.R
+++ b/R/plot.R
@@ -1053,7 +1053,7 @@ plot_pit <- function(pit,
         data = pit,
         aes(x = pit_value)
       ) +
-        geom_histogram(aes(y = stat(count) / sum(count)),
+        geom_histogram(aes(y = stat(width*density)),
           breaks = plot_quantiles,
           colour = "grey"
         ) +
@@ -1065,7 +1065,7 @@ plot_pit <- function(pit,
       data = data.frame(x = pit),
       aes(x = x)
     ) +
-      geom_histogram(aes(y = stat(count) / sum(count)),
+      geom_histogram(aes(y = stat(width*density)),
         breaks = plot_quantiles,
         colour = "grey"
       )

From a3780e6abf0e16acf2abeb85eb6e4fc7d4a7a056 Mon Sep 17 00:00:00 2001
From: nikosbosse <nikosbosse@gmail.com>
Date: Thu, 18 Aug 2022 22:58:11 +0200
Subject: [PATCH 2/3] add necessary import to namespace

---
 NAMESPACE                                     |  1 +
 R/plot.R                                      |  1 +
 .../_snaps/plot_pit/plot-pit-integer.svg      | 82 ++++++++++---------
 3 files changed, 45 insertions(+), 39 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 8d4631879..da92c314b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -104,6 +104,7 @@ importFrom(scoringRules,dss_sample)
 importFrom(scoringRules,logs_sample)
 importFrom(stats,as.formula)
 importFrom(stats,cor)
+importFrom(stats,density)
 importFrom(stats,mad)
 importFrom(stats,median)
 importFrom(stats,na.omit)
diff --git a/R/plot.R b/R/plot.R
index bdc6f63fd..52e2d39f8 100644
--- a/R/plot.R
+++ b/R/plot.R
@@ -977,6 +977,7 @@ plot_pairwise_comparison <- function(comparison_result,
 #' `num_bins`.
 #' @importFrom stats as.formula
 #' @importFrom ggplot2 geom_col
+#' @importFrom stats density
 #' @return vector with the scoring values
 #' @examples
 #' # PIT histogram in vector based format
diff --git a/tests/testthat/_snaps/plot_pit/plot-pit-integer.svg b/tests/testthat/_snaps/plot_pit/plot-pit-integer.svg
index e7385a3a2..1b6704758 100644
--- a/tests/testthat/_snaps/plot_pit/plot-pit-integer.svg
+++ b/tests/testthat/_snaps/plot_pit/plot-pit-integer.svg
@@ -43,15 +43,15 @@
   </clipPath>
 </defs>
 <g clip-path='url(#cpNDAuMTN8Mzc0LjU5fDMwMy4zNHw1NDUuMTE=)'>
-<rect x='55.34' y='462.35' width='33.78' height='71.77' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='89.12' y='487.07' width='33.78' height='47.05' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='122.90' y='486.98' width='33.78' height='47.14' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='156.69' y='471.32' width='33.78' height='62.80' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='190.47' y='511.69' width='33.78' height='22.43' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='224.25' y='480.30' width='33.78' height='53.83' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='258.03' y='457.87' width='33.78' height='76.26' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='291.82' y='480.30' width='33.78' height='53.83' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='325.60' y='457.87' width='33.78' height='76.26' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='55.34' y='389.32' width='33.78' height='144.80' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='89.12' y='439.19' width='33.78' height='94.93' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='122.90' y='439.01' width='33.78' height='95.11' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='156.69' y='407.42' width='33.78' height='126.70' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='190.47' y='488.87' width='33.78' height='45.25' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='224.25' y='425.52' width='33.78' height='108.60' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='258.03' y='380.27' width='33.78' height='153.85' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='291.82' y='425.52' width='33.78' height='108.60' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='325.60' y='380.27' width='33.78' height='153.85' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
 </g>
 <g clip-path='url(#cpMC4wMHw3MjAuMDB8MC4wMHw1NzYuMDA=)'>
 </g>
@@ -61,15 +61,15 @@
   </clipPath>
 </defs>
 <g clip-path='url(#cpMzgwLjA3fDcxNC41MnwzOS40M3wyODEuMjE=)'>
-<rect x='395.27' y='153.59' width='33.78' height='116.63' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='429.05' y='108.74' width='33.78' height='161.48' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='462.84' y='122.19' width='33.78' height='148.03' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='496.62' y='140.14' width='33.78' height='130.08' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='530.40' y='146.73' width='33.78' height='123.49' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='564.19' y='142.51' width='33.78' height='127.71' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='597.97' y='202.93' width='33.78' height='67.28' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='631.75' y='149.11' width='33.78' height='121.11' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='665.53' y='180.51' width='33.78' height='89.71' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='395.27' y='159.38' width='33.78' height='110.84' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='429.05' y='116.74' width='33.78' height='153.47' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='462.84' y='129.53' width='33.78' height='140.69' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='496.62' y='146.59' width='33.78' height='123.63' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='530.40' y='152.85' width='33.78' height='117.37' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='564.19' y='148.85' width='33.78' height='121.37' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='597.97' y='206.27' width='33.78' height='63.95' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='631.75' y='155.11' width='33.78' height='115.11' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='665.53' y='184.95' width='33.78' height='85.26' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
 </g>
 <g clip-path='url(#cpMC4wMHw3MjAuMDB8MC4wMHw1NzYuMDA=)'>
 </g>
@@ -79,15 +79,15 @@
   </clipPath>
 </defs>
 <g clip-path='url(#cpMzgwLjA3fDcxNC41MnwzMDMuMzR8NTQ1LjEx)'>
-<rect x='395.27' y='415.25' width='33.78' height='118.87' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='429.05' y='397.31' width='33.78' height='136.81' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='462.84' y='435.44' width='33.78' height='98.68' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='496.62' y='399.55' width='33.78' height='134.57' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='530.40' y='462.35' width='33.78' height='71.77' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='564.19' y='435.44' width='33.78' height='98.68' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='597.97' y='439.92' width='33.78' height='94.20' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='631.75' y='414.72' width='33.78' height='119.41' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
-<rect x='665.53' y='393.36' width='33.78' height='140.76' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='395.27' y='413.15' width='33.78' height='120.97' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='429.05' y='394.89' width='33.78' height='139.23' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='462.84' y='433.69' width='33.78' height='100.43' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='496.62' y='397.17' width='33.78' height='136.95' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='530.40' y='461.08' width='33.78' height='73.04' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='564.19' y='433.69' width='33.78' height='100.43' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='597.97' y='438.26' width='33.78' height='95.87' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='631.75' y='412.60' width='33.78' height='121.52' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
+<rect x='665.53' y='390.87' width='33.78' height='143.25' style='stroke-width: 1.07; stroke: #BEBEBE; stroke-linecap: square; stroke-linejoin: miter; fill: #595959;' />
 </g>
 <g clip-path='url(#cpMC4wMHw3MjAuMDB8MC4wMHw1NzYuMDA=)'>
 </g>
@@ -150,22 +150,26 @@
 <text x='699.32' y='556.10' text-anchor='middle' style='font-size: 8.80px; fill: #4D4D4D; font-family: sans;' textLength='17.13px' lengthAdjust='spacingAndGlyphs'>1.00</text>
 <polyline points='40.13,281.21 40.13,39.43 ' style='stroke-width: 1.07; stroke: #CCCCCC; stroke-linecap: butt;' />
 <text x='35.20' y='273.25' text-anchor='end' style='font-size: 8.80px; fill: #4D4D4D; font-family: sans;' textLength='17.13px' lengthAdjust='spacingAndGlyphs'>0.00</text>
-<text x='35.20' y='200.40' text-anchor='end' style='font-size: 8.80px; fill: #4D4D4D; font-family: sans;' textLength='17.13px' lengthAdjust='spacingAndGlyphs'>0.02</text>
-<text x='35.20' y='127.55' text-anchor='end' style='font-size: 8.80px; fill: #4D4D4D; font-family: sans;' textLength='17.13px' lengthAdjust='spacingAndGlyphs'>0.04</text>
-<text x='35.20' y='54.71' text-anchor='end' style='font-size: 8.80px; fill: #4D4D4D; font-family: sans;' textLength='17.13px' lengthAdjust='spacingAndGlyphs'>0.06</text>
+<text x='35.20' y='221.66' text-anchor='end' style='font-size: 8.80px; fill: #4D4D4D; font-family: sans;' textLength='17.13px' lengthAdjust='spacingAndGlyphs'>0.05</text>
+<text x='35.20' y='170.08' text-anchor='end' style='font-size: 8.80px; fill: #4D4D4D; font-family: sans;' textLength='17.13px' lengthAdjust='spacingAndGlyphs'>0.10</text>
+<text x='35.20' y='118.49' text-anchor='end' style='font-size: 8.80px; fill: #4D4D4D; font-family: sans;' textLength='17.13px' lengthAdjust='spacingAndGlyphs'>0.15</text>
+<text x='35.20' y='66.91' text-anchor='end' style='font-size: 8.80px; fill: #4D4D4D; font-family: sans;' textLength='17.13px' lengthAdjust='spacingAndGlyphs'>0.20</text>
 <polyline points='37.39,270.22 40.13,270.22 ' style='stroke-width: 1.07; stroke: #CCCCCC; stroke-linecap: butt;' />
-<polyline points='37.39,197.37 40.13,197.37 ' style='stroke-width: 1.07; stroke: #CCCCCC; stroke-linecap: butt;' />
-<polyline points='37.39,124.53 40.13,124.53 ' style='stroke-width: 1.07; stroke: #CCCCCC; stroke-linecap: butt;' />
-<polyline points='37.39,51.68 40.13,51.68 ' style='stroke-width: 1.07; stroke: #CCCCCC; stroke-linecap: butt;' />
+<polyline points='37.39,218.63 40.13,218.63 ' style='stroke-width: 1.07; stroke: #CCCCCC; stroke-linecap: butt;' />
+<polyline points='37.39,167.05 40.13,167.05 ' style='stroke-width: 1.07; stroke: #CCCCCC; stroke-linecap: butt;' />
+<polyline points='37.39,115.46 40.13,115.46 ' style='stroke-width: 1.07; stroke: #CCCCCC; stroke-linecap: butt;' />
+<polyline points='37.39,63.88 40.13,63.88 ' style='stroke-width: 1.07; stroke: #CCCCCC; stroke-linecap: butt;' />
 <polyline points='40.13,545.11 40.13,303.34 ' style='stroke-width: 1.07; stroke: #CCCCCC; stroke-linecap: butt;' />
 <text x='35.20' y='537.15' text-anchor='end' style='font-size: 8.80px; fill: #4D4D4D; font-family: sans;' textLength='17.13px' lengthAdjust='spacingAndGlyphs'>0.00</text>
-<text x='35.20' y='464.30' text-anchor='end' style='font-size: 8.80px; fill: #4D4D4D; font-family: sans;' textLength='17.13px' lengthAdjust='spacingAndGlyphs'>0.02</text>
-<text x='35.20' y='391.46' text-anchor='end' style='font-size: 8.80px; fill: #4D4D4D; font-family: sans;' textLength='17.13px' lengthAdjust='spacingAndGlyphs'>0.04</text>
-<text x='35.20' y='318.61' text-anchor='end' style='font-size: 8.80px; fill: #4D4D4D; font-family: sans;' textLength='17.13px' lengthAdjust='spacingAndGlyphs'>0.06</text>
+<text x='35.20' y='485.57' text-anchor='end' style='font-size: 8.80px; fill: #4D4D4D; font-family: sans;' textLength='17.13px' lengthAdjust='spacingAndGlyphs'>0.05</text>
+<text x='35.20' y='433.98' text-anchor='end' style='font-size: 8.80px; fill: #4D4D4D; font-family: sans;' textLength='17.13px' lengthAdjust='spacingAndGlyphs'>0.10</text>
+<text x='35.20' y='382.40' text-anchor='end' style='font-size: 8.80px; fill: #4D4D4D; font-family: sans;' textLength='17.13px' lengthAdjust='spacingAndGlyphs'>0.15</text>
+<text x='35.20' y='330.81' text-anchor='end' style='font-size: 8.80px; fill: #4D4D4D; font-family: sans;' textLength='17.13px' lengthAdjust='spacingAndGlyphs'>0.20</text>
 <polyline points='37.39,534.12 40.13,534.12 ' style='stroke-width: 1.07; stroke: #CCCCCC; stroke-linecap: butt;' />
-<polyline points='37.39,461.28 40.13,461.28 ' style='stroke-width: 1.07; stroke: #CCCCCC; stroke-linecap: butt;' />
-<polyline points='37.39,388.43 40.13,388.43 ' style='stroke-width: 1.07; stroke: #CCCCCC; stroke-linecap: butt;' />
-<polyline points='37.39,315.58 40.13,315.58 ' style='stroke-width: 1.07; stroke: #CCCCCC; stroke-linecap: butt;' />
+<polyline points='37.39,482.54 40.13,482.54 ' style='stroke-width: 1.07; stroke: #CCCCCC; stroke-linecap: butt;' />
+<polyline points='37.39,430.95 40.13,430.95 ' style='stroke-width: 1.07; stroke: #CCCCCC; stroke-linecap: butt;' />
+<polyline points='37.39,379.37 40.13,379.37 ' style='stroke-width: 1.07; stroke: #CCCCCC; stroke-linecap: butt;' />
+<polyline points='37.39,327.78 40.13,327.78 ' style='stroke-width: 1.07; stroke: #CCCCCC; stroke-linecap: butt;' />
 <text x='377.33' y='568.24' text-anchor='middle' style='font-size: 11.00px; font-family: sans;' textLength='17.11px' lengthAdjust='spacingAndGlyphs'>PIT</text>
 <text transform='translate(13.05,292.27) rotate(-90)' text-anchor='middle' style='font-size: 11.00px; font-family: sans;' textLength='51.98px' lengthAdjust='spacingAndGlyphs'>Frequency</text>
 <text x='40.13' y='14.56' style='font-size: 13.20px; font-family: sans;' textLength='90.26px' lengthAdjust='spacingAndGlyphs'>plot_pit_integer</text>

From dfd52e405c657087d88112bb24b97616a1bc561a Mon Sep 17 00:00:00 2001
From: Nikos Bosse <37978797+nikosbosse@users.noreply.github.com>
Date: Sun, 9 Oct 2022 17:31:15 +0200
Subject: [PATCH 3/3] Code formatting

---
 R/plot.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/plot.R b/R/plot.R
index 52e2d39f8..8834384d9 100644
--- a/R/plot.R
+++ b/R/plot.R
@@ -1054,7 +1054,7 @@ plot_pit <- function(pit,
         data = pit,
         aes(x = pit_value)
       ) +
-        geom_histogram(aes(y = stat(width*density)),
+        geom_histogram(aes(y = stat(width * density)),
           breaks = plot_quantiles,
           colour = "grey"
         ) +